Prague, Czech Republic
Prague, Czech Republic

Charles University in Prague is the oldest and largest university in the Czech Republic. Founded in 1348, it was the first university in Central Europe, east of France and north of the Alps. It is one of the oldest universities in Europe in continuous operation and ranks in the upper 1.5 percent of the world’s best universities.Its seal shows its protector Emperor Charles IV, with his coats of arms as King of the Romans and King of Bohemia, kneeling in front of St. Wenceslas, the patron saint of Bohemia. It is surrounded by the inscription, Sigillum Universitatis Scolarium Studii Pragensis . Wikipedia.

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Tierra G.,Charles University | Guillen-Gonzalez F.,University of Seville
Archives of Computational Methods in Engineering | Year: 2015

In this paper, we review some numerical methods presented in the literature in the last years to approximate the Cahn–Hilliard equation. Our aim is to compare the main properties of each one of the approaches to try to determine which one we should choose depending on which are the crucial aspects when we approximate the equations. Among the properties that we consider desirable to control are the time accuracy order, energy-stability, unique solvability and the linearity or nonlinearity of the resulting systems. In particular, we concern about the iterative methods used to approximate the nonlinear schemes and the constraints that may arise on the physical and computational parameters. Furthermore, we present the connections of the Cahn–Hilliard equation with other physically motivated systems (not only phase field models) and we state how the ideas of efficient numerical schemes in one topic could be extended to other frameworks in a natural way. © 2014, CIMNE, Barcelona, Spain.

Zhou Y.,Zhejiang Normal University | Pokornyy M.,Charles University
Nonlinearity | Year: 2010

We consider the regularity criteria for the incompressible Navier-Stokes equations connected with one velocity component. Based on the method from Cao and Titi (2008 Indiana Univ. Math. J. 57 2643-61) we prove that the weak solution is regular, provided u3 ∈ Lt(O,T;L s(ℝ3)), 2/t + 3/s ≤ 3/4 + 1/2s, s > 10/3 or provided ∇u3 ∈ Lt(O, T;Ls(ℝ3)), 2/t + 3/s ≤ 19/12 + 1/2s , if or if s ∈ (30/19, 3] or 2/t + 3/s ≤ 3/2 + 3/4s if s ∈ (3, ∞]. As a corollary, we also improve the regularity criteria expressed by the regularity of ∂p/∂x3 or ∂u3/∂x3. © 2010 IOP Publishing Ltd & London Mathematical Society.

Massy Z.A.,Charles University | De Zeeuw D.,University of Groningen
Kidney International | Year: 2013

In the majority of patients with chronic kidney disease (CKD) the total and low-density lipoprotein (LDL) cholesterol are usually normal, with the exception of patients with nephrotic-range proteinuria and in peritoneal dialysis patients. Moreover, epidemiological evidence shows that the link between serum total cholesterol or LDL cholesterol and cardiovascular disease (CVD) in CKD is not as straightforward as in the general population. In addition, atherosclerosis-related events are responsible for only ∼30% of CVD in these patients. Nevertheless, intervention trials, particularly the Study of Heart and Renal Protection, and meta-analyses showed a proportional reduction of cardiovascular risk associated with the absolute reduction in LDL cholesterol in patients with CKD similar to the general population, with apparent attenuation of this relationship in end-stage kidney disease. Therefore, the use of cholesterol-lowering agents appears to be indicated in early CKD stages to prevent atherosclerosis-related risk. However, uncertainty persists as to the optimal management of this risk in end-stage kidney disease patients. In the present review, we discuss these issues and end up with a practical plan aimed to help the nephrologist in managing atherosclerosis- related risk using cholesterol-lowering therapies in CKD patients. © 2013 International Society of Nephrology.

Krizova L.,National Institute of Public Health | Krizova L.,Charles University | Dijkshoorn L.,Leiden University | Nemec A.,National Institute of Public Health
Antimicrobial Agents and Chemotherapy | Year: 2011

To assess the diversity of AbaR genomic resistance islands in Acinetobacter baumannii European clone I (MLST clonal complex 1), we investigated 26 multidrug-resistant strains of this major clone isolated from hospitals in 21 cities of 10 European countries between 1984 and 2005. Each strain harbored an AbaR structure integrated at the same position in the chromosomal ATPase gene. AbaR3, including four subtypes based on variations in class 1 integron cassettes, and AbaR10 were found in 15 and 2 strains, respectively, whereas a new, unique AbaR variant was discovered in each of the other 9 strains. These new variants, designated AbaR11 to AbaR19 (19.8 kb to 57.5 kb), seem to be truncated derivatives of AbaR3, likely resulting from the deletions of its internal parts mediated by either IS26 elements (AbaR12 to AbaR19) or homologous recombination (AbaR11). AbaR3 was detected in all 10 strains isolated in 1984 to 1991, while AbaR11 to AbaR19 were carried only by strains isolated since 1997. Our results and those from previous publications suggest that AbaR3 is the original form of AbaR in European clone I, which may have provided strains of the lineage with a selective advantage facilitating their spread in European hospitals in the 1980s or before. Copyright © 2011, American Society for Microbiology. All Rights Reserved.

Kholova I.,University of Tampere | Ludvikova M.,Charles University | Ludvikova M.,General University Hospital in Prague
Acta Cytologica | Year: 2014

Objective: The Bethesda System for Reporting Thyroid Cytopathology (BSRTC) was introduced in thyroid cytology in 2007 and is now generally accepted. BSRTC categories include a morphologic description and risk of malignancy as well as follow-up suggestions in each group. However, the category entitled 'atypia of undetermined significance or follicular lesion of undetermined significance' (AUS/FLUS) is problematic. This category is heterogeneous and has been overused so far. Study Design: Twenty-six studies were included in a meta-analysis. In addition to AUS/FLUS percentage, we analysed repeated AUS/FLUS percentage, cytological and histological correlations, and risk of malignancy and neoplasm for AUS/FLUS. Furthermore, stratification, interand intra-observer variability, and the possibility of a switch to another category and its clinical consequences were reviewed. Results: Out of a total of 81,833 cases, AUS/FLUS accounted for 10.9%, with a 34% risk of malignancy. Persistent AUS/FLUS was found in 21.6% in repeated cytology. Cytohistological correlation was analysed from 16 studies (4,964 cases), revealing 10.4% as AUS/FLUS and a 21.5% risk of malignancy. Conclusions: An AUS/FLUS category seems to be currently reasonable with clearly defined cytomorphological criteria which do not correspond unequivocally with those of the other categories. An AUS/FLUS category is justified and possible means of its improvement with immunohistochemistry, molecular analysis and imaging are discussed. © 2014 S. Karger AG, Basel.

Maslov D.A.,University of California at Riverside | Votypka J.,Charles University | Votypka J.,Academy of Sciences of the Czech Republic | Yurchenko V.,University of Ostrava | And 2 more authors.
Trends in Parasitology | Year: 2013

Monoxenous trypanosomatids, which are usually regarded as benign dwellers of the insect alimentary tract, represent a relatively obscure group within the family Trypanosomatidae. This field of study has long been in disarray with the genus level taxonomy of this group remaining artificial, species criteria elusive, host specificity and occurrence poorly known, and their diversity mostly unexplored. The time has arrived to remedy this situation: a phylogenetic approach has been applied to taxa recognition and description, and a culture-independent (PCR-based) approach for detection and identification of organisms in nature has made it feasible to study the diversity of the group. Although more than 100 typing units have been discovered recently, these appear to represent a small segment of trypanosomatid biodiversity, which still remains to be uncovered. © 2012 Elsevier Ltd.

Havranek T.,Czech National Bank | Havranek T.,Charles University | Kokes O.,Cambridge Econometrics
Energy Economics | Year: 2015

In this paper we quantitatively synthesize empirical estimates of the income elasticity of gasoline demand reported in previous studies. The studies cover many countries and report a mean elasticity of 0.28 for the short run and 0.66 for the long run. We show, however, that these mean estimates are biased upwards because of publication bias-the tendency to suppress negative and insignificant estimates of the elasticity. We employ mixed-effects multilevel meta-regression to filter out publication bias from the literature. Our results suggest that the income elasticity of gasoline demand is on average much smaller than reported in previous surveys: the mean corrected for publication bias is 0.1 for the short run and 0.23 for the long run. © 2014 Elsevier B.V.

Catford J.A.,University of Melbourne | Vesk P.A.,University of Melbourne | Richardson D.M.,Stellenbosch University | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University
Global Change Biology | Year: 2012

Biological invasions are a global phenomenon that threatens biodiversity, and few, if any, ecosystems are free from alien species. The outcome of human-mediated introductions is affected by the invasiveness of species and invasibility of ecosystems, but research has primarily focused on defining, characterizing and identifying invasive species; ecosystem invasibility has received much less attention. A prerequisite for characterizing invasibility is the ability to compare levels of invasion across ecosystems. In this paper, we aim to identify the best way to quantify the level of invasion by nonnative animals and plants by reviewing the advantages and disadvantages of different metrics. We explore how interpretation and choice of these measures can depend on the objective of a study or management intervention. Based on our review, we recommend two invasion indices and illustrate their use by applying them to two case studies. Relative alien species richness and relative alien species abundance indicate the contribution that alien species make to a community. They are easy to measure, can be applied to various taxa, are independent of scale and are comparable across regions and ecosystems, and historical data are often available. The relationship between relative alien richness and abundance can indicate the presence of dominant alien species and the trajectory of invasion over time, and can highlight ecosystems and sites that are heavily invaded or especially susceptible to invasion. Splitting species into functional groups and examining invasion patterns of transformer species may be particularly instructive for gauging effects of alien invasion on ecosystem structure and function. Establishing standard, transparent ways to define and quantify invasion level will facilitate meaningful comparisons among studies, ecosystem types and regions. It is essential for progress in ecology and will help guide ecosystem restoration and management. © 2011 Blackwell Publishing Ltd.

Hladik M.,Charles University | Cerny M.,University of Economics in Prague
Fuzzy Sets and Systems | Year: 2012

In interval linear regression analysis, we are given crisp or interval data and we are to determine appropriate interval regression parameters. There are various methods for interval regression; many of them possess the property that while some of the resulting interval regression parameters are very wide, the other parameters are crisp. This drawback is the main limiting factor for such methods and much effort has been devoted to overcoming it. We propose a method motivated by tolerance analysis in linear systems. Our method yields intervals for regression parameters the widths of which are proportional to an in-advance given vector of parameters. Moreover, the method is computationally very cheap, and provides a natural measure of quality of a model. First we formulate the method for the basic model of crisp input-crisp output data and then extend it to crisp input-interval output and interval input-interval output models. For the interval-valued cases we study several formulations of the solution concept: possibility, strong possibility, weak possibility, necessity. Here, strong possibility is a new concept proposed as a natural counterpart to the remaining ones. We prove that the method provides optimal interval parameters meeting centrality and proportionality requirements. We also show that the method provides interval regression parameters satisfying various versions of Tanaka-Lees inclusion property. We also derive a form of a complementarity theorem for the weak possibility and necessity solution concepts. Since practical problems may be affected by outlying observations we show that our approach is easily adapted to deal with them. We illustrate the theory by examples. © 2011 Elsevier B.V. All rights reserved.

Kueffer C.,ETH Zurich | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University | Richardson D.M.,Stellenbosch University
New Phytologist | Year: 2013

Invasion science is a very active subdiscipline of ecology. However, some scientists contend that theoretical integration has been limited and that predictive power remains weak. This paper, focusing on plants, proposes a new multi-pronged research strategy that builds on recent advances in invasion science. More intensive studies on particular model organisms and ecosystems are needed to improve our understanding of the full suite of interacting factors that influence invasions ('model system research'). At the same time, comparative studies across many study systems are essential for unravelling the context-dependencies of insights that emerge from particular studies ('multi-site studies'); and quantitative synthesis based on large datasets should be constrained to well-defined theoretical domains ('focused meta-analysis'). We also suggest ways for better integration of information about species biology and ecosystem characteristics ('invasion syndromes'). We expect that a resulting theory of invasions will need to be conceived as a somewhat heterogeneous conglomerate of elements of varying generality and predictive power: laws that apply to well-specified domains, general concepts and theoretical frameworks that can guide thinking in research and management, and in-depth knowledge about the drivers of particular invasions. © 2013 The Authors. © 2013 New Phytologist Trust.

Hainzl S.,German Research Center for Geosciences | Fischer T.,Charles University | Dahm T.,Institute of Geophysics
Geophysical Journal International | Year: 2012

Two recent major swarms in Western Bohemia occurred in the years 2000 and 2008 within almost the same portion of a fault close to Novy Kostel. Previous analysis of the year 2000 earthquake swarm revealed that fluid intrusion seemed to initiate the activity whereas stress redistribution by the individual swarm earthquakes played a major role in the further swarm evolution. Here we analyse the new swarm, which occurred in the year 2008, with regard to its correlation to the previous swarm as well its spatiotemporal migration patterns. We find that (i) the main part of the year 2008 activity ruptured fault patches adjacent to the main activity of the swarm 2000, but that also (ii) a significant overlap exists where earthquakes occurred in patches in which stress had been already released by precursory events; (iii) the activity shows a clear migration which can be described by a 1-D (in up-dip direction) diffusion process; (iv) the migration pattern can be equally well explained by a hydrofracture growth, which additionally explains the faster migration in up-dip compared to the down-dip direction as well as the maximum up-dip extension of the activity. We use these observations to estimate the underlying fluid pressure change in two different ways: First, we calculate the stress changes induced by precursory events at the location of each swarm earthquake assuming that observed stress deficits had to be compensated by pore pressure increases; and secondly, we estimate the fluid overpressure by fitting a hydrofracture model to the asymmetric seismicity patterns. Both independent methods indicate that the fluid pressure increase was initially up to 30 MPa. © 2012 The Authors Geophysical Journal International © 2012 RAS.

Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University | Richardson D.M.,Stellenbosch University
Annual Review of Environment and Resources | Year: 2010

Invasive species are a major element of global change and are contributing to biodiversity loss, ecosystem degradation, and impairment of ecosystem services worldwide. Research is shedding new light on the ecological and economic consequences of invasions. New approaches are emerging for describing and evaluating impacts of invasive species, and for translating these impacts into monetary terms. The harmful effects of invasions are now widely recognized, and multiscale programs are in place in many parts of the world to reduce current and future impacts. There has been an upsurge in scientific research aimed at guiding management interventions. Among the activities that are receiving the most attention and that have the most promise for reducing problems are risk assessment, pathway and vector management, early detection, rapid response, and new approaches to mitigation and restoration. Screening protocols to reduce new introductions are becoming more accurate and have been shown cost-effective. Copyright © 2010 by Annual Reviews. All rights reserved.

Blom D.J.,University of Cape Town | Hala T.,Center for Clinical and Basic Research | Bolognese M.,Bethesda Health Research Center | Lillestol M.J.,Lillestol Research | And 12 more authors.
New England Journal of Medicine | Year: 2014

BACKGROUND: Evolocumab, a monoclonal antibody that inhibits proprotein convertase subtilisin/kexin type 9 (PCSK9), significantly reduced low-density lipoprotein (LDL) cholesterol levels in phase 2 studies. We conducted a phase 3 trial to evaluate the safety and efficacy of 52 weeks of treatment with evolocumab. METHODS: We stratified patients with hyperlipidemia according to the risk categories outlined by the Adult Treatment Panel III of the National Cholesterol Education Program. On the basis of this classification, patients were started on background lipid-lowering therapy with diet alone or diet plus atorvastatin at a dose of 10 mg daily, atorvastatin at a dose of 80 mg daily, or atorvastatin at a dose of 80 mg daily plus ezetimibe at a dose of 10 mg daily, for a run-in period of 4 to 12 weeks. Patients with an LDL cholesterol level of 75 mg per deciliter (1.9 mmol per liter) or higher were then randomly assigned in a 2:1 ratio to receive either evolocumab (420 mg) or placebo every 4 weeks. The primary end point was the percent change from baseline in LDL cholesterol, as measured by means of ultracentrifugation, at week 52. RESULTS: Among the 901 patients included in the primary analysis, the overall least-squares mean (±SE) reduction in LDL cholesterol from baseline in the evolocumab group, taking into account the change in the placebo group, was 57.0±2.1% (P<0.001). The mean reduction was 55.7±4.2% among patients who underwent background therapy with diet alone, 61.6±2.6% among those who received 10 mg of atorvastatin, 56.8±5.3% among those who received 80 mg of atorvastatin, and 48.5±5.2% among those who received a combination of 80 mg of atorvastatin and 10 mg of ezetimibe (P<0.001 for all comparisons). Evolocumab treatment also significantly reduced levels of apolipoprotein B, non-high-density lipoprotein cholesterol, lipoprotein(a), and triglycerides. The most common adverse events were nasopharyngitis, upper respiratory tract infection, influenza, and back pain. CONCLUSIONS: At 52 weeks, evolocumab added to diet alone, to low-dose atorvastatin, or to high-dose atorvastatin with or without ezetimibe significantly reduced LDL cholesterol levels in patients with a range of cardiovascular risks. Copyright © 2014 Massachusetts Medical Society.

Richardson D.M.,Stellenbosch University | Pysek P.,Academy of Sciences of the Czech Republic | Pysek P.,Charles University
New Phytologist | Year: 2012

Contents: Summary 383 I. Introduction 383 II. The introduction-naturalization-invasion continuum for conceptualizing biological invasions 384 III. The biogeographical background for studying naturalization: variation among populations and regions 385 IV. Factors determining naturalization in plants 388 Acknowledgements 392 References 392 Summary: The literature on biological invasions is biased in favour of invasive species - those that spread and often reach high abundance following introduction by humans. It is, however, also important to understand previous stages in the introduction-naturalization-invasion continuum ('the continuum'), especially the factors that mediate naturalization. The emphasis on invasiveness is partly because most invasions are only recognized once species occupy large adventive ranges or start to spread. Also, many studies lump all alien species, and fail to separate introduced, naturalized and invasive populations and species. These biases impede our ability to elucidate the full suite of drivers of invasion and to predict invasion dynamics, because different factors mediate progression along different sections of the continuum. A better understanding of the determinants of naturalization is important because all naturalized species are potential invaders. Processes leading to naturalization act differently in different regions and global biogeographical patterns of plant invasions result from the interaction of population-biological, macroecological and human-induced factors. We explore what is known about how determinants of naturalization in plants interact at various scales, and how their importance varies along the continuum. Research that is explicitly linked to particular stages of the continuum can generate new information that is appropriate for improving the management of biological invasions if, for example, potentially invasive species are identified before they exert an impact. © 2012 New Phytologist Trust.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2010.4.2-1 | Award Amount: 7.36M | Year: 2010

Assuming an annual birth rate of 10.25 births/1,000 population approximately 25,000 Extremely Low Gestational Age Newborns are born every year in the EU. Conservative figures estimate that approximately half of all these babies will develop low blood pressure and require treatment. However, no uniform criteria exist to define hypotension and the evidence to support our current management strategies is limited. Many of these interventions have been derived from adult literature and have not been validated in the newborn. Dopamine remains the most common inotrope used despite little evidence that it improves outcome. Hypotension is not only associated with mortality of preterm infants but is also associated with brain injury and impaired neurosensory development in ELGAN survivors. Preterm brain injury has far reaching implications for the child, parents, family, health service and society at large. It is therefore essential that we now design and perform the appropriate trials to determine whether the infusion of inotropic agents is associated with improved outcome. We have assembled a consortium with expertise in key areas of neonatal cardiology, neonatology, neurophysiology, basic science and pharmacology with the intention of answering these questions. The objectives of the group are as follows: 1. To perform a multinational, randomized controlled trial to evaluate whether a more restricted approach to the diagnosis and management of hypotension compared to a standard approach, with dopamine as a first line inotrope, affects survival without significant brain injury at 36 weeks gestational age in infants born less than 28 weeks gestation and affects survival without neurodevelopmental disability at 2 years corrected age 2. To perform pharmacokinetic and pharmcodynamic studies of dopamine 3. To develop and adapt a formulation of dopamine suitable for newborns in order to apply for a Paediatric Use Marketing Authorization

Agency: Cordis | Branch: FP7 | Program: CPCSA | Phase: INFRA-2011-1.2.2. | Award Amount: 16.27M | Year: 2011

EUDAT is our proposal for the next stage in the realisation of the vision of data as infrastructure. The EUDAT consortium includes representatives from each stage of the value chain that has evolved to deliver scientific knowledge to researchers, citizens, industry and society as a whole. It includes funding agencies that invest in research infrastructures and programmes of research, infrastructure operators and research communities who rely on the availability of data-management services, national data centres and providers of connectivity and, of course, the users who rely on the availability of data and services, innovators who add value to the raw results of scientific research.\n\nEUDAT is a three-year project that will deliver a Collaborative Data Infrastructure (CDI) with the capacity and capability for meeting future researchers needs in a sustainable way. Its design will reflect a comprehensive picture of the data service requirements of the research communities in Europe and beyond. This will become increasingly important over the next decade as we face the challenges of massive expansion in the volume of data being generated and preserved (the so-called data tsunami) and in the complexity of that data and the systems required to provide access to it.\n\nAlthough those user requirements will vary between scientific disciplines, the micro-systems from which each communitys services are built are largely generic. This commonality will make it easier to achieve the minimum critical mass of users necessary for significant economies of scale to be achieved. The ability to rapidly provide bespoke responses to the evolving needs of our research communities additionally strengthens the business case for those communities. With the inclusion of disciplines from across the spectrum of scientific endeavour sharing a common infrastructure, EUDAT also provides the opportunity for data-sharing between disciplines and cross-fertilisation of ideas.

Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 3.23M | Year: 2012

Novel transplant regimens are currently being developed to improve beneficial GvL effects and reduce GvHD and infections via several new forms of cellular therapies. This newly emerging supra-disciplinary field of cellular therapy and regenerative medicine is also being used to improve outcomes in autoimmune disease (such as Rheumatoid Arthritis) and cancers. The goal of this research programme is to gain insight into the mechanisms of action of GvL and GvHD in order to improve current therapies and develop and test novel ones via clinical trials and/or animal model experiments. The research is therefore necessarily multidisciplinary including clinical medicine, immunology, genomics, proteomics, molecular biology and pathology. In order to implement cellular therapies across Europe the current EU Directive 2001/83/EC applies. These regulations stipulate that the cellular therapies which are advanced therapeutic medical products (ATMP) must be produced under current Good Manufacturing Practice (cGMP). Not only is there a lack of understanding of GvL vs. GvHD effects but there is also a lack of training in cGMP for both clinical and non-clinical scientists. We aim to re-address these basic current needs, as well as those of industry, which include lack of access to clinical tissue for validation of bio-markers prior to commercialisation.

Agency: Cordis | Branch: FP7 | Program: NOE | Phase: ICT-2009.2.2 | Award Amount: 7.57M | Year: 2010

Linguistic diversity is a corner stone of our multicultural European society. To preserve this essential asset in the age of the emerging information and knowledge society, Europe needs ICT technologies and applications at affordable costs that\n\n enable communication, collaboration and participation across language boundaries\n secure their language users equal access to the information and knowledge society\n support each language in the advanced functionalities of networked ICT\n\nPrerequisites of these applications are advances in several fields of Human Language Technologies (HLT) such as\n\n machine translation (MT) including automatic translation and machine assisted human translation\n technologies for information and knowledge management including IR, crosslingual IR and corporate memories\n technologies for document and content production and management (including authoring tools, language checking and interactive content applications)\n technologies for intuitive interfaces to all types of technology (including multimodal user interfaces, speech interfaces for interactive mobile applications, robot control interfaces)\n\nBuilding a single EU information space reflecting and supporting the cultural diversity of our continent as an adequate foundation for the multilingual European information and knowledge society is a major challenge. Because of the complexity of human language and the number of languages to be included this challenge demands a large collective effort of research and language communities as well as several industrial sectors.\n\nT4ME shall seek progress by approaching open problems in collaboration with other research fields such as machine learning, social computing, cognitive systems, knowledge technologies and multimedia content. It shall mobilize and strengthen the European HLT community encompassing researchers, developers and language professionals through networking of research and by creating new schemes of sharing resources and efforts.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-1.2-6 | Award Amount: 3.86M | Year: 2009

Since the sequencing of the human genome has been completed the demand for genetic analysis in the human health care system is drastically increasing, and the extension of molecular genetic diagnostics is urgently needed. However, the majority of genetic diseases is molecularly and clinically highly heterogeneous, and until recently the available techniques lacked the required capacity to analyze several genes in parallel. The recently introduced high-throughput whole genome sequencing (WGS) technology now offers the unique opportunity to extend molecular genetic analysis by introducing these techniques, and develop taylormade medical resequencing approaches for molecular genetic diagnosis of heterogeneous disorders. This project aims to deliver crucial innovations leading to these approaches, and to deliver a proof-of-principle for its implementation in selected model disorders. The model disorders have been selected with increasing genetic complexity, and represent the majority of non-multifactorial genetic disorders. The current momentum to perform these innovations by a European consortium of clinical genetic diagnostic laboratories and research laboratories and industrial stakeholders will lead to a front-running position of European laboratories and small and medium enterprises (SMEs) in this field. The consortium putting forward this proposal consists of leading scientists and established laboratories providing cutting edge knowledge with respect to quality management aspects, ethical and societal issues, and cost effectiveness issues. This is the only approach that will warrant the development of diagnostic tools designed to restrict genetic testing to relevant medical factors. For European SMEs this proposal offers the opportunity to identify niches in the steadily increasing molecular genetic market. A specially designed training programme will take care of rapid dissemination of the acquired knowledge and tools across Europe.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: ENV.2013.6.1-6 | Award Amount: 3.70M | Year: 2013

The aim of the ECONADAPT project is to provide user-orientated methodologies and evidence relating to economic appraisal criteria to inform the choice of adaptation actions using analysis that incorporates cross-scale governance under conditions of uncertainty. A critical theme of the proposal is therefore to support the application of adaptation economics in the period following the publication of the EUs 2013 Adaptation Strategy, focusing on key decision areas that need enhanced economic information, and on the key users of such information. Key decision areas include: management of extreme weather events modified by climate change that have high impact costs in the short term; appraisal of projects where the costs of climate risks are borne over long time periods; appraisal of flows of large-scale EU funds where the case for climate resilience needs to be made; macro-economic effects of climate change risks and adaptation strategies at Member State and EU levels, and; appraisal of overseas development assistance aimed at reducing the damage costs of climate risks in less developed countries. The project will work intensively with stakeholders from e.g. relevant DGs, Member States, Regional or local policy makers, and seek to learn from, and inform, experience. The methods and approaches will be co-developed with the diverse user groups engaged in using economic data within adaptation decision making. A two-tier approach is proposed to provide detailed guidance and empirical data: first, to other economists or private sector organisations with adaptation needs, and second, to other users who may want to use light-touch methods, with the empirical data to help in scoping decision making outcomes. A strong link will be made with the European Climate Adaptation Platform (Climate-ADAPT), with the guidance and economic information designed for a wide range of users.

Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: ENV.2010.5.1.0-2 | Award Amount: 1.01M | Year: 2011

Based on indications from EC and FP7 statistics, the Central and Eastern European (CEE) countries participate at low rate in the FP7 Environment theme. On the other hand air pollution, chemical pollution and environmental risks should be handled with expressed interest in this region, due to severe environmental damages caused by decades of negligence and mishandling. CEE researchers have been conducting research in the mentioned fields since the middle of the 20th century, however, their results did not reach and influence - either the policy makers of their own country, or their academic counterparts in EU-15. The main objective of ENVIMPACT is to enrich the EU knowledge base with the environment-related results of the CEE researchers, thus inducing new collaborations under FP7/FP8 which may lead to innovative solutions for the lasting protection of our environment. Using local contacts, knowledge and the insight of expert groups consisting of relevant academic, industrial/ETP and policy representatives, the innovative environmental research practices and results originating from Central and Eastern Europe will be identified, mapped and made available for the governmental, academic and industrial stakeholders all over Europe. After analysing the presently applied dissemination and exploitation practices of CEE research results (by SWOT analysis), good and bad practices will be presented in an online catalogue. Recommendations will be prepared for the development a taylor-made toolkit. To close the communication gap, CEE researchers will be offered trainings and online mentoring services, based on the recommendations for communication and exploitation of research results. Partners from 7 NMSs will ensure the availability of local research results, while representatives from 4 EU-15 countries will help to identify and match the needs in terms of communication of CEE/EU-15 researchers and will provide the expertise in reaching the relevant stakeholders.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2007.4.1 | Award Amount: 16.56M | Year: 2008

Text that is not digital is virtually invisible. Todays readers search the internet for electronically accessible texts rather than visit the reading room of a library. Born-digital and digitised contemporary materials contain the richness that allows tools such as text mining and the semantic web to offer superior accessibility but the story is very different for historic documents. A vital part of the European heritage, encompassing more than four centuries of historic books and bound periodicals is becoming less and less visible to the public at large.\nWith the i2010 vision of a European Digital Library, the EU has launched an ambitious plan for large scale digitisation projects transforming Europes printed heritage into digitally available resources. However, lack of institutional knowledge and expertise slows down the pace with which this vision can be realised. The state-of-the-art in OCR performance and machine understanding of the original document is inadequate, especially for historically important material with archaic fonts and spellings, newspapers with complex layouts, bound volumes, microfilm or typescript.\nThe IMPACT project will remove many of these barriers. It brings together fifteen national and regional libraries, research institutions and commercial suppliers - all centres of competence with unequalled experience of large-scale text digitisation processes and technologies. The project will let them share their know-how and best practices, develop innovative tools to enhance the capabilities of OCR engines and the accessibility of digitised text and lay down the foundations for the mass-digitisation programmes that will take place over the next decade. This project will facilitate a more collaborative approach to mass-digitisation. It will build capacity and lower the barriers to entry for organisations in the early stages of their own digitisation activity.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH-2009-2.1.1. | Award Amount: 3.32M | Year: 2009

The project will contribute to the goals of the Call showing that it is possible to better address global changes in a long term time perspective (20302050), making a first development of tools new generations of models and indicators with enhanced capabilities to take into account the interaction between the economy and the environment, paradigm shifts in the energy-transport-environment nexus and the land-use and territorial functions. The objectives of PASHMINA will include: 1. production of exploratory scenarios (qualitative storylines) of future global change options up to 2030 and 2050, complemented by a quantitative analysis of key development indicators (GDP, well being, etc.) undertaken by means of global long term meta-models (WP1) 2. analysis of the consequences of the paradigm shifts in the energy-transport-environment nexus related to the urban functions: housing, mobility, recreation, etc. (WP2) 3. analysis of the possible paradigm shifts in the land use and territorial functions related to agriculture, forestry and more in general ecosystem services: e.g. biofuels, biodiversity, ecosystems metabolism, etc. (WP3) 4. first development a new generation of global indicators and models, starting from already existing sustainability accounting and general equilibrium modelling frameworks and adapting these to make them (more) sensitive to paradigm shifts in the long-term perspective (WP4) 5. pilot assessment of possible adaptation and mitigation strategies to tackle with different paradigm shifts, evaluating their trade-offs (WP5). 6. to produce a comparative evaluation of the advancements in modelling tools achieved by PASHMINA, and to disseminate those in the scientific and stakeholders communities by means of innovative dissemination tools (virtual library, wiki-web tools, webGIS application) and other dissemination activities (WP6).

Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: ENV.2008. | Award Amount: 10.33M | Year: 2009

Our capacity to effectively sustain biodiversity across spatial and temporal scales is an essential component of European environmental sustainability. Anthropogenic and environmental pressures on biodiversity act differently at different scales. Consequently, effective conservation responses to these threats must explicitly consider the scale at which effects occur, and therefore it is crucial that administrative levels and planning scales match the relevant biological scales. The SCALES project will provide the scientific and policy research needed to guide scale-dependent management actions. It will assess and model the scaling properties of natural and anthropogenic processes and the resulting scale-dependencies of the impacts of these pressures on various levels of biodiversity from genes to ecosystem functions. To facilitate these assessment methods for upscaling and downscaling biodiversity data will be reviewed and improved. SCALES will further evaluate the effectiveness of management and policy responses to biodiversity loss in terms of their scale-relevance and will develop new tools for matching their scales to relevant biological scales. Finally, a resulting methodological and policy framework for enhancing the effectiveness of European biodiversity conservation across scales will be developed and tested. This framework focuses on networks of protected areas and regional connectivity. This framework will be disseminated to a wide range of relevant users via a web based support tool kit (SCALE-TOOL) and by means of further dissemination channels, such as conferences, publications, and the mass media.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH-2010-2.1-3 | Award Amount: 3.46M | Year: 2011

World societies experience today large transformation processes both in the social, economic and environmental dimensions. These transformations are usually described under the heading of global change, to emphasize the increasing interactions between them. The objective of the proposal is three-fold: (1) to provide significant advances in the estimation of socio-economic impacts of global challenges at Global, European and regional scale; (2) to identify optimal adaptation strategies; (3) to evaluate total costs and the optimal mix of adaptation and mitigation against global changes. Work Package (WP) 1 will examine the sources, interactions and characteristics of global changes, including the emergence of fast-growing economies, environmental degradation, competition on the use of exhaustible resources, international competitiveness issues. A primary objective of the proposal is to estimate socio-economic impacts arising from global changes by using economic models. The consortium is endowed with a large set of state-of-the-art, internationally renown, modeling tools. Models will be further expanded and enriched in WP 3. Key areas of research will be: agriculture, forestry, land use, energy, EU competitiveness, labor, international trade. The socio-economic impact of these challenges on key sectors/areas will be examined with the enhanced set of models in WP 4 and WP 5. While in WP 4 impacts of global challenges will be studied assuming limited adaptive capacity, in WP 5 optimal adaptation strategies will be examined. WP 5 will also inform on total costs of global challenges and on the optimal mix of mitigation and adaptation. In WP 2 will develop empirical and theoretical insights on key issues which will have a value per se and will also be used to enhance models in WP 3. WP 6 will complement the analysis of WP 4 and WP 5 developing theoretical innovations concerning discounting, risk and ambiguity and by testing them numerically with models.

Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-ITN-2008 | Award Amount: 5.04M | Year: 2009

Storing CO2 in the subsurface to reduce global warming, finding hydrocarbon and other resources and monitoring their extraction, generating energy with Earths internal heat, and forecasting natural hazards (earthquake-induced ground motion, volcanic eruptions) requires high-resolution tomographic images of the Earths interior. The main goal of QUEST is research and training in the development of strategies for automated seismic imaging using the increasing power of 3-D simulation technology. While so far the observed information was severely reduced to determine Earths structure, the massive increase in available computational resources allows us now to make use of the complete information contained in the observations. With narrowing resources and increasing energy prizes the exploration industry is seeking highly skilled young scientists capable of driving the new computational technologies towards industrial problems. Earth Science graduating students are lacking profound theoretical and practical training in numerical methods and high-performance computing. QUEST intends to fill this gap offering the students excellent prospects in industry and academia as the combination of skills to be trained are highly in demand. We also expect substantial progress in understanding the dynamics of our planet, the quantification of natural hazards such as earthquakes, tsunamis, and volcanic eruptions. QUEST will link world-leading scientists in methodologies such as computational wave propagation, the theory of inverse problems and global tomography with two of the best industrial research laboratories in geophysics and computing world wide. QUEST will have a lasting impact on the practice of seismic tomography, leading to High-Performance-Computing solutions applicable to industrial and academic challenges, and a generation of young researchers capable of producing better Earth images that help us tackle the challenges of future energy-resource management and natural-hazard related research.

Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 3.01M | Year: 2012

Coding of biochemical information is commonly described to be based solely on nucleotides and amino acids, whereas carbohydrates, the most abundant type of molecule in Nature, appear sidelined in this respect. That carbohydrates, as part of cellular glycoconjugates, have exceptional talents for building biochemical signals is an emerging insight, at the heart of the concept of the Sugar Code. Intuitively, emergence of recognition partners for information transfer is expected, and this is the case. Thus, coding of bioinformation in glycans and information transfer via lectins is key to a wealth of medically relevant processes, e.g. infection, immune regulation and malignancy, now awaiting its full exploitation pharmaceutically. To do so, training in this exceptionally interdisciplinary field needs to be provided. With this aim, scientific and country/gender issues are strategically combined in this network. Its composition assures a continuous chain of research expertise, from computational and synthetic chemistry to state of the art biophysical chemistry and structural biology, then to biochemistry, molecular cell biology and pharmaceutical/biomedical sciences, generating innovative clinical approaches. Notably, academia is linked with industry, bringing in the essence of business acumen into the training programme. This activity and the research deliberately planned as interdisciplinary projects ensure an optimal training for young researchers in a dynamically developing area of conspicuous biopharmaceutical potential. Equally important, it lays the foundation to inspire novel strategies for the design of potent and selective inhibitors against lectins and the development of lectins (or suitably engineered variant(s)) as therapeuticals. As a boon for the success of the network, cooperations between several partners have already proven successful, especially increasing the core in Madrid and partners in Dublin, Munich and Prague.

Agency: Cordis | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2011-1.1.20. | Award Amount: 12.58M | Year: 2012

The Project promotes the access to five European Research Infrastructures, and it is structured into nine Networking Activities, plus the Management of the Consortium, and fourteen Joint Research Activities. The Project will profit of the success of the previous HadronPhysics project in FP6 and the current HadronPhysics2 in FP7, and originates from the initiative of more than 2.500 European scientists working in the field of hadron physics. Hadron physics deals with the study of strongly interacting particles, the hadrons. Hadrons are composed of quarks and gluons. Their interaction is described by Quantum Chromo Dynamics, the theory of the strong force. Hadrons form more complex systems, in particular atomic. Under extreme conditions of pressure and temperature, hadrons may loose their identity and dissolve into a new state of matter similar to the primordial matter of the early Universe. The Networking Activities are related to the organization of experimental and theoretical collaborative work concerning both ongoing activities at present Research Infrastructures and planned experiments at future facilities. In hadron physics the close interaction between experimentalists and theoreticians is of paramount importance. The Joint Research Activities concentrate on technological innovations for present and future experiments. Applications in material science, medicine, information, technology, etc., represent natural fall-outs. The main objective of this Integrating Activity is to optimize the use and development of the Research Infrastructures existing in Europe working in the field of hadron physics. The Project aims as well at structuring, on European scale, the way Research Infrastructures operate, and at fostering their joint development in terms of capacity and performance. The approach used is the bottom up approach, to respond to the needs of the scientific community in all fields of science and technology.

Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: HEALTH.2010.2.3.3-1 | Award Amount: 16.37M | Year: 2011

To address the call for proposals Biology and control of vector-borne infections in Europe launched by the European Commission, we want to investigate the biological, ecological and epidemiological components of vector-borne diseases (VBD) introduction, emergence and spread, and to propose innovative tools for controlling them, building on the basis of acquired knowledge. We have selected the main groups of arthropod vectors involved in the transmission of vector-borne diseases in Europe: ticks, mosquitoes, sandflies, and biting midges (Culicoides). We have also selected the main diseases of actual or possible importance in human and veterinary public health. Rodents, insectivores and rodent-borne diseases have also been considered, both for their direct importance in public health, and for the major role of rodents and insectivores as reservoir hosts of many pathogens. We have put a strong focus on vector- and disease-quantitative modelling. The resulting predictive models will be used to assess climate or environmental change scenarios, as well as vector or disease control strategies. Human behaviour and risk perception are an important component of VBD introduction, emergence and spread. The consequences triggered by VBD for human and veterinary public health in Europe are just starting to emerge in public awareness. We will also account for this aspect of human and veterinary public health in our proposal. Finally, the set of innovative research methods, tools and results obtained during the project will be a step forward a generic approach of VBD in terms of disease monitoring and early warning systems, and will reinforce the general framework for an integrated pest and disease management system. For all these aspects, we will benefit from, and amplify the strong scientific results, capacity building, and research networks established by EDEN project on emerging, vector-borne diseases in a changing European environment.

This research project meets the EU guidelines for youth policy and the Lisbon strategy by focusing on socially excluded youth homeless young people and those at risk of homelessness - and through promoting a dynamic understanding of their life-trajectories. It takes into account gender, ethnic minority and migrant status and its policy outcomes and programme recommendations will also apply to those with low education qualifications, and poor employment and social integration prospects. It involves the active participation of young people as co-researchers. Levels of youth homelessness vary between European countries in relation to the patterns of support available to young people and within countries in relation to gender, ethnic minority group and migrant status. However, even Mediterranean societies, with strong family support systems, have begun to experience youth homelessness amongst local as well as migrant populations. In Northern Europe interventionist programmes have been developed designed to: a) structure case work with hostel dwellers (the Netherlands 8-Steps Programme); b) prevent youth homelessness among those at risk through a cluster of local services (the UK Safe Moves programme). Working with NGOs, CSEYHP will: (1) Study the life trajectories of homeless youth populations in different national contexts, identifying risk, processes of social exclusion and points of reinsertion; (2) Introduce and investigate the use of the 8-Steps and Safe Moves programmes with NGOs working with homeless youth in NL, UK, P and CZ; (3) Investigate the roles of trusted adults, lead professionals, peer mentors and family members in delivering reinsertion strategies; and (4) Develop the concepts of risk, social exclusion and shelter exclusion both theoretically and practically. Expected impacts include change in the working practice of NGOs, empowerment for young people and national and EU recognition of the issue of youth homelessness.

Agency: Cordis | Branch: FP7 | Program: CSA | Phase: ICT-2011.9.1 | Award Amount: 486.75K | Year: 2012

We seek to bring together all major European and Israeli research centres in Optimal Control of Quantum Information Processing. This project will coordinate ongoing research activities, best practice dissemination, personnel training and public engagement as well as interaction with public stakeholders and policymakers for 17 established research groups from 15 universities in 6 countries a total of about 60 scientists and 30 PhD students, spanning a variety of nationalities, races, cultures, social backgrounds, genders and career stages.The proposed Consortium will join the forces of multiple EU and Israeli research groups to explore a radical alternative to the currently established information processing technologies quantum information processing, where bits are carried by atoms or elementary particles and dramatic acceleration is believed to be possible for several types of computational tasks. Our specific research area within Quantum Information Processing is optimal control of quantum bits a set of technologies that enable extremely accurate manipulation of quantum bits with minimal expenditure of energy.Within this Coordination Action, we aim to create a vibrant, productive and efficient European research community, to deliver value to the society and to grow a new generation of young European physicists.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: Fission-2010-1.1.2 | Award Amount: 3.26M | Year: 2011

InSOTEC aims at identifying the main socio-political challenges for implementing geological disposal and their interplay with technical challenges. It will furthermore provide the IGD-TP with concrete suggestions on how to address these entangled socio-technical challenges. The biggest challenge today lies in adapting the generic concept of geological disposal to the real world environment (both natural and social) in which it needs to be implemented and with which the whole of the waste management system will need to build and maintain a long-term sustainable relationship. Addressing this challenge will imply searching for a strong and lasting connection between the technical and social aspects of managing radioactive waste. InSOTEC wants to contribute to addressing this challenge by: - Identify and clarify socio-technical challenges for implementing geological disposal (and radioactive waste management in general). - Develop further analytical insights into these challenges by means of a number of case studies on specific topics, addressing the interplay between technical and socio-political challenges. - Advance and facilitate mutual learning, and advise and assist scientists and technological experts to develop the tools and the ability to communicate in a two way process about their work and to engage with stakeholders on technical and safety issues. - Advise the IGD-TP on how to strengthen its position and message to the world of decision-makers, through the integration of a social component within its scope of work by: o Exploring with the IGD-TP how to fulfil its ambition to link a broader range of stakeholders (of which some non-institutional) on a structured basis to the platforms Exchange Forum. o Making concrete suggestions to the IGD-TP on how to set priorities for a social sciences and multidisciplinary research agenda that will help to address the socio-technical as one single problem

Agency: Cordis | Branch: FP7 | Program: CP | Phase: Fission-2007-1.2-01 | Award Amount: 23.78M | Year: 2008

Actinide recycling by separation and transmutation is considered worldwide and particularly in several European countries as one of the most promising strategies to reduce the inventory of radioactive waste, thus contributing to make nuclear energy sustainable. Consistently with potentially viable recycling strategies, the Collaborative Project ACSEPT will provide a structured R&D framework to develop chemical separation processes compatible with fuel fabrication techniques, with a view to their future demonstration at the pilot level. Considering technically mature aqueous separation processes, ACSEPT will optimise and select the most promising ones dedicated to actinide partitioning and those featuring a group separation. These developments will be appropriately balanced with an exploratory research focused on the design of new molecules. In parallel, promising group actinide separation pyro-processes will be developed beyond the current state-of-the-art, as an alternative option, for a longer term. ACSEPT will also pave the way towards more integration between Partitioning and Transmutation by carrying dissolution as well as actinide conversion studies. All experimental results will be integrated by carrying out engineering and systems studies on aqueous and dry (pyro) processes to prepare for future demonstration at a pilot level. A training and education programme will also be implemented to share the knowledge among partitioning community and present and future generations of researchers. The challenging objectives of ACSEPT will be addressed by a multi-disciplinary consortium composed of European universities, nuclear research bodies and major industrial players. This consortium will generate fundamental improvements for a future design of an Advanced Processing Pilot Unit. ACSEPT will thus be an essential contribution to the demonstration, in the long term, of the potential benefits of actinide recycling to minimise the burden on the geological repositories.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: ENV.2007. | Award Amount: 5.10M | Year: 2008

The MEGAPOLI project brings together leading European research groups, state-of-the-art scientific tools and key players from third countries to investigate the interactions among megacities, air quality and climate. MEGAPOLI will bridge the spatial and temporal scales that connect local emissions, air quality and weather with global atmospheric chemistry and climate. The main objectives are: (i) to assess impacts of megacities and large air-pollution hot-spots on local, regional and global air quality, (ii) to quantify feedbacks among megacity air quality, local and regional climate, and global climate change, (iii) to develop improved integrated tools for prediction of air pollution in megacities. In order to achieve these objectives we will: - Develop and evaluate integrated methods to improve megacity emission data; - Investigate physical and chemical processes starting from the megacity street level, continuing to the city, regional and global scales; - Assess regional and global air quality impacts of megacity plumes; - Determine the main mechanisms of regional meteorology/climate forcing due to megacity plumes; - Assess global megacity pollutant forcing on climate; - Examine feedback mechanisms including effects of climate change on megacity air quality; - Develop integrated tools for prediction of megacity air quality; - Evaluate these integrated tools and use them in case studies; - Develop a methodology to estimate the impacts of different scenarios of megacity development on human health and climate change; - Propose and assess mitigation options to reduce the impacts of megacity emissions. We will follow a pyramid strategy of undertaking detailed measurements in one European major city, Paris, performing detailed analysis for 12 megacities with existing air quality datasets and investigate the effects of all megacities on climate. The results will be disseminated to authorities, policy community, researchers and the other megacity stakeholders.

Agency: Cordis | Branch: FP7 | Program: CP-FP-SICA | Phase: ENV.2010.1.2.3-2 | Award Amount: 4.55M | Year: 2011

The project will examine the health impacts of greenhouse gas (GHG) reduction policies in urban settings in Europe, China and India, using case studies of 3-4 large urban centres and three smaller urban centres. Sets of realistic interventions will be proposed, tailored to local needs, to meet published abatement goals for GHG Emissions for 2020, 2030 and 2050. Mitigation actions will be defined in four main sectors: power generation/industry, household energy, transport and food and agriculture. The chief pathways by which such measures influence health will be described, and models developed to quantify changes in health-related exposures and health behaviours. Models will include ones relating to outdoor air pollution, indoor air quality and temperature, physical activity, dietary intake, road injury risks and selected other exposures. Integrated quantitative models of health impacts will be based on life table methods encompassing both mortality and morbidity outcomes modelled over 20 year time horizons. Where possible, exposure-response relationships will be based on review evidence published by the Comparative Risk Assessment initiative or systematic reviews. Uncertainties in model estimates will be characterized using a mathematical framework to quantify the influence of uncertainties in both model structure and parameter estimates. Particular attention will be given to economic assessments, both in terms of behavioural choices/uptake of various forms of mitigation measure (with new surveys to address evidence gaps), and in terms of health benefits and costs calculated from societal, health service and household perspectives. A decision analysis framework will be developed to compare different mitigation options. Experts and user groups will be consulted to define the mitigation questions to be examined, and the results will be discussed in consultative workshops scheduled for the final months of the project.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-3.1-5 | Award Amount: 1.29M | Year: 2009

The inappropriate supply and consumption of non-prescribed medicines consists a public health problem of outmost importance for developed as well as for developing countries. The aims to develop new research methods and generate scientific basis to reduce the incidence of drug-related mishaps and maximize the potent effect of medicines in the provision of healthcare. The project utilizes a theory-specific approach to identify and understand primary care physicians and primary care patients behaviour towards prescription and consumption of medicines. Grounded on the theory of planned behaviour (TPB; Ajzen, 1991) seeks to identify predisposing behavioural factors that will enable the alteration of the problematic behaviour. This model also provides the basis for theory-guided interventions, tailored to address the behavioural components playing an influential role in the irrational prescription and consumption of medicines. In particular, the projects objectives include the assessment of the extent of OTC misuse in countries of southern Europe, the identification of influential factors on primary care physicians and patients intentions towards irrational prescription and misuse of medicines as well as the design and implementation of certain pilot interventions with the potential to be translated into policy. Qualitative and quantitative research methods will be employed to assess predisposing factors of inappropriate prescription practices and medicine misuse in samples of primary care physicians and primary care patients. Pilot interventions will be also devised and applied. Southern European countries will benefit from the progress and the know-how of northern European countries invited to participate in the current proposal. Another benefit will be the formation of a network consisting of various disciplines that ensures evaluation, discussion and widespread dissemination of emerging knowledge throughout European primary health care settings.

Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: HEALTH-2007-4.1-8 | Award Amount: 679.12K | Year: 2009

The EECAlink is a coordination action aimed at identification of joint research priorities of the EU and EECA countries and strengthening scientific collaboration among them. International Cooperation Partner Countries targeted by our proposal are: Armenia, Belarus, Georgia, Kazakhstan, Moldova, Russia, Ukraine and Uzbekistan. EECAlink represents (i) a measure of active encouragement of the international Health research related cooperation and allows (ii) strengthening of the existing bi-lateral scientific collaboration of all participating university/academia partners. Project consortium was balanced to be able to act as a pipe-line for communication of the (iii) research priorities of EECA countries to relevant EU policy makers and vice versa, (iv) help to coordinate future joint calls relevant to the Health Theme. Last, but not least, (v) to build capacities for proposal submission in FP7. EECAlink is proposed to run for 30 months. For the project communication and impact evaluation purposes, we have defined three major target stakeholder groups: 1. Policy makers this target group is further divided into (i) European and (ii) national. The first stakeholder group represents a key element for creation of European added value through identification of joint research opportunities for future calls in the area of Health research 2. Universities and academia partners the project is coordinated by the Charles University in Prague and represents a consortium of ten academic partners, who wish to both strengthen and extend their international collaboration in topics identified in FP7-TP Health programme 3. Wider RTD public research and innovation managers and individual scientific group leaders from participating countries interested in submitting own FP7 proposals

Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: HEALTH.2012.2.1.1-1-C | Award Amount: 17.68M | Year: 2012

Despite examples of excellent practice, rare disease (RD) research is still mainly fragmented by data and disease types. Individual efforts have little interoperability and almost no systematic connection between detailed clinical and genetic information, biomaterial availability or research/trial datasets. By developing robust mechanisms and standards for linking and exploiting these data, RD-Connect will develop a critical mass for harmonisation and provide a strong impetus for a global trial-ready infrastructure ready to support the IRDiRC goals for diagnostics and therapies for RD in close collaboration with the successful A/B projects. It will build on and transform the current state-of-the-art across databases, registries, biobanks, bioinformatics, and ethical considerations to develop a quality-assured and comprehensive integrated hub/platform in which complete clinical profiles are combined with -omics data and sample availability for RD research. The integrated, user-friendly RD-Connect platform, built on efficient informatics concepts already implemented in international research infrastructures for large-scale data management, will provide access to federated databases/registries, biobank catalogues, harmonised -omics profiles, and cutting-edge bioinformatics tools for data analysis. All patient data types will be linked via the generation of a unique identifier (RD-ID) developed jointly with the US NIH. The RD-Connect platform will be one of the primary enablers of progress in IRDiRC-funded research and will facilitate gene discovery, diagnosis and therapy development. RD-Connect has the RD field at its heart and brings together partners with a strong track record in RD research (gene discovery and development of innovative treatments), as well as committed IRDiRC funding partners and representatives of all major international RD initiatives (EU/US/AU/JP) spanning patient organisations, research and public health, to maximise impact to RD patients

Agency: Cordis | Branch: FP7 | Program: BSG-SME | Phase: SME-1 | Award Amount: 1.48M | Year: 2008

At any moment in time, the decision makers within SMEs have a wide range of development opportunities available to them to advance the competitive position of their firm. These opportunities typically include development of new products or the improvement of their process performance. However, it is very difficult to determine, ex-ante, to which combination of improvement opportunities they should devote resources in order for the firm to maximise its performance. The ValuePOLE project is focused on delivering a Model, an ICT Tool and a Methodology to answer this challenge for the SME decision maker so that they can maximise their competitive position with the minimum investment of resources. ValuePOLE, delivers - a new Predictive Performance tool for SMEs, to maximise value creation in the entire product, process life cycles. (ValuePOLE will maximise value creation by providing an infrastructure for the ex-ante, i.e. before the event, prediction of performance outcomes in planned innovations). - a model for performance Prediction and Optimisation of the product and process Lifecycles in SME value chains. - a methodology that goes beyond lean in that it enables organisations to better deploy its resources to be both operationally effective through the selective application of improvement methodologies to current organisational configurations for todays customers as well as strategically flexible in the adaptation of new configurations of products, processes, technologies, competencies, and systems that enable the satisfaction of tomorrows customers. ValuePOLE will support organisations for improvements in processes and innovations in products based on either existing or new technologies.

Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: HEALTH.2010.1.2-3 | Award Amount: 2.25M | Year: 2011

EuroGentest is an FP6 European network for the harmonization of genetic testing and for the further improvement of quality in genetic services across Europe. This proposal is to support EuroGentest2, a Coordination Action that will cover the different aspects of quality assurance of genetic practice and has all the ingredients to fulfil the needs. EuroGentest2 will be concerned with setting the targets for laboratory and health professional accreditation, by contributing to guidelines and standards, and actively interacting with the professional organizations and the policy makers. EuroGentest2 will also assist the diagnostic and clinical community and the individual laboratories and counselling units in reaching those aims by providing tools for quality management and by coordinating training activities. EuroGentest2 will extend its activities from postnatal diagnostic and predictive testing to prenatal testing, thereby building on the achievements of the FP6 SAFE network, and to direct to consumer testing. A major aim of the Coordination Action will be the creation of a European association of genetic diagnostic centres that will guarantee the future of the network. The Coordination Action will lead to the further harmonization and quality assurance of genetic practice. The patients will benefit by the improvement of the analytical and clinical quality and validity of the testing, and from improved trans-border services and information. The European diagnostics industry will benefit through a faster access of innovations to the market through the validation for diagnostic use. It will enable countries and regions with less developed health care infrastructure to develop standards for best practice of provision of clinical genetic service. The Coordination Action will also identify research needs and have the capacity to set a research agenda that corresponds to the needs of the human genetics community

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH.2013.1.3-2 | Award Amount: 3.34M | Year: 2014

During the global financial crisis and ensuing Great Recession, economists at policy-making institutions had little choice but to augment macroeconomic models with ad-hoc assumptions and adjustments in order to provide analysis and advice for policy makers. Our consortiums proposal aims to move policy-focused macroeconomic modelling beyond this approach to the endogenous modelling of the dynamics resulting from financial risks and related decision making in banks, households, firms and public institutions. We bring together four broad lines of research to systematically develop new behavioural and institutional building blocks, integrating them in policy-focused macroeconomic models and using these models in a new framework for policy evaluation. In terms of building blocks, one line of research moves beyond the assumption of representative and homo-oeconomicus-type agents to incorporate micro-behavioural realism in decision making, while a second line of research advances the modelling of financial institutions, their fragility and the dynamics of systemic risk. The third line of research integrates these new building blocks (including a selection of those developed by researchers outside the consortium) in a new generation of policy-focused macroeconomic models. In parallel, in the fourth line of research new policy evaluation tools are developed, with a focus on robust tools aimed at containing financial contagion and boom-bust cycles, maintaining fiscal sustainability and coordinating monetary, fiscal and regulatory policies in normal and crisis regimes. The consortium comprises researchers with a strong track record in advancing the frontier on behavioural and institutional modelling, highly influential macroeconomic modellers as well as seasoned veterans of model-based monetary, fiscal, and regulatory policy evaluation and design. Consortium members have strong academic backgrounds as well as substantive practical experience at policy-making institutions.

Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: NMP-2007-2.1-3;NMP-2007-1.3-5 | Award Amount: 1.46M | Year: 2008

NaPolyNet is a 36-month project involving 16 partners from 10 European countries. The objectives are: 1. to network at regional, national and international level with experts on the characterization of polymer nanostructured materials in the field of packaging, textiles and membranes, bridging the gap between scientific and engineering approaches for the improved understanding of the structure-performance correlation in polymer devices; 2. to facilitate transnational access to important and unique equipment and to train young scientists and SMEs technologists; 3. to harmonize the work necessary for new standards in the field of characterization of polymer nanostructures for packaging, textiles and membranes. NaPolyNet will also focus on latest findings for managing the safety implications of polymer nanostructure along the life-cycle of those products. The activities are grouped into 7 work-packages (WP): After setting up the procedures for managing the project (WP1), the team will map the competences in the different fields of characterization of polymer nanostructures and will set up an European Open Laboratory (EOL) open to outside the consortium partners (WP2) incorporating the best and novel characterization methodologies and expertises. The EOL will be the base of the demonstration activities planned in WP3 and for the activities reported in WP4 that aims at making soon available experimental and theoretical strategies and routines in developing stage at the EOL location. This will allow average trained users of equipment for thermal, structural, morphological, mechanical characterization to produce reliable data on nanostructured materials and correctly interpret them. An International Workshop is planned on processing-structure-dynamics and properties of polymer nanostructures (WP5) in order to further support development and design of intrinsically safe nanomaterials. WP6 is completely dedicated to harmonize the work for preparation of new standards for polymeric nanomaterials characterization. WP7 aims at disseminating, knowledge-transfer and reporting with the purpose of giving the project a significant impact beyond the consortium participants and contributing to overcome barriers to the industrial application of polymer nanostructured materials especially in SMEs.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: SEC-2007-6.4-01 | Award Amount: 3.01M | Year: 2008

EUSECON analyses the newly emerging field of European security economics by identifying the nature and scope of this research field, by bringing together the leading European research players in this field and by building new analytical and conceptual insights on the most pressing research needs in this field. By implementing these research activities, EUSECON will establish an operational network of the leading European researchers in security economics, which in turn will enable research-based policy advice on economic aspects of security. In order to achieve these aims, EUSECON builds an integrated and collaborative approach, which will lay the foundations for the development of a new European multidisciplinary research agenda in security economics and security policy. The unifying theme of the proposed research are the human drivers of the new insecurity, that is terrorism and organized crime. Specifically, EUSECON analyses the causes, dynamics and long-term effects of both human-induced insecurity threats and European security policies. The approach will promote in-depth understanding of insecurity threats emerging from terrorism and organised crime with a view to uncover the much-needed information base for effective domestic and international security policy. In terms of proven research performance in this field and relevant past policy advisory activities, the sixteen members of the consortium represent the best economists and social scientists in this field in Europe today. It is expected that EUSECON will significantly advance the European research capacity well beyond the life.-time of this project, even vis--vis the currently strongly dominant American research capacity. This will also improve the long-term viability of the European policy making capacity on security and competitiveness in this field.

Agency: Cordis | Branch: FP7 | Program: CSA-SA | Phase: SiS.2012.2.2.1-1 | Award Amount: 3.56M | Year: 2013

The aim of this teacher training project is to help transform science and mathematics teaching practice across Europe by giving teachers new skills to engage with their students, exciting new resources and the extended support needed to effectively introduce enquiry based learning into their classrooms. We will do this by working with teacher training institutions and teacher networks across Europe where we will implement innovative training programmes called enquiry labs. These will be based around the core scientific concepts and emotionally engaging activity of solving mysteries, i.e. exploring the unknown. The enquiry labs will use scientists and communication professionals (e.g. actors, communication experts, etc.) to mentor teachers through the transition to use enquiry to teach science. A spoke and hub model for coordination and delivery allows the project to both respond to local country needs while maintaining an overall EU wide sharing of best practices and reporting.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: ENV.2007. | Award Amount: 4.61M | Year: 2008

There is increasing interest in the economics of climate change to inform policy on a) long-term targets, b) the costs of inaction (the economic effects of climate change), and c) the costs and benefits of adaptation. The objectives of this study are to advance knowledge across all three areas, i.e. the full economic costs of climate change, through the following tasks: 1. To identify and develop consistent climate change and socio-economic scenarios, including mitigation scenarios; 2. To quantify in physical terms, and economic costs, the costs of inaction for these scenarios, with bottom-up disaggregated (spatial) modelling for market and non-market sectors (coasts, health, ecosystems, energy, water, infrastructure) in the EU and other major negotiator countries (US, China, India). To extend analysis to quantify and value the costs and benefits of adaptation, and the residual costs of climate change after adaptation. 3. To asses the physical effects and economic damages of a number of the most important major catastrophic events and major socially contingent effects. 4. To update the mitigation costs of GHG emission reductions for medium and long-term reduction targets/ stabilisation goals. To include (induced) technological change, non CO2 GHG and sinks, and recent abatement technologies. 5. To quantify the ancillary air quality benefits of mitigation, using a spatially detailed dis-aggregated approach to quantify in physical terms and monetary benefits, in Europe and major negotiator countries. 6. To apply a number of complementary CGM and IAM models to incorporate the information from the tasks above. 7. To bring all the information above together to provide policy relevant output, including information on physical effects and economic values, and undertake analysis of policy scenarios. The project involves a multi-disciplinary team with leading impact and economic experts. It is innovative in developing bottom-up and top-down analysis within consistent scenarios and a single integrated framework, providing highly dis-aggregated outputs on impacts and economic costs.

Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: Fusion-2007-7.1 | Award Amount: 2.48M | Year: 2008

This aim of the FUSENET project is the establishment of a European Fusion Education Network (FUSENET) for education in fusion science and technology, as part of a comprehensive package of coordination actions, in order to increase, enhance, and broaden fusion training and education activities in Europe. The project consists of eleven focused work packages, with a total proposed budget of 2,000,000 . The project brings together a broad representation of the European fusion community with 36 participants from 18 countries, of which 22 Universities and 14 Euratom Associations. The project consists of four groups of coordination actions: the establishment and running of the FUSENET network; development of individual learning opportunities and common educational goals; development of educational materials and hands-on experiments; and funding of joint educational activities. The FUSENET project will cover all education levels, from secondary school through Bachelor and Master level, to PhD. The actions of FUSENET build upon the already strongly coordinated European Fusion Research programme, coor-dinated under the European Fusion Development Agreement EFDA. The network will be given a permanent identity by the establishment of the FUSENET Association, which will provide a platform for the coordination of existing actions, the initiation, development and implementation of new EU-wide actions, and for the exchange and dissemination of fusion education information. The envisioned concrete end result of the FUSENET project is an integrated fusion education system in Europe, with strong links between fusion institutes and higher education institutes. Through a central website, the pro-gramme will offer a transparent structure of coherent educational actions, accessible and inviting, in which stu-dents and teachers can easily find their way to a variety of attractive ways to participate in the fusion research programme.

Agency: Cordis | Branch: FP7 | Program: CP-SICA | Phase: HEALTH-2007-2.2.1-10 | Award Amount: 3.35M | Year: 2009

Mental retardation (MR) is a highly heterogeneous disorder and is of genetic origin in about 50% of the cases. Despite recent progress in research the causes and the pathophysiology of MR remains obscure. It is essential to investigate this in order to develop future diagnostic and therapeutic strategies. The overall goal of this proposal is to establish an interdisciplinary Eastern Europe and Central Asia (EECA) consortium of experts with a joint programme of activities to generate knowledge about MR and the structure and dynamics of the brain as such. This project will be the first to study in depth the prevalence and incidence of MR in EECA . The objectives of the CHERISH project are to: - to develop a standardized approach for MR diagnosis through clinical workshops and courses - to create a large data-base of patients with clinically well defined MR, both syndromic and non-syndromic - identify cryptic genomic rearrangements through molecular cytogenetic analysis - sequence MR genes and analyse the molecular epidemiology of MR in Eastern European populations - develop diagnostic tools for recurrent/common mutations - identify new MR genes in X-linked and autosomal recessive forms of the disorder - increase awareness on the possible genetic origin of MR and implications for novel therapeutic strategies The project partners will join forces to create a large collection of samples and a database from MR patients which will be become the reference. All institutions involved are the referral centres for MR in their respective countries. The molecular studies will be performed in technologically-advanced genetic laboratories. A straightforward outcome of CHERISH will lay the basis for a significant improvement of clinical, educational and industrial developments. The project will contribute to improve the management of MR with the potential to reduce the high health care costs and to improve quality of life of the concerned population.

Agency: Cordis | Branch: FP7 | Program: BSG-CSO | Phase: ENV.2007. | Award Amount: 1.01M | Year: 2009

This project involves five very different Civil Society Organisations (CSOs) involved in Education for Sustainable Development in a very wide range of project types coming together to investigate two main aims, with academic assistance: 1) to develop more useful indicators to measure the impact of value/behaviour change elements in their ESD projects at the project level. This will enable them to better prioritise their resources across a wide range of project types. A considerable range of value-based projects will be considered, involving SMEs, communities and schoolchildren. The newly developed project level impact indicators will be related to those for other levels, e.g. regional, national; and those used in academic arenas. It will be necessary to particularly focus on the development of less established SD indicators such as well-being which are can be strongly affected by spiritual/faith-based values and activities (Clark and Lelkes, 2005). Indicators for this have been difficult to quantify so far in mainstream discussions, but by focussing at project impact level we believe some can be defined and refined, with CSOs working with academics. Some schools of thought suggest that reinforcing local values will lead more effectively to behaviour changes, leading to larger SD impacts; without ways to measure, such ideas cannot be tested. 2) to improve the environmental impact of projects through advice at ground level. Three of the CSO participants in this proposal are faith-based whose projects generally focus on social issues more than environmental ones. The RTDs will be asked to outline possibilities to increase the projects environmental impact within their current context, leading to suggestions and guidelines for such CSOs to allow them to be more effective at environmental impact even when this is not their main focus. Researchers officers will work extensively in the field on CSO projects, with CSO staff, for both aims.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH.2013.7.1-1 | Award Amount: 2.98M | Year: 2014

The project POst-CArbon CIties of TOmorrow foresight for sustainable pathways towards liveable, affordable and prospering cities in a world context (POCACITO) will develop an evidence-based 2050 roadmap for EU post-carbon cities. POCACITO facilitates the transition of EU cities to a forecasted sustainable or post-carbon economic model. The project focuses on towns, cities, megacities, metropolitan areas and urban clusters larger than 1 million people as well as small and medium-sized cities. POCACITOs approach uses participatory scenario development as a mutual learning and living lab environment strategy. The project recognises that post-carbon city transitions should improve urban resilience to fluctuating environmental and socio-economic pressure. Pressure in this context includes long-term changes in urban resident demographics, city and rural migration patterns, and potential city health concerns. Further, POCACITO develops innovative long-term outlooks for European post-carbon cities to address climate adaptation and urban environmental metabolism concerns by using a participatory city case study approach. Case study cities include Barcelona, Copenhagen/Malm, Istanbul, Lisbon, Litomerice, Milan/Turin, Offenburg and Zagreb. These cities will develop qualitative post-carbon visions with local stakeholders. Visions will be chosen based on selected best-practice measures and preliminary city assessments. Accompanying studies will yield a typology of post-carbon cities and a post-carbon city index. A marketplace of ideas will spread best practices from other EU cities and global cities in global emerging nations, allowing an international exchange of urban best practices. Related research will produce case study city roadmaps and an evidence-based 2050 roadmap for post-carbon EU cities within a global context. The projects research supports the sustainable development objective of the Europe 2020 strategy and the Innovation Union flagship initiative.

Agency: Cordis | Branch: FP7 | Program: CSA-SA | Phase: SiS.2013.1.2-1 | Award Amount: 3.36M | Year: 2013

The European Research Area is targeting efforts in research and innovation on the current challenges faced by society. These challenges are complex, multidimensional and require the engagement of different actors alongside researchers, particularly relating to integrated and sustainable urban development. In an effort to bridge the gap between the scientific community and society, SEiSMiC (Societal Engagement in Science, Mutual learning in Cities) aims to create a structured dialogue and mutual learning with citizens and urban actors by setting up National Networks (and expanding on existing networks where possible) in 10 countries across Europe. These networks will specifically include urban stakeholders from civil society, business, NGOs, youth, media, musea but also from research and policy). On the European level, an Advisory Group (with EU-wide urban stakeholder organisations) and an Observer Group (with JPI Urban Europe and European Parliament representatives) will also be established. The objectives of SEiSMiC as Mobilisation and Mutual Learning Action Plan are threefold. Firstly it aims to mobilise a wide range of urban stakeholders at the local level with a view to, secondly, feed the experiences and challenges of social innovation at local level into the European urban research agenda and to enhance the social dimension of the strategic research agenda of JPI Urban Europe. Thirdly, it will diffuse the initiatives, projects and results of JPI Urban Europe (and other European programmes) to all urban actors at local, regional, national and European level. It is expected that by means of this multi-level, multi-actor, integrated and inclusive approach, research activities can be increased, new concepts and solutions will be more targeted and accepted, social innovation with the social context is strengthened, and commonalities and differences in European needs, awareness and solutions in the urban field can be identified.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2013.4.1 | Award Amount: 3.97M | Year: 2013

In the last decade, the incremental advancement of mainstream research on Machine Translation (MT) has been obtained by encompassing increasingly sophisticated statistical approaches and fine-grained linguistic features that add to the surface level alignment on which these approaches are ultimately anchored.It has been ventured recently, in some leading academic and industry circles, that the incremental progress towards quality MT of this path may be asymptotically reaching a ceiling, as more fine-grained distinctions tend to be needed to aim at better translations with fewer gains in terms of quality increase.The goal of this project is to contribute to a quantum leap in quality MT by pursuing a novel approach that opens the way to higher quality translations and a new cycle of technological advancement.We build on the complementarity of the two pillars of language technology -- symbolic and probabilistic -- and seek a quantum leap in their hybridization. We explore combinations of them that amplify their strengths and mitigate their drawbacks with a new design for the intertwining of statistical and rule-based MT.The construction of deep treebanks has progressed to be delivering now the first significant Parallel DeepBanks, where pairs of synonymous sentences from different languages are annotated with their fully-fledged grammatical representations, up to the level of their semantic representation.The construction of Linked Open Data and other semantic resources, in turn, has progressed now to support impactful application of lexical semantic processing that handles and resolves referential and conceptual ambiguity.These cutting edge advances permit for the cross-lingual alignment supporting translation to be established at the level of deeper linguistic representation. The deeper the level the less language-specific differences remain among source and target sentences and new chances of success become available for the statistically based transduction.

Agency: Cordis | Branch: FP7 | Program: BSG-SME | Phase: SME-1 | Award Amount: 1.34M | Year: 2011

Scientists try to develop coatings that prevent of fouling. Development of new coating formulation takes 5 years, beginning from R&D study to the date of launching. Taking into account the marine market development and the change of low requirements connected to the environmental issues this time is too long. Formulation time distances depend mainly on testing. In Europe the only method is testing in natural conditions. Antifouling tests are carried out in different regions of the world to check performance in different biological and chemical conditions. The high price and the long time of testing cause too long payback time for SME that exist on the market. That is the reason why just big companies are able to develop new coating formulation and the marked is not available for SMEs. Significant decrease of antifouling test performance will cause large decrease of new coating formulations development time and cost, will let SMEs to enter to the market and will decrease the coatings prices.The projects idea is to develop an innovative, automated antifouling test system for professional examinations of coatings. The proposed system will let to perform tests in laboratory conditions and will decrease the test time by 500%. The fouling appearance will be measured by the image analyzer. The test system will allow to detect the fouling appearance even if it is not visible to the naked eye. The tests will be carried out automatically, 24 hours a day without supervision. The test data will be collected and stored on a continuous basis by the database and this data will be available on-line. Selected species will be so characteristic as to ensure that during laboratory tests the worst conditions for coatings that exist in natural conditions are replicated. The proposed project will let to construct relatively cheap, available for SME antifouling test set that let European SME to enter to the huge marine coatings market and become a rival company for market potentat

Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: HEALTH-2009-2.2.1-3 | Award Amount: 14.90M | Year: 2010

OPTiMiSE (OPtimization of Treatment and Management of Schizophrenia in Europe) will focus on two goals: optimising current treatments in Schizophrenia and explore novel therapeutic options for schizophrenia. The project intends to both address basic, but so far unanswered, questions in the treatment of schizophrenia and develop new and experimental interventions. It is expected that the project will lead to evidence that is directly applicable to treatment guidelines, will explore the development of novel treatments and will identify potential mechanisms for new drug development. To achieve these goals we have assembled a European team of experts that is second to none in the world. Together we will pursue the following objectives: -To use MRI to optimise treatment outcome and to facilitate prediction of response to treatment; - To provide a rational basis for antipsychotic choices in the treatment of first episode schizophrenia or schizophreniform disorder; - To improve functional outcome and reduce drug discontinuation by means of psychosocial interventions. - To explore the potential of cannabidiol CBD, a modulator of endocannabinoid functioning, as an alternative to D2 based antipsychotics - To validate a new approach to improve cognitive performance in patients with cognitive deficits on the basis of their genetic make up; - To use theoretically driven neurochemical imaging (MRS) and empirically driven genetic/genomic markers as predictors of response to treatment.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2009.4.3 | Award Amount: 10.56M | Year: 2010

In KHRESMOI, we will build a multi-lingual multi-modal search and access system for biomedical information and documents. This will be achieved by:- Effective automated information extraction from biomedical documents, including improvement using crowd sourcing and active learning, and automated estimation of the level of trust and target user expertise- Automated analysis and indexing for medical images in 2D (X-Rays), 3D (MRI, CT), and 4D (fMRI)- Linking information extracted from unstructured or semi-structured biomedical texts and images to structured information in knowledge bases- Support of cross-language search, including multi-lingual queries, and returning machine-translated pertinent excerpts- Adaptive user interfaces to assist in formulating queries and display search results via ergonomic and interactive visualizationsThe research will flow into several open source components, which will be integrated into an innovative open architecture for robust and scalable biomedical information search.The system will be evaluated in use cases by three well-defined user groups:1. Members of the general public want access to reliable and understandable medical information in their own language2. Clinicians and general practitioners need accurate answers rapidly a search on PubMed requires on average 30 minutes, while clinicians typically have 5 minutes available. Furthermore, over 40% of searches fail to provide relevant information3. Radiologists are drowning in images at larger hospitals over 100GB (over 100000 images) are produced per dayRepresentative groups of end users are available for sizable evaluations, accessed through a medical search engine with 11000 queries per day, a professional association of 2700 medical doctors, and two radiology departments with 175 radiologists.KHRESMOI is directed at Objective ICT-2009.4.3: Intelligent Information Management. It will focus on target outcome (a) capturing tractable information.

Agency: Cordis | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2008-1.1.1 | Award Amount: 18.74M | Year: 2009

The Project promotes the access to five European Research Infrastructures, and it is structured intop eight Networking Activities, plus the Management of the Consortium, and fourteen Joint Research Activities. The Project represents the continuation of the successful HadronPhysics project in FP6 and originates from the initiative of more than 2.500 European scientists working in the field of hadron physics. Hadron physics deals with the study of strongly interacting particles, the hadrons. Hadrons are composed of quarks and gluons. Their interaction is described by Quantum Chromo Dynamics, the theory of the strong force. Hadrons form more complex systems, in particular atomic. Under extreme conditions of pressure and temperature, hadrons may loose their identity and dissolve into a new state of matter similar to the primordial matter of the early Universe. The Networking Activities are related to the organization of experimental and theoretical collaborative work concerning both ongoing activities at present Research Infrastructures and planned experiments at future facilities. In hadron physics the close interaction between experimentalists and theoreticians is of paramount importance. The Joint Research Activities concentrate on technological innovations for present and future experiments. Applications in material science, medicine, information, technology, etc., represent natural fall-outs. The main objective of this Integrating Activity is to optimize the use and development of the Research Infrastructures existing in Europe working in the field of hadron physics. The Project aims as well at structuring, on European scale, the way Research Infrastructures operate, and at fostering their joint development in terms of capacity and performance. The approach used is the bottom up approach, to respond to the needs of the scientific community in all fields of science and technology.

News Article | November 18, 2015

A century ago, in November 1915, Albert Einstein published his general theory of relativity in four short papers in the proceedings of the Prussian Academy of Sciences in Berlin1. The landmark theory is often presented as the work of a lone genius. In fact, the physicist received a great deal of help from friends and colleagues, most of whom never rose to prominence and have been forgotten2, 3, 4, 5. (For full reference details of all Einstein texts mentioned in this piece, see Supplementary Information.) Here we tell the story of how their insights were woven into the final version of the theory. Two friends from Einstein's student days — Marcel Grossmann and Michele Besso — were particularly important. Grossmann was a gifted mathematician and organized student who helped the more visionary and fanciful Einstein at crucial moments. Besso was an engineer, imaginative and somewhat disorganized, and a caring and lifelong friend to Einstein. A cast of others contributed too. Einstein met Grossmann and Besso at the Swiss Federal Polytechnical School in Zurich6 — later renamed the Swiss Federal Institute of Technology (Eidgenössische Technische Hochschule; ETH) — where, between 1896 and 1900, he studied to become a school teacher in physics and mathematics. Einstein also met his future wife at the ETH, classmate Mileva Marić. Legend has it that Einstein often skipped class and relied on Grossmann's notes to pass exams. Grossmann's father helped Einstein to secure a position at the patent office in Berne in 1902, where Besso joined him two years later. Discussions between Besso and Einstein earned the former the sole acknowledgment in the most famous of Einstein's 1905 papers, the one introducing the special theory of relativity. As well as publishing the papers that made 1905 his annus mirabilis, Einstein completed his dissertation that year to earn a PhD in physics from the University of Zurich. In 1907, while still at the patent office, he started to think about extending the principle of relativity from uniform to arbitrary motion through a new theory of gravity. Presciently, Einstein wrote to his friend Conrad Habicht — whom he knew from a reading group in Berne mockingly called the Olympia Academy by its three members — saying that he hoped that this new theory would account for a discrepancy of about 43˝ (seconds of arc) per century between Newtonian predictions and observations of the motion of Mercury's perihelion, the point of its orbit closest to the Sun. Einstein started to work in earnest on this new theory only after he left the patent office in 1909, to take up professorships first at the University of Zurich and two years later at the Charles University in Prague. He realized that gravity must be incorporated into the structure of space-time, such that a particle subject to no other force would follow the straightest possible trajectory through a curved space-time. In 1912, Einstein returned to Zurich and was reunited with Grossmann at the ETH. The pair joined forces to generate a fully fledged theory. The relevant mathematics was Gauss's theory of curved surfaces, which Einstein probably learned from Grossmann's notes. As we know from recollected conversations, Einstein told Grossmann7: “You must help me, or else I'll go crazy.” Their collaboration, recorded in Einstein's 'Zurich notebook', resulted in a joint paper published in June 1913, known as the Entwurf ('outline') paper. The main advance between this 1913 Entwurf theory and the general relativity theory of November 1915 are the field equations, which determine how matter curves space-time. The final field equations are 'generally covariant': they retain their form no matter what system of coordinates is chosen to express them. The covariance of the Entwurf field equations, by contrast, was severely limited. In May 1913, as he and Grossmann put the finishing touches to their Entwurf paper, Einstein was asked to lecture at the annual meeting of the Society of German Natural Scientists and Physicians to be held that September in Vienna, an invitation that reflects the high esteem in which the 34-year-old was held by his peers. In July 1913, Max Planck and Walther Nernst, two leading physicists from Berlin, came to Zurich to offer Einstein a well-paid and teaching-free position at the Prussian Academy of Sciences in Berlin, which he swiftly accepted and took up in March 1914. Gravity was not a pressing problem for Planck and Nernst; they were mainly interested in what Einstein could do for quantum physics. Several new theories had been proposed in which gravity, like electromagnetism, was represented by a field in the flat space-time of special relativity. A particularly promising one came from the young Finnish physicist Gunnar Nordström. In his Vienna lecture, Einstein compared his own Entwurf theory to Nordström's theory. Einstein worked on both theories between May and late August 1913, when he submitted the text of his lecture for publication in the proceedings of the 1913 Vienna meeting. In the summer of 1913, Nordström visited Einstein in Zurich. Einstein convinced him that the source of the gravitational field in both their theories should be constructed out of the 'energy–momentum tensor': in pre-relativistic theories, the density and the flow of energy and momentum were represented by separate quantities; in relativity theory, they are combined into one quantity with ten different components. This energy–momentum tensor made its first appearance in 1907–8 in the special-relativistic reformulation of the theory of electrodynamics of James Clerk Maxwell and Hendrik Antoon Lorentz by Hermann Minkowski. It soon became clear that an energy–momentum tensor could be defined for physical systems other than electromagnetic fields. The tensor took centre stage in the new relativistic mechanics presented in the first textbook on special relativity, Das Relativitätsprinzip, written by Max Laue in 1911. In 1912, a young Viennese physicist, Friedrich Kottler, generalized Laue's formalism from flat to curved space-time. Einstein and Grossmann relied on this generalization in their formulation of the Entwurf theory. During his Vienna lecture, Einstein called for Kottler to stand up and be recognized for this work8. Einstein also worked with Besso that summer to investigate whether the Entwurf theory could account for the missing 43˝ per century for Mercury's perihelion. Unfortunately, they found that it could only explain 18˝. Nordström's theory, Besso checked later, gave 7˝ in the wrong direction. These calculations are preserved in the 'Einstein–Besso manuscript' of 1913. Besso contributed significantly to the calculations and raised interesting questions. He wondered, for instance, whether the Entwurf field equations have an unambiguous solution that uniquely determines the gravitational field of the Sun. Historical analysis of extant manuscripts suggests that this query gave Einstein the idea for an argument that reconciled him with the restricted covariance of the Entwurf equations. This 'hole argument' seemed to show that generally covariant field equations cannot uniquely determine the gravitational field and are therefore inadmissible9. Einstein and Besso also checked whether the Entwurf equations hold in a rotating coordinate system. In that case the inertial forces of rotation, such as the centrifugal force we experience on a merry-go-round, can be interpreted as gravitational forces. The theory seemed to pass this test. In August 1913, however, Besso warned him that it did not. Einstein did not heed the warning, which would come back to haunt him. In his lecture in Vienna in September 1913, Einstein concluded his comparison of the two theories with a call for experiment to decide. The Entwurf theory predicts that gravity bends light, whereas Nordström's does not. It would take another five years to find out. Erwin Finlay Freundlich, a junior astronomer in Berlin with whom Einstein had been in touch since his days in Prague, travelled to Crimea for the solar eclipse of August 1914 to determine whether gravity bends light but was interned by the Russians just as the First World War broke out. Finally, in 1919, English astronomer Arthur Eddington confirmed Einstein's prediction of light bending by observing the deflection of distant stars seen close to the Sun's edge during another eclipse, making Einstein a household name10. Back in Zurich, after the Vienna lecture, Einstein teamed up with another young physicist, Adriaan Fokker, a student of Lorentz, to reformulate the Nordström theory using the same kind of mathematics that he and Grossmann had used to formulate the Entwurf theory. Einstein and Fokker showed that in both theories the gravitational field can be incorporated into the structure of a curved space-time. This work also gave Einstein a clearer picture of the structure of the Entwurf theory, which helped him and Grossmann in a second joint paper on the theory. By the time it was published in May 1914, Einstein had left for Berlin. Turmoil erupted soon after the move. Einstein's marriage fell apart and Mileva moved back to Zurich with their two young sons. Albert renewed the affair he had started and broken off two years before with his cousin Elsa Löwenthal (née Einstein). The First World War began. Berlin's scientific elite showed no interest in the Entwurf theory, although renowned colleagues elsewhere did, such as Lorentz and Paul Ehrenfest in Leiden, the Netherlands. Einstein soldiered on. By the end of 1914, his confidence had grown enough to write a long exposition of the theory. But in the summer of 1915, after a series of his lectures in Göttingen had piqued the interest of the great mathematician David Hilbert, Einstein started to have serious doubts. He discovered to his dismay that the Entwurf theory does not make rotational motion relative. Besso was right. Einstein wrote to Freundlich for help: his “mind was in a deep rut”, so he hoped that the young astronomer as “a fellow human being with unspoiled brain matter” could tell him what he was doing wrong. Freundlich could not help him. The problem, Einstein soon realized, lay with the Entwurf field equations. Worried that Hilbert might beat him to the punch, Einstein rushed new equations into print in early November 1915, modifying them the following week and again two weeks later in subsequent papers submitted to the Prussian Academy. The field equations were generally covariant at last. In the first November paper, Einstein wrote that the theory was “a real triumph” of the mathematics of Carl Friedrich Gauss and Bernhard Riemann. He recalled in this paper that he and Grossmann had considered the same equations before, and suggested that if only they had allowed themselves to be guided by pure mathematics rather than physics, they would never have accepted equations of limited covariance in the first place. Other passages in the first November paper, however, as well as his other papers and correspondence in 1913–15, tell a different story. It was thanks to the elaboration of the Entwurf theory, with the help of Grossmann, Besso, Nordström and Fokker, that Einstein saw how to solve the problems with the physical interpretation of these equations that had previously defeated him. In setting out the generally covariant field equations in the second and fourth papers, he made no mention of the hole argument. Only when Besso and Ehrenfest pressed him a few weeks after the final paper, dated 25 November, did Einstein find a way out of this bind — by realizing that only coincident events and not coordinates have physical meaning. Besso had suggested a similar escape two years earlier, which Einstein had brusquely rejected2. In his third November paper, Einstein returned to the perihelion motion of Mercury. Inserting the astronomical data supplied by Freundlich into the formula he derived using his new theory, Einstein arrived at the result of 43″ per century and could thus fully account for the difference between Newtonian theory and observation. “Congratulations on conquering the perihelion motion,” Hilbert wrote to him on 19 November. “If I could calculate as fast as you can,” he quipped, “the hydrogen atom would have to bring a note from home to be excused for not radiating.” Einstein kept quiet on why he had been able to do the calculations so fast. They were minor variations on the ones he had done with Besso in 1913. He probably enjoyed giving Hilbert a taste of his own medicine: in a letter to Ehrenfest written in May 1916, Einstein characterized Hilbert's style as “creating the impression of being superhuman by obfuscating one's methods”. Einstein emphasized that his general theory of relativity built on the work of Gauss and Riemann, giants of the mathematical world. But it also built on the work of towering figures in physics, such as Maxwell and Lorentz, and on the work of researchers of lesser stature, notably Grossmann, Besso, Freundlich, Kottler, Nordström and Fokker. As with many other major breakthroughs in the history of science, Einstein was standing on the shoulders of many scientists, not just the proverbial giants4.

News Article | November 11, 2015

This 5X image of moss was designated an Image of Distinction in the 2014 Nikon Small World Photomicrophotography Competition, which recognizes excellence in photography with the optical microscope. It was taken by Viktor Sykora of Charles University in Prague, Czech Republic, using steromicroscopy and darkfield illumination.

Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: COH-2007-2.2-01-OMC-NET | Award Amount: 1.02M | Year: 2010

EuKTS addresses directly the 1st and 2nd CREST recommendations (Rec) in particular regarding: Need for providing adequate professional Knowledge Transfer (KT)/Technology Transfer (TT) training/education Rec 15, 17 and 18 from 1st Cycle and Rec 4 and 6 from 2nd Cycle from OMC CREST Expert Group on IPR and Research Need for providing quality KT/TT data through common survey and data collection Rec 13, 14 and 15 from OMC-Crest Expert Group Encourage the reform of public research centres and universities, 2nd cycle Need for organisation with KT/TT training and metrics functionality Rec 6 from OMC-Crest the Expert Group on IPR and Research, 1st Cycle EuKTS also directly follow up KT/TT recommendations made by the European Commission and accepted by the Member States at Council meeting Competitiveness on May 29th 2008 (Rec 3 and 14) EuKTS is a bottom-up initiative by the participating countries and stakeholders, which aims to complement OMC-CREST process by: Designing of European Knowledge Transfer Society (EuKTS) model with the aim to support the European R&D policy by the co-ordination of the major existing professional associations/networks and the enhancement of efficiency in providing KT metrics /focused on training & Porfession) and training standards in technology transfer field. Creating support through a bottom-up approach for EuKTS model by the involvement of policy makers in consultation procedures at European level Creating broad European support for enhancement of a common KT/TT metrics system focused on training & profession as mean to strengthen the R&D policy in Europe Creating support through a bottom-up approach to support the EuKTS model by the involvement of training providers specialised in KT/TT education Creating broad European support from training providers for the development of common training standards and competence framework for European KT/TT practitioners. To achieve objectives it is vital to involve the relevant policymakers and KT/TT stakeholders.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH.2012.1.1-3 | Award Amount: 2.75M | Year: 2013

The aim of SmartSpec is to provide substance, guidance and practical support to the EU Smart Specialisation Platform, based on the combination of leading academic and practical expertise present in the consortium. The goal is directed at operationalising the concept of smart specialisation in a manner which will be useful to actors in different regional contexts. It will do this by strengthening the analytical underpinnings of the smart specialisation concept, providing methodological guidance for practice and generating strategic intelligence for policy-makers. Through an integrated, multi-dimensional and place-based approach focused on 8 Work Packages, SmartSpec develops robust practical and analytical findings to strengthen the implementation of smart specialisation strategies. With a strong emphasis on knowledge exchange and facilitated learning, SmartSpec will deliver useful results to inform practitioners and policymakers in the development and assessment of smart specialisation strategies, whilst extending the state of the art.

Skolarikos A.,Sismanoglio Hospital | Straub M.,TU Munich | Knoll T.,University of Tübingen | Sarica K.,Dr Lutfi KIrdar Research and Teaching Hospital | And 4 more authors.
European Urology | Year: 2015

Context An optimum metabolic evaluation strategy for urinary stone patients has not been clearly defined. Objective To evaluate the optimum strategy for metabolic stone evaluation and management to prevent recurrent urinary stones. Evidence acquisition Several databases were searched to identify studies on the metabolic evaluation and prevention of stone recurrence in urolithiasis patients. Special interest was given to the level of evidence in the existing literature. Evidence synthesis Reliable stone analysis and basic metabolic evaluation are highly recommended in all patients after stone passage (grade A). Every patient should be assigned to a low- or high-risk group for stone formation. It is highly recommended that low-risk stone formers follow general fluid and nutritional intake guidelines, as well as lifestyle-related preventative measures to reduce stone recurrences (grade A). High-risk stone formers should undergo specific metabolic evaluation with 24-h urine collection (grade A). More specifically, there is strong evidence to recommend pharmacological treatment of calcium oxalate stones in patients with specific abnormalities in urine composition (grades A and B). Treatment of calcium phosphate stones using thiazides is only highly recommended when hypercalciuria is present (grade A). In the presence of renal tubular acidosis (RTA), potassium citrate and/or thiazide are highly recommended based on the relative urinary risk factor (grade A or B). Recommendations for therapeutic measures for the remaining stone types are based on low evidence (grade C or B following panel consensus). Diagnostic and therapeutic algorithms are presented for all stone types based on the best level of existing evidence. Conclusion Metabolic stone evaluation is highly recommended to prevent stone recurrences. Patient summary In this report, we looked at how patients with urolithiasis should be evaluated and treated in order to prevent new stone formation. Stone type determination and specific blood and urine analysis are needed to guide patient treatment. © 2014 European Association of Urology. All rights reserved.

Neumann F.-J.,Heart Center Bad Krozingen | Widimsky P.,Charles University | Belardi J.A.,Instituto Cardiovascular Of Buenos Aires
EuroIntervention | Year: 2012

Aims: To provide clinical outcome data from everyday practice for the new generation Resolute zotarolimuseluting stent (R-ZES). Methods and results: Patients were eligible if placement of ≥1 R-ZES was intended. There were no restrictions on clinical indication, number of treated vessels, and lesion characteristics. The primary endpoint was the adjudicated cumulative 1-year incidence of cardiac death and target vessel myocardial infarction. Twenty-five per cent of the patients were randomly selected for monitoring. We recruited 2,349 patients with 3,147 lesions (1.6±1.0 stents per patient); 46.0% of patients had acute coronary syndrome, 30.5% were diabetic, and ≥1 complex criterion for stent placement was present in 67.5% of patients. One-year follow-up was complete in 97.9% of patients. The 1-year incidence of the primary endpoint was 4.3% (95% CI: 3.5% to 5.2%) and for ARC definite and probable stent thrombosis, 0.9% (0.5% to 1.3%). Clinically driven target lesion revascularisation and target lesion failure were 3.4% (2.7% to 4.3%) and 7.0% (6.0% to 8.2%), respectively. These findings were consistent across all lesion and patient subsets analysed. There were no significant differences in outcomes between monitored and unmonitored patients. Conclusions: In everyday practice, the R-ZES performed similarly well as in the RESOLUTE All Comers randomised trial. © Europa Edition 2012. All rights reserved.

Valenta J.,Charles University | Bruhn B.,KTH Royal Institute of Technology | Linnros J.,KTH Royal Institute of Technology
Nano Letters | Year: 2011

Single silicon nanowires (Si-NWs) prepared by electron-beam lithography and reactive-ion etching are investigated by imaging optical spectroscopy under variable temperatures and laser pumping intensities. Spectral images of individual Si-NWs reveal a large variability of photoluminescence (PL) along a single Si-NW. The weaker broad emission band asymmetrically extended to the high-energy side is interpreted to be due to recombination of quasi-free 1D excitons while the brighter localized emission features (with significantly variable peak position, width, and shape) are due to localization of electron-hole pairs in surface protrusions acting like quasi-0D centers or quantum dots (QDs). Correlated PL and scanning electron microscopy images indicate that the efficiently emitting QDs are located at the Si-NW interface with completely oxidized neck of the initial Si wall. Theoretical fitting of the delocalized PL emission band explains its broad asymmetrical band to be due to the Gaussian size distribution of the Si-NW diameter and reveals also the presence of recombination from the Si-NW excited state which can facilitate a fast capture of excitons into QD centers. © 2011 American Chemical Society.

Menova P.,Czech Institute of Organic Chemistry And Biochemistry | Hocek M.,Czech Institute of Organic Chemistry And Biochemistry | Hocek M.,Charles University
Chemical Communications | Year: 2012

A method for enzymatic production of short (10-20 nt) cytosine-modified oligonucleotides was developed by nicking enzyme amplification reaction using Vent(exo-) polymerase, Nt.BstNBI nicking endonuclease and 5-substituted dCTP derivatives. The methodology including isolation was scaled up to nanomolar amounts and was proved to be suitable for production of diverse base-modified short single-stranded oligonucleotides (inaccessible by other enzymatic methods) that are of potential interest as labelled primers or functionalized aptamers. © 2012 The Royal Society of Chemistry.

Bruhn B.,KTH Royal Institute of Technology | Valenta J.,Charles University | Sangghaleh F.,KTH Royal Institute of Technology | Linnros J.,KTH Royal Institute of Technology
Nano Letters | Year: 2011

The blinking statistics of numerous single silicon quantum dots fabricated by electron-beam lithography, plasma etching, and oxidation have been analyzed. Purely exponential on- and off-time distributions were found consistent with the absence of statistical aging. This is in contrast to blinking reports in the literature where power-law distributions prevail as well as observations of statistical aging in nanocrystal ensembles. A linear increase of the switching frequency with excitation power density indicates a domination of single-photon absorption processes, possibly through a direct transfer of charges to trap states without the need for a bimolecular Auger mechanism. Photoluminescence saturation with increasing excitation is not observed; however, there is a threshold in excitation (coinciding with a mean occupation of one exciton per nanocrystal) where a change from linear to square-root increase occurs. Finally, the statistics of blinking of single quantum dots in terms of average on-time, blinking frequency and blinking amplitude reveal large variations (several orders) without any significant correlation demonstrating the individual microscopic character of each quantum dot. © 2011 American Chemical Society.

Schroder D.,Czech Institute of Organic Chemistry And Biochemistry | Budesinsky M.,Czech Institute of Organic Chemistry And Biochemistry | Roithova J.,Charles University
Journal of the American Chemical Society | Year: 2012

Despite the simplicity of the molecule, the site of single deprotonation of p-hydroxybenzoic acid upon electrospray ionization (ESI) has recently formed a subject of debate in this journal. By means of NMR experiments in solution and gas-phase studies employing ion-mobility mass spectrometry (IM-MS), the apparent controversy is resolved. It is shown that irrespective of the solvent the carboxylate tautomer is preferred in solution, while the opposite holds true for isolated ions in the gas phase. The tautomer distribution sampled in the gas phase very much depends on the actual solvent used in ESI, the pH value, as well as the total concentration. Moreover, the occurrence of gas-phase reactions in the course of the ESI process influences the tautomer ratio. Implications for correlations between ESI mass spectra and solution-phase chemistry are discussed. © 2012 American Chemical Society.

Kotora M.,Charles University | Kotora M.,Czech Institute of Organic Chemistry And Biochemistry
Pure and Applied Chemistry | Year: 2010

N-oxides possessing the pyridine framework are strong Lewis bases that can activate the C-Si bond of allylhalosilanes to such an extent that they catalyze reactions with aldehydes. N-oxides embedded in chiral scaffolds are usually capable of highly selective chirality transfer to the derived products. Our goal was to develop a general synthetic method allowing the preparation of structurally varied N,N'-dioxides suitable for enantioselective organocatalysis. The underlying synthetic strategy was based on [2 + 2 + 2]-cyclotrimerization of suitably substituted diynes with nitriles catalyzed by Co-complexes to generate the desired bipyridines, their further oxidation and resolution of which furnished the corresponding chiral N,N'-dioxides. The prepared compounds were used in catalytic allylation of aromatic aldehydes to homoallyl alcohols with high enantioselectivity (up to 96 % ee). Enantioselectivity, enantiodiscrimination, and the reaction mechanism are controlled by the choice of solvent. © 2010, IUPAC.

Nachtigall P.,Charles University | Delgado M.R.,University of the Balearic Islands | Nachtigallova D.,Czech Institute of Organic Chemistry And Biochemistry | Arean C.O.,University of the Balearic Islands
Physical Chemistry Chemical Physics | Year: 2012

Gas adsorption on zeolites constitutes the base of many technological applications of these versatile porous materials. Quite often, especially when dealing with small molecules, individual extra-framework (exchangeable) cations are considered to be the adsorption site on which molecules coming from a gas phase form the corresponding adsorption complex. Nonetheless, while that can be the case in some instances, recent research work that combines variable temperature infrared spectroscopy with periodic DFT calculations showed that some types of adsorption sites involve two or more cations, which constitute dual and multiple cation sites, respectively. Adsorption complexes formed on these cationic adsorption sites differ in both structure and stability from those formed on a single cation alone. Examples concerning CO, CO 2 and H 2 adsorption on alkali and alkaline-earth metal exchanged zeolites are reviewed, with the double purpose of clarifying concepts and highlighting their relevance to practical use of zeolites in such fields as gas separation and purification, gas storage and heterogeneous catalysis. © the Owner Societies 2012.

Motloch P.,Charles University | Valterov I.,Czech Institute of Organic Chemistry And Biochemistry | Kotora M.,Charles University
Advanced Synthesis and Catalysis | Year: 2014

The enantioselective allylation of thiophene- 2-carbaldehyde with allyltrichlorosilane under Lewis base catalysis has been studied. The use of catalytic amount (1 mol%) of chiral bipyridine N,N'-dioxides provided the corresponding 1-(thiophen-2-yl)- but-3-en-1-ol with asymmetric induction reaching 97% ee. The prepared chiral (S)-1-(thiophen-2-yl)- but-3-en-1-ol was used as the crucial chiral building block in a formal total synthesis of duloxetine. © 2014 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim.

Kim N.H.,University of California at San Diego | Delcroix M.,University Hospitals of Leuven | Jenkins D.P.,Papworth Hospital | Channick R.,Massachusetts General Hospital | And 7 more authors.
Journal of the American College of Cardiology | Year: 2013

Since the last World Symposium on Pulmonary Hypertension in 2008, we have witnessed numerous and exciting developments in chronic thromboembolic pulmonary hypertension (CTEPH). Emerging clinical data and advances in technology have led to reinforcing and updated guidance on diagnostic approaches to pulmonary hypertension, guidelines that we hope will lead to better recognition and more timely diagnosis of CTEPH. We have new data on treatment practices across international boundaries as well as long-term outcomes for CTEPH patients treated with or without pulmonary endarterectomy. Furthermore, we have expanded data on alternative treatment options for select CTEPH patients, including data from multiple clinical trials of medical therapy, including 1 recent pivotal trial, and compelling case series of percutaneous pulmonary angioplasty. Lastly, we have garnered more experience, and on a larger international scale, with pulmonary endarterectomy, which is the treatment of choice for operable CTEPH. This report overviews and highlights these important interval developments as deliberated among our task force of CTEPH experts and presented at the 2013 World Symposium on Pulmonary Hypertension in Nice, France. © 2013 by the American College of Cardiology Foundation. Published by Elsevier Inc.

Gurlebeck N.,University of Bremen | Gurlebeck N.,Charles University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2014

In this article, we derive source integrals, i.e., quasilocal expressions, for multipole moments in axially symmetric and static spacetimes. Usually, these multipole moments are read off the asymptotics of the metric close to spatial infinity. Whereas for the evaluation of the here derived source integrals the geometry has to be known in the region containing all sources, i.e., matter as well as singularities. The source integrals can be written either as volume integrals over such a region or as integrals over the surface of that region. Eventually, these source integrals allow assigning to any spacetime regions its contribution to the total multipole moments of the spacetime. Finally, we give an exemplary application that outlines the usefulness and applicability of the source integrals in, e.g., (non)existence proofs. © 2014 American Physical Society.

Scheiber I.F.,Charles University | Mercer J.F.B.,Deakin University | Dringen R.,University of Bremen | Dringen R.,Center for Environmental Research and Sustainable Technology
Progress in Neurobiology | Year: 2014

Copper is an important trace element that is required for essential enzymes. However, due to its redox activity, copper can also lead to the generation of toxic reactive oxygen species. Therefore, cellular uptake, storage as well as export of copper have to be tightly regulated in order to guarantee sufficient copper supply for the synthesis of copper-containing enzymes but also to prevent copper-induced oxidative stress. In brain, copper is of importance for normal development. In addition, both copper deficiency as well as excess of copper can seriously affect brain functions. Therefore, this organ possesses ample mechanisms to regulate its copper metabolism. In brain, astrocytes are considered as important regulators of copper homeostasis. Impairments of homeostatic mechanisms in brain copper metabolism have been associated with neurodegeneration in human disorders such as Menkes disease, Wilson's disease and Alzheimer's disease. This review article will summarize the biological functions of copper in the brain and will describe the current knowledge on the mechanisms involved in copper transport, storage and export of brain cells. The role of copper in diseases that have been connected with disturbances in brain copper homeostasis will also be discussed. © 2014 Elsevier Ltd.

Parkan K.,Institute of Chemical Technology Prague | Pohl R.,Czech Institute of Organic Chemistry And Biochemistry | Kotora M.,Charles University
Chemistry - A European Journal | Year: 2014

A convenient synthetic pathway enabling D-glucal and D-galactal pinacol boronates to be prepared in good isolated yields was achieved. Both pinacol boronates were tested in a series of cross-coupling reactions under Suzuki-Miyaura cross-coupling conditions to obtain the corresponding aryl, heteroaryl, and alkenyl derivatives in high isolated yields. This methodology was applied to the formal synthesis of the glucopyranoside moiety of papulacandin D and the first total synthesis of bergenin. Building blocks with boron: A convenient synthetic route to D-glucal and D-galactal pinacol boronates was developed, and the boronates were used in cross-coupling reactions to generate the corresponding aryl, heteroaryl, and alkenyl derivatives in high yields (see scheme). This methodology was applied to the formal synthesis of the glucopyranoside moiety of papulacandin D and the total synthesis of bergenin. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Roithova J.,Charles University | Roithova J.,Czech Institute of Organic Chemistry And Biochemistry | Milko P.,Czech Institute of Organic Chemistry And Biochemistry
Journal of the American Chemical Society | Year: 2010

The reaction mechanism of copper(II)-mediated naphthol coupling in the presence of TMEDA (N,N,N',N'-tetramethylethylenediamine) is studied using infrared multiphoton dissociation (IRMPD) spectroscopy and DFT calculations. It is shown that the coupling reaction proceeds in ad hoc formed binuclear clusters [(1-H)2Cu2Cl(TMEDA)2]+, where (1-H) is a deprotonated naphthol molecule (methyl ester of 3-hydroxy-2-naphthoic acid). The IRMPD spectra of the isolated cluster in the gas phase reveal that it contains two uncoupled naphtholate subunits and only the irradiation promotes the coupling reaction, which is thus observed as a genuine gas-phase reaction. The driving force for the C-C coupling is a keto-enol tautomerization of the initial coupling product, and the formation of the corresponding binol in the cluster is exothermic by 0.61 eV. In contrast, analogous C-O and O-O couplings are endothermic reactions. © 2010 American Chemical Society.

Pepke-Zaba J.,Papworth Hospital | Jansa P.,Charles University | Kim N.H.,University of California at San Diego | Naeije R.,Free University of Colombia | Simonneau G.,University Paris - Sud
European Respiratory Journal | Year: 2013

Chronic thromboembolic pulmonary hypertension (CTEPH) is a progressive disease with poor prognosis if not treated. The treatment of choice is surgery with pulmonary endarterectomy. However, a significant percentage of patients are deemed non-operable due to distal distribution of the disease and arteriopathy in the non-occluded areas that is indistinguishable from pulmonary arterial hypertension (PAH). The overlap in clinical presentation, pathological features and pathogenesis between PAH and CTEPH provides a compelling rationale for exploring the efficacy of PAH-targeted therapies in CTEPH. These therapies are often considered for non-operable patients and are also used in operable patients as a bridge to surgery or as post-pulmonary endarterectomy therapy for persistent pulmonary hypertension, despite the fact they are not licensed for CTEPH. Two randomised clinical trials have been performed in non-operable CTEPH patients. The BENEFiT study, with the endothelin receptor antagonist bosentan, did not show improvement in walking distance. Recently, the CHEST-1 trial, with the soluble guanylate cyclase stimulator riociguat, met study end-point and demonstrated significant improvement in walking distance in patients with non-operable CTEPH. There is an urgent need for more randomised clinical trials designed to clarify whether administration of PAH-targeted therapies improves clinically meaningful end-points in various CTEPH populations. Copyright © ERS 2013.

Dringen R.,University of Bremen | Scheiber I.F.,Charles University | Mercer J.F.B.,Deakin University
Frontiers in Aging Neuroscience | Year: 2013

This short review will summarize the current knowledge on the uptake, storage, and export of copper ions by astrocytes and will address the potential roles of astrocytes in copper homeostasis in the normal and diseased brain. Astrocytes in culture efficiently accumulate copper by processes that include both the copper transporter Ctr1 and Ctr1-independent mechanisms. Exposure of astrocytes to copper induces an increase in cellular glutathione (GSH) content as well as synthesis of metallothioneins, suggesting that excess of copper is stored as complex with GSH and in metallothioneins. Furthermore, exposure of astrocytes to copper accelerates the release of GSH and glycolytically generated lactate. Astrocytes are able to export copper and express the Menkes protein ATP7A. This protein undergoes reversible, copper-dependent trafficking between the trans-Golgi network and vesicular structures. The ability of astrocytes to efficiently take up, store and export copper suggests that astrocytes play a key role in the supply of neurons with copper and that astrocytes should be considered as target for therapeutic interventions that aim to correct disturbances in brain copper homeostasis. © 2013 Dringen, Scheiber and Mercer.

Kristoufek L.,Czech Institute of Information Theory And Automation | Kristoufek L.,Charles University | Kristoufek L.,University of Warwick
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2015

We propose a framework combining detrended fluctuation analysis with standard regression methodology. The method is built on detrended variances and covariances and it is designed to estimate regression parameters at different scales and under potential nonstationarity and power-law correlations. The former feature allows for distinguishing between effects for a pair of variables from different temporal perspectives. The latter ones make the method a significant improvement over the standard least squares estimation. Theoretical claims are supported by Monte Carlo simulations. The method is then applied on selected examples from physics, finance, environmental science, and epidemiology. For most of the studied cases, the relationship between variables of interest varies strongly across scales. © 2015 American Physical Society.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2009.2.2 | Award Amount: 3.76M | Year: 2010

The FAUST project will develop machine translation (MT) systems which respond rapidly and intelligently to user feedback. Current web-based MT systems provide high-volume translation without real-time. Most systems provide no opportunity for users to offer opinions or corrections for translation results. Other systems ask users for feedback on translation, however the user does not see any benefit to providing feedback: the translation does not change in response to the feedback. Our goal is to develop high-volume translation systems capable of adapting to user feedback in real-time.\n\nWe will build on the current leading commercial statistical MT systems developed by Language Weaver and deployed by Softissimo Inc at Our research will be based on translation in five bidirectional language pairs in these EU official languages: Czech-English, French-English, Romanian-English, Spanish-English, and Spanish-Catalan. We will also study translation from Arabic and Chinese into English. The systems we develop will be used directly by users at the website. We will develop novel feedback collection mechanisms which encourage users to interact with the systems and to provide feedback. In this way we will collect the data, in the form of user judgements of translation quality and feedback for translation correction, which will guide our research.\n\nOur objectives are to :\nEnhance the high-volume, translation website with an experimental and evaluation infrastructure that will enable the study of instantaneous user feedback in MT.\n\nDeploy novel web-oriented, feedback collection mechanisms that reduce noise in feedback provided by users and increase the utility of the web contributions.\n\nAutomatically acquire novel data collections to study translation as informed by user feedback.\nDevelop mechanisms for instantaneously incorporating user feedback into the machine translation engines that are used in production environments, such as those that power the website.\n\nCreate novel automatic metrics of translation quality which reflect preferences learned from user feedback.\nDevelop new translation models driven by user feedback data and integrate natural language generation directly into MT to improve translation fluency and reduce negative feedback from users.

Agency: Cordis | Branch: FP7 | Program: MC-IRSES | Phase: FP7-PEOPLE-2011-IRSES | Award Amount: 38.00K | Year: 2012

The overall objective of the project is to bring together an international and interdisciplinary research teams for the purpose of forming a center for research and transfer of knowledge in the area of international migration. Migration is an international phenomenon that transcends national boundaries. It is no longer limited to only few areas of the world, with many new migration systems having established themselves over the last 20 years. The project will take predominantly economic and socio-economic perspective. The team will commence its work from a clear standpoint: migration phenomena are similar across the world and there are many tools to investigate them that can be used successfully in various geographic areas. Promoting universal scientific approach, the project is going to trespass geographical and political fragmentation of this study area. Instead it will focus on commonalities across three migration systems: European Union Mediterranean countries Russian Federation Commonwealth of Independent States European Union Commonwealth of Independent States The exchange program will facilitate the following technical cooperation: 1. Exchange of expertise as regards measurement of various types of money transfers and their impact; 2. Exchange of expertise on researching criminal activities in labour market in various migration systems; 3. Exchange of experience in analyzing of the factors determining the formation of the centres of labour gravity and sharing the methodology of estimating the dynamics of human capital flows. In order to achieve these aims, the partners will engage in five work packages that will include both research collaboration and hands-on experience. The first will be achieved through interactive exchanges and structured seminars and workshops, as well as supporting lectures; the second will be achieved by focused field visits.

Agency: Cordis | Branch: FP7 | Program: MC-IRSES | Phase: FP7-PEOPLE-2010-IRSES | Award Amount: 374.30K | Year: 2011

Scanning probe microscopy (SPM) is an established technique for the characterisation of materials and structures at the nanoscale and is increasingly bridging traditional disciplines including the biosciences. As such, it is of fundamental and practical interest across the sciences and industry. The geometry of the tip is the critical factor which determines the resolution of an SPM sensor. In an attempt to achieve ultra high spatial resolution, carbon nanotubes have been widely investigated and shown some promise. However, it is extremely difficult to control the properties of these tubes, especially the electrical behaviour and growth geometry. Equally, their manipulation is a daunting task. We propose to use III-V semiconductor nanowires as functioning sensors at the apex of scanning probes. These structures can be directly grown on the substrates or SPM cantilevers with controllable properties at the nanometre scale. Using these nanowires offers excellent new avenues for the integration of established semiconducting devices onto the tip of a scanning probe. This will improve the sensitivity and functionality of scanning probe methods. An example of potential applications for such a novel probe is the detection of virus based on their electrical response which can be coupled to that of nanowires under appropriate conditions. Within the framework of this project, we will combine the complementary expertise of various internationally leading institutions for the creation of integrated individual semiconductor nanowire SPM probes exhibiting enhanced functionalities.

Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2010-ITN | Award Amount: 5.09M | Year: 2011

Background and motivation: The combination of cloud computing, service-orientation, and on-demand application delivery is bringing about a paradigm shift in our ways of computer usage. As the software industry moves closer to service-based application engineering and cloud-based application delivery, the traditional models, methodologies, and technologies for developing and offering software applications are becoming increasingly challenged. Emerging questions and research challenges form a vibrant new field with tremendous industrial innovation potential in which Europe needs to establish excelling research. Timely and focused education of future researchers in this area is therefore essential. Major objectives: The RELATE Initial Training Network aims to establish a network of international academic and industrial partners for a joint research training effort in the area of engineering and provisioning service-based cloud applications. The training is intended to not only shape high-level academic researchers, but also educate next generation experts and innovators in the European software industry. Through an integrative and multidisciplinary research approach, RELATE aims to promote the advancement of the state of the art in the related areas of model-driven engineering and formal methods, service-based mash-ups and application integration, security, performance, and trust in service-based cloud applications, and quality management and business model innovation. Consortium: The RELATE Initial Training Network joins organisations with internationally recognised research activities in the area of engineering and provisioning of service-based applications. At its core, the network consists of five academic organisations and two companies from Germany, Greece, France, UK and Czech Republic, and is complemented by six additional industrial and academic associated partners from Germany, Greece, and France.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH.2011.4.3-1 | Award Amount: 3.23M | Year: 2012

In an era of global flux, emerging powers and growing interconnectedness, transatlantic relations appear to have lost their bearings. As the international system fragments into different constellations of state and non-state powers across different policy domains, the US and the EU can no longer claim exclusive leadership in global governance. Not only the ability, but also the willingness of the US and the EU to exercise leadership together can no longer be taken for granted. Political, economic, and social elites on both shores of the Atlantic express different views on whether the US and the EU should be bound together, freelance, or seek alternative partnerships in a confusing multipolar world. Traditional paradigms to understand the transatlantic relationship are thus wanting. A new approach is needed to pinpoint the direction transatlantic relations are taking. TRANSWORLD provides such an approach. By combining an inter-disciplinary analysis of transatlantic relations, including desk research, in-depth interviews, an elite survey and a sophisticated Delphi exercise to elaborate solid policy proposals, TRANSWORLD would: a) ascertain, differentiating among four policy domains (economic, security, environment, and human rights/democracy), whether transatlantic relations are drifting apart, adapting along an ad hoc cooperation-based pattern, or evolving into a different but resilient special partnership; b) assess the role of a re-defined transatlantic relationship in the global governance architecture; c) provide tested policy recommendations on how the US and the EU could best cooperate to enhance the viability, effectiveness, and accountability of governance structures. In so doing, TRANSWORLD, which features a thirteen-partner transatlantic consortium of attested academic, policy, dissemination and management excellence, would contribute to an inter-disciplinary transatlantic research area, with in-built connections to policy-making.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2011.2.4.3-1 | Award Amount: 8.89M | Year: 2012

Patients with diabetes are at risk of developing diabetic nephropathy, which will ultimately result in the requirement for renal replacement therapy and is also associated with high cardiovascular morbidity and mortality. Detection of low concentrations of albuminuria in urine (microalbuminuria) is the current clinical standard for detecting those at significant risk and targeting preventive treatment. However, albuminuria is of low specificity at early stages of disease, and of considerable biological variability, hence a poor predictor at early stages of disease. In two independent studies we have demonstrated that urinary proteomics offers the prospect of detecting nephropathy earlier in the preclinical phase, enabling targeted treatment at an earlier stage. We propose to assess the potential of this technology to identify normoalbuminuric patients at risk and to target therapy with an aldosterone receptor antagonist (spironolactone) as add-on to recommended therapy including angiotensin converting enzyme (ACE) inhibition or angiotensin II receptor blockers (ARBs) according to national guidelines. We will test the following hypotheses: (1) urinary proteomics predicts progression of albuminuria (as a surrogate marker for the development of overt nephropathy) in a cohort of 3280 type 2 diabetic patients with normal urinary albumin excretion, and (2) early initiation of intensive preventive therapy directed by urinary proteomics reduces progression of albuminuria in those 20 % at high risk and thereby delay progression to overt nephropathy and spare treatment for those with low risk, paving the way of personalised medicine. This will be the first biomarker-directed therapy trial for primary prevention of diabetic kidney disease. Additional clinical and circulating biomarkers will be assessed and models to predict progression of albuminuria including clinical factors, biomarkers and proteomics will be developed.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2011.3.3-1 | Award Amount: 3.36M | Year: 2011

The need to deal with health inequalities is now on the agenda of key supranational institutions, such as the European Commission (EC). To tackle the so-called causes of the causes of health inequity, the focus should be put on structural policies, policies that especially in the current times of financial and employment crisis influence patterns of social stratification, living and working conditions, and thus peoples health. The SOPHIE project aims to generate new evidence on the impact and effectiveness of structural policies in reducing health inequalities, and to develop innovative methodologies for the evaluation of these policies in Europe. We will study major policy areas, including macro-economy, welfare state, labour market and employment relations, built environment, housing, as well as gender-oriented and immigration-related policies. Examples of these policies at the European, national and local levels will be examined, in addition to their impacts on health inequalities by social class, gender and migrant status. The project will develop theoretical frameworks as well as quantitative and qualitative methods for evaluating the effectiveness of such policies in different contexts. Novel methods that are useful for evaluating the impact of complex social interventions will be employed, including realist reviews, explanatory case studies and concept mapping. Particular attention will be given to increasing the involvement of affected stakeholders (civil society and deprived population groups) in the identification, design and evaluation of policies to tackle health inequalities. Affected communities and stakeholders will work with responsible policymakers in activities of dissemination of results, knowledge transfer and translation of findings into policy recommendations. Through SOPHIE, the EC will gain knowledge on the impact on health and health inequalities of social and economic policies which may be implemented or recommended to Member States

Agency: Cordis | Branch: FP7 | Program: MC-IRSES | Phase: FP7-PEOPLE-2012-IRSES | Award Amount: 138.60K | Year: 2013

The concept of the NIDYFICS project is to connect researchers in environmental geosciences for high level discussions and exchanges and for transfer of knowledge between European and Brazilian institutions. A key point is the training of young researchers in a promising research field by working with and sharing knowledge with experts. Pyrometallurgical process of metallic ores generates large amounts of wastes, considered as hazardous materials, as they contain potentially toxic elements, like nickel. Wastes are reused for construction or reprocessed, but a significant fraction is commonly dumped on soil surface or into lakes, where their dispersal by wind or water may have environmental impact on large areas. Another way of reuse could be in agronomy as soil additive. The purpose of the NIDYFICS project is to characterize the dynamics of Ni and other associated metals in the soil-waste-plant-water continuum in the ultramafic massif of Barro Alto (Goas, Brazil), which is considered as a biodiversity hotspot. Thus, it is crucial to unravel the solid speciation of metals, which controls their potential release and mobility to assess the environmental impact of wastes spreading onto soils. Moreover, to understand and quantify the metal dynamics, the measure of metal isotopic ratios is a key tool to trace their sources and fate in the environment. Finally, the benefits and also the risk of metal contamination associated to the waste reutilization in the sugar cane production will be assessed at pot and field scales. This pluridisciplinary project involves soil scientists, spectroscopists, geochemists and agronomists, who already started to work in synergy on this topic. This joint research and exchange project will lead to the acquisition of basic results about Ni geochemistry, to the proposition of valorization strategies for the pyrometallurgical wastes, and to the training of young scientists who will later be involved in academic or applied research.

Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: HEALTH-2009-2.1.1-2 | Award Amount: 13.75M | Year: 2010

The International Cancer Genome Consortium (ICGC) has the goal of obtaining a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumour types and/or subtypes, with the aim of elucidating the genomic changes present in the many forms of cancers that contribute to the burden of disease throughout the world. We present a proposal for a European contribution to this effort through application of state-of-the-art approaches to the genomics of the most common form of renal cell cancer (RCC). RCC is of particular importance within Europe where the highest global incidence rates are observed. Disease incidence has increased over the last two decades, and it is now the 8th most common cancer in the EU. CAGEKID brings clinical and epidemiological resources that are unique worldwide together with the necessary genetics and genomics expertise required for this effort. In the first phase of the study, we will provide a full genomic characterisation of 100 matched pairs of DNA extracted from the tumour and constitutional samples. DNA will be completely sequenced, and the data brought together with those from whole genome transcript and methylation analyses. Follow-up studies of potential targets will be made in further samples. The results acquired will be relied to targeted protein analyses. The primary data will be made available to the scientific community, and the programme will contribute to establishing norms for the manipulation and storage of biological samples. CAGEKID will provide the first systematic analysis of this tumour site providing new insights into disease aetiology with application for diagnosis and treatment. It addresses a major need to identify new biological markers for renal cell cancer, one of very few tumour types for which there are currently no biological markers in routine clinical use. Renal cancer is not yet supported by any of the members of the ICGC.

Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: HEALTH-2007-2.1.1-2 | Award Amount: 14.61M | Year: 2008

The project is focused on the definition of a comprehensive genetic epidemiological model of complex traits like Essential Hypertension (EH) and intermediate phenotypes of hypertension dependent/associated Target Organ Damages (TOD). To identify the common genetic variants relevant for the pathogenesis of EH and TODs, we will perform a Whole Genome Association (WGA) study of 4.000 subjects recruited from historical well-characterized European cohorts. Genotyping will be done with the Illumina Human 1M BeadChip. Well-established multi-variate techniques and innovative genomic analyses through machine learning techniques will be used for the WGA investigations. Using machine learning approach we aim at developing a disease model of EH integrating the available information on EH and TOD with relevant validated pathways and genetic/environmental information to mimic the clinicians recognition pattern of EH/TOD and their causes in an individual patient. Our statistical design is with two samples run in parallel, each with 1,000 cases and 1,000 controls, followed by a replication/joint analysis. This design is more powerful than replication alone and allows also a formal testing of the potential heterogeneity of findings compared to a single step (one large sample) design. The results represent the source to build a customized and inexpensive genetic diagnostic chip that can be validated in our existing cohorts (n=12,000 subjects). HYPERGENES is in the unique position to propose a ground-breaking project, improving the methodology of genetic epidemiology of chronic complex diseases that have a high prevalence among EU populations. Designing a comprehensive genetic epidemiological model of complex traits will also help us to translate genetic findings into improved diagnostic accuracy and new strategies for early detection, prevention and eventually personalised treatment of a complex trait. The ultimate goal will be to promote the quality of life of EU populations.

Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: HEALTH-2007-2.4.2-2 | Award Amount: 14.92M | Year: 2008

Fighting Aneurysmal Diseases (FAD) is a public health in EU, because of the ageing population. In the absence of intervention, aneurysms evolve towards rupture and death. The translational objectives of the project are to accelerate the acquisition of knowledge, and to develop new diagnostic and therapeutic tools for FAD in humans. The project innovates by integrating two different localizations differing in their initial etiologies but similar in their evolution. FAD will be built by pooling existing and new clinical & biological databases in EU. Tissue and cell banks will be constituted. The deliverables will be the standardization of clinical and biological procedures and the recording of all the material available in the consortium. These databases will provide a basis for genetic studies. Pathophysiology of aneurysms will be explored through human tissue and experimental models in transgenic animals, focusing on the role of proteases and their source within diseased tissues. Human databases, genetic & pathophysiological concepts will provide basis for the development of new diagnostic tools: genetic screening, identification of new surrogate markers, validation of candidate markers and discovery of new ones by proteomic approaches; and functional imaging, visualizing in situ various biological activities. These new molecules/cells of interest will be targeted in preclinical therapeutic approaches, using animal models, and by developing clinical trials. The objective of FAD will be achieved through the organization of a consortium, grouping 15 partners, integrating numerous medical and scientific disciplines. The consortium includes academic partners from 10 different EU countries, a Turkish research team, and 3 industrial partners. The acquired scientific and technological knowledges will be disseminated through training sessions, participation in European meetings, communication toward industry, and direct relationships with patient associations.

Agency: Cordis | Branch: FP7 | Program: CP-CSA | Phase: Fission-2012-4.2.1 | Award Amount: 5.40M | Year: 2013

Safety issues are of fundamental importance for the acceptance and sustainable application of nuclear energy. Actinides play a central role in the nuclear fuel cycle from mining, fuel fabrication, energy production, up to treatment of used fuel by reprocessing, partitioning and transmutation and/or finally management and disposal of radioactive waste. A fundamental understanding of actinide properties and behaviour in fuel materials, during the separation processes and once in geological repository is an imperative prerequisite to tackle all the related safety issues. Unravelling the complexity of the principal actinide components of used nuclear fuel certainly represents one of the grand challenges in nuclear science. In order to meet the needs of the safe and sustainable management of nuclear energy, it is therefore essential to maintain highest level of expertise in actinide sciences in Europe and to prepare the next generation of scientists and engineers who will contribute to develop safe actinide management strategies. Because actinides are radioactive elements, their study requires specific tools and facilities that are only available to a limited extent in Europe. Only a few academic and research organisations have the capabilities and licenses to work on these elements under safe conditions. It is therefore strategic to coordinate the existing actinide infrastructures in Europe, and to strengthen the community of European scientists working on actinides. In the continuation of ACTINET-6 and ACTINET-I3, TALISMAN will foster the networking between existing European infrastructures in actinide sciences open them widely to any European scientists by offering and supporting transnational access to unique facilities. To meet its objectives, TALISMAN will animate and organize a network of actinide facilities across the EU that will increase our knowledge for a safer management of actinides fostering training and education.

Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-ITN-2008 | Award Amount: 1.66M | Year: 2010

The main objective of PLANTORIGINS-ITN is to improve career prospects of young researchers in the growing field of plant evolutionary developmental biology through a programme of research, training and transfer of knowledge that integrates new discoveries and approaches in the fields of plant morphology, systematics, and developmental genetics with the overall goal of understanding the origins of form in plants. Much research in plant evolutionary developmental biology focuses on comparatively modern groups within the flowering plants, especially on economically important crops. But, as the field develops, it is becoming increasingly important and feasible to extend the scope of research to address questions of a fundamental nature in plants. The overarching and long term scientific question of PLANTORIGINS-ITN is: how did the major tissues and organ systems of plants evolve and what is their genetic regulatory basis? PLANTORIGINS-ITN brings together into a cohesive network a group of eight leading academic and industrial partners to provide unique state of the art training in these key areas. Because of the highly multidisciplinary nature of this network, transfer of knowledge within and between sectors is given high priority in our training programme. We regard this as fundamental to fostering the development and exploitation of research in this field. Our two industrial partners contribute state of the art analytical skills in the area of gene expression (microarray technology) and complementary business skills in the area of intellectual property rights and will provide valuable direction and feedback. The skills and competencies developed by the eight young researchers that we will train are directly transferable to the plant biotechnology sector, which is recognised as a strategically important industry that makes a key contribution to Europes agricultural competitiveness, sustainable development and economic growth.

Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: NMP.2013.1.1-1 | Award Amount: 9.30M | Year: 2013

The present project is aimed to the development of a multi-step process for the production of second-generation biofuels from lignocellulosic biomass in a cost-efficient way through the use of tailored nanostructured catalysts. The proposed process is based on the cascade combination of three catalytic transformations: catalytic pyrolysis, intermediate deoxygenation and hydrodeoxygenation. The sequential coupling of catalytic steps will be an essential factor for achieving a progressive and controlled biomass deoxygenation, which is expected to lead to liquid biofuels with a chemical composition and properties similar to those of oil-derived fuels. According to this strategy, the best nanocatalytic system in each step will be selected to deal with the remarkable chemical complexity of lignocellulose pyrolysis products, as well as to optimize the bio-oil yield and properties. Since hydrodeoxygenation (HDO) is outlined in this scheme as the ultimate deoxygenation treatment, the overall hydrogen consumption should be strongly minimized, resulting in a significant improvement of the process economic profitability. The use of nanostructured catalysts will be the key tool for obtaining in each chemical step of the cascade process, the optimum deoxygenation degree, as well as high efficiency, in terms both of matter and energy, minimizing at the same time the possible environmental impacts. The project will involve experiments at laboratory, bench and pilot plant scales, as well as a viability study of its possible commercial application. Thereby, the integrated process will be assessed according to technical, economic, social, safety, toxicological and environmental criteria. The consortium will be formed by 17 partners, including 4 research institutions, 6 universities, 5 large industries and 2 SME.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2011.4.2-2 | Award Amount: 3.88M | Year: 2011

In 2010 a widely marketed drug for the treatment of type 2 diabetes (T2DM) (rosiglitazone) was taken from the market as it was associated with an increased risk of myocardial infarction, a T2DM complication it was actually supposed to prevent. This example shows several things. First, the approval requirements do not guarantee a longer term positive benefit risk profile. Second, large scale postmarketing studies are desperately needed to monitor the benefit risk profile throughout the lifecycle of T2DM drugs, and to achieve the required scale collaboration across countries is mandatory. Many novel T2DM drugs have come to the market, all on the basis of the same surrogate endpoints. New safety issues are constantly arising, such as potential associations with pancreatitis, pancreas cancer, bladder cancer, acute renal failure, etc. In the SAFEGUARD Consortium we have assembled an excellent multidisciplinary group of experts who collaboratively aim to quantify the cardiovascular, cerebrovascular and pancreatic safety risk of the T2DM drugs, in particular the more novel drugs by investigating 1) published clinical trials and observational studies; 2) spontaneously reported adverse event reports in national and international pharmacovigilance databases; 3) data from nine population-based health care databases in six countries capturing longitudinal drug exposure and event data on more than 1.7 million T2DM patients. Data elaboration will be distributed but standardized through common protocols, data models and scripts. To put the epidemiological results into perspective, intensive monitoring mechanistic studies in human will be conducted to further understand how and why these T2DM drugs may affect the cardiovascular, digestive or renal system. The SAFEGUARD consortium will yield a harmonized epidemiological data platform on a large T2DM population, which could easily be used to address newly occurring safety issues in the future.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2012.3.2-1 | Award Amount: 3.76M | Year: 2012

The proposed research responds to the call for research into the Quality, Efficiency and Solidarity of Health Systems. European countries are reforming their health systems to improve health care delivery. One of the ways they are doing this is by changing skill mix within teams delivering health services: extending the roles of existing health professions and introducing new ones. This project will undertake a systematic evaluation of the impact of these new professional roles on practice, outcomes and costs in a range of different health care settings within European Union and Associate Countries. It will detail the nature, scope and contribution of the new professional roles, evaluate their impact on clinical practice and outcomes, and identify their scope to improve the integration of care. It will conduct economic evaluation to identify the cost effectiveness of the new professional roles, identify optimal models for delivery of health care and the consequences of these for management of human resources and workforce planning. Study design is cross-sectional and multi-level. A mixed methods approach will combine analysis of routinely collected data and primary data generated through interviews and questionnaires to health professionals, managers and patients. Data analysis will employ multi-level modelling techniques.

Agency: Cordis | Branch: FP7 | Program: ERC-SG | Phase: ERC-SG-PE1 | Award Amount: 849.00K | Year: 2010

The proposed project aims at analyzing fundamental problems from combinatorics using the most current methods available and at providing new structural and algorithmic insights to such problems. The problems considered will be treated on a general level of classes of combinatorial objects of the same kind and the developed general methods will also be applied to specific open problems. Classes of dense and sparse objects will be treated using different techniques. Dense combinatorial objects appear in extremal combinatorics and tools developed to handle them found their applications in different areas of mathematics and computer science. The project will focus on extending known methods to new classes of combinatorial objects, in particular those from algebra, and applying the most current techniques including Razborov flag algebras to problems from extremal combinatorics. Applications of the obtained results in property testing will also be considered. On the other hand, algorithmic applications often include manipulating with sparse objects. Examples of sparse objects are graphs embeddable in a fixed surface and more general minor-closed classes of graphs. The project objectives include providing new structural results and algorithmic metatheorems for classes of sparse objects using both classical tools based on the theory of graph minors as well as new tools based on the framework of classes of nowhere-dense structures.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: NMP-2007-2.2-2 | Award Amount: 3.25M | Year: 2008

We are proposing a Collaborative Project, NAMASTE, on nanostructured dilute magnetic semiconductor and metal materials. The key ideas are to control and manipulate the nanoscale properties of magnetic materials by local strain and electric fields making possible new types of magneto-electronic and spintronic devices. This is a co-ordinated programme of theoretical, experimental and technological research by a consortium of European academic and industrial research groups, each of which is internationally leading in the complementary, multidisciplinary research fields essential to the project delivery. The proposal builds on recent advances in the state-of-the-art by the consortium members and is based on the design of materials whose specific nanostructure yields the required tailored properties. NAMASTE should significantly advance the understanding of nanostructured magnetic materials and magnetic phenomena at the nanoscale. The project has a high probability of major medium and long term impact on many aspects of spintronics, magnetic data storage and processing, and magnetic sensors.

Agency: Cordis | Branch: FP7 | Program: CSA-SA | Phase: ENV.2009. | Award Amount: 1.21M | Year: 2009

The purpose of the GEO Network for Capacity Building (GEO-Net-CaB) project is to create the conditions for the improvement and increase of the GEO capacity building activities and framework, with special emphasis on developing countries, new EU member states (and EU neighbouring states) and climate monitoring and will serve the bigger goal of improved effectiveness and efficiency of GEO capacity building for application in the GEO societal benefit areas. Coinciding with this purpose, successful brokerage with (potential) clients for earth observation products and services will be facilitated. The project will deliver the following output: 1. Capacity building needs in earth observation are identified (at a generic and global level, but with emphasis on the target regions). 2. Specifications for earth observation capacity buildings are described. 3. Resource providers are identified. 4. Sustainable brokerage between stakeholders (including resource providers) is established. 5. A mechanism to facilitate cooperation between stakeholders and providers is established. 6. A global base of technical expertise for education and training in earth observation is established (with emphasis on developing countries, new EU member states and climate monitoring). 7. Monitoring and evaluation mechanisms for determining the efficacy of GEO capacity building efforts are established. To achieve maximum impact demonstration projects will be carried out in Southern Africa, the French-speaking African region, Czechia and Poland, with spin-offs to EU neighbouring countries and Latin America and Asia. The project (with a duration of three years) will be carried out by a strong consortium of partners from the Netherlands, France, South Africa, Morocco, Czechia and Poland, supervised by an advisory board with worldwide representation and strong connections to GEO.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: NMP.2012.1.1-1 | Award Amount: 4.96M | Year: 2012

chipCAT aims at the knowledge-driven development of a novel type of thin-film catalysts for silicon-based on-chip micro fuel cells (u-FCs). Combining fundamental surface-science, model catalysis, and first-principles computational studies, a detailed understanding of the surface chemistry on complex nanostructured catalysts will be achieved. This microscopic-level understanding will be used to tailor active sites and their mutual interplay at the nanoscale in order to maximize activity and selectivity and to reduce deactivation and poisoning. Starting from new oxide-based materials with minor demand for noble metals, new material concepts will be explored. Target structures defined by fundamental research will then by transferred to standard FC and u-FC catalysis by using advanced thin-film preparation techniques, such as magnetron sputtering and vacuum deposition. Knowledge-transfer between real and model catalysis will be guaranteed with atomic-level control, using a broad spectrum of surface spectroscopies, in-situ/operando spectroscopies, and microscopies with atomic resolution. Using modern microtechnologies, the novel tailor-made catalyst materials will be integrated into working FC test devices. Prototype devices will be fabricated for performance tests with results fed back to fundamental research. Finally, a process for laboratory-scale production of u-FC batches will be developed. Thus, we will connect surface science, model catalysis, state-of-the-art theory, thin-film-technology, applied heterogeneous catalysis, and microtechnology in an interdisciplinary approach, aiming at the development of a new generation of metal-oxide FC catalysts with improved performance and stability. This project not only will allow to drastically reduce or replace usage of critical materials in the related applications but also will open the pathway to groundbreaking energy storage technologies for mobile devices.

Agency: Cordis | Branch: FP7 | Program: CP-IP | Phase: NMP-2008-2.4-1 | Award Amount: 11.62M | Year: 2009

A major challenge facing European industry involves the development of more specific, energy saving processes with less environmental impact. The recent development of Metal Organic Frameworks (MOFs) may prove a major milestone in achieving these goals. MACADEMIA project is an extension to an FP6 STREP (DeSANNS) which highlighted some MOF materials for CO2 capture and storage. It will expand and continue this work on a much larger scale. The three Total branches will focus on bringing MOFs to key market sectors - gas separation and storage, liquid separation and catalysis. The Total-led consortium, with 11 academic partners from across EU, one leading South Korean partner, among world leaders among their particular domain of MOF science, will be contributing to the project, with a dedicated management partner. MACADEMIA intends to produce new MOFs and optimise those already of promising interest, characterise MOFs using specialised techniques, test MOFs using a three-tiered process, use predictive modelling and demonstrate the use of MOFs in key industrial processes. It will target separation processes in gas / vapour phase (propene/propane, acid gases separation, CO2 and H2 purification), in liquid phase (xylene separations, recovery of N- and/or S-compounds from hydrocarbons), and in catalysis (Lewis-acid MOFs as catalysts for epoxide polymerization, redox-active MOFs as catalysts for hydrocarbon autoxidation). Several of MACADEMIAs targets are expected to reach pilot scale whereas a blue sky approach will be taken for others giving room for innovation and step change. An attractive project, it is open to young researchers with industrially coordinated research to counterbalance competition from USA and Japan and able to contribute to a strong ERA.

Agency: Cordis | Branch: FP7 | Program: CSA-SA | Phase: HEALTH-2007-2.2.2-4 | Award Amount: 840.61K | Year: 2008

AIM. To investigate the reasons for the exclusion of the elderly in clinical trials and to provide solutions for this problem. INTRODUCTION. Although the elderly account for high drug consumption, they are underrepresented in clinical trials. With an increasingly ageing European population it is essential to demonstrate the efficacy and safety of drugs. Clinical trials need to take into account the relevant issues of this population, i.e. changed metabolism, multiple chronic conditions and poly-pharmacy. To examine this issue and effect a paradigm shift it is necessary to target gatekeepers and stakeholders of clinical trials. METHODS. The project will be coordinated by the Medical Economics and Research Centre, Sheffield, with guidance from the Centre for Interdisciplinary Research on Ageing at Keele University, UK. The 5 work packages (WP) will be carried out by a multi-disciplinary team of highly qualified experts in Geriatrics, Gerontology and social sciences. WP1 will involve a systematic review of the literature and review of ongoing clinical trials to assess the extent of exclusion of the elderly. Based on these findings WP2 and WP 3 will investigate why the elderly are underrepresented in clinical trials and what can be done to improve their participation. This will be carried out in 9 countries: UK, Spain, Holland, Italy, Poland, Lithuania, Romania, Israel and the Czech Republic. WP2 will research the views of health professionals and ethicists using structured questionnaires. WP3 will explore the perceptions of older patients and carers using a focus group methodology. For WP4, the recommendations from WP2 and WP3 will be used to develop a charter for the elderly in clinical trials. WP5 will disseminate and implement the findings. CONCLUSION. PREDICT will promote the inclusion of the elderly in clinical trials in Europe. This project will facilitate the improvement of the rights of older people and the quality of health care for the ageing population.

Rasic D.,Dalhousie University | Hajek T.,Dalhousie University | Hajek T.,Charles University | Alda M.,Dalhousie University | And 2 more authors.
Schizophrenia Bulletin | Year: 2014

Objective: Offspring of parents with severe mental illness (SMI; schizophrenia, bipolar disorder, major depressive disorder) are at an increased risk of developing mental illness. We aimed to quantify the risk of mental disorders in offspring and determine whether increased risk extends beyond the disorder present in the parent. Method: Meta-analyses of absolute and relative rates of mental disorders in offspring of parents with schizophrenia, bipolar disorder, or depression in family high-risk studies published by December 2012. Results: We included 33 studies with 3863 offspring of parents with SMI and 3158 control offspring. Offspring of parents with SMI had a 32% probability of developing SMI (95% CI: 24%-42%) by adulthood (age >20). This risk was more than twice that of control offspring (risk ratio [RR] 2.52; 95% CI 2.08-3.06, P <. 001). High-risk offspring had a significantly increased rate of the disorder present in the parent (RR = 3.59; 95% CI: 2.57-5.02, P <. 001) and of other types of SMI (RR = 1.92; 95% CI: 1.48-2.49, P <. 001). The risk of mood disorders was significantly increased among offspring of parents with schizophrenia (RR = 1.62; 95% CI: 1.02-2.58; P =. 042). The risk of schizophrenia was significantly increased in offspring of parents with bipolar disorder (RR = 6.42; 95% CI: 2.20-18.78, P <. 001) but not among offspring of parents with depression (RR = 1.71; 95% CI: 0.19-15.16, P =. 631). Conclusions: Offspring of parents with SMI are at increased risk for a range of psychiatric disorders and one third of them may develop a SMI by early adulthood. © 2013 The Author.

Hyvl J.,Czech Institute of Organic Chemistry And Biochemistry | Roithova J.,Charles University
Organic Letters | Year: 2014

Reductive elimination of ethane from the palladium(IV) complex [PdMe 3(bpy)I] (bpy = 2,2′-bipyridine) is studied by electrospray ionization mass spectrometry. Palladium(IV) complexes can be detected as binuclear clusters [Pd2Me6I(bpy)2]+ or as complexes [PdMe3(bpy)(L)]+ stabilized by an electron-donating ligand L. Fragmentation of all palladium(IV) complexes is dominated by elimination of ethane which corresponds to the reductive elimination coupling of the methyl groups. The associated energy demands for different complexes reveal that the mononuclear complexes with poorly electron-donating ligands provide the fastest reaction. © 2013 American Chemical Society.

ATLANTA--(BUSINESS WIRE)--In recognition of National Black HIV/AIDS Awareness Month, AIDS Healthcare Foundation (AHF) partnered with the Center for Civil and Human Rights (CCHR) to unveil “Atlanta’s HIV+ Population Now” art sculpture yesterday. The unveiling of this very powerful artistic presentation was preceded by a short luncheon update for the media on the status of HIV in our community and the work of AID Atlanta, one of the oldest and largest HIV/AIDS service organizations in the south-east, in addressing the current crisis. Created through support from the AHF Grant Fund, “Atlanta’s HIV+ Population Now”, an 8-foot arts installation, designed by local Atlanta artist Matthew Terrell, shows audiences the ever-growing problem of new HIV diagnoses in the Atlanta metro area. Taking inspiration from the iconic “Atlanta’s Population Now” sign located on Peachtree Street, which has charted our city’s growth since 1965, the “Atlanta’s HIV+ Population Now” sign uses data from the CDC (which has been compiled by the AIDSvu Map project at Emory University) to show how many people are diagnosed every day with HIV in the Atlanta Metro Area. The piece, which takes the form of a pyramidal sign, simple text, and interchangeable marquee-style digits, will stay on display in the lower, external courtyard area of CCHR through June 27th, National HIV/AIDS Testing Day. To further exemplify the impact of the HIV epidemic in the Atlanta community, and to encourage public engagement, every Friday at 12 noon, the artist will update the numbers in the marquee and will be on hand to discuss HIV with visitors, and to talk about the meaning of the project. Recent statistics by AIDSvu show that, nationally, the downtown Atlanta corridor has one of the highest rates of people living with an HIV diagnosis. The Centers for Disease Control and Prevention (CDC) has also reported that the HIV prevalence rate among people living in urban poverty areas is very high (2.1%) and exceeds the 1% cut-off that defines a generalized HIV epidemic. “As AHF continues to address the HIV/AIDS epidemic in communities across the nation, we have found the arts to be a powerful tool for breaking down the barriers of stigma and judgment, providing awareness and encouraging powerful and transformative dialogue on how diverse communities can work to combat this major public health issue,” shared Imara Canady, AHF Southern Bureau Regional Director for Communications and Community Engagement. “Through this artistic expression, we hope to both continue the awareness of the impact of the HIV epidemic in Atlanta and to work with the Center for Civil and Human Rights team, to create thought-provoking public discourse on how this community can address this epidemic. AIDS Healthcare Foundation (AHF), the largest global AIDS organization, currently provides medical care and/or services to over 694,000 individuals in 35 countries worldwide in the US, Africa, Latin America/Caribbean, the Asia/Pacific Region and Eastern Europe. To learn more about AHF, please visit our website:, find us on Facebook: and follow us on Twitter: @aidshealthcare and Instagram: @aidshealthcare Matthew Terrell works as an artist, writer, and communication professional in the fine city of Atlanta. His work focuses on issues such as HIV/AIDS, drag culture, queer Southern identity, and the intersection of sexuality and technology. Terrell's visual art has shown in San Francisco, Atlanta, and Savannah. He contributes reviews, essays, and articles for publications including BURNAWAY Magazine, VICE, Huffington Post, Creative Loafing, and ArtsATL. Terrell has spoken about issues related to HIV (including organ donation, PrEP, and other prevention initiatives), for NPR's Here and Now, Georgia Public Broadcasting's On Second Thought, and WABE's Closer Look. His proudest moment was, while researching an article on Keith Haring’s work in Atlanta, finding a missing fragment of the original Haring mural. Terrell helped return the piece to Children's Healthcare of Atlanta. Terrell has attended Djerassi Resident Artist Program, Atlantic Center for the Arts, The Studios of Key West, and Serenbe Artist Residency. He has a BFA and MFA in writing from SCAD, and an MA in communications from Georgia State University. Terrell was a Rotary Ambassadorial Scholar in Prague, and studied international media at Charles University 2008-2009. He is an alum of Arts Leaders of Metro Atlanta class of 2016, Burnaway Emerging Arts Writers Mentorship Program in 2015, and NPR's Next Generation Radio in 2006. About the Center for Civil and Human Rights: The Center for Civil and Human Rights in Downtown Atlanta is an engaging cultural attraction that connects The American Civil Rights Movement to today’s Global Human Rights Movements. The Center features a continuously rotating exhibit from The Morehouse College Martin Luther King, Jr. Collection, which includes many of Dr. King’s documents and personal items. Visitors will be immersed in experiential exhibits through powerful and authentic stories, historic documents, compelling artifacts, and interactive activities. The Center is a source for ongoing dialogue — hosting educational forums and attracting world-renowned speakers and artists who work on a variety of human rights topics.

The synthesis of 2′-deoxyribonucleoside triphosphates (dNTPs) either by classical triphosphorylation of nucleosides or by aqueous cross-coupling reactions of halogenated dNTPs is discussed. Different enzymatic methods for synthesis of modified oligonucleotides and DNA by polymerase incorporation of modified nucleotides are summarized, and the applications in redox or fluorescent labeling, as well as in bioconjugations and modulation of interactions of DNA with proteins, are outlined. © 2014 American Chemical Society.

Jungwirth T.,ASCR Institute of Physics Prague | Jungwirth T.,University of Nottingham | Wunderlich J.,ASCR Institute of Physics Prague | Wunderlich J.,Hitachi Cambridge Laboratory | And 8 more authors.
Reviews of Modern Physics | Year: 2014

Over the past two decades, the research of (Ga,Mn)As has led to a deeper understanding of relativistic spin-dependent phenomena in magnetic systems. It has also led to discoveries of new effects and demonstrations of unprecedented functionalities of experimental spintronic devices with general applicability to a wide range of materials. This is a review of the basic material properties that make (Ga,Mn)As a favorable test-bed system for spintronics research and a discussion of contributions of (Ga,Mn)As studies in the general context of the spin-dependent phenomena and device concepts. Special focus is on the spin-orbit coupling induced effects and the reviewed topics include the interaction of spin with electrical current, light, and heat. © 2014 American Physical Society.

Fonseca R.M.,University of Lisbon | Malinsky M.,Charles University | Staub F.,University of Bonn
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2013

We work out a set of simple rules for adopting the two-loop renormalization group equations of a generic gauge field theory given in the seminal works of Machacek and Vaughn to the most general case with an arbitrary number of Abelian gauge factors and comment on the extra subtleties possibly encountered upon matching a set of effective gauge theories in such a framework. © 2013 Elsevier B.V.

Turek I.,Academy of Sciences of the Czech Republic | Kudrnovsky J.,ASCR Institute of Physics Prague | Carva K.,Charles University
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We present results of systematic fully relativistic first-principles calculations of the uniaxial magnetic anisotropy energy (MAE) of a disordered and partially ordered tetragonal Fe-Co alloy using the coherent potential approximation (CPA). This alloy has recently become a promising system for thin ferromagnetic films with a perpendicular magnetic anisotropy. We find that existing theoretical approaches to homogeneous random bulk Fe-Co alloys, based on a simple virtual crystal approximation (VCA), overestimate the maximum MAE values obtained in the CPA by a factor of 4. This pronounced difference is ascribed to the strong disorder in the minority spin channel of real alloys, which is neglected in the VCA and which leads to a broadening of the d-like eigenstates at the Fermi energy and to the reduction of the MAE. The ordered Fe-Co alloys with a maximum L10-like atomic long-range order can exhibit high values of the MAE, which, however, get dramatically reduced by small perturbations of the perfect order. © 2012 American Physical Society.

Bertolini S.,International School for Advanced Studies | Di Luzio L.,Karlsruhe Institute of Technology | Malinsky M.,Charles University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

We analyze the relation between the present (and foreseen) bounds on matter stability and the presence of TeV-scale color octet scalar states in nonsupersymmetric SO(10) grand unification with one adjoint Higgs representation triggering the symmetry breaking. This scenario, discarded long ago due to tree-level tachyonic instabilities appearing in all phenomenologically viable breaking patterns, has been recently revived at the quantum level. By including the relevant two-loop corrections we find a tight correlation between the octet mass and the unification scale which either requires a light color octet scalar within the reach of the LHC or, alternatively, a proton lifetime accessible to the forthcoming megaton-scale facilities. © 2013 American Physical Society.

Wong K.S.,Charles University | Masin D.,Charles University | Ng C.W.W.,Hong Kong University of Science and Technology
Computers and Geotechnics | Year: 2014

The shear modulus at very small strains (less than 0.001%) is an important parameter in the design of geotechnical structures subjected to static and cyclic loadings. Although numerous soil models are available for predicting shear modulus of saturated and dry soils, only a few ones can predict shear stiffness at very small strains of unsaturated soils correctly. In this study, a few unsaturated soil models are evaluated critically and compared with a newly developed model. This newly proposed model is verified by using measured shear modulus at very small strains for three different low plasticity fine grained soils available in the literature. It is found that this new model can predict shear modulus at very small strain resulting from an increase and a decrease in mean net stress at constant matric suction for low plasticity fine grained soils. Moreover, this model is able to give a reasonably good prediction on shear stiffness at very small strain during wetting of a collapsible unsaturated soil. In addition, the newly proposed model is illustrated to capture a consistent trend with experimental data of shear stiffness at very small strain for non-collapsible soils obtained during drying-wetting cycles. This evaluation revealed that the newly proposed model has better predictive capabilities than some earlier formulations of the same simplicity. In addition, the proposed model with fewer parameters has similar predictive capability as compared with a more complex model. © 2013 Elsevier Ltd.

Chaplick S.,Charles University | Ueckerdt T.,Karlsruhe Institute of Technology
Journal of Graph Algorithms and Applications | Year: 2013

A graph is Bk-VPG when it has an intersection representation by paths in a rectangular grid with at most k bends (turns). It is known that all planar graphs are B3-VPG and this was conjectured to be tight. We disprove this conjecture by showing that all planar graphs are B2-VPG. We also show that the 4-connected planar graphs constitute a subclass of the intersection graphs of Z-shapes (i.e., a special case of B2-VPG). Additionally, we demonstrate that a B2-VPG representation of a planar graph can be constructed in O(n3/2) time. We further show that the triangle-free planar graphs are contact graphs of: L-shapes, Γ-shapes, vertical segments, and horizontal segments (i.e., a special case of contact B1-VPG). From this proof we obtain a new proof that bipartite planar graphs are a subclass of 2-DIR.

Grasselli M.,Polytechnic of Milan | Prazak D.,Charles University
Interfaces and Free Boundaries | Year: 2011

We consider a system which describes the behavior of a binary mixture of immiscible incompressible fluids with shear dependent viscosity by means of the diffuse interface approach. This system consists of Navier-Stokes type equations, characterized by a nonlinear stress-strain law, which are nonlinearly coupled with a convective Cahn-Hilliard equation for the order parameter. We analyze the corresponding dynamical system and, by means of the short trajectory method, we prove the existence of global and exponential attractors. We also discuss the dependence of an upper bound of the fractal dimension on the physical parameters of the system. © European Mathematical Society 2011.

Havrdova E.,Charles University | Galetta S.,University of Pennsylvania | Stefoski D.,Rush University Medical Center | Comi G.,San Raffaele Scientific Institute
Neurology | Year: 2010

Background: Multiple sclerosis (MS) shares many pathologic features with other immune-mediated inflammatory diseases, such as rheumatoid arthritis, Crohn disease, and psoriasis. The development of effective biologic agents for rheumatoid arthritis has resulted in a treatment paradigm shift such that disease remission is now an explicit goal. Expert Clinical Opinion: The traditional immunomodulatory disease-modifying therapies for MS (interferon beta and glatiramer acetate) delay disease progression and reduce activity on brain MRI to varying degrees; however, they have not been demonstrated to induce disease remission. Therefore, the concept of disease remission or freedom from disease activity in MS has received little attention from the neurology community. We discuss some potential definitions of disease remission in MS and whether freedom from disease activity can become an increasingly useful measure of therapeutic response. Future Directions: Future research should be directed at determining the long-term significance of freedom from disease activity during a short-term clinical trial in relapsing-remitting MS. Copyright © 2010 by AAN Enterprises, Inc. All rights reserved.

Varga E.,Charles University | Babuin S.,ASCR Institute of Physics Prague | Skrbek L.,Charles University
Physics of Fluids | Year: 2015

We report a comprehensive study of turbulent superfluid 4He flow through a channel of square cross section. We study for the first time two distinct flow configurations with the same apparatus: coflow (normal and superfluid components move in the same direction), and counterflow (normal and superfluid components move in opposite directions). We realise also a variation of counterflow with the same relative velocity, but where the superfluid component moves while there is no net flow of the normal component through the channel, i.e., pure superflow. We use the second-sound attenuation technique to measure the density of quantised vortex lines in the temperature range 1.2 K ≲ T ≲ Tλ ≈ 2.18 K and for flow velocities from about 1 mm/s up to almost 1 m/s in fully developed turbulence. We find that both the steady-state and temporal decay of the turbulence significantly differ in the three flow configurations, yielding an interesting insight into two-fluid hydrodynamics. In both pure superflow and counterflow, the same scaling of vortex line density with counterflow velocity is observed, L ∝ V2 cf , with a pronounced temperature dependence; in coflow instead, the vortex line density scales with velocity as L ∝ V3/2 and is temperature independent; we provide theoretical explanations for these observations. Further, we develop a new promising technique to use different second-sound resonant modes to probe the spatial distribution of quantised vortices in the direction perpendicular to the flow. Preliminary measurements indicate that coflow is less homogeneous than counterflow/superflow, with a denser concentration of vortices between the centre of the channel and its walls. © 2015 AIP Publishing LLC.

Schulmann K.,University of Strasbourg | Jezek J.,Charles University
International Journal of Earth Sciences | Year: 2012

During the ascent, emplacement and post-emplacement deformation of igneous rocks, two or more phases of deformation that overprint each other are often depicted. These overprints, when magnetic minerals are present, are recorded in magnetic fabric. In this contribution, overprints are studied by means of numerical modeling, following several basic scenarios common to igneous rocks. Biotite and amphibole that occur often together in igneous rocks are considered as carriers of the anisotropy of magnetic susceptibility. Modeling shows that (1) a constrictional fabric with a low degree of anisotropy as commonly recorded in magmatic rocks may result from a deformation overprint and not necessarily from an extensional/transtensional regime, and (2) that the constrictional AMS fabrics originates from orthogonal superimposition of a deformation event on an AMS fabric inherited from earlier magma emplacement history. Therefore, the interpretation of a constrictional fabric must be performed with caution. Numerical modeling may provide a suitable help in strengthening the interpretation of real magnetic fabric data. © 2011 Springer-Verlag.

Kysely J.,ASCR Institute of Physics Prague | Plavcova E.,ASCR Institute of Physics Prague | Plavcova E.,Charles University
Journal of Geophysical Research: Atmospheres | Year: 2010

The study compares daily maximum (Tmax) and minimum (T min) temperatures in two data sets interpolated from irregularly spaced meteorological stations to a regular grid: the European gridded data set (E-OBS), produced from a relatively sparse network of stations available in the European Climate Assessment and Dataset (ECA&D) project, and a data set gridded onto the same grid from a high-density network of stations in the Czech Republic (GriSt). We show that large differences exist between the two gridded data sets, particularly for Tmin. The errors tend to be larger in tails of the distributions. In winter, temperatures below the 10% quantile of Tmin, which is still far from the very tail of the distribution, are too warm by almost 2°C in E-OBS on average. A large bias is found also for the diurnal temperature range. Comparison with simple average series from stations in two regions reveals that differences between GriSt and the station averages are minor relative to differences between E-OBS and either of the two data sets. The large deviations between the two gridded data sets affect conclusions concerning validation of temperature characteristics in regional climate model (RCM) simulations. The bias of the E-OBS data set and limitations with respect to its applicability for evaluating RCMs stem primarily from (1) insufficient density of information from station observations used for the interpolation, including the fact that the stations available may not be representative for a wider area, and (2) inconsistency between the radii of the areal average values in high-resolution RCMs and E-OBS. Further increases in the amount and quality of station data available within ECA&D and used in the E-OBS data set are essentially needed for more reliable validation of climate models against recent climate on a continental scale. Copyright 2010 by the American Geophysical Union.

Iorio A.,Charles University | Lambiase G.,University of Salerno | Lambiase G.,National Institute of Nuclear Physics, Italy
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

We find that, for a very specific shape of a monolayer graphene sample, a general relativistic-like description of a back-ground spacetime for graphene's conductivity electrons is very natural. The corresponding electronic local density of states is of finite temperature. This is a Hawking-Unruh effect that we propose to detect through an experiment with a Scanning Tunneling Microscope. © 2012 Elsevier B.V.

Broz P.,Academy of Sciences of the Czech Republic | Broz P.,Charles University | Hauber E.,German Aerospace Center
Journal of Geophysical Research E: Planets | Year: 2013

Hydrovolcanism is a common natural phenomenon on Earth and should be common on Mars, too, since its surface shows widespread evidence for volcanism and near-surface water. We investigate fields of pitted cones in the Nephentes/Amenthes region at the southern margin of the ancient impact basin, Utopia, which were previously interpreted as mud volcanoes. The cone fields contain pitted and breached cones with associated outgoing flow-like landforms. Based on stratigraphic relations, we determined a Hesperian or younger model age. We test the hypothesis of a (hydro)volcanic origin. Based on a detailed morphological and morphometrical analysis and an analysis of the regional context, an igneous volcanic origin of these cones as hydrovolcanic edifices produced by phreatomagmatic eruptions is plausible. Several lines of evidence suggest the existence of subsurface water ice. The pitted cones display well-developed wide central craters with floor elevations below the preeruptive surface. Their morphometry and the overall appearance are analogous to terrestrial tuff cones and tuff rings. Mounds that are also observed in the same region resemble terrestrial lava domes. The hydrovolcanic interaction between ascending magma and subsurface water and/or water ice may explain the formation of the pitted cones, although other scenarios such as mud volcanism cannot be ruled out. Together with the mounds, the cones might represent effusive and explosive edifices of a monogenetic volcanic field composed of lava domes, tuff rings, tuff cones, and possibly maars. © 2013. American Geophysical Union. All Rights Reserved.

Jurco B.,Charles University | Schupp P.,Jacobs University Bremen | Schupp P.,Heriot - Watt University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

We propose an effective action for a p '-brane with open p-branes ending on it. The action has dual descriptions similar to the commutative and non-commutative ones of the DBI action for D-branes and open strings. The Poisson structure governing the non-commutativity of the D-brane is replaced by a Nambu structure and the open-closed string relations are generalized to the case of p-branes utilizing a novel Nambu sigma model description of p-branes. In the case of an M5-brane our action interpolates between M5-actions already proposed in the literature and matrix-model like actions involving Nambu structures. © 2012 Elsevier B.V.

Dvorak J.,Charles University | Jensen E.B.V.,University of Aarhus
Journal of Microscopy | Year: 2013

In this paper, we propose a semiautomatic procedure for estimation of particle surface area. It uses automatic segmentation of the boundaries of the particle sections and applies different estimators depending on whether the segmentation was judged by a supervising expert to be satisfactory. If the segmentation is correct the estimate is computed automatically, otherwise the expert performs the necessary measurements manually. In case of convex particles we suggest to base the semiautomatic estimation on the so-called flower estimator, a new local stereological estimator of particle surface area. For convex particles, the estimator is equal to four times the area of the support set (flower set) of the particle transect. We study the statistical properties of the flower estimator and compare its performance to that of two discretizations of the flower estimator, namely the pivotal estimator and the surfactor. For ellipsoidal particles, it is shown that the flower estimator is equal to the pivotal estimator based on support function measurements along four perpendicular rays. This result makes the pivotal estimator a powerful approximation to the flower estimator. In a simulation study of prolate and oblate ellipsoidal particles, the surfactor also performs well for particles which are not extremely elongated. In particular, the surfactor is not very much affected by the singularity in the surfactor formula or by possible inaccuracies in the necessary angle measurements. We also assess the performance of the semiautomatic procedure in a study of somatostatin positive inhibitory interneurons from mice hippocampi. Only 35% of the cells needed to be analysed manually and an important decrease in workload was obtained by using the semiautomatic approach. © 2013 Royal Microscopical Society.

Iorio A.,Charles University | Lambiase G.,University of Salerno | Lambiase G.,National Institute of Nuclear Physics, Italy
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2014

The solutions of many issues, of the ongoing efforts to make deformed graphene a tabletop quantum field theory in curved spacetimes, are presented. A detailed explanation of the special features of curved spacetimes, originating from embedding portions of the Lobachevsky plane into R3, is given, and the special role of coordinates for the physical realizations in graphene is explicitly shown, in general, and for various examples. The Rindler spacetime is reobtained, with new important differences with respect to earlier results. The de Sitter spacetime naturally emerges, for the first time, paving the way to future applications in cosmology. The role of the Bañados, Teitelboim, and Zanelli (BTZ) black hole is also briefly addressed. The singular boundary of the pseudospheres, "Hilbert horizon," is seen to be closely related to the event horizon of the Rindler, de Sitter, and BTZ kind. This gives new, and stronger, arguments for the Hawking phenomenon to take place. An important geometric parameter, c, overlooked in earlier work, takes here its place for physical applications, and it is shown to be related to graphene's lattice spacing, . It is shown that all surfaces of constant negative curvature, K=-r-2, are unified, in the limit c/r→0, where they are locally applicable to the Beltrami pseudosphere. This, and c=, allow us (a) to have a phenomenological control on the reaching of the horizon; (b) to use spacetimes different from the Rindler spacetime for the Hawking phenomenon; and (c) to approach the generic surface of the family. An improved expression for the thermal LDOS is obtained. A nonthermal term for the total LDOS is found. It takes into account (i) the peculiarities of the graphene-based Rindler spacetime; (ii) the finiteness of a laboratory surface; and (iii) the optimal use of the Minkowski quantum vacuum, through the choice of this Minkowski-static boundary. © 2014 American Physical Society.

Berger L.,University of Savoy | Bernard-Demanze L.,Charles University
Gait and Posture | Year: 2011

The aim of this study was to evaluate the age-related changes in postural control during a simple quiet standing task and a dual-task paradigm (applying a memory-spatial task and quiet standing).Thirty-five subjects were divided in two age-related groups: both younger (Y: 20-26 years) and older (O: 60-77 years) groups performed a simple postural task (quiet standing) and a dual-task (a visual memory task combined with quiet standing). Measures of the center of pressure (CoP) were recorded and its two components, the center of gravity (CG) and the differential CoP-CG, were evaluated.An age-related effect was observed in static postural performance during dual-tasking. Postural stability led to improved performance in younger subjects during the dual-task and but not in the elderly.Of the results suggest there is a " cognition first" principle for the younger adults, that is, the mirror image of the " posture first" principle observed in older adults under dual-tasking situations. © 2010 Elsevier B.V.

Vanikova Z.,Gilead Sciences | Hocek M.,Gilead Sciences | Hocek M.,Charles University
Angewandte Chemie - International Edition | Year: 2014

5-[(2-Nitrobenzyl)oxymethyl]-2′-deoxyuridine 5′-O-triphosphate was used for polymerase (primer extension or PCR) synthesis of photocaged DNA that is resistant to the cleavage by restriction endonucleases. Photodeprotection of the caged DNA released 5-hydroxymethyluracil-modified nucleic acids, which were fully recognized and cleaved by restriction enzymes. Stability: A modified nucleoside triphosphate is incorporated into DNA sequences using polymerase. The resulting photocaged DNA is resistant against cleavage by restriction endonucleases (REs) and fully replicable by polymerase chain reaction (PCR) or primer extension (PEX). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Heneberg P.,Charles University | Rezac M.,Czech Republic Crop Research Institute
Ecological Engineering | Year: 2014

Although the value of the habitat lost by quarrying is widely known, awareness of the conservation value of the newly formed habitat is negligible. We provide evidence on the conservation value of both active and disused sandpits and gravel-sandpits for epigeic spiders and harvestmen, commonly considered important indicator species. We focus on xerothermophilous habitats within sandpits subjected to near-natural succession or other reclamation efforts. We show that xerothermophilous sandpit microhabitats are used by 323.8. ±. 23.9 epigeic spider species and 8.5. ±. 1.1 harvestmen species, with the species spectrum changing dramatically during spontaneous succession and if the habitat is subject to other forms of reclamation, with low species dominance across all habitats tested. We found 81 spider species recognized as critically endangered, endangered, vulnerable or nearly threatened. Of these, 72 (89%) were present at spontaneously formed xerothermophilous habitats of various ages, and 40 (49%) at the reclaimed sites. We analyzed the species-specific habitat preferences of the red-listed spider species in relation to both abiotic (altitude, slope, soil penetration resistance, soil shear strength resistance, soil texture) and biotic (vegetation cover, plant diversity, diversity of red-listed plants) factors. The xerothermophilous sandpit habitats served as important refuges for Central European steppe and aeolian sand dune species, which had nearly disappeared from the surrounding intensively cultivated cultural landscape. © 2014 Elsevier B.V.

Kolar M.,Gilead Sciences | Kolar M.,Charles University | Hobza P.,Gilead Sciences | Hobza P.,Palacky University | Hobza P.,Pohang University of Science and Technology
Journal of Chemical Theory and Computation | Year: 2012

Until recently, the description of halogen bonding by standard molecular mechanics has been poor, owing to the lack of the so-called σ hole localized at the halogen. This region of positive electrostatic potential located on top of a halogen atom explains the counterintuitive attraction of halogenated compounds interacting with Lewis bases. In molecular mechanics, the σ hole is modeled by a massless point charge attached to the halogen atom and referred to as an explicit σ hole (ESH). Here, we introduce and compare three methods of ESH construction, which differ in the complexity of the input needed. The molecular mechanical dissociation curves of three model complexes containing bromine are compared with accurate CCSD(T)/CBS data. Furthermore, the performance of the Amber force field enhanced by the ESH on geometry characteristics is tested on the casein kinase 2 protein complex with seven brominated inhibitors. It is shown how various schemes depend on the selection of the ESH parameters and to what extent the energies and geometries are reliable. The charge of 0.2e placed 1.5 Å from the bromine atomic center is suggested as a universal model for the ESH. © 2012 American Chemical Society.

Frank O.,J. Heyrovsky Institute of Physical Chemistry | Vejpravova J.,ASCR Institute of Physics Prague | Holy V.,Charles University | Kavan L.,J. Heyrovsky Institute of Physical Chemistry | Kalbac M.,J. Heyrovsky Institute of Physical Chemistry
Carbon | Year: 2014

We present a comprehensive study of graphene grown by chemical vapor deposition on copper single crystals with exposed (1 0 0), (1 1 0) and (1 1 1) faces. Direct examination of the as-grown graphene by Raman spectroscopy using a range of visible excitation energies and microRaman mapping shows distinct strain and doping levels for individual Cu surfaces. Comparison of results from Raman mapping with X-ray diffraction techniques and atomic force microscopy shows it is neither the crystal quality nor the surface topography responsible for the specific strain and doping values, but it is the Cu lattice orientation itself. We also report an exceptionally narrow Raman 2D band width caused by the interaction between graphene and metallic substrate. The appearance of this extremely narrow 2D band with full-width-at-half maximum (FWHM) as low as 16 cm-1 is correlated with flat and undoped regions on the Cu(1 0 0) and (1 1 0) surfaces. The generally compressed (∼0.3% of strain) and n-doped (Fermi level shift of ∼250 meV) graphene on Cu(1 1 1) shows the 2D band FWHM minimum of ∼20 cm-1. In contrast, graphene grown on Cu foil under the same conditions reflects the heterogeneity of the polycrystalline surface and its 2D band is accordingly broader with FWHM >24 cm-1. © 2013 Elsevier Ltd. All rights reserved.

Ng C.W.W.,Hong Kong University of Science and Technology | Boonyarak T.,Hong Kong University of Science and Technology | Masin D.,Charles University
Canadian Geotechnical Journal | Year: 2013

Tunnel driving inevitably induces changes in stress and deformation in the ground, which could cause ultimate and serviceability problems to an adjacent tunnel. The effects of induced stress on an existing tunnel and crossing-tunnel interaction are still not fully understood. In this study, a series of three-dimensional centrifuge tests were carried out to investigate the responses of an existing tunnel in sand to the excavation of a new tunnel perpendicularly below it. Three-dimensional tunnel advancement was simulated using a novel technique that considers the effects of both volume and weight losses. This novel technique involves using a "donut" to control volume loss and mimic soil removal in-flight. To improve fundamental understanding of the stress transfer mechanism during the new tunnel advancement, measured results were back-analyzed threedimensionally using the finite element method. The maximum measured settlement of the existing tunnel induced by the new tunnel constructed underneath was about 0.3% of tunnel diameter, which may be large enough to cause serviceability problems. The observed large settlement of the existing tunnel was caused not only by a sharp reduction in vertical stress at the invert, but also by substantial stress transfer of overburden pressure at the crown. The section of the existing tunnel directly above the new tunnel was compressed vertically because the incremental normal stress on the existing tunnel was larger in the vertical direction than in the horizontal direction. The tensile strain and shear stress induced in the existing tunnel exceeded the cracking tensile strain and allowable shear stress limit given by the American Concrete Institute.

Novak P.,ASCR Institute of Physics Prague | Chlan V.,Charles University
Physical Review B - Condensed Matter and Materials Physics | Year: 2010

The hyperfine field is an important probe of the magnetism of solids, yet its calculation from the first principles in the compounds of 3d metals proved to be difficult. For iron we circumvent this problem by calculating the spin magnetic moments of the 3d electrons and the valence 4s electrons and express the contact hyperfine field as their linear combination. After adding the contributions of the on-site interaction of the nuclear spin with the orbital and spin moment of the 3d electrons, the coefficients of the linear combination are calculated by comparison with the hyperfine field experimentally determined in a number of iron compounds. The method brings the theoretical contact fields within ∼1?T of the values deduced from experiment. © 2010 The American Physical Society.

Raindlova V.,Gilead Sciences | Pohl R.,Gilead Sciences | Hocek M.,Gilead Sciences | Hocek M.,Charles University
Chemistry - A European Journal | Year: 2012

5-(5-Formylthienyl)-, 5-(4-formylphenyl)- and 5-(2-fluoro-5-formylphenyl) cytosine 2′-deoxyribonucleoside mono- (dC RMP) and triphosphates (dC RTP) were prepared by aqueous Suzuki-Miyaura cross-coupling of 5-iodocytosine nucleotides with the corresponding formylarylboronic acids. The dC RTPs were excellent substrates for DNA polymerases and were incorporated into DNA by primer extension or PCR. Reductive aminations of the model dC RMPs with lysine or lysine-containing tripeptide were studied and optimized. In aqueous phosphate buffer (pH 6.7) the yields of the reductive aminations with tripeptide III were up to 25 %. Bioconjugation of an aldehyde-containing DNA with a lysine-containing tripeptide was achieved through reductive amination in yields of up to 90 % in aqueous phosphate buffer. Joining forces: DNA-peptide conjugation through reductive amination of aldehyde-modified DNA with lysine-containing peptides was developed (see scheme). Formylaryl-linked dCTP derivatives were prepared by cross-coupling and incorporated into DNA by polymerases. The reductive amination of aldehyde-modified nucleotides and DNA was studied and optimized. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Agency: Cordis | Branch: FP7 | Program: CSA-SA | Phase: SiS-2009- | Award Amount: 3.77M | Year: 2010

The aim of ESTABLISH is to facilitate and implement an inquiry based approach in the teaching and learning of science and technology across Europe, mainly focussed, through the collaborative actions of the consortium, on appropriate teacher education and support using trialled and tested resource material particularly suited to inquiry based teaching. Inquiry based teaching methodologies are encouraged to engage students in science and mathematics by increasing their interest in science and also by stimulating teacher motivation. However, widespread implementation of such a methodology will only occur with inclusion and participation of all partners in education, both formal and informal. ESTABLISH addresses this by drawing together over 60 partners from across 11 European countries to work together on a 48 month multidisciplinary project to encourage and promote the more widespread use of inquiry-based science teaching techniques in second level schools through appropriate teacher education, creation of authentic learning environments and actions to bridge the gap between the science education research community, science teachers, students, parents, local industry as well as policy makers in order to facilitate the uptake of inquiry-based science teaching. The outcomes of this project will firstly be a large team of teachers across Europe who are skilled and confident in their delivery of inquiry based teaching. Further outcomes will be the identification of suitable model(s) of teacher education, at both pre- and in-service levels, for inquiry based teaching and also identification of best practice in guiding change through all the stakeholders involved in science and science education. Teachers are active partners as developers, researchers and agents so that real change in classroom practice can be achieved. ESTABLISH is committed to sharing and disseminating best practice in inquiry-based methods through European teacher networks, conferences and publications.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2007.2.2 | Award Amount: 5.94M | Year: 2009

Europe faces a growing economic and societal challenge due to its vast diversity of languages, and machine translation (MT) technology holds promise as a means to address this challenge. EuroMatrix Plus will\n- continue the rapid advance of MT technology, creating example systems for every official EU language, and providing other MT developers with our infrastructure for building statistical translation models,\n- continue and broaden the controlled systematic investigation of different approaches and techniques to accellerate the scientific evolution of novel methods, including both selection and crossfertilization. The aim is to to arrive at scientifically well understood novel combinations of methods that are provenly superior to the state of the art,\n- contribute to the growth and competitiveness of the European MT research scene and infrastructure through open evaluations and living community supported surveys of resources, tools, systems and their respective capabilities,\n- focus on bringing MT to the users, in addition to focusing on scientific advances. Because our statistical models are derived from example translations, we can build and exploit a synergistic relationship in which users suggest improvements to the system by post-editing its output, and the system improves itself by learning from user feedback.\nEuroMatrix Plus focuses on two types of users: professional translators and translation agencies working for private corporations, administrations, and other organisations, and lay users who create content on a volunteer basis by translating foreign materials into their own languages. We will investigate how these users can benefit from state of the art in MT, and conversely, how MT can benefit from user corrections, and create an openly accessible sample application that enables users to automatically translate news stories and web pages from any EU language into any other, and whose corrections will be exploited for improving MT technology.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2009.8.5 | Award Amount: 7.94M | Year: 2010

Future software-intensive systems, such as sensor networks, power grids, satellite and robot swarms, will generally exhibit a number of characteristic features:* Massive numbers of nodes, nodes with complex behavior, or complex interactions between nodes.* Operation in open and non-deterministic environments with variable network topology.* Need for adaptation, e.g., to changing environments and requirements.We call this future generation of software-intensive systems ensembles. The potentially huge impact - both positive and negative - of ensembles means that we need to understand ways to reliably and predictably model, design, and program them.Although there is a lot of research in this area, so far no theoretically well-founded technique for building ensembles exists. The goal of the ASCENS project is to develop such a method and to demonstrate its feasibility in three important application domains: robot swarms, cloud computing and e-mobility.

Kielkowski P.,Gilead Sciences | Fanfrlik J.,Gilead Sciences | Hocek M.,Gilead Sciences | Hocek M.,Charles University
Angewandte Chemie - International Edition | Year: 2014

A series of 7-substituted 7-deazaadenine and 5-substituted cytosine 2′-deoxyribonucleoside triphosphates (dNTPs) were tested for their competitive incorporations (in the presence of dATP and dCTP) into DNA by several DNA polymerases by using analysis based on cleavage by restriction endonucleases. 7-Aryl-7-deazaadenine dNTPs were more efficient substrates than dATP because of their higher affinity for the active site of the enzyme, as proved by kinetic measurements and calculations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Agency: Cordis | Branch: FP7 | Program: MC-ITN | Phase: PEOPLE-2007-1-1-ITN | Award Amount: 3.75M | Year: 2008

The scientific aims of the ELDEL project are: 1) to produce a model elucidating the relationships among psychological (psycholinguistic, cognitive) and environmental (orthographic, linguistic, educational/instructional, cultural) factors determining the development of literacy skills in European languages, and 2) to uncover the key components of an effective, culture-appropriate intervention program for the prevention and remediation of literacy problems in the languages under study. The research program comprises a number of overlapping cross-linguistic studies that will reveal the language-specific and language-general factors affecting literacy development. This multidisciplinary network includes partners with expertise in developmental, educational, and clinical psychology, experimental psycholinguistics, speech and language therapy, and an industrial partner specialising in the creation of software for the assessment and training of literacy skills. Each partner will also contribute to the networks training aims, to provide training in generic as well as in state-of-the-art domain-specific research skills. Participants will offer training in one or more of the following specialist areas: (a) specific literacy skills (e.g., phonological skills, spelling, reading comprehension), (b) typical vs. clinical populations (e.g., children with developmental disorders, dyslexia), (c) research methodology (e.g., longitudinal, intervention, experimental psycholinguistic, naturalistic), and (d) use and development of measurement tools (computer-generated, eye tracking, cross-linguistic tests). Additional training in relevant skills will be provided by visiting researchers during workshops and short courses. The projects are conceived to promote mobility within the network and allow young researchers to benefit from the training most relevant to them. This ITN will equip Early Stage and Experienced Researchers for successful careers in cutting-edge literacy research.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: SSH.2012.3.2-2 | Award Amount: 3.06M | Year: 2013

DISCIT aims to produce new knowledge enabling Member States, affiliated European countries and the European Union to achieve full and effective participation of persons with disabilities in society and the economy. In investigating the social and political conditions for making such participation a reality, the project adopts a multifaceted understanding of Active Citizenship. Adopting a multilevel and institutional perspective, DISCIT examines how different types of policies (social benefits, social services and social regulation instruments) can be mutually supportive in enhancing Active Citizenship for persons with disabilities. Using the UN Convention on the Rights of Persons with Disabilities (CRPD) as a framework of reference, DISCIT identifies more effective ways to remove and prevent physical, attitudinal, social and organisational barriers to Active Citizenship and participation on an equal basis with others, in a context of rapid social and economic change and evolving conceptions of disability across European societies. DISCIT synthesises policy lessons from a strategic sample of European states: Liberal (Ireland, United Kingdom), Conservative (Germany, Italy), Social Democratic (Norway, Sweden) and Post-Communist (Czech Republic, Serbia) regimes. DISCIT involves consortium members from all these countries in addition to Switzerland and Belgium. DISCITs results provide new insight into how the European Union can support Member States and affiliated European countries in working towards the realization of the rights of persons with disabilities as expressed in the Fundamental Rights under the EC Treaty and the CRPD. By clarifying the possibilities for a strengthened synergy between policies at diverse levels of governance, DISCIT contributes to knowledge for realizing the ambitions of the EU Disability Strategy 2010-2020 and the Europe 2020 Strategy for Smart, Sustainable and Inclusive Growth. DISCIT has a duration of 36 months; is coordinated by Norwegian Social Research (NOVA); the consortium members are universities, research institutes and two civil society organisations (EDF and MDRI-S). The consortium is supported by a Scientific Advisory Committee with distinguished members mainly from countries not covered by the consortium members, a European Stakeholder Committee and eight National Stakeholder Committees.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: ENV.2011.4.2.2-1 | Award Amount: 1.65M | Year: 2011

In the last four years, Beyond GDP indicators have rapidly risen up the political agenda and enjoyed greater public awareness. High profile initiatives have included nefs Happy Planet Index, launched in 2006, the EUs Beyond GDP initiative starting with the Beyond GDP conference in 2007, the OECDs Measuring the Progress of Societies project, and in 2009, the publication of the recommendations of the Commission on the Measurement of Economic Performance and Social Progress, led by economists Stiglitz, Sen and Fitoussi. Despite a growing number of critiques of GDP, and the emergence of an impressive array of alternative indicators, GDP maintains a central place amongst policy makers, planning offices, media and other target groups. Some data on what may be considered Beyond GDP indicators are being collected by official statistics offices, but they appear not to be considered in policy making or are given a peripheral role. The central assumption of the project is that indicators, if effectively embedded in the policy making process, are an effective transmission mechanism to connect research and policy. The aim of the project is therefore to enhance and speed up both the development and the effective use of indicators that can balance the use of GDP so as to support the sustainable development policy process in the EU. Ideally, indicator users need to be aware of the knowledge that exists, and vice versa indicator producers need to be aware of the context(s) in which the indicators will be used. Indicators should be developed as part of an interactive process with multiple feedbacks that ensure that user demands are taken up in the production of alternative indicators. Besides this knowledge gap, it needs also to be understood as part of a change process, in which one has to overcome various other barriers that prevent the existing research from being acted on. The BRAINPOoL project approaches this problem as a mismatch between demand and supply and aims to solve this via action research and knowledge brokerage activities. This is done by: Structuring the research reservoir on Beyond GDP indicators by synthesising existing overviews of Beyond GDP indicators, and assessing the degree to which they have been taken up in policy making; Increasing the understanding of the user context of Beyond GDP indicators; Stimulating user-producer interactions by organising meetings, discussions and workshops and improving the relation between users and producers at different levels; Consolidating and structuring a follow-up beyond the duration of BRAIN POoL by establishing institutional structures and/or feeds into existing ones in such a way that interactions between indicator producers and users will be sustained. Throughout the project linkages will be established with relevant target groups, such as policy makers on different levels, statistical offices, and planning agencies.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2007.1.2 | Award Amount: 4.68M | Year: 2008

The Q-ImPrESS project aims at bringing service orientation to critical software systems, such as industrial production control, telecommunication and critical enterprise applications. All these domains share a need for guaranteed end-to-end quality of service, but also a need to evolve over their long lifetimes. The Q-ImPrESS project targets this challenge by providing a method to allow developers, users and maintainers to foresee the impact of design decisions and evolutionary changes to the system not only on its overall quality of service, but also on its internal quality properties such as maintainability. Therefore, a new service architecture meta-model is developed which is accompanied by tool-supported model-driven quality of service prediction approaches and automated quality assessment. The consortium bundles outstanding European research groups on the field of quality assessment and prediction together with leading case study providers and agile and highly innovative SMEs which guarantee practicability, sustainability and open dissemination of the results.

Agency: Cordis | Branch: FP7 | Program: CP | Phase: ICT-2007.5.1 | Award Amount: 11.42M | Year: 2008

The aim of METABO is to set up a comprehensive platform, running both in clinical settings and in every-day life environments, for continuous and multi-parametric monitoring of the metabolic status in patients with, or at risk of, diabetes and associated metabolic disorders. The type of parameters that will be monitored, in addition to traditional clinical and biomedical parameters, will also include subcutaneous glucose concentration, dietary habits, physical activity and energy expenditure, effects of ongoing treatments, and autonomic reactions. The data produced by METABO will be integrated with the clinical data and the history of the patient and will be used in two major interrelated contexts of care: 1. Setting up a dynamic model of the metabolic behaviour of the individual to predict the influence and relative impact of specific treatments and of single parameters on glucose level. 2. Building personalized care plans integrated in the current clinical processes linking the different actors in primary and secondary care and improving the active role of the Patient.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-1.4-7 | Award Amount: 3.61M | Year: 2008

Stem cells offer a promising avenue to therapy for a wide range of complaints. However, for this potential to be realized, a consistent and plentiful supply of well-characterised stem cells is essential. There has been relatively little progress in the development of new culture technologies for the large-scale manufacture of mesenchymal stem cells (MSCs). There is a strong possibility that this limited ability to produce stem cells will result in delays to the translation of new therapies to the clinic. This will have a direct negative effect on the health of European citizens suffering from diseases untreatable by conventional medical technology and delay European efforts to promote NanoMedicine - Nanotechnology for Health. PurStem will progress the state of the art in the production of mesenchymal stem cells (MSCs) in large quantities. The current state of the art has several weaknesses - there are no standards for characterisation, isolation or identification of MSCs from any tissue, nor are there standard protocols for differentiation of MSCs to various lineages. Additionally, surface markers used for MSC characterization lack specificity and cryopreservation protocols are not standardized. Critically, current production methods for MSC require the use of animal products with major contaminant implications. PurStem will Identify the MSC receptome and Use this repertoire of growth factor receptors to Develop novel serum-free media for MSC production. PurStem will also result in novel antibody reagents for specific MSC characterization and contribute to GMP manufacturing standards to enable rapid progression to production of serum-free MSC for clinical applications. The impact on a range of therapeutic and research domains of having a reliable supply of industrial levels of categorised MSCs will be significant. PurStem represents a key enabler for stem cell applications in a range of therapeutic fields.

Agency: Cordis | Branch: FP7 | Program: CSA-CA | Phase: SEC-2007-7.0-02 | Award Amount: 815.08K | Year: 2008

Identifying the Needs of Medical First Responder in Disasters (NMFRDisaster) is a project coordinating medical first responders with research institutes in order to identify need for further research in the following areas: 1) Training methodology and technology used to train medical first responders for disasters. 2) Understanding the human impact of disaster on first responders. 3) Ethical and legal issues influencing the medical response to disasters. 4) Personal Protective equipment used in Chemical and Biological incidents. 5) Use of blood and blood products in disasters. This will be achieved through a preliminary research on existing know how followed by a work shop where the needs of the first responders will be identified, matched with existing knowledge and products, then setting the roadmap for future needed R&D.

Agency: Cordis | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2007-2.2-01 | Award Amount: 5.63M | Year: 2008

The ultimate goal of CLARIN is the construction and operation of a shared distributed infrastructure that aims at making language resources and technology available to the humanities and social sciences research communities at large. The preparatory phase will pave the way for implementation along 4 dimensions: Funding and governance: The aim is to bring together the funding agencies and to work out a ready-to-sign draft agreement between the funding agencies in the participating countries about governance, financing, construction and operation of the infrastructure. Technical: The technical objective is to provide a detailed specification of the infrastructure, agreement on data and interoperability standards to be adopted, and a running, validated prototype based on these specifications. The validation should cover technical, linguistic and user aspects. Language: For the validation the prototype will be populated with a selection of language resources and technologies for all participating languages. The objective is to deliver a sufficiently populated, and thoroughly tested prototype that demonstrates the adequacy of the approach for all participating languages. User: In order to fully exploit the potential of what language resources and technology have to offer to the humanities and social sciences communities we will: (i) make an analysis of current practice in the use of language technology in the humanities in order to establish the needs; (ii) launch and monitor typical humanities projects in order to validate the prototype and its specifications; (iii) create awareness in the humanities and social sciences communities of the potential of the use of language resources and technology to improve or innovate their research; (iv) bring together the humanities and language technology communities in order to ensure lasting synergies.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: NMP-2009-1.2-1 | Award Amount: 4.12M | Year: 2010

The overall objective of the project is to develop new Nanomaterials with New Production Technologies and to fabricate silicon quantum dot tandem solar cells to achieve increased efficiencies. The understanding of electrical transport and recombination mechanisms in these newly developed nanomaterials will enable us to design new tandem solar cell structures - based on Si thin-film or wafer solar cells - that help to overcome the efficiency limits of these conventional concepts. In order to reach our goals, considerable R\D work has to be performed on semiconductor bulk materials, thin layers and hetero-structures for such solar cells. These topics have not yet or only in parts been investigated and are also of high scientific interest for novel photonic and charge storage devices incorporating Si nanocrystals embedded in Si alloys. The consortium of this project, also including two companies, merges the scientific and technological competences that are necessary to find answers to these questions. Another objective is the compatibility of the newly developed technologies with high-throughput processing to ensure further cost-reduction. The expected significant jump in the solar cell and processing evolution will lead to higher efficiencies for solar cells and to ongoing cost-reduction also with a long-term perspective and will help to strengthening the European leadership in PV technologies. Thus it will also have a positive impact on the acceptance of photovoltaics by the public and by politics. Moreover, since energy efficiency is a big subject in the public discussion, photovoltaics will be an example of one of the highest electricity production efficiencies that have been achieved of all power generators. To sum up, we believe that this project will have a direct and positive impact on the European PV industry and its status in material science and it will contribute to the very ambitious goals of the EU commission in CO2 reduction in general.

Grund J.P.C.,Addiction Research Center | Grund J.P.C.,Charles University | Latypov A.,Columbia University | Harris M.,London School of Hygiene and Tropical Medicine
International Journal of Drug Policy | Year: 2013

Background: Krokodil, a homemade injectable opioid, gained its moniker from the excessive harms associated with its use, such as ulcerations, amputations and discolored scale-like skin. While a relatively new phenomenon, krokodil use is prevalent in Russia and the Ukraine, with at least 100,000 and around 20,000 people respectively estimated to have injected the drug in 2011. In this paper we review the existing information on the production and use of krokodil, within the context of the region's recent social history. Methods: We searched PubMed, Google Advanced Search, Google Scholar, YouTube and the media search engine for peer reviewed or media reports, grey literature and video reports. Survey data from HIV prevention and treatment NGOs was consulted, as well as regional experts and NGO representatives. Findings: Krokodil production emerged in an atypical homemade drug production and injecting risk environment that predates the fall of communism. Made from codeine, the active ingredient is reportedly desomorphine, but - given the rudimentary 'laboratory' conditions - the solution injected may include various opioid alkaloids as well as high concentrations of processing chemicals, responsible for the localized and systemic injuries reported here. Links between health care and law enforcement, stigma and maltreatment by medical providers are likely to thwart users seeking timely medical help. Conclusion: A comprehensive response to the emergence of krokodil and associated harms should focus both on the substance itself and its rudimentary production methods, as well as on its micro and macro risk environments - that of the on-going syndemic of drug injecting, HIV, HCV, TB and STIs in the region and the recent upheaval in local and international heroin supply. The feasibility of harm reduction strategies for people who inject krokodil may depend more on political will than on the practical implementation of interventions. The legal status of opioid substitution treatment in Russia is a point in case. © 2013 Elsevier B.V.

Helicobacter pylori has been recently detected in the oral cavity and oropharynx. However, the role it plays in oral and oropharyngeal pathogenesis remains unclear. The virulence of H. pylori strains can be distinguished according to the virulence factors genes carried. Our research has been focused on realtime PCR analysis of cagA and vacA genes of H. pylori strains in tonsils and tonsillar squamous cell cancer and their comparison with H. pylori strains obtained from the gastric mucosa of the same patients. Urea breath test (UBT) test was used to detect a gastric H. pylori infection in 20 patients with previously proven H. pylori in the oropharynx. Genotyping of H. pylori in gastric biopsies was performed in patients with positive gastric infection. Out of 20 patients positive for oropharyngeal H. pylori, 8 were positive for concurrent gastric H. pylori infection. In 6 of them gastric biopsies were obtained. Comparison of oropharyngeal and stomach H. pylori genotypes showed important differences. Four of 6 patients had different H. pylori strains in the oropharynx and stomach. The differences were found in cagA gene as well as in vacA gene. The finding of oral presence of H. pylori without concurrent stomach infection was confirmed using UBT. The results show that more than one H. pylori strain can be present in oropharynx and stomach in the same patient. The oropharyngeal infection seems to be independent to the gastric infection.

Lorenz-Meyer D.,Charles University
Science Technology and Human Values | Year: 2012

This article notes that research policy and early laboratory studies resonate in foregrounding the laboratory as an important place and agent in producing valued research output but tend to gloss over the complex processes by which laboratories are built and sustained over time as well as the significance of non-Western histories. Drawing on multisited ethnography in laboratories located in the geopolitical East of Europe, it examines the articulations and tensions between performing laboratories as locales and as locations of scientific excellence across a range of heretofore underexamined online and offline sites, including group seminars and institutional Web pages. By drawing attention to enterprising modes of performing achievement and lab organization, the article shows how the laboratory is also a policy actor and reproduces Westward-oriented knowledge geographies. Pointing to care as a mode of ordering, it further explores different forms of material and affective labor that are obfuscated in such performances but build and sustain the lab as local-global assemblage. The article concludes by discussing the policy implications of making this labor visible. © SAGE Publications 2012.

Masin D.,Charles University
Unsaturated Soils - Proceedings of the 5th International Conference on Unsaturated Soils | Year: 2011

The paper presents a model for the dependency of a water retention curve (WRC) on void ratio. The approach is based on the effective stress principle for unsaturated soils and several underlying assumptions. The model describes the unsaturated soil behaviour along the main drying and wetting branches of WRC, it therefore does not incorporate the effects of hydraulic hysteresis. It leads to the dependency of a water retention curve (WRC) on void ratio, which does not require any material parameters apart from the parameters specifying WRC for the reference void ratio. Its predictive capabilities are demonstrated by comparing predictions with the experimental data on several different soils. © 2011 Taylor & Francis Group, London.

Skalova S.,Charles University
Arab journal of nephrology and transplantation | Year: 2013

Gitelman syndrome (GS) is a very rare autosomal recessive tubulopathy due to loss-of-function or mutation in solute carrier family12, member 3 gene (SLC12A3 gene) encoding thiazide-sensitive NaCl co-transporter in the distal convoluted tubule, leading to hypokalemia, metabolic alkalosis, hypomagnesemia, hypocalciuria and low-to-normal blood pressure. Clinical signs are mostly secondary to chronic hypokalemia and include dizziness, fatigue, constipation and weakness. Patients can also present with muscle cramps, tetany, fatigue and convulsions due to severe metabolic alkalosis or hypomagnesemia. Manifestations of GS are rarely apparent before the age of five, and the syndrome is usually diagnosed during adolescence or adulthood. Here we describe a case of GS presenting in infancy with hypokalemia and psychomotor retardation. We present an 18-month-old boy who presented with psychomotor retardation and failure to thrive. Investigations revealed hypokalemia at 2.7 mmol/L, metabolic alkalosis, hypocalciuria and normal serum magnesium level. The diagnoses of Barter syndrome (BS) and Gitelman syndrome (GS) were considered. Genetic studies confirmed the diagnosis of GS and three different mutations of in SLC12A3 gene were detected. Two mutations (c.2576T>C and c.2929C>Ty) were considered as causal ones, with the patient's parents being the heterozygous carriers. Oral potassium supplementation resulted in normalisation of the hypokalemia and psychomotor improvement. We report a rare case of psychomotor retardation occurring at an early age in genetically confirmed GS. In spite of being a rare disorder, GS has to be considered in children with developmental delay and muscle weakness. With adequate treatment, GS patients have an excellent prognosis.

Fuchs O.,Institute of Hematology and Blood Transfusion | Fuchs O.,Charles University
Current Molecular Pharmacology | Year: 2010

Nuclear factor-kappaB (NF-κB) upregulates the transcription of proteins that promote cell survival, stimulate growth, induce angiogenesis and reduce susceptibility to apoptosis. NF-κB signaling pathway is constitutively activated in myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), acute lymphocytic leukemia (ALL), chronic myeloid leukemia (CML), chronic lymphocytic leukemia (CLL), lymphomas and in multiple myeloma (MM). Inactive NF-κB is bound in the cytoplasm to its inhibitor IκB, which masks its nuclear localisation signal. Two protein kinases with a high degree of sequence similarity, IKKα and IKKβ, mediate phosphorylation of IκB proteins and represent a convergence point for most signal transduction pathways leading to NF-κB activation. The overexpression of NF-κB and its antiapoptotic cytoprotective effect suggest that it might be a useful therapeutic target for the treatment of hematologic malignancies. Several drugs effective for the treatment of MM, including proteasome inhibitors, thalidomide, lenalidomide and arsenic trioxide, block NF-κB activation. New agents with NF-κB inhibitory activity enhance the anti-MM effects of conventional chemotherapeutic agents and reduce different side-effects. Triptolide (diterpenoid triepoxyde), a purified component of a traditional Chinese medicine, extracted from a shrub-like vine named Trypterygium wilfordii Hook F (TWHF) inhibits transcriptional activation of NF-κB and downregulates the expression of various NF-κB-regulated genes. Triptolide (10-80 ng/ml) induces apoptosis of MM cells and effectively inhibits cell growth of MM cells. NF-κB activation can be also inhibited by IKKβ-selective inhibitors, PS-1145dihydrochloride, MLN120B (both Millennium Pharmaceuticals, Cambridge, MA) and BMS-345541 (Bristol-Myers Squibb, Princeton, NJ). LC-1, the dimethylamino-parthenolide (DMAPT) derivative demonstrated significant cytotoxicity to AML blasts targeting NF-κB. © 2010 Bentham Science Publishers Ltd.

Two CE methods with contactless conductivity detection have been developed for determining the oral antidiabetic drug metformin in human urine and blood. The determination of metformin is performed on a separation capillary with an effective length of 14. cm, using a maximum voltage of 30. kV and with a small injection of 50-fold diluted urine into the capillary. Under these conditions, the migration time of metformin is 35. s and the LOD is 0.3. μM. Large-volume sample stacking was used to determine low metformin levels in serum. The injection of a sample of serum deproteinized with acetonitrile was 10 times greater compared to the injected amount of urine. This enabled reduction of the LOD to 0.03. μM and the metformin migration time equalled 86. s. The undesirable solvent from sample zone was forced out of the capillary to ensure rapidity and good repeatability of the determination. The RSD values for the migration time are 0.1% for urine and 0.7% for serum; RSD for the peak areas equalled 1.4% for urine and 2.6% for serum. The developed CE technique was tested on performance of routine analyses of metformin in the urine and serum of patients suffering from type II diabetes mellitus. © 2014 Elsevier B.V.

There is substantial clinical and experimental evidence that ammonia is a major factor in the pathogenesis of hepatic encephalopathy. In the article is demonstrated that in hepatocellular dysfunction, ammonia detoxification to glutamine (GLN) in skeletal muscle, brain, and likely the lungs, is activated. In addition to ammonia detoxification, enhanced GLN production may exert beneficial effects on the immune system and gut barrier function. However, enhanced GLN synthesis may exert adverse effects in the brain (swelling of astrocytes or altered neurotransmission) and stimulate catabolism of branched-chain amino acids (BCAA; valine, leucine, and isoleucine) in skeletal muscle. Furthermore, the majority of GLN produced is released to the blood and catabolized in enterocytes and the kidneys to ammonia, which due to liver injury escapes detoxification to urea and appears in peripheral blood. As only one molecule of ammonia is detoxified in GLN synthesis whereas two molecules may appear in GLN breakdown, these events can be seen as a vicious cycle in which enhanced ammonia concentration activates synthesis of GLN leading to its subsequent catabolism and increase in ammonia levels in the blood. These alterations may explain why therapies targeted to intestinal bacteria have only a limited effect on ammonia levels in patients with liver failure and indicate the needs of new therapeutic strategies focused on GLN metabolism. It is demonstrated that each of the various treatment options targeting only one the of the ammonia-lowering mechanisms that affect GLN metabolism, such as enhancing GLN synthesis (BCAA), suppressing ammonia production from GLN breakdown (glutaminase inhibitors and alpha-ketoglutarate), and promoting GLN elimination (phenylbutyrate) exerts substantial adverse effects that can be avoided if their combination is tailored to the specific needs of each patient. © 2013 The Author(s).

Vajtr D.,Charles University
Soudní lékarství / casopis Sekce soudního lékarstvi Cs. lékarské spolecnosti J. Ev. Purkyne | Year: 2012

Introduction: Traumatic brain injury (TBI) triggers a series of reactions resulting in cytoskeletal-related changes varying between focal and diffuse injuries. Methods: The patients (n=38) were divided into group of diffuse axonal injuries (DAI, n=10) and focal (n=28) injuries. Serum hyperphosphorylated neurofilaments (NF-H) and glial fibrillary acidic protein (GFAP) were measured by Biovendor immunoassay, and serum S-100B protein was measured by Cobas e411 (Roche) by immunoassay. Immunohistochemistry was performed with monoclonal antibodies (Chemicon, USA). Results: The median serum S-100B concentration was higher in patients with focal mass lesions (1.72±0.4 μg/l vs. 0.37±0.1 μg/l, p<0,05) compared to patients with DAI during 10 days of hospitalisation. With respect to all patients, the highest peak of serum S-100B values (4.21±1.1 μg/l) and GFAP (8.58±2.4 μg/l) were found in expansive lesions. The median serum NF-H was higher in DAI compared to focal TBI (0.625±0.14 vs 0.139±0.02 ng/l, p<0.05) during all 10 days after admission. Further, immunohistochemical investigation, in deceased patients with DAI , using NF-H antibody proved positive varicose and waving axons, and retraction balls. Time-dependent profile of serum NF-H demonstrated the increase of values within 4th up to 10th day in both groups. Values ranged from 0.263 up to 1.325 ng/l in DAI, and from 0.103 up to 1.108 ng/l in focal injuries. Patients with expansive contusions had similar levels of serum NF-H as patients without expansive lesions. Immunohistochemistry of cytoskeletal proteins presented strong positive staining of vinculin, vimentin in vessels, GFAP, and S-100B in DAI compared to weak staining in expansive lesions. Conclusion: The time-profile kinetics of all markers may reflect different types of pathophysiological changes of the BBB or axonal damage in focal and diffuse injuries. Keywords: brain contusions - diffuse axonal injury - S-100B protein - GFAP - hyperphosphorylated neurofilaments.

Pawlas Z.,Charles University
Kybernetika | Year: 2011

Summary characteristics play an important role in the analysis of spatial point processes. We discuss various approaches to estimating summary characteristics from replicated observations of a stationary point process. The estimators are compared with respect to their integrated squared error. Simulations for three basic types of point processes help to indicate the best way of pooling the subwindow estimators. The most appropriate way depends on the particular summary characteristic, edge-correction method and also on the type of point process. The methods are demonstrated on a replicated dataset from forestry.

Cizkova H.,Charles University | Bina C.R.,Northwestern University
Earth and Planetary Science Letters | Year: 2013

Trench rollback has been a widely discussed phenomenon in recent years, and multiple studies have concentrated on various parameters that may influence trench migration and related aspects of slab deformation in the (upper) mantle. Here we concentrate on the effects of rheological description (yield stress, lower-mantle viscosity, viscosity of crust) in controlling the rollback and associated stagnation of slabs in the transition zone (410-660 km depth). We perform numerical simulations of slab evolution in a 2D Cartesian model with strongly nonlinear rheology combining diffusion creep, dislocation creep and a power-law stress limiter. We demonstrate that trench retreat develops in most models considered, regardless of the subducting plate age or prescribed strength. Rollback then mostly produces slabs that are horizontally deflected at the 660-km phase boundary and remain subhorizontal at the bottom of the transition zone. Slab morphologies are in agreement with stagnant, horizontally deflected structures reported in the transition zone by seismic tomography. Furthermore, if the strength of the slab is limited to less than 0.5 GPa, the slab experiences a significant amount of horizontal buckling. The amplitude of the rollback velocity is sensitive to several model parameters. As one might expect, it increases with the age of the subducting plate, thus reflecting its increasingly negative buoyancy. On the other hand, rollback velocity decreases if we increase the viscosity of the crust and thereby strengthen the coupling between the subducting and overriding plates. High friction on the contact between the subducting and overriding plates may even result in slabs penetrating into the lower mantle after a period of temporary stagnation. Also, reducing the additional negative buoyancy imparted by the 410-km exothermic phase transition suppresses trench rollback. Interpretation of the controls on slab rollback and stagnation may be rather complex in strongly nonlinear rheological models, where, for example, buoyancy effects may be counteracted by associated yield-stress weakening. © 2013 Elsevier B.V.

Zahradnik J.,Charles University | Plesinger A.,Academy of Sciences of the Czech Republic
Bulletin of the Seismological Society of America | Year: 2010

Broadband observations of small earthquakes at short epicentral distances reveal a mixture of near-field effects and instrumental artifacts. We investigated these phenomena at a station equipped with an STS-2 and CMG-40T sensor situated almost above shallow M 3.0 to 3.8 events (peak ground acceleration 2 × 10-1 m/sec2). The horizontal components were systematically accompanied by tiltlike disturbances, and the tilt obtained from the STS-2 records exceeded more than 10 times the values predicted by the source model. We also observed a so far uncommonly recognized type of disturbance, whose shape is the first derivative of the tiltlike disturbance. The most likelyexplanationseemstobeclippingofhigh-frequency signal peaks within the sensor system. A computational model of a broadband feedback velocimeter as a linear dynamic system with saturation proved this interpretation on a qualitative level. Generally, any asymmetry in the transfer of high frequencies in the feedback velocimeter would produce along-period disturbance of this type.Users of near-faultbroad-band velocigrams may numerically simulate the disturbances, without any knowledge of their physical nature, and subtract them from the records. The decontaminated records still may have a strange, bow-shaped form, related to the near-field ramp and the static displacement (of the order of 1 × 10-5 m in this article). The effects studied in this article seem to have a general character, for apparently any feedback-controlled broadband velocimeter.

Vargova L.,Charles University | Sykova E.,Charles University
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2014

Volume transmission is a form of intercellular communication that does not require synapses; it is based on the diffusion of neuroactive substances across the brain extracellular space (ECS) and their binding to extrasynaptic high-affinity receptors on neurons or glia. Extracellular diffusion is restricted by the limited volume of the ECS, which is described by the ECS volume fraction α, and the presence of diffusion barriers, reflected by tortuosity λ, that are created, for example, by fine astrocytic processes or extracellular matrix (ECM) molecules. Organized astrocytic processes, ECM scaffolds or myelin sheets channel the extracellular diffusion so that it is facilitated in a certain direction, i.e. anisotropic. The diffusion properties of the ECS are profoundly influenced by various processes such as the swelling and morphological rebuilding of astrocytes during either transient or persisting physiological or pathological states, or the remodelling of the ECM in tumorous or epileptogenic tissue, during Alzheimer's disease, after enzymatic treatment or in transgenic animals. The changing diffusion properties of the ECM influence neuron-glia interaction, learning abilities, the extent of neuronal damage and even cell migration. From a clinical point of view, diffusion parameter changes occurring during pathological states could be important for diagnosis, drug delivery and treatment. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Louthan O.,Charles University
Folia Biologica (Czech Republic) | Year: 2011

Chromogranin A (CgA) is a hydrophilic acidic one-chain peptide containing 439 amino acids, preceded by NH2-terminal 18-amino-acid signal peptide; the complete pre-chromogranin A molecule thus encompasses 457 amino acids. It is a member of the chromogranin family that comprises several proteins. The CgA gene is a single-copy gene localized in the locus 14q32. Chromogranin A is produced by endocrine and neuroendocrine cells. The largest amount of CgA occurs in chromaffin granules of adrenal medulla and in the dense-core vesicles of sympathetic nerves. Its biological functions have not been completely elucidated, but it is known that it acts as a precursor of many biologically active peptides generated by cleavage at specific sites. It is the major soluble protein co-stored and co-released along with resident catecholamines and polypeptide hormones or cell-specific neurotransmitters. Because of its widespread distribution in neuroendocrine tissue, it can be used both as immunohistochemical marker and serum marker of neuroendocrine tu- mours. CgA has been used as a rather reliable tumour marker because its level is significantly increased in neuroendocrine tumours and changes of its level reflect the tumour response to therapy or tumour recurrence. © 2006 - 2013 Folia Biologica.

There is increasing awareness that the negative effects of anthropogenic stressors may be magnified in the presence of natural stressors. Very few of these studies have included physiology, yet including physiological studies may help learning about the mechanistic base of such synergisms at the life history level and identify synergistic interactions not translated in life history traits. We studied in Enallagma cyathigerum damselfly larvae potential synergistic effects between exposure to the pesticide glyphosate and predator cues on a key life history trait, growth rate, its associated behavioural trait, food intake, and three types of physiological traits known to be affected by both stressors in isolation: the stress protein Hsp70, energy storage and variables related to oxidative stress and damage. The pesticide and predator cues reduced growth rate in an additive way. Food intake increased under pesticide exposure and was not affected by the predator cues, indicating physiological mediation of the growth reduction. One potential physiological mechanism was that both stressors additively increased Hsp70 levels, this may also have contributed to the reduced levels of total carbohydrates when exposed to predator cues. Chronic exposure to predator cues reduced oxygen consumption, possibly to avoid too high costs of an increased metabolic rate. This reduction did not occur in the presence of the pesticide, reflecting the need for energetically expensive defence mechanisms (such as Hsp70 upregulation). When both stressors were combined, there was a reduction of the antioxidant enzyme superoxide dismutase activity (SOD) and an associated increase of oxidative damage in lipids. While synergistic interactions were not present for growth rate and food intake, they were identified for antioxidant defence and oxidative damage. This novel type of "hidden" synergistic interaction may have profound fitness implications, and when ignored will lead to underestimations of the impact of pollutants in natural populations where predators are omnipresent. © 2013 Elsevier B.V.

Barto L.,McMaster University | Barto L.,Charles University
Proceedings - Symposium on Logic in Computer Science | Year: 2011

A central open question in the study of non-uniform constraint satisfaction problems (CSPs) is the dichotomy conjecture of Feder and Vardi stating that the CSP over a fixed constraint language is either NP-complete, or tractable. One of the main achievements in this direction is a result of Bulatov (LICS'03) confirming the dichotomy conjecture for conservative CSPs, that is, CSPs over constraint languages containing all unary relations. Unfortunately, the proof is very long and complicated, and therefore hard to understand even for a specialist. This paper provides a short and transparent proof. © 2011 IEEE.

Flegr J.,Charles University | Striz I.,Institute of Clinical and Experimental Medicine
BMC Infectious Diseases | Year: 2011

Background: About 30% of the population worldwide are infected with the protozoan parasite Toxoplasma gondii. Latent toxoplasmosis has many specific behavioral and physiological effects on the human organism. Modified reactivity of the immune system has been suggested to play a key role in many of these effects. For example, the immunosuppression hypothesis explains the higher probability of the birth of male offspring observed in Toxoplasma-positive humans and mice by the protection of the (more immunogenic) male embryos against abortion.Methods: Here we searched for indices of immunosuppression in Toxoplasma-positive subjects by comparing clinical records of immunology outpatients.Results: Our cohort study showed that the male patients with latent toxoplasmosis had decreased and the Toxoplasma-positive women had increased leukocyte, NK-cell and monocyte counts in comparison with controls. The B-cell counts were reduced in both Toxoplasma-positive men and women. The difference between Toxoplasma-positive and Toxoplasma-negative subjects diminished with the decline of the specific Toxoplasma antibody titre (a proxy for the length of infection), which is consistent with the observed decreasing strength of the effect of latent toxoplasmosis on human reproduction. The prevalence of toxoplasmosis in 128 male patients was unusually low (10.9%) which contrasted with normal prevalence in 312 female patients (23.7%) and in general population Prague (20-30%).Conclusions: Latent toxoplasmosis has immunomodulatory effects in human and probably protects men against some classes of immunopathological diseases. The main limitation of the present study was the absence of the data on the immunoreactivity of immune cells subpopulations. Therefore further studies are needed to search for indices of immunosuppression in human using more specific markers. © 2011 Flegr and Stříž; licensee BioMed Central Ltd.

Paulusova V.,Charles University
Acta medica (Hradec Králové) / Universitas Carolina, Facultas Medica Hradec Králové | Year: 2012

Oral Lichen planus (OLP) is chronic inflammatory oral mucosal disease of unknown etiology. Basement membrane damage and T-cell migration in OLP may be mediated by matrix metalloproteinases (MMPs). We examined the expression of matrix metalloproteinase 9 to support this hypothesis. The study population consisted of 71 patients with OLP and 10 control patients with oral fibromas. Indirect immunohistochemistry was used for detection of MMP 9 expression (polyclonal rabbit anti-human MMP antibody). In all cases of OLP, the MMP-9 expression was seen mainly in the area oflymphocytic inflammatory infiltrate in the lamina propria including lymphocytes within the overlying epithelium. In addition, it was observed in the epithelial keratinocytes, particularly in the stratum basale and stratum spinosum with occasional positivity in the superficial layer. Fibroblasts and endothelium of small vessels in the lamina propria showed MMP9 expression as well. In all cases of oral mucosal fibromas, the MMP-9 expression was seen only in fibroblasts and in endothelium of small vessels with occasional positivity within the overlying epithelium. It remains unclear, whether MMP-9 is directly connected to OLP pathogenesis.

Battiato M.,Uppsala University | Carva K.,Uppsala University | Carva K.,Charles University | Oppeneer P.M.,Uppsala University
Physical Review Letters | Year: 2010

We propose a semiclassical model for femtosecond laser-induced demagnetization due to spin-polarized excited electron diffusion in the superdiffusive regime. Our approach treats the finite elapsed time and transport in space between multiple electronic collisions exactly, as well as the presence of several metal films in the sample. Solving the derived transport equation numerically we show that this mechanism accounts for the experimentally observed demagnetization within 200 fs in Ni, without the need to invoke any angular momentum dissipation channel. © 2010 The American Physical Society.

Uhlirova K.,Charles University | Prokleska J.,Charles University | Sechovsky V.,Charles University
Physical Review Letters | Year: 2010

A Comment on the Letter by D. Kaczorowski et al., Phys. Rev. Lett.PRLTAO0031-9007 103, 027003 (2009)10.1103/PhysRevLett.103.027003. The authors of the Letter offer a Reply. © 2010 The American Physical Society.

Mancal T.,Charles University | Valkunas L.,Lithuanian Academy of Sciences | Valkunas L.,Vilnius University
New Journal of Physics | Year: 2010

In this paper, we consider the dynamics of a molecular system subjected to external pumping by a light source. Within a completely quantum mechanical treatment, we derive a general formula, which enables us to assess the effects of different light properties on the photo-induced dynamics of excitations in a molecular system. We show that, once the properties of light are known in terms of a certain two-point correlation function, the only information needed to reconstruct the system dynamics is the reduced evolution superoperator. The latter quantity is, in principle, accessible through ultrafast nonlinear spectroscopy. Considering a direct excitation of a small molecular antenna by incoherent light, we find that excitation of coherences is possible due to the overlap of homogeneous line shapes associated with different excitonic states. In Markov and secular approximations, the amount of coherence is significant only under fast relaxation, and both the populations and coherences between exciton states become static at long times. We also study the case when the excitation of a photosynthetic complex is mediated by a mesoscopic system. We find that such a case can be treated by the same formalism with a special correlation function characterizing ultrafast fluctuations of the mesoscopic system. We discuss bacterial chlorosome as an example of such a mesoscopic mediator and propose that the properties of energy-transferring chromophore-protein complexes might be specially tuned to the fluctuation properties of their associated antennae. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

BACKGROUND: This study was motivated by the growth in the number of elderly with dementia and consequent need to help family caregivers who face the daily stress for long periods of time. The aim was to describe the frequency of some common psychosomatic symptoms in self-assessed health status and to determine whether there are gender differences in these symptoms and the perception of one's own health in family caregivers. METHODS: The first results of cross-sectional survey design as the first phase of a longitudinal cohort study are presented. The participants in this investigation (n=73) were family caregivers of outpatients suffering from moderate (59 cases = 80.8%) or mild (14 cases = 19.2%) stage of Alzheimer' s disease (AD). RESULTS: The group of caregivers consisting of 61 (83.6%) women and 12 men (16.4%). Participants of this study were recruited from the Department of Psychiatry, Prague, Czech Republic. Data from caregivers were collected by using a self-administered questionnaire containing various items to measure self-perceived health including some common psychosomatic symptoms in relationship with their caregiving role. CONCLUSIONS: The following symptoms appeared the most frequent among family caregivers: chronic fatigue and sleeping disturbances. Most caregivers of patients with moderate stage of AD evaluated their own health as poor and experienced more symptoms in comparison with caregivers of patients with mild stage of Alzheimer's disease, who scored their own health as good or very good. A follow-up of the survey population seems to be necessary. ©2012 Neuroendocrinology Letters.

Background: Darwin's evolutionary theory could easily explain the evolution of adaptive traits (organs and behavioral patterns) in asexual but not in sexual organisms. Two models, the selfish gene theory and frozen plasticity theory were suggested to explain evolution of adaptive traits in sexual organisms in past 30 years.Results: The frozen plasticity theory suggests that sexual species can evolve new adaptations only when their members are genetically uniform, i.e. only after a portion of the population of the original species had split off, balanced on the edge of extinction for several generations, and then undergone rapid expansion. After a short period of time, estimated on the basis of paleontological data to correspond to 1-2% of the duration of the species, polymorphism accumulates in the gene pool due to frequency-dependent selection; and thus, in each generation, new mutations occur in the presence of different alleles and therefore change their selection coefficients from generation to generation. The species ceases to behave in an evolutionarily plastic manner and becomes evolutionarily elastic on a microevolutionary time-scale and evolutionarily frozen on a macroevolutionary time-scale. It then exists in this state until such changes accumulate in the environment that the species becomes extinct.Conclusion: Frozen plasticity theory, which includes the Darwinian model of evolution as a special case - the evolution of species in a plastic state, not only offers plenty of new predictions to be tested, but also provides explanations for a much broader spectrum of known biological phenomena than classic evolutionary theories. © 2010 Flegr; licensee BioMed Central Ltd.

Tyrosine hydroxylase deficiency manifests mainly in early childhood and includes two clinical phenotypes: an infantile progressive hypokinetic-rigid syndrome with dystonia (type A) and a neonatal complex encephalopathy (type B). The biochemical diagnostics is exclusively based on the quantitative determination of the neurotransmitters or their metabolites in cerebrospinal fluid (CSF). The implementation of neurotransmitter analysis in clinical praxis is necessary for early diagnosis and adequate treatment. Neurotransmitter metabolites in CSF were analyzed in 82 children (at the age 1 month to 17 years) with clinical suspicion for neurometabolic disorders using high performance liquid chromatography (HPLC) with electrochemical detection. The CSF level of homovanillic acid (HVA) was markedly decreased in three children (64, 79 and 94 nmol/l) in comparison to age related controls (lower limit 218-450 nmol/l). Neurological findings including severe psychomotor retardation, quadruspasticity and microcephaly accompanied with marked dystonia, excessive sweating in the first patient was compatible with the diagnosis of tyrosine hydroxylase (TH) deficiency (type B) and subsequent molecular analysis revealed two novel heterozygous mutations c.636A>C and c.1124G>C in the TH gene. The treatment with L-DOPA/carbidopa resulted in the improvement of dystonia. Magnetic resonance imaging studies in two other patients with microcephaly revealed postischaemic brain damage, therefore secondary HVA deficit was considered in these children. Diagnostic work-up in patients with neurometabolic disorders should include analysis of neurotransmitter metabolites in CSF.

Ptacek R.,Charles University
Prague medical report | Year: 2010

Attention deficit hyperactivity disorder (ADHD) is a common child diagnosis with frequent comorbidities (Quinn, 2008). According to present studies eating disorders may represent one of them (Mikami et al., 2008). Several studies reported ADHD relation to the higher predisposition to obesity (Altafas, 2002), higher values of signs of overnutrition, as body mass index (Waring and Lapane, 2008) or higher value of fat (Ptacek et al., 2009a, c). These characteristics are considered to be directly related to the disorder. They can be caused by impulsivity and probable specific feeding customs of ADHD patients. The presence of eating disorders in ADHD patients could partially explain previously described growth and weight changes.

Kamlar M.,Charles University | Putaj P.,Charles University | Vesely J.,Charles University
Tetrahedron Letters | Year: 2013

Organocatalytic alkynylation of nucleophilic fluorocarbons using hypervalent iodine compounds under cinchona-based catalysis, namely using O-allyl N-anthracenyl cinchona alkaloid derivative II, is described. The reaction gives the final fluoro-propargyl compounds in good to excellent yields (up to 91%) and with moderate to low enantioselectivity (up to 61% ee). The reaction represents the first example of the use of hypervalent iodine compounds for the construction of fluorinated compounds and opens access to the preparation of biologically attractive compounds such as 1,2,3-triazoles. © 2013 Elsevier Ltd. All rights reserved.

Reischig T.,Charles University
Expert Review of Anti-Infective Therapy | Year: 2010

The adverse impact of cytomegalovirus (CMV) infection after solid organ transplantion is currently believed to be mediated primarily by its immunomodulatory effects. There is a large body of evidence showing that both CMV disease and asymptomatic viremia are independent risk factors for the development of allograft rejection. The aim of this article is to summarize mechanisms whereby CMV is involved in the development and progression of allograft rejection, with particular emphasis on renal transplant recipients. The article will also address the potential of anti-CMV preventive protocols designed to favorably affect the incidence of allograft rejection. © 2010 Expert Reviews Ltd.

Tashpulatov S.N.,Charles University | Tashpulatov S.N.,Academy of Sciences of the Czech Republic
Energy Policy | Year: 2013

Price fluctuations that partially comove with demand are a specific feature inherent to liberalized electricity markets. The regulatory authority in Great Britain, however, believed that sometimes electricity prices were significantly higher than what was expected and, therefore, introduced price-cap regulation and divestment series. In this study, I analyze how the introduced institutional changes and regulatory reforms affected the dynamics of daily electricity prices in the England and Wales wholesale electricity market during 1990-2001.This research finds that the introduction of price-cap regulation did achieve the goal of lowering the price level at the cost of higher price volatility. Later, the first series of divestments is found to be successful at lowering price volatility, which however happens at the cost of a higher price level. Finally, this study also documents that the second series of divestments was more successful at lowering both the price level and volatility. © 2013 Elsevier Ltd.

Bibliometric indicators increasingly affect careers, funding, and reputation of individuals, their institutions and journals themselves. In contrast to author self-citations, little is known about kinetics of journal self-citations. Here we hypothesized that they may show a generalizable pattern within particular research fields or across multiple fields. We thus analyzed self-cites to 60 journals from three research fields (multidisciplinary sciences, parasitology, and information science). We also hypothesized that the kinetics of journal self-citations and citations received from other journals of the same publisher may differ from foreign citations. We analyzed the journals published the American Association for the Advancement of Science, Nature Publishing Group, and Editura Academiei Române. We found that although the kinetics of journal self-cites is generally faster compared to foreign cites, it shows some field-specific characteristics. Particularly in information science journals, the initial increase in a share of journal self-citations during post-publication year 0 was completely absent. Self-promoting journal self-citations of top-tier journals have rather indirect but negligible direct effects on bibliometric indicators, affecting just the immediacy index and marginally increasing the impact factor itself as long as the affected journals are well established in their fields. In contrast, other forms of journal self-citations and citation stacking may severely affect the impact factor, or other citation-based indices. We identified here a network consisting of three Romanian physics journals Proceedings of the Romanian Academy, Series A, Romanian Journal of Physics, and Romanian Reports in Physics, which displayed low to moderate ratio of journal self-citations, but which multiplied recently their impact factors, and were mutually responsible for 55.9%, 64.7% and 63.3% of citations within the impact factor calculation window to the three journals, respectively. They did not receive nearly any network self-cites prior impact factor calculation window, and their network self-cites decreased sharply after the impact factor calculation window. Journal selfcitations and citation stacking requires increased attention and elimination from citation indices. © 2016 Petr Heneberg. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Frynta D.,Charles University
PloS one | Year: 2010

Parrots are one of the most frequently kept and bred bird orders in captivity. This increases poaching and thus the potential importance of captive populations for rescue programmes managed by zoos and related institutions. Both captive breeding and poaching are selective and may be influenced by the attractiveness of particular species to humans. In this paper, we tested the hypothesis that the size of zoo populations is not only determined by conservation needs, but also by the perceived beauty of individual parrot species assessed by human observers. For the purpose of data collection, we defined four sets of species (40 parrots, 367 parrots, 34 amazons, 17 macaws). Then, we asked 776 human respondents to evaluate parrot pictures of the selected species according to perceived beauty and we analyzed its association with color and morphological characters. Irrespective of the species set, we found a good agreement among the respondents. The preferred species tended to be large, colorful, and long-tailed. We repeatedly confirmed significant, positive association between the perceived beauty and the size of worldwide zoo population. Moreover, the range size and body size appeared to be significant predictors of zoo population size. In contrast, the effects of other explanatory variables, including the IUCN (International Union for Conservation of Nature) listing, appeared insignificant. Our results may suggest that zoos preferentially keep beautiful parrots and pay less attention to conservation needs.

Ouda L.,Academy of Sciences of the Czech Republic | Druga R.,Charles University | Syka J.,Academy of Sciences of the Czech Republic
Brain Structure and Function | Year: 2012

SMI-32 antibody recognizes a non-phosphorylated epitope of neurofilament proteins, which are thought to be necessary for the maintenance of large neurons with highly myelinated processes. We investigated the distribution and quantity of SMI-32-immunoreactive(-ir) neurons in individual parts of the rat auditory system. SMI-32-ir neurons were present in all auditory structures; however, in most regions they constituted only a minority of all neurons (10-30%). In the cochlear nuclei, a higher occurrence of SMI-32-ir neurons was found in the ventral cochlear nucleus. Within the superior olivary complex, SMI-32-ir cells were particularly abundant in the medial nucleus of the trapezoid body (MNTB), the only auditory region where SMI-32-ir neurons constituted an absolute majority of all neurons. In the inferior colliculus, a region with the highest total number of neurons among the rat auditory subcortical structures, the percentage of SMI-32-ir cells was, in contrast to the MNTB, very low. In the medial geniculate body, SMI-32-ir neurons were prevalent in the ventral division. At the cortical level, SMI-32-ir neurons were found mainly in layers III, V and VI. Within the auditory cortex, it was possible to distinguish the Te1, Te2 and Te3 areas on the basis of the variable numerical density and volumes of SMI-32-ir neurons, especially when the pyramidal cells of layer V were taken into account. SMI-32-ir neurons apparently form a representative subpopulation of neurons in all parts of the rat central auditory system and may belong to both the inhibitory and excitatory systems, depending on the particular brain region. © 2011 Springer-Verlag.

Hadrava P.,Czech Republic Astronomical Institute | Cechura J.,Czech Republic Astronomical Institute | Cechura J.,Charles University
Astronomy and Astrophysics | Year: 2012

Aims. We investigate the anisotropy of stellar winds in binaries to improve the models of accretion in high-mass X-ray binaries. Methods. We model numerically the stellar wind from a supergiant component of a binary in radial and three-dimensional radiation hydrodynamic approximation taking into account the Roche potential, Coriolis force, and radiative pressure in the continuum and spectral lines. Results. The Coriolis force influences substantially the mass loss and thus also the accretion rate. The focusing of the stellar wind by the gravitational field of the compact companion leads to the formation of a gaseous tail behind the companion. © 2012 ESO.

Cmielova J.,Charles University | Rezacova M.,Charles University
Journal of Cellular Biochemistry | Year: 2011

Protein p21 Cip1/Waf1 is a cyclin-dependent kinase inhibitor, which is important in the response of cells to genotoxic stress and a major transcriptional target of p53 protein. Based on the localization, p21 Cip1/Waf1 protein executes various functions in the cell. In the nucleus p21 Cip1/Waf1 binds to and inhibits the activity of cyclin dependent kinases Cdk1 and Cdk2 and blocks the transition from G1 phase into S phase or from G2 phase into mitosis after DNA damage. This enables the repair of damaged DNA. p21 Cip1/Waf1 was also found as an important protein for the induction of replication senescence as well as stress-induced premature senescence. In the cytoplasm, p21 Cip1/Waf1 protein has an anti-apoptotic effect. It is able to bind to and inhibit caspase 3, as well as the apoptotic kinases ASK1 and JNK. The function of p21 Cip1/Waf1 in response to a DNA damage probably depends on the extent of the damage. In the case of low-level DNA damage, the expression of p21 Cip1/Waf1 is increased, it induces cell cycle arrest, and performs also anti-apoptotic activities. However, after extensive DNA damage the amount of p21 Cip1/Waf1 protein is decreased and the cell undergoes apoptosis. Dual function of p21 Cip1/Waf1 was also observed in cancerogenesis. On the one hand, p21 Cip1/Waf1 acts as a tumor suppressor; on the other hand it prevents apoptosis and acts as an oncogene. Better understanding of the role of p21 Cip1/Waf1 in various conditions would help to develop better cancer-treatment strategies. © 2011 Wiley Periodicals, Inc.

Urbanek P.,Charles University
Kidney and Blood Pressure Research | Year: 2012

Within the last few decades, the incidence and prevalence of both hepatitis B and C infections have decreased among kidney disease patients. Significant advances have been made in the prevention of hepatitis B and C virus transmission in these high-risk populations; however, the transmission risk is still not negligible. Viral hepatitis infections represent a significant problem among kidney disease patients; patients on regular dialysis, as well as renal transplant recipients (RTRs) due to their epidemiological, virological, and clinical features. Chronic hepatitis B and C have a strong impact on the clinical course of kidney disease as well as on the clinical course after kidney transplantation. The purpose of this review is to focus on the epidemiology, transmission modes, natural courses, and treatment options of hepatitis B and C infections in both chronic kidney disease patients and RTRs. Copyright © 2012 S. Karger AG, Basel.

Mocikova H.,Charles University
Prague medical report | Year: 2010

Lymphocytopenia is a poor prognostic marker in initial staging of non- Hodgkin lymphomas (below 1.0 x 10(9)/l) and Hodgkin lymphoma (below 0.6 x 10(9)/l) and in relapsed diffuse large B cell lymphoma. Early lymphocyte recovery > or =0.5 x 10(9)/l after autologous and allogeneic stem cell transplantation is a significant predictor of tumor control and survival in lymphomas. Natural killer cells are involved in tumor cell killing and are the only subset of lymphocytes associated with disease outcome in initial staging and after autologous stem cell transplantation in lymphomas. The antitumor effect of various NK cell subsets should be defined.

Stetkarova I.,Charles University | Stetkarova I.,Na Homolce Hospital | Kofler M.,Hochzirl Hospital
Clinical Neurophysiology | Year: 2013

Objective: The cutaneous silent period (SP) is a spinal inhibitory reflex, which suppresses activity in spinal motor nuclei. Transcranial magnetic stimulation (TMS) elicits a cortical SP, which represents GABAB receptor-mediated inhibition of cortical excitability. Baclofen as a strong GABAB agonist effectively reduces muscle hypertonia, however, it is not known whether intrathecal baclofen (ITB) may modulate spinal inhibitory circuits. Methods: We evaluated clinical and neurophysiological effects of ITB in ten patients with severe spasticity due to spinal cord injury (n=9) and chronic progressive multiple sclerosis (n=1). Neurophysiological assessment included H reflex and cutaneous and cortical SPs, before and 15, 30, 60, 90, 120, and 180. min after ITB bolus administration. Results: ITB suppressed soleus H reflex as early as 15. min after lumbar bolus injection; MAS scores declined after 1. h. Cortical SP end latency and duration increased progressively with a significant maximum 3. h following ITB bolus, whereas cutaneous SP latency and duration did not change significantly. Conclusion: The present findings suggest that baclofen does not affect the cutaneous SP, but prolongs the cortical SP. Significance: The spinal inhibitory circuitry of the cutaneous SP is not modulated by GABAB receptor-mediated activity, in contrast to the cortical inhibitory circuitry of the cortical SP, which is subject to powerful GABAB control. © 2012 International Federation of Clinical Neurophysiology.

AIM: To evaluate the novel triplex polymerase chain reaction (PCR) assay for the analysis of polymorphic Y-chromosomal short tandem repeat loci (Y-STR). METHODS: A total of 14 Y-STR loci was analyzed. Allele frequencies for 3 tetrameric Y-STR loci (DYS449, DYS456, and DYS458) and extended haplotype loci typed by Y-PLEXTM 12 system were investigated in a sample of 50 unrelated healthy Czech male donors. We computed the relevant intra-population statistic parameters for our data (gene diversity, average gene diversity over loci, and mean number of pairwise differences) and compared our sample set with other Central European populations using RST pairwise genetic distance. RESULTS: We focused on the comparison of genetic diversity between the Y-STR extended haplotype loci and that of the 3 additional loci, and on the benefit of using DYS449, DYS456, and DYS458 in forensic and population genetics applications. Total gene diversity in our sample set was 0.998367 when using all 14 loci. Our data analysis revealed very high genetic diversity at DYS449 locus (0.876735), which surpasses even the diversity at DYS385a/b (0.819592). Population comparison showed no difference between Czech, Bavarian, Austrian, and Saxon sample set. A minor difference was found between Czech and Polish sample set. CONCLUSION: Typing of 3 Y-chromosomal microsatellite polymorphisms may provide a useful complement to already established sets of Y-STRs.

Bauer M.,Charles University | Bauer M.,Academy of Sciences of the Czech Republic | Cassar A.,University of San Francisco | Chytilova J.,Charles University | And 2 more authors.
Psychological Science | Year: 2014

In suggesting that new nations often coalesce in the decades following war, historians have posed an important psychological question: Does the experience of war generate an enduring elevation in people's egalitarian motivations toward their in-group? We administered social-choice tasks to more than 1,000 children and adults differentially affected by wars in the Republic of Georgia and Sierra Leone. We found that greater exposure to war created a lasting increase in people's egalitarian motivations toward their in-group, but not their out-groups, during a developmental window starting in middle childhood (around 7 years of age) and ending in early adulthood (around 20 years of age). Outside this window, war had no measurable impact on social motivations in young children and had only muted effects on the motivations of older adults. These "war effects" are broadly consistent with predictions from evolutionary approaches that emphasize the importance of group cooperation in defending against external threats, though they also highlight key areas in need of greater theoretical development. © The Author(s) 2013.

Vichova T.,Charles University | Motovska Z.,Charles University
Experimental and Clinical Cardiology | Year: 2013

The role of oxidative stress in cardiovascular disease processes, such as atherogenesis, ischemic-reperfusion injury and cardiac remodelling, has been increasingly recognized in the past few decades. Currently, an increasing number of studies suggest that levels of oxidative stress markers in body fluids correlate with atherosclerotic disease activity. This finding may lead to novel clinical approaches in patients with coronary artery disease. Assessment of oxidative stress markers could modify risk stratification and treatment of patients with suspected coronary artery disease or myocardial infarction. © 2013 Pulsus Group Inc. All rights reserved.

Seeman T.,Charles University
Current Hypertension Reports | Year: 2012

Hypertension is a common and serious complication after renal transplantation. It is an important risk factor for graft loss and adverse cardiovascular outcomes. Blood pressure (BP) in transplanted children should be measured not only by clinic BP (cBP) measurement, but also by ambulatory blood pressure monitoring (ABPM), because ABPM has distinct advantages over cBP, specifically the ability to reveal nocturnal, masked or white-coat hypertension. These types of hypertension are common in transplanted children (nocturnal hypertension 36-71 %, masked hypertension 24-45 %). It may also reveal uncontrolled hypertension in treated children, thereby improving control of hypertension. Regular use of ABPM and ABPM-guided therapy of hypertension may help to decrease cardiovascular and renal target organ damage in transplanted children. Therefore, ABPM should be routinely performed in all transplanted children at least once a year, regardless of the values of cBP. © Springer Science+Business Media, LLC 2012.

Danhel A.,Charles University | Barek J.,Charles University
Current Organic Chemistry | Year: 2011

This review with 119 references describes applications of amalgam electrodes in organic electrochemistry. Possible detection arrangements and useful techniques utilizing voltammetric and amperometric methods are briefly discussed. However, main attention is paid to the description of mechanisms of electrode reactions of investigated organic compounds determined at amalgam electrodes during last ten years. Selected derivatives of aromatic hydrocarbons, azo dyes, herbicides, pharmaceuticals, vitamins and biomolecules (e.g. amino acids, peptides, nucleobases and/or nucleic acids) are discussed. The understanding of the discussed methods gives a reader an overview of application possibilities offered by modern electroanalytical methods using amalgam electrodes. © 2011 Bentham Science Publishers.

Polycystic ovary syndrome (PCOS) is a common endocrinopathy affecting women of fertile age. It is associated with several risk factors and long-term health consequences. Chronic anovulation combined with relative estrogen excess and consequent prolonged stimulatory effect on the endometrium can lead to the pathogenesis of hormonal dependant carcinoma. PCOS is thus traditionally reported to be associated with increased risk of endometrial, as well as breast and ovarian cancers. This article provides a critical literature review of the relationship between PCOS and the incidence of estrogen-dependant gynecological tumours, and it then discusses whether the commonly cited risk factor association can be substantiated by high quality studies which comply with the requirements of evidence-based medicine. © 2013 Informa UK, Ltd.

Svacina S.,Charles University
Advances in Experimental Medicine and Biology | Year: 2013

Fat accumulation is a typical phenomenon in the pathogenesis of Type 2 diabetes. Also Type 1 diabetics are getting obese these days living in an environment with typical caloric overfeeding and low physical activity. Weight reduction is an important part of therapy in all obese diabetic patients. Orlistat is the only accessible antiobesity drug today. Weight neutral antidiabetics like metform in and DPP-4 inhibitors can be also used. Incretin analogues (exenatide and liraglutide) are also very important drugs inducing weight loss in diabetic and also in nondiabetic patients. Insulin therapy causes mostly weight gain. Long acting insulin analogues are able to induce small weight loss in Type 1 diabetes or only a small weight increase or weight loss in Type 2 diabetic pat ients. Procedures of bariatric surgery are very important in the treatment being able to induce remission of Type 2 diabetes. Weight reduction can be supported also using the new class of antiadiabetic drugs-SGLT inhibitors which are blocking glucose absorption in kidneys. The use of new incretine analogues injected at the interval of one to two weeks is the most important strategy for the treatment of obese Type 2 diabetic patients and perhaps also of Type 1 diabetic patients even in combination with insulin. © 2012 Landes Bioscience and Springer Science+Business Media.

Bartonicek J.,Charles University
Archives of Orthopaedic and Trauma Surgery | Year: 2010

Surgery in the first half of the nineteenth century was primarily dominated by pain and fear of lethal infections. Therefore, the absolute majority of fractures and dislocations were treated non-operatively. Development of operative treatment of fractures was influenced by three major inventions: anaesthesia (1846), antisepsis (1865) and X-rays (1895). The first to use external fixation is traditionally considered to be Malgaigne (1843). However, his devices cannot be considered as external fixation. Von der Höhe, in 1843, fixed a non-union of the femur by inserting into both fragments a couple of screws transversely connected outside the wound. Von Langenbeck in 1855 treated a non-union of the humerus with screws connected by a devise designed for this purpose. A predecessor of nailing of acute diaphyseal fractures may be considered to be fixation of diaphyseal non-unions of the femur, humerus and tibia with ivory intramedullary pegs, performed by Dieffenbach in 1846. Nevertheless, until 1885, osteosynthesis was still a Cinderella having at its disposal mainly wires, ivory pegs and very primitive types of external fixation. During the following 35 years (1886-1921), operative treatment of fractures witnessed an unprecedented revolution. Radiology became an integral part of bone and joint surgery. All types of osteosynthesis, i.e. plates (Hansmann 1886), external fixation (Parkhill 1897) and intramedullary nails (Schöne 1913) were introduced into clinical practice. Basic experiments were undertaken, surgical approaches described and the first textbooks on osteosynthesis published. © 2010 Springer-Verlag.

The similarity search in theoretical mass spectra generated from protein sequence databases is a widely accepted approach for identification of peptides from query mass spectra produced by shotgun proteomics. Growing protein sequence databases and noisy query spectra demand database indexing techniques and better similarity measures for the comparison of theoretical spectra against query spectra. We employ a modification of previously proposed parameterized Hausdorff distance for comparisons of mass spectra. The new distance outperforms the original distance, the angle distance and state-of-the-art peptide identification tools OMSSA and X!Tandem in the number of identified peptides even though the q-value is only 0.001. When a precursor mass filter is used as a database indexing technique, our method outperforms OMSSA in the speed of search. When variable modifications are not searched, the search time is similar to X!Tandem. We show that the precursor mass filter is an efficient database indexing technique for high-accuracy data even though many variable modifications are being searched. We demonstrate that the number of identified peptides is bigger when variable modifications are searched separately by more search runs of a peptide identification engine. Otherwise, the false discovery rates are affected by mixing unmodified and modified spectra together resulting in a lower number of identified peptides. Our method is implemented in the freely available application SimTandem which can be used in the framework TOPP based on OpenMS.

Liberko M.,Charles University | Kolostova K.,Charles University | Bobek V.,Charles University
Critical Reviews in Oncology/Hematology | Year: 2013

The major cause of death due to cancer is its metastatic deposit in numerous tissues and organs. The metastatic process requires the migration of malignant cells from primary sites to distant environments. Even for tumors initially spreading through lymphatic vessels, hematogenous transport is the most common metastatic pathway. The detachment of cancer cells from a primary tumor into the blood stream is called epithelial-mesenchymal transition (EMT). As these cells circulate further in the bloodstream they are known as circulating tumor cells (CTCs). The CTC population is highly resilient, enabling the cells to colonize a foreign microenvironment. Alternatively, cancer stem cells (CSCs) may arise from differentiated cancer cells through EMT and an embryonic transdifferentiation process. The presence of CTCs/CSCs in blood seems to be a determining factor of metastasis.This paper reviews various methods of clinical cancer detection as well as the biology and molecular characterization of CTCs/CSCs. Our goal was to summarize clinical studies which used CTC/CSCs for prognosis in patients with breast, colorectal, prostate, lung, ovarian, and bladder cancer. © 2013 Elsevier Ireland Ltd.

Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ.Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III), genetic revolution model of Mayr (class IV) or the frozen plasticity theory of Flegr (class V), suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation - while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III) or elastic (class IV and V) on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation.The punctuational theories have many evolutionary and ecological implications. Most of these predictions could be tested empirically, and should be analyzed in greater depth theoretically. The punctuational theories offer many new predictions that need to be tested, but also provide explanations for a much broader spectrum of known biological phenomena than classical gradualistic evolutionary theories.This article was reviewed by Claus Wilke, Pierre Pantarotti and David Penny (nominated by Anthony Poole). © 2013 Flegr; licensee BioMed Central Ltd.

Necas P.,Charles University | Hejna P.,Charles University
Forensic Science, Medicine, and Pathology | Year: 2012

The phenomenon of eponymous terms in forensic pathology is described in this paper. The authors analyzed representative textbooks (monographs) dealing with forensic pathology in both English and German and identified several eponymous terms. The paper aims to present to the reader the most important eponymous terms in forensic pathology. Included in the paper are the following terms: Beckwith's Sign, Casper's Rule, Krönlein's Shot, Lichtenberg's Figures, Nysten's Law, Paltauf's Spots, Puppe's Rule, Sehrt's Sign, Simon's Sign, Sveshnikov's Sign, Tardieu's Spots, Wischnewski Spots, Wydler's Sign. The spread of eponymous terms throughout various languages is mentioned. The linguistic basis of such terms as well as their advantages and disadvantages in specialist fields, and indeed in even wider circles, is discussed. The authors state that the main function of these terms is to facilitate the open flow of unambiguous information among scholars. Eponymous terms in forensic pathology are characteristic for the German speaking countries and for all countries influenced by the German school of forensic pathology. Their usage in the Anglo-Saxon world is much less widespread, meaning they do not occur very often in English monographs and textbooks. © 2012 Springer Science+Business Media, LLC.

Salac T.,Charles University
Complex Analysis and Operator Theory | Year: 2013

In this paper we construct particular differential operators which are invariant with respect to the canonical action of the principal group of a particular type of parabolic geometry. These operators form sequences which are related to the minimal resolutions of the {Mathematical expression}-Dirac operator studied in Clifford analysis. © 2013 Springer Basel.

Rotational thromboelastometry (ROTEM) is increasingly used in practice to monitor coagulation status of severely bleeding patients and it helps to provide aimed therapy. The main advantage of ROTEM is detection of fibrinolysis. To get fast results, the reagents for activation, either extrinsic or intrinsic pathway of coagulation, are used. Although this method gives information about whole blood coagulation, in some cases, the patient is bleeding despite normal values of ROTEM. We present a case of a bleeding patient with normal values of activated ROTEM method (EXTEM, INTEM). However, nonactivated method (NATEM) was able to detect fibrinolysis and no clot was found in the cuvette. When tranexamic acid was added to the cuvette, the trace came back to normal value and a clot was formed inside the cuvette. According to this finding, the patient was effectively treated with antifibrinolytic drugs and stopped bleeding. In this case, we want to demonstrate that NATEM, as nonactivated ROTEM, seems to be more sensitive to coagulation changes, especially in detection of fibrinolysis, than activated ROTEM methods. Copyright © 2015 YEAR Wolters Kluwer Health, Inc. All rights reserved.

Sykora J.,Charles University
Journal of Pediatric Gastroenterology and Nutrition | Year: 2016

OBJECTIVES:: Abdominal pain-related functional gastrointestinal disorders in children include functional dyspepsia, functional abdominal pain, irritable bowel syndrome and abdominal migraine. We aimed to evaluate a possible association between functional abdominal pain disorders and Helicobacter pylori (H.pylori) infection as well as faecal calprotectin level. METHODS:: Prospective observational study including consecutive children with functional gastrointestinal disorders fulfilling Rome III criteria (cases) and age/gender-matched healthy controls. H.pylori has been detected by biopsy-based tests and stool-antigen detection, faecal calprotectin by ELISA. RESULTS:: A total of 56 cases (27 with functional dyspepsia) and 56 controls were enrolled. H. pylori being detected in 17/56 cases (30.4%) and 4/56 controls (7.1%, OR: 5.7; 95% CI:1.8–18.2, p?=?0.003). H. pylori was detected significantly more frequently in cases with functional dyspepsia (14/27, 51.9% OR: 14.0; 95% CI: 3.9–49.7, p?=?0.00001) than in controls and not in cases with other well-recognized functional gastrointestinal complaints (3/29, 10.3%). The median faecal calprotectin level was similar in cases (7,8ug/g, 95% CI: 7.8–8.4) including those with gastritis, and controls (9.1?ug/g, 95% CI: 7.8–11.3). Gastritis features were more frequent in H.pylori infected and non-infected cases with functional dyspepsia (27/27,100%) than in cases with other abdominal functional complaints (15/29, 51.7%, p?=?0.007). CONCLUSION:: H.pylori gastritis and non-infectious gastritis were associated with functional dyspepsia in children referred for abdominal-pain related functional gastrointestinal disorders while faecal calprotectin is not a predictor of gastritis and is similar in children with functional abdominal pain symptoms and in controls. © 2016 by European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology,

Bakhouche H.,Charles University
Prague medical report | Year: 2012

Pharmacogenetics is a discipline that investigates how genetic variation relates to the drug efficacy and safety. The goal of pharmacogenetics is a personalized treatment, where according to genotype we would be able to prescribe the most effective drug at the most appropriate dose for an individual patient. The aim of this review is to summarize pharmacogenetics as a specialization with its own background, research, methods, including barriers and promises for the future.

Hladik M.,Charles University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2016

We deal with an interval parametric system of linear equations, and focus on the problem how to find an optimal preconditioning matrix for the interval parametric Gauss-Seidel method. The optimality criteria considered are to minimize the width of the resulting enclosure, to minimize its upper end-point or to maximize its lower end-point. We show that such optimal preconditioners can be computed by solving suitable linear programming problems. We also show by examples that, in some cases, such optimal preconditioners are able to significantly decrease an overestimation of the results of common methods. © Springer International Publishing Switzerland 2016.

Certikova-Chabova V.,Charles University | Tesar V.,Charles University
Minerva Medica | Year: 2013

Nephrotic syndrome is characterized by heavy proteinuria followed by hypoproteinemia, hypercholestrolemia, lipiduria, and edema. The glomerular filtration barrier (GFB) consists of glomerular endothelial cells covered with glycocalyx, the basement membrane, subpodocyte space and podocytes with foot processes and slit membranes between them. The coordinated function of GFB has been considered to be the major barrier against filtration of plasma proteins to urine. However, new hypothesis suggesting more permeable GFB has emerged. According to this, proteinuria might be prevented by tubular protein reabsorbtion. Experments and human studies have revealed numerous putative permeability factors in idiopathic nephrotic syndrome (minimal change disease/focal segmental glomerulosclerosis). New antigens and antibodies have been suggested in "idiopathic" membranous nephropathy as well. Formation of nephrotic edema, the role of oncotic pressure and of different sodium and water retaining hormones have been subject of intensive study. These findings should pave the way to new therapeutic modalities targeted more precisely to the pathogenic mechanisms.

Kovanda J.,Charles University | Weinzettel J.,Charles University | Weinzettel J.,Norwegian University of Science and Technology
Environmental Science and Policy | Year: 2013

This article presents a comparison of indicators based on an economy-wide material flow analysis, namely imports, exports, domestic material consumption, raw material equivalents of imports, raw material equivalents of exports and raw material consumption. These indicators were calculated for the Czech Republic for 1995-2010 using, besides an economy-wide material flow analysis, the hybrid input-output life cycle assessment method, which allows for a calculation of raw material equivalents of imports and exports. The results show that a calculation of indicators, which include raw material equivalents, is useful, as it provides some important information which is not obvious from imports, exports and domestic material consumption indicators. We have proved that the latter group of indicators provide the incorrect information regarding the environmental pressure trend related to material flows, underestimate the overall pressure related to foreign trade and provide incorrect information on the importance of various material categories in particular indicators. Consequently, in the case of the Czech Republic, the implications stemming from these points such as the very high dependency of the Czech production system on metal ores from abroad and a rather unequal distribution of environmental pressures between the Czech Republic and its trading partners have not been more thoroughly addressed by Czech economic, environmental and sustainability policies so far and present unresolved issues which will have to be dealt with in the future. © 2013 Elsevier Ltd.

Tacheci I.,Charles University
Acta medica (Hradec Králové) / Universitas Carolina, Facultas Medica Hradec Králové | Year: 2010

Non-steroidal anti-inflammatory drug (NSAIDs) induced enteropathy represents an important complication of one of the most commonly used drugs worldwide. Due to previous diagnostics difficulties the real prevalence of this disease was underestimated for a long time. The pathogenesis of NSAID-enteropathy is more multifactorial and complex than formerly assumed but has still not been fully uncovered. A combination of the local and systemic effect plays an important role in pathogenesis. Thanks to novel enteroscopy methods (wireless capsule endoscopy, double balloon enteroscopy), small bowel lesions are described in a substantial section of NSAID users although most are clinically asymptomatic. The other non-invasive tests (small bowel permeability, faecal calprotectin, scintigraphy using faecal excretion of 111-indium-labelled leukocytes etc.) proposed for diagnostics are not generally used in clinical practice, mainly because of their non-specificity. Despite intensive research into possible treatment, the main measure for patients with NSAID-enteropathy is still withdrawal of NSAIDs. Double balloon enteroscopy plays an important role in the treatment of complications (bleeding, strictures).

Iorio A.,Charles University
Journal of Physics: Conference Series | Year: 2015

We offer some arguments in favor of the construction of an experimental facility, where to test fundamental theories of Nature by using co-responding systems. Co-responding systems are physical systems such that certain behaviors of one system are clearly related to certain behaviors of the other system. Physical systems available at our energy scales, co-responding to the unreachable high-energy systems, are what we need, to attack from an experimental perspective the open questions beyond the reach of CERN. The focus here is on two scenarios with which we have some familiarity: hadron production in high energy scattering processes as a Unruh phenomenon, and graphene as a quantum field theory in a curved spacetime, the latter being our prime bet. © Published under licence by IOP Publishing Ltd.

Behounkova M.,Charles University | Tobie G.,CNRS Nantes Laboratory of Planetology and Geodynamics | Choblet G.,CNRS Nantes Laboratory of Planetology and Geodynamics | Cadek O.,Charles University
Icarus | Year: 2012

The intense activity at the south pole of Enceladus hints at an internal water reservoir. However, there is no direct evidence of liquid water at present and its long-term stability in the interior remains problematic. By modeling heat production and transfer in the ice shell in a spherical geometry, we show that tidal heating naturally leads to a concentration of convective hot upwellings in the south polar region, favoring the preservation of liquid water at depth. We show that large volumes of water are produced within the ice shell at the south pole during periods of elevated orbital eccentricity (3-5 times the present-day value). Strong lateral variations in the melt production and crystallization rates result in stress concentration in the south polar region, thus providing an explanation for the tectonic activity observed today. We predict that an internal ocean may be sustained over the long term as the consequence of repeated periods with elevated orbital eccentricity, leading to episodic melting and resurfacing events. © 2012 Elsevier Inc.

Hladik M.,Charles University
Journal of Global Optimization | Year: 2016

The classical αBB method is a global optimization method the important step of which is to determine a convex underestimator of an objective function on an interval domain. Its particular point is to enclose the range of a Hessian matrix in an interval matrix. To have a tighter estimation of the Hessian matrices, we investigate a linear parametric form enclosure in this paper. One way to obtain this form is by using a slope extension of the Hessian entries. Numerical examples indicate that our approach can sometimes significantly reduce overestimation on the objective function. However, the slope extensions highly depend on a choice of the center of linearization. We compare some naive choices and also propose a heuristic one, which performs well in executed examples, but it seems there is no one global winner. © 2015, Springer Science+Business Media New York.

Matolin M.,Charles University
Journal of Environmental Radioactivity | Year: 2016

The radiometric map of the Czech Republic is based on uniform regional airborne radiometric total count measurements (1957-1959) which covered 100% of the country. The airborne radiometric instrument was calibrated to a 226Ra point source. The calibration facility for field gamma-ray spectrometers, established in the Czech Republic in 1975, significantly contributed to the subsequent radiometric data standardization. In the 1990's, the original analogue airborne radiometric data were digitized and using the method of back-calibration (IAEA, 2003) converted to dose rate. The map of terrestrial gamma radiation expressed in dose rate (nGy/h) was published on the scale 1:500,000 in 1995. Terrestrial radiation in the Czech Republic, formed by magmatic, sedimentary and metamorphic rocks of Proterozoic to Quaternary age, ranges mostly from 6 to 245 nGy/h, with a mean of 65.6 ± 19.0 nGy/h. The elevated terrestrial radiation in the Czech Republic, in comparison to the global dose rate average of 54 nGy/h, reflects an enhanced content of natural radioactive elements in the rocks.The 1995 published radiometric map of the Czech Republic was successively studied and verified by additional ground gamma-ray spectrometric measurements and by comparison to radiometric maps of Germany, Poland and Slovakia in border zones. A ground dose rate intercomparison measurement under participation of foreign and domestic professional institutions revealed mutual dose rate deviations about 20 nGy/h and more due to differing technical parameters of applied radiometric instruments. Studies and verification of the radiometric map of the Czech Republic illustrate the magnitude of current deviations in dose rate data. This gained experience can assist in harmonization of dose rate data on the European scale. © 2016 Elsevier Ltd.

Hyperammonemia and severe amino acid imbalances play central role in hepatic encephalopathy (HE). In the article is demonstrated that the main source of ammonia in cirrhotic subjects is activated breakdown of glutamine (GLN) in enterocytes and the kidneys and the main source of GLN is ammonia detoxification to GLN in the brain and skeletal muscle. Branched-chain amino acids (BCAA; valine, leucine, and isoleucine) decrease due to activated GLN synthesis in muscle. Aromatic amino acids (AAA; phenylalanine, tyrosine, and tryptophan) and methionine increase due to portosystemic shunts and reduced ability of diseased liver. The effects on aminoacidemia of the following variables that may affect the course of liver disease are discussed: nutritional status, starvation, protein intake, inflammation, acute hepatocellular damage, bleeding from varices, portosystemic shunts, hepatic cancer, and renal failure. It is concluded that (1) neither ammonia nor amino acid concentrations correlate closely with the severity of liver disease; (2) BCAA/AAA ratio could be used as a good index of liver impairment and for early detection of derangements in amino acid metabolism; (3) variables potentially leading to overt encephalopathy exert substantial but uneven effects; and (4) careful monitoring of ammonia and aminoacidemia may discover important break points in the course of liver disease and indicate appropriate therapeutic approach. Of special importance might be isoleucine deficiency in bleeding from varices, arginine deficiency in sepsis, and a marked rise of GLN and ammonia levels that may appear in all events leading to HE. © 2015 Elsevier Inc.

Stefanics G.,ETH Zurich | Stefanics G.,University of Zürich | Kremlacek J.,Charles University | Czigler I.,Hungarian Academy of Sciences
Frontiers in Human Neuroscience | Year: 2014

An increasing number of studies investigate the visual mismatch negativity (vMMN) or use the vMMN as a tool to probe various aspects of human cognition. This paper reviews the theoretical underpinnings of vMMN in the light of methodological considerations and provides recommendations for measuring and interpreting the vMMN. The following key issues are discussed from the experimentalist's point of view in a predictive coding framework: (1) experimental protocols and procedures to control “refractoriness” effects; (2) methods to control attention; (3) vMMN and veridical perception. © 2014 Stefanics, Kremláček and Czigler.

Bartak R.,Charles University
ICAART 2012 - Proceedings of the 4th International Conference on Agents and Artificial Intelligence | Year: 2012

Workflow is a formal description of a process or processes. There exist tools for interactive and visual editing of workflows such as the FlowOpt Workflow Editor. During manual editing of workflows, it is common to introduce flaws such as cycles of activities. Hence one of the required features of workflow management tools is verification of workflows, which is a problem of deciding whether the workflow describes processes that can be realized in practice. In this paper we deal with the theoretical complexity of verifying workflows with a nested structure and with extra constraints. The nested structure forces users to create valid workflows but as we shall show, introduction of extra causal, precedence, and temporal synchronization constraints makes the problem of deciding whether the workflow represents a realizable process hard. In particular, we will show that this problem is NP-complete.

Heneberg P.,Charles University
Critical Reviews in Oncology/Hematology | Year: 2016

Growth stimuli in cancer growth resemble those exhibited in wound healing. However, the process of nemosis is absent in cancer-associated fibroblasts (CAFs), which remain constitutively active. CAFs are present in almost all solid tumors but are most abundant in breast, prostate and pancreatic cancers. TGF-β1, TGF-β2, PDGF, IL-6, bFGF, reactive oxide species and protein kinase C are considered the key players in tumor-induced transdifferentiation of surrounding fibroblasts. Full-extent transdifferentiation was obtained only when the medium contained TGF-β1 or TGF-β2 (with or without other factors), whereas PDGF, bFGF or IL-6 (each alone) induced only partial transdifferentiation. Recent evidence suggests that the fibroblasts associated with primary cancers differ from those associated with metastases. The metastases-associated fibroblasts are converted by a metastasis-specific spectrum of factors. A large portion of paracrine tumor signaling is mediated by cancer cell-derived vesicles termed exosomes and microvesicles. The cancer cell-derived exosomes contain abundant and diverse proteomes and a number of signaling factors (TGF-ß1, TGF-ß2, IL-6, MMP2 and MMP9), particularly under hypoxic conditions. In contrast to the traditional view, the clonal expansion and selection of neoplastic cells should not be viewed outside the host body context. It is vital for a neoplastic cell to achieve the ability to re-program host body cells into CAFs and by this influence to modulate its microenvironment and receive positive feedback for growth and drug resistance. Neoplastic cells, which fail to develop such capacity, do not pass critical barriers in tumorigenesis and remain dormant and benign. © 2015 Elsevier Ireland Ltd.

Cendelin J.,Charles University
Cerebellum | Year: 2016

Stem cell-based and regenerative therapy may become a hopeful treatment for neurodegenerative diseases including hereditary cerebellar degenerations. Neurotransplantation therapy mainly aims to substitute lost cells, but potential effects might include various mechanisms including nonspecific trophic effects and stimulation of endogenous regenerative processes and neural plasticity. Nevertheless, currently, there remain serious limitations. There is a wide spectrum of human hereditary cerebellar degenerations as well as numerous cerebellar mutant mouse strains that serve as models for the development of effective therapy. By now, transplantation has been shown to ameliorate cerebellar function, e.g. in Purkinje cell degeneration mice, Lurcher mutant mice and mouse models of spinocerebellar ataxia type 1 and type 2 and Niemann-Pick disease type C. Despite the lack of direct comparative studies, it appears that there might be differences in graft development and functioning between various types of cerebellar degeneration. Investigation of the relation of graft development to specific morphological, microvascular or biochemical features of the diseased host tissue in various cerebellar degenerations may help to identify factors determining the fate of grafted cells and potential of their functional integration. © 2015, Springer Science+Business Media New York.

Korbel M.,Charles University
Acta medica (Hradec Králové) / Universitas Carolina, Facultas Medica Hradec Králové | Year: 2013

Periprosthetic fractures are the third most common reason for revision total hip arthroplasty. Surgical treatment of periprosthetic fractures belongs to the most difficult procedures due to the extensive surgery, elderly polymorbid patients and the high frequency of other complications. The aim of this study was to evaluate the results of operatively treated periprosthetic femoral fractures after total hip arthroplasty. We evaluated 47 periprosthetic fractures in 40 patients (18 men and 22 women) operated on between January 2004 and December 2010. The mean follow-up period was 27 months (within a range of 12-45 months). For the clinical evaluation, we used modified Merle d'Aubigné scoring system. In group of Vancouver A fractures, 3 patients were treated with a mean score of 15.7 points (good result). We recorded a mean score of 14.2 points (fair result) in 6 patients with Vancouver B1 fractures, 12.4 points (fair result) in 24 patients with Vancouver B2 fractures and 12.7 points (fair result) in 7 patients with Vancouver B3 fractures. In group of Vancouver C fractures, we found a mean score of 16.2 points (good result) in 7 patients. Therapeutic algorithm based on the Vancouver classification system is, in our opinion, satisfactory. Accurate differentiation of B1 and B2 type of fractures is essential. Preoperative radiographic images may not be reliable. If in doubt, checking the stability of the prosthesis fixation during surgery should be performed.

Heneberg P.,Charles University
European Journal of Orthopaedic Surgery and Traumatology | Year: 2011

An increasing number of national and international funding and statistical agencies utilize Web of Science (WOS) as a source of data influencing their decisions and analyses of research outcome. However, currently existing data sources for scientometric research, including WOS, are far from being perfect. Most of the imperfections are caused by uneven coverage, errors or changes in indexing policies, or mistaken or ineffective retrieval strategies employed by the users. Thus, it is important to be aware of the critical elements of scientometric evaluation, as inappropriately designed search procedures may lead to confusing or false-positive results. This paper presents the analysis of a series of previously published papers, which were affected by errors of omission and commission due to changes in WOS abstracting policies. When comparing WOS Topic search with WOS Title search, substantial differences arose. Number of papers published every year on cruciate ligament was shown to remain unchanged since early 1980s, when employing WOS Title search. Similarly, trends in number of citations on this topics remain unchanged through the long period of time, reflecting only increasing amount of citable papers available. The findings differ from those reported previously based on WOS Topic search, as improvement in the search protocol fully explained and rejected the previously reported steep increase in publications on cruciate ligament, air pollution, and oral lesions since 1991. The different outcomes compared to the other search protocols were caused by variations in WOS abstracting policies, such as exclusion of the address field, keywords, and exclusion or changes of the country codes or names. Despite the percentage of WOS records lacking these fields is decreasing in time, inclusion of such records hinders the ability to use the respective fields in any long-term searches using the WOS database. The results suggest thatWOS Topic search is not the appropriate tool to search for time-dependent changes in publication productivity. © Springer-Verlag 2010.

Ettler V.,Charles University
Applied Geochemistry | Year: 2016

This review summarizes over 160 studies focused on soil contamination near non-ferrous metal smelters. The methods of these investigations were examined with an emphasis on the combinations of traditional (geo)chemical approaches with various mineralogical and metal isotope techniques that are particularly helpful for depicting the fate of smelter-derived contamination in the soil. Differences in the distributions and binding of metal(loid)s in smelter-affected soils from temperate and (sub)tropical climatic zones indicate the greater vulnerability of the latter. Prevailing wind direction is a key factor affecting the dispersion of smelter emissions and their subsequent deposition into the soils, with greater importance found especially in arid areas. Whereas the greatest contamination is generally observed in the surface soil layers, downward migration of metal(loid)s in the soil profiles has been documented at numerous sites. Contamination of smelter soils significantly affects both plants and soil organisms, but suitable remediation techniques (such as chemical stabilization of soils by amendments) can be used for reducing the bioavailability of contaminants. © 2015.

Safrankova J.,Charles University | Nemecek Z.,Charles University | Prech L.,Charles University | Zastenker G.N.,Russian Academy of Sciences
Physical Review Letters | Year: 2013

This Letter shows the first results from the solar wind monitor onboard the Spektr-R spacecraft which measures plasma moments with a time resolution of 31 ms. This high-time resolution allows us to make direct observations of solar wind turbulence below ion kinetic length scales. We present examples of the frequency spectra of the density, velocity, and thermal velocity. Our study reveals that although these parameters exhibit the same behavior at the magnetohydrodynamic scale, their spectra are remarkably different at the kinetic scale. © 2013 American Physical Society.

Vesely A.,Charles University
Policy Sciences | Year: 2016

This article argues that policy advice can be understood as a special kind of “policy work” that depends upon a diverse set of factors operating at different levels. The basic aim of the article is to disentangle this multi-level and multifaceted phenomenon into a conceptual framework that can be used for empirical analysis and theory building. In that framework, policy advice is conceptualized as a never-ending interaction among various actors in a specific institutional context, through which routines and norms are both reproduced and abolished. First, it is explained why policy advice is most fruitfully understood as a special kind of policy work, and then how it relates to other policy work activities. Second, problems with single-level approaches are discussed and the need for a multi-level approach is explained. Third, a multi-level conceptual framework is formulated and described. Fourth, some possible applications of the framework are illustrated with examples from current empirical research. The article concludes with implications for research and theory building. © 2016 Springer Science+Business Media New York

Fischer T.,Charles University | Guest A.,GeomechanicsGG
Geophysical Research Letters | Year: 2011

We apply rock mechanics concepts to the seismological observations in order to explain why during hydraulic injection some events display tensile and some shear deformation. The presence of non-shear components depends on the differential stress and the fracture orientation with respect to the σ 1 direction. Provided the slip vector is parallel to the traction we define four types of earthquakes according to the ratio of the shear and tensile components. Assuming a Griffith failure envelope, hybrid events containing both shear and tensile components can occur for fractures striking within 22.5 ofσ 1. We argue that pure tensile fractures striking parallel to σ 1 are unlikely in the presence of natural fractures. The low shear traction of tensile events also implies their small stress drops. By applying the analysis to two different data sets, Soultz-sous-Forets and Cotton Valley, we show that different orientations of natural fractures and differential stress in the targeted formations made each region favorable for different non-DC components in the injection-induced seismicity. Copyright 2011 by the American Geophysical Union.

Lin X.,Uppsala University | Novotny M.,Charles University | Soderhall K.,Uppsala University | Soderhall I.,Uppsala University
Journal of Biological Chemistry | Year: 2010

Hematopoiesis is the process by which hemocytes mature and subsequently enter the circulation. Vertebrate prokineticins (PKs) are known to take part in this process, as are the invertebrate prokineticin domain proteins, astakines. In Pacifastacus leniusculus, astakine 1 is essential for the release of new hemocytes into the open circulatory system of these animals. In addition to astakine 1, we have now cloned a homologue of astakine 1 with an insert of 13 amino acids, named as astakine 2. Both crustacean astakines lack the N-terminal AVIT motif, which is present in vertebrate PKs, and hence receptor binding differs from that of vertebrate PKs. We have found astakine-like sequences in 19 different invertebrate species, and the sequences show that some motifs are conserved among invertebrate groups. Previously we showed that astakine 1 is directly involved in hematopoiesis, and now we show that astakine 1 and astakine 2 have different roles in hemocyte lineage differentiation. Astakine 1 can stimulate proliferation of hematopoietic tissue (Hpt) cells (precursor of hemocytes) as well as specifically induce differentiation of Hpt cells along the semigranular cell lineage, whereas astakine 2 plays a role in granular cell differentiation. Moreover, we discuss the impact of the putative structures of different astakines in comparison with the vertebrate prokineticins. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

FryDlova P.,Charles University | Frynta D.,Charles University
Biological Journal of the Linnean Society | Year: 2010

In a model group of giant reptiles, we explored the allometric relationships between male and female body size and compared the effects of sexual and fecundity selection, as well as some proximate causes, on macroevolutionary patterns of sexual size dimorphism (SSD). Monitor lizards are a morphologically homogeneous group that has been affected by extreme changes in body size during their evolutionary history, resulting in 14-fold differences among the body sizes of recent species. Here, we analysed data concerning the maximum and/or mean male and female snout-vent lengths in 42 species of monitor lizard from literary sources and supplemented these data with measurements made in zoos. There was a wide scale of SSD from nearly monomorphic species belonging mostly to the subgenus Odatria and Prasinus group of the Euprepriosaurus to apparently male-larger taxa. The variable best explaining SSD was the body size itself; the larger the species, the higher the SSD. This pattern agrees with the currently discussed Rensch's rule, claiming that the relationship between male and female body size is hyperallometric, i.e. the allometric exponent of this relationship exceeds unity and thus SSD increases with body size in the case of male-larger taxa. All our estimates of the reduced major axis regression slopes of this relationship ranged from 1.132 to 1.155. These estimates are significantly higher than unity, and thus unequivocally corroborate the validity of Rensch's rule in this reptilian group. In spite of our expectation that the variation in SSD can be alternatively explained by variables reflecting the strength of sexual selection (presence of male combat), fecundity selection (e.g. clutch size and mass) and/or proximate ecological factors (habitat type), none of these variables had consistent effects on SSD, especially when the data were adjusted to phylogenetic dependence and/or body size. © 2010 The Linnean Society of London.

Zobel M.,University of Tartu | Moora M.,Academy of Sciences of the Czech Republic | Herben T.,Charles University
Oikos | Year: 2010

Patterns of clonal growth and their controls on the level of individuals have been studied thoroughly, but little is known about the actual clonal mobility of plant individuals in vegetation and about its role in generating vegetation patterns and influencing species coexistence. Current evidence shows that communities are composed of spatially nonmobile 'matrix-forming species' and mobile 'inter-matrix' species, while local between-species variation in clonal mobility has been shown to be positively correlated to small-scale richness. We identify two major gaps in the knowledge. (1) Clonal mobility has a strong species-specific component, but the existing information is mainly qualitative and describes the potential mobility of species the best. Also, species may respond by their clonal growth in a plastic way to some environmental stimuli, such as neighbors or abiotic environment, but this data comes almost exclusively from artificial conditions. We know very little of the actual spatial mobility of clonal plant individuals in the field and of the factors that determine it. (2) Theoretical research indicates that localized dispersal plays prime role in determination of community structure. While clonal mobility shares many important features with the seed dispersal, it also shows important differences to it, such as in dispersal kernel (non-monotonic in clonal dispersal), role of microsite limitation, and role of plasticity. We have little information how systematic are these differences, and whether these differences in dispersal can play any role in shaping community dynamics. We conclude that clonal mobility has an important role in structuring plant communities in a small scale and propose further studies to address specific mechanisms, as well as community context of evolution of clonality. © 2010 The Authors.

Neustupa J.,Charles University | Skaloud P.,Charles University
Plant Ecology and Evolution | Year: 2010

Background and aims - Knowledge on diversity and distribution of algae and cyanobacteria in subaerial habitats still lags behind those of freshwater and marine environments. Notably, data on diversity of microalgae in tropical corticolous habitats are still scarce. We investigated species composition of subaerial epixylic algae and cyanobacteria from two Singaporean rainforest localities. We asked whether there are differences in species composition and alpha-diversity of samples taken in different areas and in different habitat types (bark vs. decaying bare wood). In addition, we asked whether there are differences in species turnover (beta-diversity) among different habitat types and areas. Methods - The cultivation-based approach and the microscopic analysis of populations were used. In total, 20 samples of bark and decaying wood from two forested areas were analyzed. Statistical analyses involved the non-metric multidimensional scaling (NMDS) of species data. Significance of differences in algal composition between groups of samples was evaluated by the non-parametric two-way ANOSIM (Analysis of Similarities) using the crossed design with permutations in blocks. The SIMPER method was used to identify species that characteristically discriminate between habitat types and sampling areas. Key results - In total, 57 species were identified. Green algae (Trebouxiophyceae, Chlorophyceae, Trentepohliales) were dominant, and Cyanobacteria were the second most frequent group. The dominants of the subaerial assemblages differed from corresponding temperate habitats and, in addition, their alpha-diver-sity was considerably higher. Several green algal morphospecies were characteristic for the bark localities (e.g. Dictyochloropsis spp., Pseudomarvania aerophytica, Printzina effusa and Printzina lagenifera). The alpha-diversity was similar in both habitat types, but the species turnover among samples (beta-diversity) was significantly higher in the decaying wood samples. Conclusions - Tropical corticolous habitats probably harbour higher diversity than corresponding temperate habitats. High beta-diversity of decaying wood illustrates general importance of this substrate for biodiversity of subaerial algae in the tropics. © 2010 National Botanic Garden of Belgium and Royal Botanical Society of Belgium.

Hedl R.,Academy of Sciences of the Czech Republic | Kopecky M.,Academy of Sciences of the Czech Republic | Kopecky M.,Charles University | Komarek J.,Agency for Nature Conservation and Landscape Protection of the Czech Republic
Diversity and Distributions | Year: 2010

Aim: Lowland woodlands in Europe went through dramatic changes in management in the past century. This article investigates the influence of two key factors, abandonment of coppicing and increased pressure of ungulates, in thermophilous oakwoods. We focused on three interconnected topics: (1) Has the assumed successional trend lead to impoverishment of the vegetation assemblages? (2) Has it resulted in vegetation homogenization? (3) Are the thermophilous oakwoods loosing their original character? Location: Czech Republic, Central Europe. Methods: The vegetation in 46 semi-permanent plots was recorded three times: firstly, shortly after the abandonment of coppicing (1953) and then, after four to six decades of secondary succession and strong game impact (1992 and 2006). Overall trends and changes in species spectra were analysed. Results: There is a marked successional shift towards species-poorer communities growing in cooler, moister and nutrient-richer conditions. The change was significantly different in parts affected and unaffected by high numbers of ungulates yet only for herbs, not the woody species. However, observed change in species composition was not accompanied by significant homogenization process that is the general process reported from elsewhere. A sharp decline in plant species typical for thermophilous woodland communities and in endangered species indicates that the original character of the woodland has been gradually lost. Main conclusions: Thermophilous oakwoods have been largely replaced by mesic forests. Lowland oakwoods in continental parts of Europe historically depended on active management, which kept the understorey conditions light and warm. Successional processes in the 20th century caused a critical loss of species diversity at various spatial levels. However, artificially high numbers of ungulates, which otherwise have a negative impact, probably held up succession, so that the changes may still be reversible. © 2010 Blackwell Publishing Ltd.

Vitek L.,Charles University
Frontiers in Pharmacology | Year: 2012

Bilirubin belongs to a phylogenetically old superfamily of tetrapyrrolic compounds, which have multiple biological functions. Although for decades bilirubin was believed to be only a waste product of the heme catabolic pathway at best, and a potentially toxic compound at worst; recent data has convincingly demonstrated that mildly elevated serum bilirubin levels are strongly associated with a lower prevalence of oxidative stress-mediated diseases. Indeed, serum bilirubin has been consistently shown to be negatively correlated to cardiovascular diseases (CVD), as well as to CVD-related diseases and risk factors such as arterial hypertension, diabetes mellitus, metabolic syndrome, and obesity. In addition, the clinical data are strongly supported by evidence arising from both in vitro and in vivo experimental studies. This data not only shows the protective effects of bilirubin per se; but additionally, of other products of the heme catabolic pathway such as biliverdin and carbon monoxide, as well as its key enzymes (heme oxygenase and biliverdin reductase); thus, further underlining the biological impacts of this pathway. In this review, detailed information on the experimental and clinical evidence between the heme catabolic pathway and CVD, and those related diseases such as diabetes, metabolic syndrome, and obesity is provided. All of these pathological conditions represent an important threat to human civilization, being the major killers in developed countries, with a steadily increasing prevalence. Thus, it is extremely important to search for novel markers of these diseases, as well as for novel therapeutic modalities to reverse this unfavorable situation. The heme catabolic pathway seems to fulfill the criteria for both diagnostic purposes as well as for potential therapeutical interventions. © 2012 Vítek.

Stych P.,Charles University
Acta Universitatis Carolinae, Geographica | Year: 2011

The aim of this article is to compare the effects of altitude and slope inclination on the spatial distribution of selected categories of land use.This study is based on Czechia's LUCC database 1845-1948-1990-2000.The database contains nearly 9,000 basic territorial units (BTUs) and 8 LUCC categories that can be compared in all of the time periods mentioned. For the purpose of calculating the average altitude and slope inclination of all BTUs, a digital terrain model (DTM) of Czechia was created using interpolation methods. The average altitude and slope inclination of each BTU constituted the primary input variables for the correlation analysis. The strength of the relationship between these factors and the relevant categories was examined. Evidence concerning the increasing significance of inclination In the spatial distribution of arable land and grasslands after 1948 may be the most important finding. While in 1845, the first year in the database, altitude basically determined the location of arable land; after the World War II, there was a turn in this trend. Mainly in connection with the development of agro-industrial forms (the introduction of modern heavy machinery, the automation of modern cultivation methods, etc.), inclination became more important in determining the abandonment of arable land.

Kucerova S.,Charles University
Acta Universitatis Carolinae, Geographica | Year: 2011

The article deals with evaluation of the process of education as an instrument enabling an individual to acquire certain competencies (a kind of capital). These when used in an active way, may help him/her to reach different personal benefits, or even benefits for the whole society in a given territory. Possible relationships between education and different types of capital are shown. Special attention is given to a relatively new and in this context less discussed concept of social capital. Traditionally the concept of education is regarded asan investment into human capital. For example in the case of Czechia education process is perceived mostly as acquisition of individual knowledge and skills relevant for living, for holding social roles or performing job. Despite its very problematic nature, education should be also regarded as an investment into social capital. However, it remains unclear whether investment into social capital is beneficial. Its returns are less easily definable and harder to specify. Moreover, it is also unclear who benefits from this investment. Only those who are connected to the affected networks or the local/regional society as a whole?

Bouzarovski S.,Charles University | Bassin M.,Södertörn University College
Annals of the Association of American Geographers | Year: 2011

The relationship between energy systems, on the one hand, and narratives and practices of identity building at different scales, on the other, has received little attention in the mainstream human geography and social science literature. There is still a paucity of integrated theoretical insights into the manner in which energy formations are implicated in the rise of particular cultural self-determinations, even though various strands of work on energy and identity are frequently present throughout the wide-and rather disparate-corpus of social science energy research. Therefore, this article explores themanner in which the exploitation and management of energy resources is woven into discourses and debates about national identity, international relations, a nation's path of future development, and its significance on the global arena using the case of Russia. We investigate some of the policies, narratives, and discourses that accompany the attempt to represent this country as a global "energy superpower" in relation to the resurrection of its domestic economy and material prosperity, on the one hand, and the restoration of its global status as a derzhava (or "Great Power"), on the other. Using ideas initially developed within the field of critical discourse analysis, we pay special attention to the national identity-building role played by geographical imaginations about the country's past and present energy exports to neighboring states. We argue that they have created a hydrocarbon landscape in which the discursive and material have become mutually entangled to create an infrastructurally grounded vision of national identity. © 2011 by Association of American Geographers Initial submission, March 2010.

Nesvorny D.,Southwest Research Institute | Vokrouhlicky D.,Charles University
Astrophysical Journal | Year: 2014

We develop an analytic model for transit timing variations produced by orbital conjunctions between gravitationally interacting planets. If the planetary orbits have tight orbital spacing, which is a common case among the Kepler planets, the effect of a single conjunction can be best described as: (1) a step-like change of the transit timing ephemeris with subsequent transits of the inner planet being delayed and those of the outer planet being sped up, and (2) a discrete change in sampling of the underlying oscillations from eccentricity-related interaction terms. In the limit of small orbital eccentricities, our analytic model gives explicit equations for these effects as a function of the mass and orbital separation of planets. We point out that a detection of the conjunction effect in real data is of crucial importance for the physical characterization of planetary systems from transit timing variations. © 2014. The American Astronomical Society. All rights reserved..

This paper presents an overview of past and current debates over the conceptualization of migration into rural areas - counterurbanization. It begins with the history of the term itself, leading us from its original use to the contemporary plurality of its meanings. Key issues in the process of defining counterurbanization are examined, in light of the term's historical development. The article illustrates a shift in counterurbanization research from the study of the settlement system to the study of local dimensions of counterurbanization and finally to the discursive production of counterurbanization. Secondly, contemporary residential decentralization in Czechia and the theoretical framing of counterurbanization are linked together in order to discuss the relevance of the counterurbanization research agenda in Czechia. The article concludes by stating the need for new ways to approach migration into rural areas. © Česká geografická společnost, 2011 (Czech Geographic Society).

Vokrouhlicky D.,Charles University | Nesvorny D.,Southwest Research Institute
Astrophysical Journal | Year: 2014

Although not yet detected, pairs of exoplanets in 1:1 mean motion resonance probably exist. Low eccentricity, near-planar orbits, which in the comoving frame follow horseshoe trajectories, are one of the possible stable configurations. Here we study transit timing variations (TTVs) produced by mutual gravitational interaction of planets in this orbital architecture, with the goal to develop methods that can be used to recognize this case in observational data. In particular, we use a semi-analytic model to derive parametric constraints that should facilitate data analysis. We show that characteristic traits of the TTVs can directly constrain the (1) ratio of planetary masses and (2) their total mass (divided by that of the central star) as a function of the minimum angular separation as seen from the star. In an ideal case, when transits of both planets are observed and well characterized, the minimum angular separation can also be inferred from the data. As a result, parameters derived from the observed transit timing series alone can directly provide both planetary masses scaled to the central star mass. © 2014. The American Astronomical Society. All rights reserved.

Cerna B.,Charles University | Engel Z.,Charles University
Earth Surface Processes and Landforms | Year: 2011

This study presents rock strength variations at granite outcrops and in subsurface vertical profiles in the Jizerské hory Mountains, Czech Republic. Schmidt hammer rebound values in subsurface profiles change gradually from the bedrock surface downward. An exponential relation has been observed between the R-values and depth in rock outcrops to a depth of around 4·5 m. The exponential nature of the curve indicates that rock hardness increases more rapidly with depth in the uppermost 1 m section of the rock profile. A detailed study of rebound values obtained from both intact and polished rock exposures reveal effects of surface grinding on results of the Schmidt hammer method. The range of data collected increases after grinding, allowing more precise discrimination of rock surfaces in respect of age and weathering. The Schmidt hammer method may be used effectively as a relative-age dating tool for rock surfaces that originated during the Late Pleistocene. It is concluded that this time limitation can be significantly mitigated by surface grinding before measurement. © 2010 John Wiley & Sons, Ltd.

Kratky M.,Charles University | Vinsova J.,Charles University
Current Medicinal Chemistry | Year: 2012

Isocitrate lyase plays a key role for survival of Mycobacterium tuberculosis in the latent form during a chronic stage of infection. This enzyme is important for M. tuberculosis during steady stage growth when it converts isocitrate to succinate and glyoxylate. Then, the glyoxylate is condensed with acetyl-CoA to form malate by malate synthase. The carbon conserving glyoxylate pathway has not been observed in mammals; therefore, it has been determined as a potential drug target for discovery of a new antituberculosis agent. Novel active molecules should shorten the duration of therapy, prevent resistance development and eliminate latent disease. The review summarizes recent progresses in isocitrate lyase inhibitors, overviews structural analogues of several metabolic intermediates (3-nitropropionate, 3-bromopyruvate, itaconate, itaconic anhydride), peptide inhibitors, and recently developed inhibitors with various chemical structures. The largest inhibitory activity against isocitrate lyase (IC50 of 0.10 ± 0.01 μM) and concomitantly a significant antimycobacterial activity has been presented by fluoroquinolone derivative 1-cyclopropyl-7-[3,5-dimethyl-4-(3-nitropropanoyl)piperazin-1-yl]-6- fluoro-8-methoxy-4-oxo-1,4-dihydroquinoline-3-carboxylic acid, which has incorporated 3-nitropropionyl group as one of the structural analogue of succinate, a metabolic intermediate. © 2012 Bentham Science Publishers.

Bobek V.,Charles University
Anti-Cancer Agents in Medicinal Chemistry | Year: 2012

The effect of anticoagulant adjuvant anti-tumor therapy depends on the cancer type and stage and on the type of the used anticoagulant drug. A striking response rate was described in experiments involving human patients with lung cancer. The aim of this study is to review anticoagulant and fibrinolytic drugs as antitumor agents with focus on their clinical use. The first part of the review evaluates the results of clinical studies. The results of early clinical research are promising and observations suggest novel approaches to the experimental therapy of lung cancer. The second part of the review shortly describes the problem of thrombosis in patients with lung cancer (incidence of thromboembolic disease and its pathogenesis). The third part briefly describes the antimetastatic and antitumor attributes of anticoagulants and fibrinolytics. © 2012 Bentham Science Publishers.

Mancal T.,Charles University
Journal of Physical Chemistry B | Year: 2013

We formulate a classical pure dephasing system-bath interaction model in a full correspondence to the well-studied quantum model of natural light-harvesting antennae. The equations of motion of our classical model not only represent the correct classical analogy to the quantum description of excitonic systems, but they also have exactly the same functional form. We demonstrate derivation of classical dissipation and relaxation tensor in second order perturbation theory. We find that the only difference between the classical and quantum descriptions is in the interpretation of the state and in certain limitations imposed on the parameters of the model by classical physics. The effects of delocalization, transfer pathway interference, and the transition from coherent to diffusive transfer can be found already in the classical realm. The only qualitatively new effect occurring in quantum systems is the preference for a downhill energy transfer and the resulting possibility of trapping the energy in the lowest energy state. © 2013 American Chemical Society.

Mikula P.,Charles University
Ardea | Year: 2014

Birds inhabiting urban areas have to cope with novel conditions. Unlike natural habitats, birds in urban environments are exposed to an increased human presence which often induces stress. Urban birds with reduced sensitivity to human disturbance can obtain benefits such as longer foraging time or decreased energy costs for escape. Here, I tested the hypothesis that the decrease in flight initiation distance (FID) to a potential predator (an approaching human) reflects adaptation to the level of disturbance expressed as pedestrian density. Moreover, I studied the Influence of habitat type and species on observed FIDs. I analysed 2117 flight distances (20 species of European birds) located in ten localities in Prague. I found that species and pedestrian density play a more important role in determining FIDs than the type of habitat. Moreover, urban populations exposed to increased pedestrian density had consistently shorter flight distances. This study provides empirical documentation of changes in anti-predator behaviour, which strongly correlate with the pedestrian density gradient. It could support the idea that the establishment of FID can be highly plastic process depending on local conditions, as it is highly affected by a bird's individuality and its ability to adapt to the local level of disturbance by learning.

Skoumalova A.,Charles University | Hort J.,Charles University | Hort J.,St Annes University Hospital Brno
Journal of Cellular and Molecular Medicine | Year: 2012

Alzheimer′s disease (AD) represents a highly common form of dementia, but can be diagnosed in the earlier stages before dementia onset. Early diagnosis is crucial for successful therapeutic intervention. The introduction of new diagnostic biomarkers for AD is aimed at detecting underlying brain pathology. These biomarkers reflect structural or biochemical changes related to AD. Examination of cerebrospinal fluid has many drawbacks; therefore, the search for sensitive and specific blood markers is ongoing. Investigation is mainly focused on upstream processes, among which oxidative stress in the brain is of particular interest. Products of oxidative stress may diffuse into the blood and evaluating them can contribute to diagnosis of AD. However, results of blood oxidative stress markers are not consistent among various studies, as documented in this review. To find a specific biochemical marker for AD, we should concentrate on specific metabolic products formed in the brain. Specific fluorescent intermediates of brain lipid peroxidation may represent such candidates as the composition of brain phospholipids is unique. They are small lipophilic molecules and can diffuse into the blood stream, where they can then be detected. We propose that these fluorescent products are potential candidates for blood biomarkers of AD. © 2012 The Authors Journal of Cellular and Molecular Medicine © 2012 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

Subr L.,Charles University | Haas J.,Charles University
Astrophysical Journal | Year: 2014

The center of our Galaxy hosts almost two hundred very young stars, a subset of which is orbiting the central supermassive black hole (SMBH) in a relatively thin disk-like structure. First analyses indicated a power-law surface density profile of the disk, Σ ∞ Rβ with β = -2. Recently, however, doubts about this profile arose. In particular, it now seems to be better described by a sort of broken power law. By means of both analytical arguments and numerical N-body modeling, we show that such a broken power-law profile is a natural consequence of the two-body relaxation of the disk. Due to the small relative velocities of the nearby stars in co-planar Keplerian orbits around the SMBH, two-body relaxation is effective enough to affect the evolution of the disk on timescales comparable to its estimated age. In the inner, densest part of the disk, the profile becomes rather flat (β ≈, 1) while the outer parts keep imprints of the initial state. Our numerical models show that the observed projected surface density profile of the young stellar disk can result from two-body relaxation driven evolution of a disk with initial single power-law profile with -2≲β ≲ -1.5. In addition, we suggest that two-body relaxation may have caused a significant radial migration of the S-stars toward the central SMBH, thus playing an important role in their formation scenario. © 2014. The American Astronomical Society. All rights reserved.

Drlik M.,Charles University | Kocvara R.,Charles University
Journal of Pediatric Urology | Year: 2013

The current opinion on spermatic cord torsion is discussed in this review, with special attention to natural history, value of diagnostic tools, evidence for surgical management, outcome and management of atypical forms of torsion. © 2012 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

Protein tyrosine phosphatases (PTPs) are increasingly recognized as important effectors of host-pathogen interactions. Since Guan and Dixon reported in 1990 that phosphatase YopH serves as an essential virulence determinant of Yersinia, the field shifted significantly forward, and dozens of PTPs were identified in various microorganisms and even in viruses. The discovery of extensive tyrosine signaling networks in non-metazoan organisms refuted the moth-eaten paradigm claiming that these organisms rely exclusively on phosphoserine/phosphothreonine signaling. Similarly to humans, phosphotyrosine signaling is thought to comprise a small fraction of total protein phosphorylation, but plays a disproportionately important role in cell-cycle control, differentiation, and invasiveness. Here we summarize the state-of-art knowledge on PTPs of important non-metazoan pathogens (Listeria monocytogenes, Staphylococcus aureus, Porphyromonas gingivalis, Caulobacter crescentus, Yersinia, Synechocystis, Leishmania, Plasmodium falciparum, Entamoeba histolytica, etc.), and focus also at the microbial proteins affecting directly or indirectly the PTPs of the host (Mycobacterium tuberculosis MTSA-10, Bacillus anthracis anthrax toxin, streptococcal β protein, Helicobacter pylori CagA and VacA, Leishmania GP63 and EF-1α, Plasmodium hemozoin, etc.). This is the first review summarizing the knowledge on biological activity and pharmacological inhibition of non-metazoan PTPs, with the emphasis of those important in host-pathogen interactions. Targeting of numerous non-metazoan PTPs is simplified by the fact that they act either as ectophosphatases or are secreted outside of the pathogen. Interfering with tyrosine phosphorylation represents a powerful pharmacologic approach, and even though the PTP inhibitors are difficult to develop, lifting the fog of phosphatase inhibition is of the great market potential and further clinical impact. © 2012 Bentham Science Publishers.

Percutaneous coronary interventions (PCIs) have become the most commonly performed coronary revascularization procedures. At the same time, there is an increased likelihood that patients with intracoronary stents will need to undergo surgery. Two serious consequences emerge from this situation: (i) stent thrombosis in relation to discontinuation of antiplatelet therapy, and (ii) major bleeding in relation to continuation of antiplatelet therapy. The best solution to overcome the risks resulting from surgery performed in patients after stent implantation is to postpone the operation until after re-endothelialization of the vessel surface is completed. Expert recommendations advise that patients can be sent for non-cardiac surgery 3 months after bare-metal stent PCI and 12 months after drug-eluting stent PCI, with continuation of aspirin therapy. Difficult decisions regarding antiplatelet management arise when a patient that is still receiving dual antiplatelet therapy with aspirin and a thienopyridine has to undergo surgery that cannot be postponed. Discussions between the treating cardiologist, the surgeon and the anaesthesiologist about this situation are recommended in order to achieve a reasonable expert consensus. © 2011 Adis Data Information BV. All rights reserved.

Lhotakova Y.,Charles University
PloS one | Year: 2012

Novel biomaterials based on hydrophilic polycaprolactone and polyurethane (Tecophilic®) nanofibers with an encapsulated 5,10,5,20-tetraphenylporphyrin photosensitizer were prepared by electrospinning. The doped nanofiber textiles efficiently photo-generate O(2)((1)Δ(g)), which oxidize external chemical and biological substrates/targets. Strong photo-virucidal effects toward non-enveloped polyomaviruses and enveloped baculoviruses were observed on the surface of these textiles. The photo-virucidal effect was confirmed by a decrease in virus infectivity. In contrast, no virucidal effect was detected in the absence of light and/or the encapsulated photosensitizer.

Cerna K.,Charles University
Limnologica | Year: 2010

Spatial patterns on a very small scale (10 cm), and the effect of artificial barriers on the composition of phytobenthic algal assemblages along two transects within different microhabitat types were investigated. Samples were taken in a peat bog along linear transects on a scale of 10 cm, and water chemistry was examined. The distribution of algae along both transects was influenced by both spatial distance and environmental conditions in similar proportions. Differences in species composition in various parts of the transects were observed, but this pattern was primarily related to the abundance of species, rather than to their presence/absence in samples. Similarity in species composition correlated with spatial distance and environmental parameters in both microhabitat types. I concluded that, given a homogenous environment on a small scale, spatial distribution of algae is affected by both the environmental conditions of the microhabitats and their dispersal limitations. Moreover, an artificial barrier constituted an obstruction for water and nutrient flow, as well as algal migration, and had an impact on species composition. © 2010 Elsevier GmbH.

Palacky J.,Charles University | Vorlickova M.,Academy of Sciences of the Czech Republic | Vorlickova M.,Masaryk University | Kejnovska I.,Academy of Sciences of the Czech Republic | And 2 more authors.
Nucleic Acids Research | Year: 2013

DNAconcentrationhasbeenrecentlysuggestedtobe the reason why different arrangements are revealed for K+-stabilized human telomere quadruplexes by experimental methods requiring DNA concentrations differing by orders of magnitude. AsRamanspectroscopy can be applied to DNA samples ranging from those accessible by absorption and CD spectroscopies up to extremely concentrated solutions, gels and even crystals; it has been used here to clarify polymorphism of a core human telomeric sequence G3(TTAG 3)3 in the presence of K+and Na+ ions throughout wide range of DNA concentrations. We demonstrate that the K+-structure of G3(TTAG3)3 at low DNA concentration is close to the antiparallel fold of Na+-stabilized quadruplex. On the increase of G 3(TTAG3)3 concentration, a gradual transition from antiparallel to intramolecular parallel arrangement was observed, but only for thermodynamically equilibrated K+-stabilized samples. The transition is synergically supported by increased K+ concentration. However, even for extremely high G3(TTAG3)3 and K +concentrations, an intramolecular antiparallel quadruplex is spontaneously formed from desalted non-quadruplex single-strand after addition of K+ ions. Thermal destabilization or long dwell time are necessary to induce interquadruplex transition. On the contrary, Na+-stabilized G 3(TTAG3)3 retains its antiparallel folding regardless of the extremely high DNA and/or Na+concentrations, thermal destabilization or annealing. © 2012 The Author(s).

A mixture of 29 organic acids (OAs) occurring in urine was analyzed by capillary electrophoresis (CE) with capacitively coupled contactless conductivity detection (C4D) and UV photometric detection. The optimized analytical system involved a 100cm long polyacrylamide-coated capillary (50μm i.d.) and the background electrolyte of 20mM 2-morpholinoethanesulfonic acid (MES)/NaOH+10% (v/v) methanol, pH 6.0 (pH is related to the 20mM MES/NaOH buffer in water). The LOD values obtained by C4D for the OAs which do not absorb UV radiation range from 0.6μM (oxalic acid) to 6.8μM (pyruvic acid); those obtained by UV photometry for the remaining OAs range from 2.9μM (5-hydroxy-3-indoleacetic acid) to 10.2μM (uric acid). The repeatability of the procedure developed is characterized by the coefficients of variation, which vary between 0.3% (tartaric acid) and 0.6% (5-hydroxy-3-indoleacetic acid) for the migration time and between 1.3% (tartaric acid) and 3.5% (lactic acid) for the peak area. The procedure permitted quantitation of 20 OAs in a real urine sample and was applied to monitoring of the occurrence of the inborn metabolic fault of methylmalonic aciduria. © 2010 Elsevier B.V.

Vesely J.,Charles University | Rios R.,University of Southampton
Chemical Society Reviews | Year: 2014

Nucleophilic addition to carbon-nitrogen double bonds (imines) represents one of the most common strategies for the synthesis of amine derivatives. In order to circumvent the problem associated with low reactivity of imines in nucleophilic addition, various imines with electron-withdrawing groups at nitrogen have been studied, and many of them were successfully applied in asymmetric methodologies. Especially N-carbamoyl imines were found to be useful in the enantioselective synthesis of various organic compounds, due to their increased reactivity toward nucleophiles as well as limited difficulties connected with the removal of the carbamoyl moiety in target molecules. The aim of this review is to cover enantioselective methods based on N-carbamoyl imines, focusing on synthetically useful protocols. © The Royal Society of Chemistry.

Novakova L.,Charles University | Havlikova L.,Charles University | Vlckova H.,Charles University
TrAC - Trends in Analytical Chemistry | Year: 2014

In recent years, the popularity of hydrophilic interaction chromatography (HILIC) in the analysis of small polar and ionizable molecules increased substantially. A large number of new stationary phases with sub-2-μm and superficially porous particles were developed and used in various applications, including pharmaceuticals, metabolites, biomarkers, amino acids and peptides. Applications of HILIC in ultra-high performance liquid chromatography (UHPLC) mode constitute only about 10% of all current HILIC applications. This review presents an overview of UHPLC in HILIC mode, including the importance of the final sample diluent, a discussion on available stationary phases and approaches to detection, and a comparison of performance with other chromatographic modes. © 2014 Elsevier B.V.

Maya F.,University of the Balearic Islands | Horstkotte B.,Charles University | Estela J.M.,University of the Balearic Islands | Cerda V.,University of the Balearic Islands
TrAC - Trends in Analytical Chemistry | Year: 2014

The dispersive liquid-liquid microextraction (DLLME) technique is simple, efficient and environment friendly. One of the main limitations to its further development is the lack of approaches to its automation. In this work, we describe and review recent applications of a novel approach to perform fully-automated in-syringe DLLME based on the use of computer-controlled bi-directional syringe pumps. The in-syringe-DLLME technique enables precise flow control over the extractant and the concomitant detection of the analytes "in-syringe", within a peripheral flow network, or by introduction into coupled detectors. © 2014 Elsevier B.V.

Vandenabeele P.,Ghent University | Edwards H.G.M.,University of Bradford | Jehlicka J.,Charles University
Chemical Society Reviews | Year: 2014

The applications of analytical Raman spectroscopy in the characterisation of materials associated with archaeologically excavated artefacts, forensic investigations of drugs of abuse, security and crime scenes, minerals and rocks and future astrobiological space missions are now well established; however, these applications have emphasised the need for new developments in the area of miniaturised instrumentation which extends the concept and breadth of the analytical requirement to facilitate the provision of data from 'in field' studies. In this respect, the apparently unrelated themes of art and archaeology, forensic science, geological science and astrobiology as covered by this review are unified broadly by the ability to record data nondestructively and without resorting to sampling and the subsequent transfer of samples to the analytical laboratory. In studies of works of art there has long been a requirement for on-site analysis, especially for valuable paintings held under strict museum security and for wall paintings which cannot physically be removed from their setting; similarly, the use of portable Raman spectroscopy in archaeological and geological field work as a first-pass screening device which obviates the necessity of multiple and wasteful specimen collection is high on the wish-list of practicing spectroscopists. As a first-pass screening probe for forensic crime scenes, Raman spectroscopy has proved to be of inestimable value for the early detection of dangerous and prohibited materials such as drugs of abuse, explosives and their chemical precursors, and banned contraband biomaterials such as ivories and animal products; in these applications the advantage of the Raman spectroscopic technique for the recognition of spectral signatures from mixtures of inorganic and organic compounds is paramount and not afforded by other less portable instrumental techniques. Finally, in astrobiological work, these requirements also apply but with the additional prerequisite for system operation remotely-often over distances of several hundred million kilometres-as part of instrumental suites on robotic spacecraft and planetary landers; this necessitates robust and reliable instrumentation for the observation of unique and characteristic spectral features from the planetary geological surface and subsurface which are dependent on the assignment of both biological and geological band signatures. This journal is © the Partner Organisations 2014.

Roth W.J.,J. Heyrovsky Institute of Physical Chemistry | Roth W.J.,Jagiellonian University | Nachtigall P.,Charles University | Morris R.E.,University of St. Andrews | Cejka J.,J. Heyrovsky Institute of Physical Chemistry
Chemical Reviews | Year: 2014

Zeolites are well-known as valuable crystalline solids with framework structures containing discrete micropores of molecular dimensions that accommodate exchangeable extra-framework cation sites. Lamellar zeolites combine useful benefits of both classes, high catalytic activity, microporosity, thermal stability, and chemical resistance of zeolites with structural flexibility of 2D solids, enabling their postsynthetic modification, both structural and compositional. The main category of 2D zeolites is the layered precursors, which are viewed as primary forms because they are the starting materials for further modifications. The various modifications may be an end product (IEZ-stabilized) or they may be further modifiable, like intercalated and swollen derivatives. Synthesis method, either via direct synthesis or by postsynthetic modification, is another criterion for classifying layered zeolite materials. New precursors can also be obtained from a regular zeolite by selective chemical degradation.

Vokrouhlicky D.,Charles University | Nesvorn D.,Southwest Research Institute
Astronomical Journal | Year: 2011

Disruptive collisions in the asteroid belt produced groups of fragments known as the asteroid families. The studies of identified asteroid families help us to better understand issues related to impact physics, space weathering, asteroid interior, and collisional evolution of the main belt. Here, we analyze a family near the central main belt asteroid (2384) Schulhof. We show that the previously found group of objects around (81337) 2000 GP36 is actually a sub-cluster in the larger Schulhof family. Using backward integrations we demonstrate that the orbits of sub-cluster asteroids converge to that of (2384) Schulhof at 780 ± 100 kyr ago, suggesting that the breakup event happened very recently. Interestingly, a similar analysis of the two newly discovered members of the Schulhof family may indicate a second event ≲ 100 kyr ago (e.g., secondary collision, fission, satellite instability). If confirmed, the formation history of the Schulhof family would suggest that small asteroids may have very colorful lifetimes. Additional astrometric observations of the two new member asteroids will be needed to improve their present orbit and better constrain their past histories. © 2011. The American Astronomical Society. All rights reserved.

Caltova K.,Charles University
Acta medica (Hradec Králové) / Universitas Carolina, Facultas Medica Hradec Králové | Year: 2012

The aim of our study was to determine the effect of selected cytostatics on a human ovarian cancer cell line A2780 as a model system for ovarian cancer treatment. This cell line is considered cisplatin-sensitive. Panel of tested cytostatics included cisplatin, paclitaxel, carboplatin, gemcitabine, topotecan and etoposide. These cytostatics have a different mechanism of action. To evaluate cytotoxic potential of the tested compounds, the methods measuring various toxicological endpoints were employed including morphological studies, MTT assay, dynamic monitoring of cell proliferation with xCELLigence, cell cycle analysis, caspase 3 activity and expression of proteins involved in cell cycle regulation and cell death. The A270 cell line showed different sensitivity towards the selected cytostatics, the highest cytotoxic effect was associated with paclitaxel and topotecan.

Harmanec P.,Charles University | Prsa A.,Villanova University
Publications of the Astronomical Society of the Pacific | Year: 2011

The increasing precision of astronomical observations of stars and stellar systems is gradually getting to a level where the use of slightly different values of the solar mass, radius, and luminosity, as well as different values of fundamental physical constants, can lead to measurable systematic differences in the determination of basic physical properties. An equivalent issue with an inconsistent value of the speed of light was resolved by adopting a nominal value that is constant and has no error associated with it. Analogously, we suggest that the systematic error in stellar parameters may be eliminated by (1) replacing the solar radius Rȯ and luminosity Lȯ by the nominal values that are by definition exact and expressed in SI units: 1 RN ȯ = 6.95508 × 108 m and 1 LN ȯ = 3.846 × 1026 W; (2) computing stellar masses in terms of Mȯ by noting that the measurement error of the product GMȯ is 5 orders of magnitude smaller than the error in G; (3) computing stellar masses and temperatures in SI units by using the derived values M2010 ȯ = 1:988547 × 1030 kg and T2010 ȯ = 5779.57 K; and (4) clearly stating the reference for the values of the fundamental physical constants used. We discuss the need and demonstrate the advantages of such a paradigm shift. © 2011.

Battiato M.,Uppsala University | Carva K.,Uppsala University | Carva K.,Charles University | Oppeneer P.M.,Uppsala University
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

Femtosecond laser excitation of a ferromagnetic material creates energetic spin-polarized electrons that have anomalous transport characteristics. We develop a semiclassical theory that is specifically dedicated to capture the transport of laser-excited nonequilibrium (NEQ) electrons. The randomly occurring multiple electronic collisions, which give rise to electron thermalization, are treated exactly and we include the generation of electron cascades due to inelastic electron-electron scatterings. The developed theory can, moreover, treat the presence of several different layers in the laser-irradiated material. The derived spin-dependent transport equation is solved numerically and it is shown that the hot NEQ electron spin transport occurs neither in the diffusive nor ballistic regime, it is superdiffusive. As the excited spin majority and minority electrons in typical transition-metal ferromagnets (e.g., Fe, Ni) have distinct, energy-dependent lifetimes, fast spin dynamics in the femtosecond (fs) regime is generated, causing effectively a spin current. As examples, we solve the resulting spin dynamics numerically for typical heterostructures, specifically, a ferromagnetic/nonmagnetic metallic layered junction (i.e., Fe/Al and Ni/Al) and a ferromagnetic/nonmagnetic insulator junction (Fe or Ni layer on a large band-gap insulator as, e.g., MgO). For the ferromagnetic/nonmagnetic metallic junction where the ferromagnetic layer is laser-excited, the computed spin dynamics shows that injection of a superdiffusive spin current in the nonmagnetic layer (Al) is achieved. The injected spin current consists of screened NEQ, mobile majority-spin electrons and is nearly 90% spin-polarized for Ni and about 65% for Fe. Concomitantly, a fast demagnetization of the ferromagnetic polarization in the femtosecond regime is driven. The analogy of the generated spin current to a superdiffusive spin Seebeck effect is surveyed. © 2012 American Physical Society.

Cabala R.,Charles University | Bursova M.,Charles University
Journal of Chromatography A | Year: 2012

We have developed a new microextraction technique for equilibrium, non-exhaustive analyte preconcentration from aqueous solutions into organic solvents lighter than water. The key point of the method is application of specially designed and optimized bell-shaped extraction device, BSED. The technique has been tested and applied to the preconcentration of selected volatile and semi volatile compounds which were determined by gas chromatography/mass spectrometry in spiked water samples. The significant parameters of the extraction have been found using chemometric procedures and these parameters were optimized using the central composite design (CCD) for two solvents. The analyte preconcentration factors were in a range from 8.3 to 161.8 (repeatability from 7 to 14%) for heptane, and 50.0-105.0 (repeatability from 0 to 5%) for tert-butyl acetate. The reproducibility of the technique was within 1-8%. The values of limits of detection and determination were 0.1-3.3ngmL -1 for heptane and 0.3-10.7ngmL -1 for tert-butyl acetate. The new microextraction technique has been found to be a cheap, simple and flexible alternative to the common procedures, such as SPME or LLME. This BSED-LLME technique can also be combined with other separation methods, e.g., HPLC or CE. © 2012 Elsevier B.V.

Fischerova D.,Charles University
Ultrasound in Obstetrics and Gynecology | Year: 2011

This Review documents examination techniques, sonographic features and clinical considerations in ultrasound assessment of gynecological tumors. The methodology of gynecological cancer staging, including assessment of local tumor extent, lymph nodes and distant metastases, is described. With increased technical quality, sonography has become an accurate staging method for early and advanced gynecological tumors. Other complementary imaging techniques, such as computed tomography and magnetic resonance imaging, can be used as an adjunct to ultrasound in specific cases, but are not essential to tumor staging if sonography is performed by a specialist in gynecological oncology. Ultrasound is established as the method of choice for evaluating local extent of endometrial cancer and is the most important imaging method for the differential diagnosis of benign and malignant ovarian tumors. Ultrasound can be used to detect early as well as locally advanced cancers that extend from the vagina, cervix or other locations to the paracolpium, parametria, rectum and sigmoid colon, urinary bladder and other adjacent organs or structures. In cases of ureteric involvement, ultrasound is also helpful in locating the site of obstruction. Furthermore, it is specific for the detection of extrapelvic tumor spread to the abdominal cavity in the form of parietal or visceral carcinomatosis, omental and/or mesenteric infiltration. Ultrasound can be used to assess changes in infiltrated lymph nodes, including demonstration of characteristic sonomorphologic and vascular patterns. Vascular patterns are particularly well visualized in peripheral nodes using high resolution linear array probes or in the pelvis using high-frequency probes. The presence of peripheral or mixed vascularity or displacement of vessels seems to be the sole criterion in the diagnosis of metastatic or lymphomatous nodes. In the investigation of distant metastases, if a normal visceral organ or characteristic diffuse or focal lesions (such as a simple cyst, hepatic hemangioma, renal angiomyolipoma, fatty liver (steatosis)) are identified on ultrasound, additional examinations using complementary imaging methods are not required. If, however, less characteristic findings are encountered, especially when the examination result radically affects subsequent therapeutic management, an additional examination using a complementary imaging method (e.g. contrast-enhanced ultrasound, computed tomography, magnetic resonance imaging, positron emission tomography) is indicated. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.

Kristoufek L.,Charles University | Kristoufek L.,Czech Institute of Information Theory And Automation
Physica A: Statistical Mechanics and its Applications | Year: 2012

In this paper, we present the results of Monte Carlo simulations for two popular techniques of long-range correlation detection - classical and modified rescaled range analyses. A focus is put on an effect of different distributional properties on an ability of the methods to efficiently distinguish between short-term memory and long-term memory. To do so, we analyze the behavior of the estimators for independent, short-range dependent, and long-range dependent processes with innovations from eight different distributions. We find that apart from a combination of very high levels of kurtosis and skewness, both estimators are quite robust to distributional properties. Importantly, we show that RS is biased upwards (yet not strongly) for short-range dependent processes, while M-RS is strongly biased downwards for long-range dependent processes regardless of the distribution of innovations. © 2012 Elsevier B.V. All rights reserved.

Mazurova S.,Charles University
Prague medical report | Year: 2013

Barth syndrome is an X-linked recessive disorder that is caused by mutations in Taffazin gene (TAZ), leading to severe cardiolipin deficiency which results in respiratory chain dysfunction. Barth syndrome is characterized by cardiomyopathy, neutropenia, skeletal myopathy, growth deficiency and 3-methylglutaconic aciduria. In this paper, we present clinical, biochemical and molecular data of the first four Czech patients from four unrelated families diagnosed with this rare disease. The mean age of onset was 5.5 ± 3.8 months. One child suffered from sudden cardiac death at the age of 2 years, the age of living patients is between 3 and 13 years. Muscle hypotonia was present in all four patients; cardiomyopathy and growth retardation in three and neutropenia in two of them. Two patients manifested a dilated and one patient a hypertrophic cardiomyopathy. A characteristic laboratory abnormality was the intermittently increased excretion of 3-methylglutaconic acid. Three novel hemizygous mutations in the TAZ gene were found (c.584G>T; c.109+6T>C; c.86G>A). We conclude that Barth syndrome should be included in differential diagnosis of cardiomyopathy in childhood, especially in the cooccurrence of dilated cardiomyopathy and 3-methylglutaconic aciduria.

Kvasnicka P.,Charles University
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment | Year: 2011

During the past years, the DEPFET collaboration undertook an extensive program of beam test studies as a part of the development of new generations of DEPFET pixel detectors. The beam tests in 2006, 2007 and 2008 on the CERN SPS beam have demonstrated high performance of ILC-type DEPFET matrices: S/N over 100, and spatial resolutions below 2 μm. The extensive data set of the 2008 beam test allowed us to start detailed studies of the detector properties, such as response homogeneity and resolution mapping. © 2010 Elsevier B.V. All rights reserved.

Dinicolantonio J.J.,Wegmans Pharmacy | Dinicolantonio J.J.,Charles University
International Journal of Cardiology | Year: 2013

Objective Ascertain platelet inhibition and patient outcomes (PLATO) trial conduct. Methods We examined information from the FDA complete response review. Results FDA Medical Review indicated that (1) patients on ticagrelor monitored by the study sponsor had a lower odds ratio for the primary endpoint (p = 0.0004) versus ticagrelor patients monitored by a third party Clinical Research Organisation (CRO) independent of the study sponsor, (2) a significant interaction existed between ticagrelor and regions monitored by the study sponsor for all cause mortality through study end in favor of ticagrelor (p = 0.006), (3) ticagrelor faired worse than clopidogrel when regions were monitored independent of the study sponsor by a third party Contract Research Organisation (United States, Russia and Georgia), (OR = 1.21, 95% CI: 0.91 to 1.59, p = 0.2022), (4) 46% of all primary endpoint events favoring ticagrelor came from just two countries (Poland and Hungary), (5) PLATO was easy to unblind by breaking open a clopidogrel/dummy clopidogrel tablet with at least 452 patients being unblinded prior to the database lock, (6) significantly more cardiac events submitted for clopidogrel counted in the primary analysis as a myocardial infarction (MI) compared to those submitted for ticagrelor (p < 0.0001), (7) significantly more ticagrelor subjects hospitalized after an index event/hospitalization were not being reported as having a primary event compared to clopidogrel (p = 0.002 in favor of ticagrelor), (8) site-reported MI was not significantly reduced with ticagrelor versus clopidogrel, (9) an estimated 23 definite or possible cardiovascular events or deaths on ticagrelor were either not submitted for adjudication, inactivated, deleted or were downgraded to "softer" endpoints (this was not shown in the FDA review for clopidogrel), and (10) four FDA reviewers voted for non-approval of ticagrelor. Discussion The FDA report highlights what appear to be multiple serious deficiencies in the reporting of the PLATO results, which clinicians will not have gleaned from the primary publication alone. Individual clinicians may therefore wish to carefully reconsider their practice of ticagrelor prescription for this indication. Guideline bodies should also evaluate the information in its totality. © 2013 Elsevier Ireland Ltd.

Sebesta I.,Charles University
Advances in Chronic Kidney Disease | Year: 2012

Serum uric acid concentrations are governed by the balance of urate production and excretion. Besides well-known secondary causes of hyperuricemia, such as myeloproliferative diseases, decreased renal function, and excessive dietary purine intake, there are a number of genetic disorders that result in hyper- or hypouricemia. Renal impairment in these disorders may be associated with the development of chronic kidney disease, acute kidney injury, or urate nephrolithiasis. These conditions are frequently misdiagnosed, not because the diagnosis is complicated and difficult to ascertain, but rather because of a lack of awareness of the particular condition. The first important step in the diagnosis is obtaining a detailed family history, with evaluation of serum and urinary urate concentrations. This review will aid physicians in identifying these inherited kidney disorders associated with hyperuricemia and hypouricemia. Identification of these conditions will help to explain the pathogenesis of different types of gout, and may extend insights into the urate transport and chronic kidney disease. © 2012 National Kidney Foundation, Inc.

Sonka K.,Charles University | Susta M.,Charles University
Therapeutic Advances in Neurological Disorders | Year: 2012

Central hypersomnias are diseases manifested in excessive daytime sleepiness (EDS) not caused by disturbed nocturnal sleep or misaligned circadian rhythms. Central hypersomnias includes narcolepsy with and without cataplexy, recurrent hypersomnia, idiopathic hypersomnia, with and without long sleep time, behaviorally induced insufficient sleep syndrome, hypersomnia and narcolepsy due to medical conditions, and finally hypersomnia induced by substance intake. The Epworth Sleepiness Scale is a subjective tool mostly used for EDS assessment, while the Multiple Sleep Latency Test serves as an objective diagnostic method for narcolepsy and idiopathic hypersomnias. As for symptomatic therapy of EDS, the central nervous system stimulants modafinil and methylphenidate seem to work well in most cases and in narcolepsy and Parkinson's disease; sodium oxybate also has notable therapeutic value. © 2012 The Author(s).

Vorel V.,Charles University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2016

First, we show that universality and other properties of general jumping finite automata are undecidable, which answers questions asked by Meduna and Zemek in 2012 [12]. Second, we close a study started by Černo and Mráz in 2010 [3] by proving that a clearing restarting automaton using contexts of length two can accept a binary noncontext- free language. © IFIP International Federation for Information Processing 2016.

This article presents the results of analysis of relationships between stream regulations and the geomorphic effects of floods for the case of the Blanice river basin in the Czech Republic, which was at the center of an extreme flooding event that impacted Central Europe in August 2002. The assessment is based on a geostatistical analysis of data on the distribution of flood effects and stream modifications acquired by field survey and completed by historical maps and digital cartography. Using the cluster analysis and regression tree classification, relationships between the occurrence of erosion and deposition forms, and the parameters of stream modification and general physiography were tested. The results indicate a limited relationship between stream modifications and the occurrence of geomorphic effects of the flood. The cluster analysis detected different sets of parameters linked to erosion and accumulation. The accumulation was related to physiographic properties of stream, while erosion was related to the presence of weirs in the stream segment. The regression tree classification demonstrates the potentially critical combinations of stream modifications related to the occurrence of flood effects. © 2009 Springer Science+Business Media B.V.

Farkas P.,Charles University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2016

Although vitalism, denoting a dismissed concept in biology (life sciences), is a term rooted in the late 18th century, we still may abstractly think of vitalism even today — in a very different context. The use of this term has changed in the course of centuries, and has been used across different disciplines. Reflecting texts of modern philosophers as well as architects, urban planners and thinkers, this essay is setting the term of vitalism into urban environment and aims to examine the philosophical qualities of space, rationalization, function and beauty in the 21st century. Cities are viewed here as interfaces to interact with. At the same time, Interaction Design (IxD) has tools for making the world a better place from the viewpoint of users: User-Centered Design is widely established and used term. I propose that urban vitalism may stand on qualities valued in Human-Computer Interaction (HCI) and I am trying to open paths for new concepts in understanding urban life by actualizing the patterns of interaction with the technological layer in our environments. © Springer International Publishing Switzerland 2016.

Bousova I.,Charles University | Skalova L.,Charles University
Drug Metabolism Reviews | Year: 2012

Many studies reviewed herein demonstrated the potency of some flavonoids to modulate the activity and/or expression of glutathione S-transferases (GSTs). Because GSTs play a crucial role in the detoxification of xenobiotics, their inhibition or induction may significantly affect metabolism and biological effects of many drugs, industrials, and environmental contaminants. The effect of flavonoids on GSTs strongly depends on flavonoid structure, concentration, period of administration, as well as on GST isoform and origin. Moreover, the results obtained in vitro are often contrary to the vivo results. Based on these facts, the revelation of important flavonoid-drug or flavonoid-pollutant interaction has been complicated. However, it should be borne in mind that ingestion of certain flavonoids in combination with drugs or pollutants (e.g., acetaminophen, simvastatin, cyclophosphamide, cisplatine, polycyclic aromatic hydrocarbons, chlorpyrifos, acrylamide, and isocyanates), which are GST substrates, could have significant pharmacological and toxicological consequences. Although reasonable consumptions of a flavonoids-rich diet (that may lead to GST induction) are mostly beneficial, the uncontrolled intake of high concentrations of certain flavonoids (e.g., quercetin and catechins) in dietary supplements (that may cause GST inhibition) may threaten human health. © 2012 Informa Healthcare USA, Inc.

Horvathova E.,Charles University
Ecological Economics | Year: 2012

We examine the intertemporal effect of environmental performance on financial performance and propose a method to assess the environmental performance in a fuller manner based on the weighting various pollutants according to their dangerousness to environment. Using our improved measures of environmental performance applied to the firm level data from the Czech Republic, the results suggest that while the effect of environmental performance on financial performance is negative for environmental performance lagged by 1. year lag, it becomes positive for 2. years lag. As a consequence, our findings indicate that Porter hypothesis holds in the long-run. © 2012 Elsevier B.V.

Barto L.,Charles University | Kozik M.,Jagiellonian University
Journal of the ACM | Year: 2014

We prove that constraint satisfaction problems without the ability to count are solvable by the local consistency checking algorithm. This settles three (equivalent) conjectures: Feder-Vardi [SICOMP'98], Bulatov [LICS'04] and Larose-Zádori [AU'07]. © 2014 ACM.

Stulc T.,Charles University | Sedo A.,Charles University
Diabetes Research and Clinical Practice | Year: 2010

Inhibitors of dipeptidyl peptidase-IV (DPP-IV) are a novel class of anti-diabetes drugs; inhibiting the breakdown of incretins, they increase their biological availability and decrease thus blood glucose levels. However, in addition to regulating glucose homeostasis, DPP-IV has many diverse functions, such as modulating cell growth, differentiation and transformation and immune function. Within the immune system, DPP-IV exerts mainly stimulating effects, while its relation to malignancies is highly variable. Therefore, long-term inhibition of this enzyme could have serious side effects including immune dysregulation or increased risk of cancer. Although the data on the effects of DPP-IV inhibitors in humans are scarce, the increased risk of infections and the tendency towards a higher incidence of some tumours fall in line with experimental evidence suggesting the possibility of their adverse immunological and oncological effects. Further research is obviously needed to clarify the effector mechanisms of DPP-IV inhibitors on immune function and tumour biology. Most important, however, is obtaining reassuring safety data from adequately powered, long-term trials of DPP-IV inhibitors in humans. In the meantime, all the potential risks of DPP-IV inhibitors should be kept in mind, and this class of drugs needs to be regarded with some degree of caution. © 2010 Elsevier Ireland Ltd.

Zimmermann T.,Charles University | Burda J.V.,Charles University
Dalton Transactions | Year: 2010

Interactions of hydrated cisplatin complexes cis-[Pt(NH3) 2Cl(H2O)]+ and cis-[Pt(NH3) 2(OH)(H2O)]+ with cysteine and methionine in an aqueous solution at constant pH were explored using computational methods. Thermodynamic parameters of considered reactions were studied in a broad pH range, taking up to 4 protonation states of each molecule into account. Reaction free energies at constant pH were obtained from standard Gibbs free energies using the Legendre transformation. Solvation free energies and pKa values were calculated using the PCM model with UAHF cavities, recently adapted by us for transition metal complexes. The root mean square error of pK a values on a set of model platinum complexes and amino acids was equal to 0.74. At pH 7, the transformed Gibbs free energies differ by up to 15 kcal mol-1 from the Gibbs free energies of model reactions with a constant number of protons. As for cysteine, calculations confirmed a strong preference for κS monodenate bonding in a broad pH range. The most stable product of the second reaction step, which proceeds from monodentate to chelate complex, is the κ2S,N coordinated chelate. The reaction with methionine is more complex. In the first step all three considered methionine donor atoms (N, S and O) are thermodynamically preferred products depending on the platinum complex and the pH. This is in accordance with the experimental observation of a pH dependent migration between N and S donor atoms in a chemically related system. The most stable chelates of platinum with methionine are κ2S,N and κ2N,O bonded complexes. The comparison of reaction free energies of both amino acids suggests, that the bidentate methionine ligand can be displaced even by the monodentate cysteine ligand under certain conditions. © The Royal Society of Chemistry 2010.

Kaiser R.,Charles University
Journal of Spinal Disorders and Techniques | Year: 2015

STUDY DESIGN:: Retrospective, blinded analysis of imaging studies. OBJECTIVE:: The aim of this study is compare the use of magnetic resonance imaging (MRI) to lateral radiograph using bolster in the evaluation of Scheuermann kyphosis (SK) curve flexibility measurement. SUMMARY AND BACKGROUND DATA:: The flexibility of the thoracic curve [thoracic kyphosis (TK)] in SK is of primary importance in its preoperative planning. Several methods have been described for SK curve flexibility measurement. The most commonly used method is lateral hyperextension radiography on hard bolster [hyperextension radiograph (HE)]. No current methods use MRI for flexibility assessment. MATERIALS AND METHODS:: Flexibility of TK in SK patients was measured as a difference between standing radiograph and bolster-assisted lateral HE or supine MRI. The sagittal Cobb angle of the TK was measured between the superior endplate of T4 and the inferior endplate of T12 vertebral body. Flexibilities measured by these 2 methods were compared and analyzed using the generalized estimating equation analysis and the correlation analysis. RESULTS:: We assessed 18 SK patients (14 males and 4 females) with mean age of 20.06±6.03 years. The standing TK x-rays showed 83.8±6.1 degrees. On HE, TK curve reduced by 39.3 degrees (95% confidence interval, 35.8–42.9) to 44.5±6.2 degrees (P<0.001). Preoperative MRI images showed TK of 53.8±5.9 degrees which means reduction by 30 degrees (95% confidence interval, 26.6–33.4) from the standing radiographs (P<0.001). Linear dependency between HE and MRI flexibility with a mean difference of 9.3 degrees was found (R=0.61, P<0.001). CONCLUSIONS:: Our study shows that preoperative MRI can be used for SK flexibility assessment with similar predictive value as routinely used bolster-assisted hyperextension lateral radiograph. Consequently, patient exposure to preoperative hyperextension ionizing radiation may be reduced. Copyright © 2015 Wolters Kluwer Health, Inc. All rights reserved.

Jasik J.,Charles University | Gerlich D.,Charles University | Gerlich D.,TU Chemnitz | Roithova J.,Charles University
Journal of the American Chemical Society | Year: 2014

The structure of doubly ionized benzene has been spectroscopically studied for the first time. Helium-tagged complexes were prepared at temperatures below 4 K and analyzed using infrared predissociation spectroscopy. Double ionization of benzene yields primarily high-energy dications with a six-membered-ring structure. Some of the dications undergo rearrangement to a more stable pyramidal isomer with a C5H5 base and CH at the apex. By means of isomer-selective heating by a CO2 laser, infrared predissociation spectra of both the classical and pyramidal dications were obtained. © 2014 American Chemical Society.

Repko A.,Charles University | Reinhard P.-G.,Friedrich - Alexander - University, Erlangen - Nuremberg | Nesterenko V.O.,Joint Institute for Nuclear Research | Kvasil J.,Charles University
Physical Review C - Nuclear Physics | Year: 2013

The nature of E1 low-energy strength (LES), often denoted as a "pygmy dipole resonance", is analyzed within the random-phase approximation (RPA) in 208Pb using Skyrme forces in a fully self-consistent manner. A first overview is given by the strength functions for the dipole, compressional, and toroidal operators. More detailed insight is gained by averaged transition densities and currents where the latter provide a very illustrative flow pattern. The analysis reveals clear isoscalar toroidal flow in the low-energy bin 6.0-8.8 MeV of the LES and a mixed isoscalar/isovector toroidal/compression flow in the higher bin 8.8-10.5 MeV. Thus the modes covered by LES embrace both vortical and irrotational motion. The simple collective picture of the LES as a "pygmy" mode (oscillations of the neutron excess against the nuclear core) is not confirmed. © 2013 American Physical Society.

Lin J.-P.,U.S. National Institutes of Health | Vitek L.,Charles University | Schwertner H.A.,Clinical Research
Clinical Chemistry | Year: 2010

BACKGROUND: Serum bilirubin has been consistently shown to be inversely related to cardiovascular disease (CVD). Recent studies showed serum bilirubin to be associated with CVD-related factors such as diabetes, metabolic syndrome, and body mass index. Although the association of serum bilirubin with CVD has been found in both retrospective and prospective studies, less information is available on the role of genes that control bilirubin concentrations and their association with CVD. CONTENT: In this review, we provide detailed information on the identity of the major genes that control bilirubin concentrations and their association with serum bilirubin concentrations and CVD risk. We also update the results of the major studies that have been performed on the association between serum bilirubin, CVD, and CVD-related diseases such as diabetes or metabolic syndrome. Studies consistently indicate that bilirubin concentrations are inversely associated with different types of CVD and CVD-related diseases. A conditional linkage study indicates that UGT1A1 is the major gene controlling serum bilirubin concentrations, and this finding has been confirmed in recent genomewide association studies. Studies also indicate that individuals homozygous for UGT1A1*28 have a significantly lower risk of developing CVD than carriers of the wildtype alleles. SUMMARY: Serum bilirubin has a protective effect on CVD and CVD-related diseases, and UGT1A1 is the major gene controlling serum bilirubin concentrations. Pharmacologic, nonpharmacologic, or genetic interventions that increase serum bilirubin concentrations could provide more direct evidence on the role of bilirubin in CVD prevention. © 2010 American Association for Clinical Chemistry.

Kasaova L.,Charles University
Acta medica (Hradec Králové) / Universitas Carolina, Facultas Medica Hradec Králové | Year: 2011

This study aimed to evaluate prostate volume changes and prostate motions during radiotherapy. In 2010, twenty-five patients were treated for prostate cancer by external beam radiotherapy with implanted fiducial markers. Coordinates of three gold markers on kilovoltage images were calculated daily. Volume changes in target structure were observed through changes in intermarker distances. Differences in patient position between laser-tattoo alignment and gold marker localization were evaluated. Intrafraction motion was assessed by measuring marker displacement on kilovoltage images acquired before and after fraction delivery. Prostate shrinkage was observed in 60% of patients. The average shrinkage was 7% of the prostate's initial volume. Corrections after laser-tattoo alignment remained mostly below 1 cm. The difference between marker centroid position on the actual images and the planning images was 2 +/- 1 mm on average. The extension of intrafraction movements was 7.6 +/- 0.2 mm on average. In our retrospective study, the possibility for prostate volume changes during radiotherapy was revealed. Intrafraction movements turned out to be the limiting factor in safety margin reduction.

While the effect of spatial variability on the probability of unsatisfactory performance in geotechnical applications is relativelywell understood, comparatively less attention has been given in the literature to the effects of experimental (measurement scatter) and sampling (insufficient numberof samples) uncertainties. In this paper, a general approach is developed to incorporate experimental and sampling uncertainties into probabilistic analyses based on random field methods. It is shown that, when compared with the standard approach which attributes the measured total soil variability to spatial variability, consideration of experimental uncertainty may significantly reduce the calculated probability of unsatisfactory performance. It is argued that this may be one of the reasons for an overestimation of the probability of unsatisfactory performance in geotechnical probabilistic simulations (another important reason is the spatial averaging of soil properties). Evaluation of the sampling uncertainty reveals that, although a relatively large number of samples is needed for spatial variability characterisation, a limited number of samples is sufficient to quantify the experimental uncertainty. It is pointed out that no adjustments of the existing random field-based software are needed to consider the additional uncertainties. To illustrate the proposed approach, two extensive experimental data sets on sand are presented: one reflecting total variability and the other quantifying experimental uncertainty. A hypoplastic model is calibrated against the two data sets and adopted in random field analyses of strip footing settlement. © 2015, ICE Publishing. All rights reserved.

Tashiro S.,Hiroshima University | Lanctot C.,Charles University
Nucleus | Year: 2015

The eukaryotic genome adopts in the cell nucleus a 3-dimensional configuration that varies with cell types, developmental stages and environmental condition as well as between normal and pathological states. Understanding genome function will therefore require the elucidation of the structure-function relationship of the cell nucleus as a complex, dynamic biological system, referred to as the nucleome. This exciting and timely task calls for a multi-faceted, interdisciplinary and multi-national effort. We propose the establishment of an International Nucleome Consortium to coordinate this effort worldwide. © Satoshi Tashiro and Christian Lactôot.

Kozak M.,Charles University | Trojanek F.,Charles University | Maly P.,Charles University
Optics Letters | Year: 2012

We report on time-resolved photoluminescence of a free-exciton in IIa chemical vapor deposition diamond crystal. Large difference between decay times for one- and two-photon excitation processes was observed. The longest roomtemperature exciton photoluminescence lifetime τFE = 220 ns was obtained under two-photon excitation with a photon energy of 4.7 eV. The role of diffusion and surface recombination velocity in exciton photoluminescence dynamics was studied using a new optical method based on two-photon excited time-resolved photoluminescence. The measured room-temperature value of diffusion coefficient in diamond was D = 40 cm 2/s. © 2012 Optical Society of America.

Branis M.,Charles University | Safranek J.,Charles University
Environmental Research | Year: 2011

We investigated the mass concentration, mineral composition and morphology of particles resuspended by children during scheduled physical education in urban, suburban and rural elementary school gyms in Prague (Czech Republic). Cascade impactors were deployed to sample the particulate matter. Two fractions of coarse particulate matter (PM10-2.5 and PM2.5-1.0) were characterized by gravimetry, energy dispersive X-ray spectrometry and scanning electron microscopy. Two indicators of human activity, the number of exercising children and the number of physical education hours, were also recorded. Lower mass concentrations of coarse particulate matter were recorded outdoors (average PM10-2.5 4.1-7.4γgm-3 and PM2.5-1.0 2.0-3.3γgm-3) than indoors (average PM10-2.5 13.6-26.7γgm-3 and PM2.5-1.0 3.7-7.4γgm-3). The indoor concentrations of coarse aerosol were elevated during days with scheduled physical education with an average indoor-outdoor (I/O) ratio of 2.5-16.3 for the PM10-2.5 and 1.4-4.8 for the PM2.5-1.0 values. Under extreme conditions, the I/O ratios reached 180 (PM10-2.5) and 19.1 (PM2.5-1.0). The multiple regression analysis based on the number of students and outdoor coarse PM as independent variables showed that the main predictor of the indoor coarse PM concentrations is the number of students in the gym. The effect of outdoor coarse PM was weak and inconsistent. The regression models for the three schools explained 60-70% of the particular dataset variability. X-ray spectrometry revealed 6 main groups of minerals contributing to resuspended indoor dust. The most abundant particles were those of crustal origin composed of Si, Al, O and Ca. Scanning electron microscopy showed that, in addition to numerous inorganic particles, various types of fibers and particularly skin scales make up the main part of the resuspended dust in the gyms. In conclusion, school gyms were found to be indoor microenvironments with high concentrations of coarse particulate matter, which can contribute to increased short-term inhalation exposure of exercising children. © 2011 Elsevier Inc.

Slama J.,Charles University | Dundr P.,Charles University | Dusek L.,Masaryk University | Cibula D.,Charles University
Gynecologic Oncology | Year: 2013

Objectives: Metastatic involvement of the sentinel nodes (SN) is one of the main prognostic factors in cervical cancer which determines the disease management. The results of intra-operative SN examination would make it possible to triage patients in a one-step protocol. The studies carried out on the subject so far have, however, failed to demonstrate adequate accuracy of frozen section examination (FS) and, moreover, they only involved small cohorts. Methods: The study included 225 patients with cervical cancer FIGO IA2-IIB in whom at least one SN has been detected and intra-operatively processed. The prevalence of macrometastases, micrometastases and isolated tumour cells (ITC) in the SN was evaluated and the results of FS and final SN ultrastaging were compared. Results: Metastatic involvement of the SN was detected by pathologic ultrastaging in 73 cases (32.4%); macrometastases, micrometastases and ITC were found in 48, 17 and 8 patients, respectively. Intra-operative SN assessment established the SN status correctly in as few as 41 cases (56.2%), or in 49 cases (63%) if ITC had been excluded. Final ultrastaging of intra-operatively negative SN confirmed macrometastases, micrometastases, and ITC in additional 8, 18 and 8 patients, respectively. The false negative rate of FS was higher in bigger tumours (> 20 cm3) and in the presence of LVSI. Conclusions: Frozen section examination of SN is not sufficiently reliable; it has a high false negative rate mainly due to its limited ability to detect micrometastases. A possible solution would be a more detailed intra-operative pathologic processing or two-step surgical management. © 2013 Elsevier Inc. All rights reserved.

Kvacek Z.,Charles University
Bulletin of Geosciences | Year: 2010

An attempt is made to follow the extent of forest types during the Palaeocene and Eocene in time and space over Europe. Problems that hinder producing more detailed maps of potential Eocene vegetation are the different palaeogeographic configuration of land and sea and changing relief due to orogeny, the variation in global climate, atmospheric circulation and the world ocean. The early Palaeogene palaeofloristic sites in Europe are widely spaced and the data so far obtained are of varying quality from one site to another. The differences between zonal, intrazonal (azonal) and extrazonal formations and impact of precipitation must be considered. Objective definitions of units based on diversity percentages of components are still to be elaborated. The macropalaeobotanical data thus far available allow us to distinguish intuitively three zonal vegetation types: 1) Broad-leaved evergreen/semi-evergreen quasi-paratropical forest with a high diversity of woody angiosperms related to tropical families, ferns and a low diversity of conifers (mostly Doliostrobus), 2) Broad-leaved nothophyllous evergreen forest with evergreen Fagaceae, Lauraceae, Altingiaceae, Myrtaceae and some conifers (Pinus, Doliostrobus, Cephalotaxus) and 3) Polar deciduous to mixed mesophytic forest with well diversified angiosperms predominantly deciduous and moderate representation of Ginkgo, conifers and ferns. Intrazonal (azonal) formations include riparian gallery forests, coal-forming swamp forests, and poorly developed mangroves with marginal freshwater wetland/aquatic vegetation. The Eocene extrazonal vegetation is less distinct in Europe, consisting probably of pine forests in high mountains and lowland sclerophyllous scrub on specific substrates.

Masin D.,Charles University
International Journal for Numerical and Analytical Methods in Geomechanics | Year: 2010

The paper presents an approach to predicting variation of a degree of saturation in unsaturated soils with void ratio and suction. The approach is based on the effective stress principle for unsaturated soils and several underlying assumptions. It focuses on the main drying and wetting processes and does not incorporate the effects of hydraulic hysteresis. It leads to the dependency of water retention curve (WRC) on void ratio, which does not require any material parameters apart from the parameters specifying WRC for the reference void ratio. Its validity is demonstrated by comparing predictions with the experimental data on four different soils taken over from the literature. Good correlation between the measured and predicted behaviour indirectly supports applicability of the effective stress principle for unsaturated soils. Copyright © 2009 John Wiley & Sons, Ltd.

We deal with the problem of an investor who is using a mean-risk model for accessing efficiency of investment opportunities. Our investor employs value at risk on several risk levels at the same time which corresponds to the approach called risk shaping. We review several data envelopment analysis (DEA) models which can deal with negative data. We show that a diversification–consistent extension of the DEA models based on a directional distance measure can be used to identify the Pareto–Koopmans efficient investment opportunities. We derive reformulations as chance constrained, nonlinear and mixed-integer problems under particular assumptions. In the numerical study, we access efficiency of US industry representative portfolios based on empirical distribution of random returns. We employ bootstrap and jackknife to investigate the empirical properties of the efficiency estimators. © 2015, Springer-Verlag Berlin Heidelberg.

Schulz J.,Charles University | Jasikova L.,Charles University | Skriba A.,Charles University | Roithova J.,Charles University
Journal of the American Chemical Society | Year: 2014

The gas phase structures of gold(I) complexes formed by intermolecular oxidation of selected terminal (phenylacetylene) and internal alkynes (2-butyne, 1-phenylpropyne, diphenylacetylene) were investigated using tandem mass spectrometry and ion spectroscopy in conjunction with quantum-chemical calculations. The experiments demonstrated that the primarily formed β-gold(I) vinyloxypyridinium complexes readily undergo rearrangement, dependent on their substituents, to either gold(I) α-oxo carbenenoids (a synthetic surrogate of the α-oxo carbenes) or pyridine adducts of gold(I) enone complexes in the condensed phase and that the existence of naked α-oxo carbenes is highly improbable. Isotopic labeling experiments performed with the reaction mixtures clearly linked the species that exist in solution to the ions transferred to the gas phase. The ions were then fully characterized by CID experiments and IRMPD spectroscopy. The conclusions based on the experimental observations perfectly correspond with the results from quantum-chemical calculations. © 2014 American Chemical Society.

Amlerova J.,Charles University
Epilepsy & behavior : E&B | Year: 2012

Hyperfamiliarity is a type of paramnesia characterized by an increased feeling of familiarity to unfamiliar faces. This dysfunction has been associated with frontal and temporal lobe pathology. The study investigated hyperfamiliarity in patients with temporal lobe epilepsy (TLE) by assessing their ability to recognize both familiar and unfamiliar faces. We evaluated 61 patients with pharmacoresistant TLE (33 right-sided, 28 left-sided) and 16 controls. The ability to recognize familiar faces was similar in patients and controls, although patients with left-sided TLE showed poorer performance in familiar face naming compared to both right-sided TLE patients and controls. Hyperfamiliarity was observed in a significantly higher number of patients with TLE compared to controls; in subgroup analysis, only right-sided TLE patients expressed hyperfamiliarity. Overall, patients with right-sided TLE showed more severe impairment compared to patients with left-sided TLE. It is proposed that hyperfamiliarity can be a relatively common symptom in patients with treatment-refractory TLE and right-sided focus. Copyright © 2012 Elsevier Inc. All rights reserved.

Lencova E.,Charles University
Acta medica academica | Year: 2013

To characterize the oral health-related attitudes and behaviour of Czech parents of preschool children. A representative sample of 796 parents was recruited for the cross-sectional questionnaire survey. Study data were collected using a validated questionnaire with 44 attitudinal items related to different aspects of caries prevention. The data were analyzed by explorative factor analysis, extracted factors were subjected to reliability analysis and Kruskal-Wallis ANOVA was used to test differences in the factor scores in respondents with different levels of education and self-perceived SES. The factor analysis extracted 3 factors, labelled "Toothbrushing - perceived significance and parental efficacy" ; "External caries control" and "Internal caries control". They explained 28.9% of the data variability. The comparison of the factor scores in groups with different SES and education of mothers showed highly significant differences. For all three factors, median values of the aggregated Likert scale increased with increasing SES and education of the mother. The parents report that they are aware of their responsibility for the prevention of tooth decay in their children. In caries prevention they concentrate on toothbrushing. Dietary measures do not seem to be of similar importance to them. The increasing self-perceived SES of the family and the education level of the mother have a significantly positive effect on the caries-preventive attitudes of the parents. Based on the study results, the message to the public health sector in the Czech Republic should include the need to highlight the importance of a non-cariogenic diet and the role of fluorides in caries prevention. Copyright © 2013 by Academy of Sciences and Arts of Bosnia and Herzegovina.

Ovesleova H.,Charles University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2016

Lately, elearning has been making a comeback not only in business education of global corporations but in academia as well. Offer of classes for masses of population, regardless of time, place or social status, has become a norm in great world centers of learning. One of the most respected MOOC portals, Coursera, joins 138 partners from over 28 countries in its portfolio. Majority of universities offer a comprehensive portfolio of open or paid courses of wide range of specialization, from technical fields to humanities. Rising popularity of this type of education is well documented by the number of students, which reaches 17.5 million [1]. This way, even those whose life circumstances do not allow them to become full-time students can take part in classes. This form of education also enables suitable social conditions for inclusion, which is a welcomed bonus in current situation of population exodus. In the Czech Republic, MOOC projects are among top priorities of the Ministry of Education for 2016 [2]. Design of education systems and applications has undergone distinctive changes lately. Modern technologies, such as mobile and wearable technologies, cloud services and global expansion of the Internet make education accessible for almost anybody and make it largely available. Structure of users and their learning activities expand, which logically brings about a call for better personalization of learning environment. This paper examines what role the user interface plays in the learning process and what requirements on management system the education process reflects. © Springer International Publishing Switzerland 2016.

Rosero A.,Charles University | Zarsky V.,Charles University | Zarsky V.,Academy of Sciences of the Czech Republic | Cvrckova F.,Charles University
Journal of Experimental Botany | Year: 2013

Plant cell growth and morphogenesis depend on remodelling of both actin and microtubule cytoskeletons. AtFH1 (At5g25500), the main housekeeping Arabidopsis formin, is targeted to membranes and known to nucleate and bundle actin. The effect of mutations in AtFH1 on root development and cytoskeletal dynamics was examined. Consistent with primarily actin-related formin function, fh1 mutants showed increased sensitivity to the actin polymerization inhibitor latrunculin B (LatB). LatB-treated mutants had thicker, shorter roots than wild-type plants. Reduced cell elongation and morphological abnormalities were observed in both trichoblasts and atrichoblasts. Fluorescently tagged cytoskeletal markers were used to follow cytoskeletal dynamics in wild-type and mutant plants using confocal microscopy and VAEM (variable-angle epifluorescence microscopy). Mutants exhibited more abundant but less dynamic F-actin bundles and more dynamic microtubules than wild-type seedlings. Treatment of wild-type seedlings with a formin inhibitor, SMIFH2, mimicked the root growth and cell expansion phenotypes and cytoskeletal structure alterations observed in fh1 mutants. The results suggest that besides direct effects on actin organization, the in vivo role of AtFH1 also includes modulation of microtubule dynamics, possibly mediated by actin-microtubule cross-talk. © 2012 © 2012 The Authors.

Sgall J.,Charles University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2012

We give a simple proof and a generalization of the classical result which says that the (asymptotic) approximation ratio of BestFit algorithm is 1.7. We generalize this result to a wide class of algorithms that are allowed to pack the incoming item to any bin with load larger than 1/2 (if it fits), instead to the most full bin, and at the same time this class includes the bounded-space variants of these algorithms. © 2012 Springer-Verlag Berlin Heidelberg.

Angulithes galea (Fritsch in Fritsch & Schlönbach, 1872) and Angulithes westphalicus (Schlüter, 1872) are representatives of Angulithes Montfort, 1808, occurring in the Late Cretaceous of Europe, from the Late Turonian to the Late Campanian. Following examination of the majority of specimens representing these species and their specific morphology, a detailed revision was made. Both species undergo significant morphological changes during their ontogeny, changing the shape of the ventral side and whorl cross-section attended by onset and loss of ventral keel and changing of the shell surface (by A. galea). Comparing these changes with the ontogeny of recent Nautilus suggests they are expressions of the approach and attainment of maturity. Due to this comparison, comparable changes in other taxa can be similarly interpreted, e.g. representatives of the genus Deltocymatoceras. The changes undergone by A. galea are at maturity accompanied by additional features such as strong radial ribbing, which is comparable with the ribbing in Deltocymatoceras. The affinity (ventral keel, suture, ontogeny and stratigraphy) of this genus with Angulithes is a topic for discussion.

Prusa D.,Czech Technical University | Mraz F.,Charles University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2012

We present a new model of a two-dimensional computing device called sgraffito automaton and demonstrate its significance. In general, the model is simple, allows a clear design of important computations and defines families exhibiting good properties. It does not exceed the power of finite-state automata when working over one-dimensional inputs. On the other hand, it induces a family of picture languages that strictly includes REC and the deterministic variant recognizes languages in DREC as well as those accepted by four-way automata. © 2012 Springer-Verlag.

Sukova P.,Charles University | Semerak O.,Charles University
Monthly Notices of the Royal Astronomical Society | Year: 2013

We continue the study of time-like geodesic dynamics in exact static, axially and reflection symmetric space-times describing the fields of a Schwarzschild black hole surrounded by thin discs or rings. In the first paper of this series, the rise (and decline) of geodesic chaos with ring/disc mass and position and with test particle energy was revealed on Poincaré sections and on time series of position or velocity and their power spectra. In the second paper, we compared these results with those obtained by two recurrence methods, focusing on 'sticky' orbits whose different parts show different degrees of chaoticity. Here, we complement the analysis by using several Lyapunov-type coefficients which quantify the rate of orbital divergence. After comparing the results with those obtained by the previous methods, we specifically consider a system involving a black hole surrounded by a small thin disc or a large ring, having in mind the configuration which probably occurs in galactic nuclei. Within the range of parameters which roughly corresponds to our Galactic centre, we found that the black hole accretion disc does not have a significant gravitational effect on the dynamics of free motion at larger radii, while the inner circumnuclear molecular ring (concentrated above 1 pc radius) can only induce some irregularity in motion of stars ('particles') on smaller radii if its mass reaches 10 to 30 per cent of the central black hole (which is the upper estimate given in the literature), if it is sufficiently compact (which does not hold but maybe for its inner rim) and if the stars can get to its close vicinity. The outer dust ring between 60 and 100 pc appears to be less important for the geodesic dynamics in its interior. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Bar T.,Labonnet Ltd. | Kubista M.,TATAA Biocenter | Kubista M.,Academy of Sciences of the Czech Republic | Tichopad A.,Academy of Sciences of the Czech Republic | Tichopad A.,Charles University
Nucleic Acids Research | Year: 2012

Quantitative real-time PCR (qPCR) is the method of choice for specific and sensitive quantification of nucleic acids. However, data validation is still a major issue, partially due to the complex effect of PCR inhibition on the results. If undetected PCR inhibition may severely impair the accuracy and sensitivity of results. PCR inhibition is addressed by prevention, detection and correction of PCR results. Recently, a new family of computational methods for the detection of PCR inhibition called kinetics outlier detection (KOD) emerged. KOD methods are based on comparison of one or a few kinetic parameters describing a test reaction to those describing a set of reference reactions. Modern KOD can detect PCR inhibition reflected by shift of the amplification curve by merely half a cycle with specificity and sensitivity >90. Based solely on data analysis, these tools complement measures to improve and control pre-analytics. KOD methods do not require labor and materials, do not affect the reaction accuracy and sensitivity and they can be automated for fast and reliable quantification. This review describes the background of KOD methods, their principles, assumptions, strengths and limitations. Finally, the review provides recommendations how to use KOD and how to evaluate its performance. © 2012 The Author(s).

Elias M.,University of Ostrava | Elias M.,Charles University | Brighouse A.,University of Cambridge | Gabernet-Castello C.,University of Cambridge | And 2 more authors.
Journal of Cell Science | Year: 2012

The presence of a nucleus and other membrane-bounded intracellular compartments is the defining feature of eukaryotic cells. Endosymbiosis accounts for the origins of mitochondria and plastids, but the evolutionary ancestry of the remaining cellular compartments is incompletely documented. Resolving the evolutionary history of organelle-identity encoding proteins within the endomembrane system is a necessity for unravelling the origins and diversification of the endogenously derived organelles. Comparative genomics reveals events after the last eukaryotic common ancestor (LECA), but resolution of events prior to LECA, and a full account of the intracellular compartments present in LECA, has proved elusive. We have devised and exploited a new phylogenetic strategy to reconstruct the history of the Rab GTPases, a key family of endomembrane-specificity proteins. Strikingly, we infer a remarkably sophisticated organellar composition for LECA, which we predict possessed as many as 23 Rab GTPases. This repertoire is significantly greater than that present in many modern organisms and unexpectedly indicates a major role for secondary loss in the evolutionary diversification of the endomembrane system. We have identified two Rab paralogues of unknown function but wide distribution, and thus presumably ancient nature; RabTitan and RTW. Furthermore, we show that many Rab paralogues emerged relatively suddenly during early metazoan evolution, which is in stark contrast to the lack of significant Rab family expansions at the onset of most other major eukaryotic groups. Finally, we reconstruct higher-order ancestral clades of Rabs primarily linked with endocytic and exocytic process, suggesting the presence of primordial Rabs associated with the establishment of those pathways and giving the deepest glimpse to date into pre-LECA history of the endomembrane system. © 2012. Published by The Company of Biologists Ltd.

Declerck P.,Charles University
Environmental Microbiology | Year: 2010

Legionella pneumophila, the aetiological agent of 90% of legionellosis cases, is a common inhabitant of natural and anthropogenic freshwater environments, where it resides in biofilms. Biofilms are defined as complex, natural assemblages of microorganisms that involve a multitude of trophic interactions. A thorough knowledge and understanding of Legionella ecology in relation to biofilm communities is of primary importance in the search for innovative and effective control strategies to prevent the occurrence of disease cases. This review provides a critical update on the state-of-the-art progress in understanding the mechanisms and factors affecting the biofilm life cycle of L. pneumophila. Particular emphasis is given to discussing the different strategies this human pathogen uses to grow and retain itself in biofilm communities. Biofilms develop not only at solid-water interfaces (substrate-associated biofilms), but also at the water-air interface (floating biofilms). Disturbance of the water surface can lead to liberation of aerosols derived from the floating biofilm into the atmosphere that allow transmission of biofilm-associated pathogens over considerable distances. Recent data concerning the occurrence and replication of L. pneumophila in floating biofilms are also elaborated and discussed. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

PruSa V.,Charles University | Rajagopal K.R.,Texas A&M University
Journal of Non-Newtonian Fluid Mechanics | Year: 2012

Starting with an implicit constitutive relation between the stress and relative deformation gradient histories to describe the response of a fluid, and using the assumption of fading memory, we show that both rate type and differential type fluid representations can be obtained, as approximations in retarded motions, that have the same form as the Maxwell, Oldroyd-B, Rivlin-Ericksen, and other popular fluid models. This result provides further evidence that the recently proposed implicit constitutive framework provides a very robust and general methodology to describe fluid response. Thus, fluids defined through an implicit constitutive relation between the stress and relative deformation gradient histories can be seen as an appropriate generalization of the notion of simple fluids and rate type fluids. © 2012.

Benakova N.,Charles University
Acta Dermatovenerologica Croatica | Year: 2011

This article reviews recent literature on phototherapy for psoriasis, particularly narrowband UVB. The efficacy, safety, tolerability and acceptance of phototherapy are discussed. It focuses in detail on how to improve the efficacy and safety in practice by trying to optimize the protocols, using combination therapy, monitoring the cumulative dose and providing skin cancer surveillance. Careful patient selection, individualized treatment, long-term therapy plan and complex approach to patients are the prerequisites for this. Narrowband UVB as the most widely used modality of phototherapy for psoriasis has a relatively good efficacy, cost, availability and minimal side effects. It represents a valuable treatment, which deserves more utilization and research. Although not so dynamic as in systemic drugs, research into phototherapy is ongoing. Even in the era of biologics, phototherapy remains an important therapeutic modality for psoriasis and other dermatoses and represents an essential part of modern dermatological therapy.

Fox R.J.,Cleveland Clinic | Miller D.H.,University College London | Phillips J.T.,Baylor Research Institute | Hutchinson M.,Park University | And 8 more authors.
New England Journal of Medicine | Year: 2012

BACKGROUND: BG-12 (dimethyl fumarate) is in development as an oral treatment for relapsing-remitting multiple sclerosis, which is commonly treated with parenteral agents (interferon or glatiramer acetate). METHODS: In this phase 3, randomized study, we investigated the efficacy and safety of oral BG-12, at a dose of 240 mg two or three times daily, as compared with placebo in patients with relapsing-remitting multiple sclerosis. An active agent, glatiramer acetate, was also included as a reference comparator. The primary end point was the annualized relapse rate over a period of 2 years. The study was not designed to test the superiority or noninferiority of BG-12 versus glatiramer acetate. RESULTS: At 2 years, the annualized relapse rate was significantly lower with twice-daily BG-12 (0.22), thrice-daily BG-12 (0.20), and glatiramer acetate (0.29) than with placebo (0.40) (relative reductions: twice-daily BG-12, 44%, P<0.001; thrice-daily BG-12, 51%, P<0.001; glatiramer acetate, 29%, P = 0.01). Reductions in disability progression with twice-daily BG-12, thrice-daily BG-12, and glatiramer acetate versus placebo (21%, 24%, and 7%, respectively) were not significant. As compared with placebo, twicedaily BG-12, thrice-daily BG-12, and glatiramer acetate significantly reduced the numbers of new or enlarging T 2-weighted hyperintense lesions (all P<0.001) and new T 1-weighted hypointense lesions (P<0.001, P<0.001, and P = 0.002, respectively). In post hoc comparisons of BG-12 versus glatiramer acetate, differences were not significant except for the annualized relapse rate (thrice-daily BG-12), new or enlarging T 2-weighted hyperintense lesions (both BG-12 doses), and new T 1-weighted hypointense lesions (thrice-daily BG-12) (nominal P<0.05 for each comparison). Adverse events occurring at a higher incidence with an active treatment than with placebo included flushing and gastrointestinal events (with BG-12) and injection-related events (with glatiramer acetate). There were no malignant neoplasms or opportunistic infections reported with BG-12. Lymphocyte counts decreased with BG-12. CONCLUSIONS: In patients with relapsing-remitting multiple sclerosis, BG-12 (at both doses) and glatiramer acetate significantly reduced relapse rates and improved neuroradiologic outcomes relative to placebo. (Funded by Biogen Idec; CONFIRM number, NCT00451451.) Copyright © 2012 Massachusetts Medical Society.