Turku, Finland
Turku, Finland

The University of Turku , located in Turku in southwestern Finland, is the second largest university in the country as measured by student enrollment, after University of Helsinki. It was established in 1920 and also has faculties at Rauma, Pori and Salo. The university is a member of the Coimbra Group. Wikipedia.


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The invention is based on a finding that silencing CIP2A (KIAA1524) gene sensitizes cancer cells for apoptosis-inducing activity of certain small molecule chemotherapeutic agents. Thus, the invention is directed to a respective combination therapy, sensitization method and pharmaceutical compositions. The invention further relates to a method of selecting cancer therapy for a subject on the basis of CIP2A and p53 expression and/or protein activity in a sample obtained from said subject.


Heinosaari T.,University of Turku | Miyadera T.,Kyoto University
Journal of Physics A: Mathematical and Theoretical | Year: 2017

Two quantum channels are called compatible if they can be obtained as marginals from a single broadcasting channel; otherwise they are incompatible. We derive a characterization of the compatibility relation in terms of concatenation and conjugation, and we show that all pairs of sufficiently noisy quantum channels are compatible. The complement relation of incompatibility can be seen as a unifying aspect for several important quantum features, such as impossibility of universal broadcasting and unavoidable measurement disturbance. We show that the concepts of entanglement breaking channel and antidegradable channel can be completely characterized in terms compatibility. © 2017 IOP Publishing Ltd.


Intestinal-type adenocarcinoma is the second most frequent sinonasal adenocarcinoma. High incidence of these tumors is seen among workers with occupational wood dust exposure, particularly of hardwood dusts. Intestinal-type adenocarcinoma has striking histomorphologic and immunophenotypic similarities with colorectal adenocarcinomas, but on the level of molecular pathologic mechanisms these tumors have their own specific features different from gastrointestinal tumors. This article provides an update on current histopathologic classification of intestinal-type adenocarcinomas, their immunophenotypic properties, recent advances in molecular pathologic features and differential diagnostic considerations. © 2017 The Author(s)


It is often argued that the fact that intellectual objects-objects like ideas, inventions, concepts, and melodies-can be used by several people simultaneously makes intellectual property rights impossible or particularly difficult to morally justify. In this article, I assess the line of criticism of intellectual ownership in connection with a central category of intellectual property rights, economic rights to intellectual property. I maintain that it is unconvincing.


Nyberg H.,University of Turku
Journal of Forecasting | Year: 2017

This paper introduces a regime switching vector autoregressive model with time-varying regime probabilities, where the regime switching dynamics is described by an observable binary response variable predicted simultaneously with the variables subject to regime changes. Dependence on the observed binary variable distinguishes the model from various previously proposed multivariate regime switching models, facilitating a handy simulation-based multistep forecasting method. An empirical application shows a strong bidirectional predictive linkage between US interest rates and NBER business cycle recession and expansion periods. Due to the predictability of the business cycle regimes, the proposed model yields superior out-of-sample forecasts of the US short-term interest rate and the term spread compared with the linear and nonlinear vector autoregressive (VAR) models, including the Markov switching VAR model. © 2017 John Wiley & Sons, Ltd.


Mulo P.,University of Turku | Medina M.,University of Zaragoza
Photosynthesis Research | Year: 2017

Ferredoxin–NADP+ reductase (FNR) catalyzes the last step of linear electron transfer in photosynthetic light reactions. The FAD cofactor of FNR accepts two electrons from two independent reduced ferredoxin molecules (Fd) in two sequential steps, first producing neutral semiquinone and then the fully anionic reduced, or hydroquinone, form of the enzyme (FNRhq). FNRhq transfers then both electrons in a single hydride transfer step to NADP+. We are presenting the recent progress in studies focusing on Fd:FNR interaction and subsequent electron transfer processes as well as on interaction of FNR with NADP+/H followed by hydride transfer, both from the structural and functional point of views. We also present the current knowledge about the physiological role(s) of various FNR isoforms present in the chloroplasts of higher plants and the functional impact of subchloroplastic location of FNR. Moreover, open questions and current challenges about the structure, function, and physiology of FNR are discussed. © 2017 Springer Science+Business Media Dordrecht


Isolauri E.,University of Turku
Nestle Nutrition Institute Workshop Series | Year: 2017

Obesity is globally the most prevalent nutritional disorder. Multifaceted therapeutic approaches are called for to halt the cascade from neonatal adiposity/high birth weight to childhood excessive weight gain/adult obesity with comorbidities. Recent experimental and clinical data provide one new target for interventions aiming to close this vicious circle: the microbiota. An aberrant gut microbiota, dysbiosis, induces immune and metabolic disturbances both locally and, consequent upon impaired gut barrier function, also systemic low-grade inflammation, which is causally linked to insulin resistance. The gut microecology could thus fill the gap between energy intake and expenditure by processing nutrients and regulating their access to and storage in the body, producing chemicals of hormonal nature and controlling the secretion of proinflammatory mediators locally and systemically. Conversely, being highly sensitive to environmental impacts, particularly to early feeding, the compositional development of the gut microbiota may prove the target of choice in efforts to reduce the risk of obesity. It has been demonstrated that a lower number of bifidobacteria precedes the development of obesity, and a dearth of butyrate-producing bacteria and an overall richness of bacteria increase the risk of metabolic disease; moreover, recognition that practices known to disrupt the early gut microbiota, e.g., cesarean section delivery and antibiotic exposure, contribute to obesity, encourages to pursue this line of research. © 2017 Nestec Ltd., Vevey/S. Karger AG, Basel.


Salminen S.,University of Turku
Nestle Nutrition Institute Workshop Series | Year: 2017

Human milk oligosaccharides are key components of human milk and appear in various compositions and concentrations in all human milks. In regulatory sense human milk oligosaccharides are classified as novel foods or novel food ingredients requiring safety assessment. In addition, if any health messages are intended to be used also health claim regulations apply. This chapter reviews the regulatory settings and studies human milk oligosaccharides are required to fulfill to be able to enter markets in European Union or United States or elsewhere. Examples include Lacto-N-neotetraose and 2-fucosyllactose with safety assessment in European Union and United States. © 2017 Nestec Ltd., Vevey/S. Karger AG, Basel.


Rautava S.,University of Turku
Nestle Nutrition Institute Workshop Series | Year: 2017

Early-life interaction with indigenous intestinal microbes is a prerequisite for healthy immune and metabolic maturation. Human infants acquire their gut microbiota predominantly from the mother. A considerable inoculum of microbes is received by the neonate during vaginal delivery. Recent observations suggest that human gut colonization may be initiated prenatally by microbes in amniotic fluid, but the significance of this phenomenon remains unknown. After birth, neonatal gut colonization is guided by human milk factors, which selectively promote the growth of specific microbes, as well as by live microbes present in human milk. Aberrant gut colonization in early life has been associated with an increased risk of noncommunicable diseases in later life. Epidemiological and experimental studies suggest a causal relationship between early-life gut microbiota perturbations and disease risk. Perinatal antibiotic exposure, cesarean section delivery, postnatal antibiotic administration, and formula feeding, which may disrupt intestinal microecology, have been associated with disease development in later life. The modulation of gut microbiota in the perinatal period by pre- and probiotics, for example, may offer a means to reduce the risk of chronic diseases. © 2017 Nestec Ltd., Vevey/S. Karger AG, Basel.


Grabsztunowicz M.,University of Turku | Koskela M.M.,University of Turku | Mulo P.,University of Turku
Frontiers in Plant Science | Year: 2017

Post-translational modifications (PTMs) of proteins enable fast modulation of protein function in response to metabolic and environmental changes. Phosphorylation is known to play a major role in regulating distribution of light energy between the Photosystems (PS) I and II (state transitions) and in PSII repair cycle. In addition, thioredoxin-mediated redox regulation of Calvin cycle enzymes has been shown to determine the efficiency of carbon assimilation. Besides these well characterized modifications, recent methodological progress has enabled identification of numerous other types of PTMs in various plant compartments, including chloroplasts. To date, at least N-terminal and Lys acetylation, Lys methylation, Tyr nitration and S-nitrosylation, glutathionylation, sumoylation and glycosylation of chloroplast proteins have been described. These modifications impact DNA replication, control transcriptional efficiency, regulate translational machinery and affect metabolic activities within the chloroplast. Moreover, light reactions of photosynthesis as well as carbon assimilation are regulated at multiple levels by a number of PTMs. It is likely that future studies will reveal new metabolic pathways to be regulated by PTMs as well as detailed molecular mechanisms of PTM-mediated regulation. © 2017 Grabsztunowicz, Koskela and Mulo.


Poutanen J.,University of Turku | Poutanen J.,KTH Royal Institute of Technology
Astrophysical Journal | Year: 2017

Rosseland mean opacity plays an important role in theories of stellar evolution and X-ray burst models. In the high-temperature regime, when most of the gas is completely ionized, the opacity is dominated by Compton scattering. Our aim here is to critically evaluate previous works on this subject and to compute the exact Rosseland mean opacity for Compton scattering over a broad range of temperature and electron degeneracy parameter. We use relativistic kinetic equations for Compton scattering and compute the photon mean free path as a function of photon energy by solving the corresponding integral equation in the diffusion limit. As a byproduct we also demonstrate the way to compute photon redistribution functions in the case of degenerate electrons. We then compute the Rosseland mean opacity as a function of temperature and electron degeneracy and present useful approximate expressions. We compare our results to previous calculations and find a significant difference in the low-temperature regime and strong degeneracy. We then proceed to compute the flux mean opacity in both free-streaming and diffusion approximations, and show that the latter is nearly identical to the Rosseland mean opacity. We also provide a simple way to account for the true absorption in evaluating the Rosseland and flux mean opacities. © 2017. The American Astronomical Society. All rights reserved..


Lilja J.,University of Turku
Nature Cell Biology | Year: 2017

SHANK3, a synaptic scaffold protein and actin regulator, is widely expressed outside of the central nervous system with predominantly unknown function. Solving the structure of the SHANK3 N-terminal region revealed that the SPN domain is an unexpected Ras-association domain with high affinity for GTP-bound Ras and Rap G-proteins. The role of Rap1 in integrin activation is well established but the mechanisms to antagonize it remain largely unknown. Here, we show that SHANK1 and SHANK3 act as integrin activation inhibitors by sequestering active Rap1 and R-Ras via the SPN domain and thus limiting their bioavailability at the plasma membrane. Consistently, SHANK3 silencing triggers increased plasma membrane Rap1 activity, cell spreading, migration and invasion. Autism-related mutations within the SHANK3 SPN domain (R12C and L68P) disrupt G-protein interaction and fail to counteract integrin activation along the Rap1–RIAM–talin axis in cancer cells and neurons. Altogether, we establish SHANKs as critical regulators of G-protein signalling and integrin-dependent processes. © 2017 Nature Publishing Group


Tynkkynen N.,University of Turku
Marine Policy | Year: 2017

The EU enlargement brought the Baltic Sea into the sphere of EU environmental policymaking, making the sea, with the exception of Russia, an EU inland sea. Yet, the state of the Baltic Sea environment is deteriorating at an alarming pace. This paper describes the evolution of the EU governance of the Baltic Sea environment, focussing on governance barriers. The findings demonstrate how the choice of analytical lens influences the construction of governance barriers and the respective intervention strategies. Such understanding can help policy practitioners in their search for successful measures to improve the governance situation in the Baltic Sea region. © 2017 Elsevier Ltd


Abolmasov P.,University of Turku | Abolmasov P.,Moscow State University | Poutanen J.,University of Turku | Poutanen J.,KTH Royal Institute of Technology
Monthly Notices of the Royal Astronomical Society | Year: 2017

The GeV-range spectra of blazars are shaped not only by non-thermal emission processes internal to the relativistic jet but also by external pair-production absorption on the thermal emission of the accretion disc and the broad-line region (BLR). For the first time, we compute here the pair-production opacities in the GeV range produced by a realistic BLR accounting for the radial stratification and radiation anisotropy. Using photoionization modelling with the CLOUDY code, we calculate a series of BLR models of different sizes, geometries, cloud densities, column densities and metallicities. The strongest emission features in the model BLR are Ly α and He II Ly α. Contribution of recombination continua is smaller, especially for hydrogen, because Ly continuum is efficiently trapped inside the large optical depth BLR clouds and converted to Lyman emission lines and higher order recombination continua. The largest effects on the gamma-ray opacity are produced by the BLR geometry and localization of the gamma-ray source. We show that when the gamma-ray source moves further from the central source, all the absorption details move to higher energies and the overall level of absorption drops because of decreasing incidence angles between the gamma-rays and BLR photons. The observed positions of the spectral breaks can be used to measure the geometry and the location of the gamma-ray emitting region relative to the BLR. Strong dependence on geometry means that the soft photons dominating the pair-production opacity may be actually produced by a different population of BLR clouds than the bulk of the observed broad line emission. © 2016 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society.


Molkov S.,Russian Academy of Sciences | Lutovinov A.,Moscow Institute of Physics and Technology | Falanga M.,International Space Science Institute ISSI | Tsygankov S.,University of Turku | Bozzo E.,University of Geneva
Monthly Notices of the Royal Astronomical Society | Year: 2017

In this paper, we investigated the long-term evolution of the pulse period in the high-mass X-ray binary LMC X-4 by taking advantage of more than 43 yr of measurements in the X-ray domain. Our analysis revealed for the first time that the source is displaying near-periodical variations of its spin period on a time-scale of roughly 6.8 yr, making LMC X-4 one of the known binary systems showing remarkable long-term spin torque reversals. We discuss different scenarios to interpret the origin of these torque reversals. © 2016 The Authors.


De Propris R.,University of Turku
Monthly Notices of the Royal Astronomical Society | Year: 2017

We derive the galaxy luminosity function in the Ks band for galaxies in 24 clusters to provide a local reference for higher redshift studies and to analyse how and if the luminosity function varies according to environment and cluster properties. We use new, deep K-band imaging and match the photometry to available redshift information and to optical photometry from the SDSS or the UKST/POSS: More than 80 per cent of the galaxies to K ~ 14.5 have measured redshifts. We derive composite luminosity functions, for the entire sample and for cluster subsamples. We consider the luminosity functions for red-sequence and blue cloud galaxies. The full composite luminosity function has K * = 12.79 ± 0.14 (MK =-24.81) and α = -1.41 ± 0.10. We find that K * is largely unaffected by the environment, but that the slope a increases towards lower mass clusters and clusters with Bautz-Morgan type < II. The red-sequence luminosity function seems to be approximately universal (within errors) in all environments: It has parameters K * = 13.16 ± 0.15 (MK = -24.44) and α = -1.00 ± 0.12 (for all galaxies). Blue galaxies do not show a good fit to a Schechter function, but the best values for its parameters are K * = 13.51 ± 0.41 (MK =-24.09) and α =-1.60 ± 0.29: We do not have enough statistics to consider environmental variations for these galaxies. We find some evidence that K * in clusters is brighter than in the field and a is steeper, but note that this comparison is based (for the field) on 2MASS photometry, while our data are considerably deeper. © 2016 The Authors.


Terava J.,University of Turku | Hokkanen E.,University of Turku | Pihlasalo S.,University of Turku
Nanoscale | Year: 2017

Nonspecific assays utilizing time-resolved luminescence resonance energy transfer (TR-LRET) are developed for two applications: to monitor protein adsorption efficiency and to assess the degree of surface coverage on the solid phase. We successfully measure the adsorption efficiency of non-sedimenting nanoparticles since this has been notoriously difficult to determine. Monitoring of the protein adsorption on nanoparticles does not require the nanoparticles with the adsorbed protein to be washed and it is based on the competitive adsorption between the non-adsorbed analyte protein and the acceptor-labeled protein to donor europium(iii) polystyrene nanoparticles. The application for assessing the degree of surface coverage is performed with the final coated and washed analyte nanoparticles and it requires no fluorescent labeling of the studied protein. This application utilizes the competitive adsorption of the acceptor-labeled protein on analyte nanoparticles partly covered with protein and donor europium(iii) polystyrene nanoparticles. The developed methods detect either non-adsorbed protein or uncovered nanoparticle surface, not the proteins adsorbed on the nanoparticles. This is not achievable with the traditional total protein quantification assays applied for monitoring protein adsorption since both non-adsorbed and adsorbed protein are detected and their separation is required. Thus, the developed application for monitoring protein adsorption is user-friendly, requires no centrifugal instrumentation, and is applicable also for small nanoparticles requiring ultracentrifugation. No special expertise or investment in costly instruments is required compared to the existing methods, such as spectroscopic techniques, isothermal titration calorimetry, and surface plasmon resonance. The application for assessing the degree of surface coverage is compared to a reference literature method that comprised the analysis of adsorbed fluorescently labeled protein. The saturation reached at similar protein concentrations showing the reliability of the assay. Our results suggest that the developed applications could be exploited as rapid tools for protein adsorption studies on nanoparticles and for quality control and characterization of the coating processes. © The Royal Society of Chemistry.


Kuusela T.A.,University of Turku
American Journal of Physics | Year: 2017

We describe photon statistics experiments using pseudothermal light that can be performed in an undergraduate physics laboratory. We examine the light properties in terms of a second-order coherence function, as determined either by measuring the light intensity as a function of time or via coincidence analysis of a pair of photon detectors. We determine the coherence time and intensity distribution of the pseudothermal light source that exhibits either Gaussian or non-Gaussian statistics as a function of their optical parameters, and then compare the results with theoretical predictions. The simple photodiode method can be used for the qualitative analysis of the coherence time, but more accurate measurements are achieved using the coincidence method. © 2017 American Association of Physics Teachers.


Chruscinski D.,Nicolaus Copernicus University | Macchiavello C.,National Institute of Nuclear Physics, Italy | Maniscalco S.,University of Turku | Maniscalco S.,Aalto University
Physical Review Letters | Year: 2017

We provide an analysis on non-Markovian quantum evolution based on the spectral properties of dynamical maps. We introduce the dynamical analog of entanglement witness to detect non-Markovianity and we illustrate its behavior with several instructive examples. It is shown that for several important classes of dynamical maps the corresponding evolution of singular values and/or eigenvalues of the map provides a simple non-Markovianity witness. © 2017 American Physical Society.


Vainio J.,University of Turku | Holmberg K.,University of Turku
Scientometrics | Year: 2017

In this study we examined who tweeted academic articles that had at least one Finnish author or co-author affiliation and that had high altmetric counts on Twitter. In this investigation of national level altmetrics we chose the most tweeted scientific articles from four broad areas of science (Agricultural, Engineering and Technological Sciences; Medical and Health Sciences; Natural Sciences; Social Sciences and Humanities). By utilizing both quantitative and qualitative methods of analysis, we studied the data using research techniques such as keyword categorization, co-word analysis and content analysis of user profile descriptions. Our results show that contrary to a random sample of Twitter users, users who tweet academic articles describe themselves more factually and by emphasizing their occupational expertise rather than personal interests. The more field-specific the articles were, the more research-related descriptions dominated in Twitter profile descriptions. We also found that scientific articles were tweeted to promote ideological views especially in instances where the article represented a topic that divides general opinion. © 2017 Akadémiai Kiadó, Budapest, Hungary


Raduly-Baka C.,University of Turku | Johnsson M.,Mentor Graphics | Nevalainen O.S.,University of Turku
Computers and Operations Research | Year: 2017

The assembly of electronic components on printed circuit boards is performed in a line of automated placement machines, each equipped with a feeder unit that contains the component reels required for a product type. Assembling multiple product types by a single machine requires the replacement of certain components in the feeder unit. Increasingly, assembly machines are equipped with modular feeder units, enabling the replacement of a larger group of component reels. To minimize the machine setup time, component reel modules can be preassigned with the necessary component types, thus requiring only the loading of a suitable module set for each product. This work introduces and analyzes the problem of constructing the minimum number of component reel modules, with the objective that a set of jobs can be manufactured without individual component reel changes. We show that the problem is NP-hard and provide an integer programming formulation for it. We also introduce two heuristics based on job grouping, and analyze the results. © 2016 Elsevier Ltd


Koskivaara E.,University of Turku
Pacific Asia Conference on Information Systems, PACIS 2016 - Proceedings | Year: 2016

Physical activity (PA) is a major contributor for both physical and mental wellbeing, and it is also needed to maintain our working capability. PA is not only about sports and exercise, but also being active at work, home, in commuting and during leisure time. According to WHO physical inactivity accounts globally for more than 3 million deaths annually. Evidence-based interventions to understand and increase our PA behaviour are therefore important. Activity monitors provide a means to set targets for daily activity and to follow the intensity, frequency, and duration of PA. Monitoring daily activity has been shown to motivate for PA but more information is needed to understand our daily PA behaviour. Our daily PA is correlated to our daily habits such as steps and calories burned and sleeping time. The current randomized control trail study try to understand by visualising and clustering daily PA (>3.5 MET), steps, calories and sleep of the baseline and the week 8 in working days, from Monday to Friday. The data analysis is based on self-organizing maps (SOMs) technique. The data clusters reveal changes and differences the intervention has occurred between men and women in their PA behaviour.


Saarela A.,University of Turku
Leibniz International Proceedings in Informatics, LIPIcs | Year: 2017

We solve a long-standing open problem on word equations by proving that if the words xo,⋯,xn satisfy the equation xk 0 = xk 1⋯ xk n for three positive values of k, then the words commute. One of our methods is to assign numerical values for the letters, and then study the sums of the letters of words and their prefixes. We also give a geometric interpretation of our methods. © Aleksi Saarela.


Sillanpaa M.,University of Turku | Schmidt D.,Epilepsy Research Group
Seizure | Year: 2017

Purpose To review the long-term outcome of epilepsy in population-based studies. Method Analysis of population-based studies. Results About two of three patients with new-onset epilepsy will, in the long run, enter five-year terminal remission. Chances for remission are best for those with idiopathic or cryptogenic epilepsy. It is unclear whether the seizure outcome has improved over the last several decades. Social outcome, however, may have become better because of the improved level of knowledge on and public attitudes toward people with epilepsy, and possibly fewer prejudices at home, daycare, school, military and labor market. Conclusion While we still do not have a cure for epilepsy for all patients, relief of the medical and social consequences is available for many and hope is on the horizon for people with epilepsy. © 2016 British Epilepsy Association


Bell P.C.,Loughborough University | Hirvensalo M.,University of Turku | Potapov I.,University of Liverpool
Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms | Year: 2017

In this paper, we show that the problem of determining if the identity matrix belongs to a finitely generated semigroup of 2 × 2 matrices from the modular group PSL2(Z) and thus the Special Linear group SL2(Z) is solvable in NP. From this fact, we can immediately derive that the fundamental problem of whether a given finite set of matrices from SL2(Z) or PSL2(Z) generates a group or free semigroup is also decidable in NP. The previous algorithm for these problems, shown in 2005 by Choffrut and Karhumaki, was in EXPSPACE mainly due to the translation of matrices into exponentially long words over a binary alphabet fs; rg and further constructions with a large nondeterministic finite state automaton that is built on these words. Our algorithm is based on various new techniques that allow us to operate with compressed word representations of matrices without explicit expansions. When combined with the known NP-hard lower bound, this proves that the membership problem for the identity problem, the group problem and the freeness problem in SL2(Z) are NP-complete. Copyright © by SIAM.


Parvinen K.,University of Turku
Evolutionary Ecology Research | Year: 2016

Question: How does the mechanistic underpinning of a discrete-time model affect the possibility for evolutionary suicide? Mathematical methods: Adaptive dynamics. Relevant theory on attractor families and bifurcations. Features of model: A discrete-time population model derived from a continuous-time resource-consumer model with processes of harvesting resource, mate finding, and egg production. Results: A population-level multiplicative parameter is affected both by the probability of egg survival and harvest effort. Higher survival probability is selected for, which can result in a period-doubling cascade to chaos, and in evolutionary suicide through a global bifurcation. Also, higher harvest effort is selected for, but it becomes a scaling factor for the model without qualitatively affecting its dynamics, and demographically stochastic extinction occurs. Conclusion: Evolutionary predictions should be based on individual-level traits. © 2016 Kalle Parvinen.


Nevalainen J.,University of Tampere | Oja H.,University of Turku | Datta S.,University of Florida
Statistics in Medicine | Year: 2017

Clustered data are often encountered in biomedical studies, and to date, a number of approaches have been proposed to analyze such data. However, the phenomenon of informative cluster size (ICS) is a challenging problem, and its presence has an impact on the choice of a correct analysis methodology. For example, Dutta and Datta (2015, Biometrics) presented a number of marginal distributions that could be tested. Depending on the nature and degree of informativeness of the cluster size, these marginal distributions may differ, as do the choices of the appropriate test. In particular, they applied their new test to a periodontal data set where the plausibility of the informativeness was mentioned, but no formal test for the same was conducted. We propose bootstrap tests for testing the presence of ICS. A balanced bootstrap method is developed to successfully estimate the null distribution by merging the re-sampled observations with closely matching counterparts. Relying on the assumption of exchangeability within clusters, the proposed procedure performs well in simulations even with a small number of clusters, at different distributions and against different alternative hypotheses, thus making it an omnibus test. We also explain how to extend the ICS test to a regression setting and thereby enhancing its practical utility. The methodologies are illustrated using the periodontal data set mentioned earlier. © 2017 John Wiley & Sons, Ltd.


Okhotin A.,Saint Petersburg State University | Okhotin A.,University of Turku | Salomaa K.,Queen's University
Journal of Computer and System Sciences | Year: 2017

The family of languages recognized by deterministic input-driven pushdown automata (IDPDA; a.k.a. visibly pushdown automata, a.k.a. nested word automata) is known to be closed under concatenation, Kleene star and reversal (under natural assumptions on the partition of the alphabet). As shown by Alur and Madhusudan (2004) , the Kleene star and the reversal of an n-state IDPDA can be represented by an IDPDA with 2O(n2) states, while concatenation of an m-state and an n-state IDPDA is represented by an IDPDA with 2O((m+n)2) states. This paper presents more efficient constructions for the Kleene star and for the reversal, which yield 2Θ(nlog n) states, as well as an m2Θ(nlog n)-state construction for the concatenation. These constructions are optimal up to a factor in the exponent, due to the close lower bounds previously established by Piao and Salomaa (2009) © 2017 Elsevier Inc.


Selonen V.,University of Turku | Wistbacka R.,University of Oulu
Ecology and Evolution | Year: 2017

The lifetime movements of an individual determine the gene flow and invasion potential of the species. However, sex dependence of dispersal and selective pressures driving dispersal have gained much more attention than dispersal at different life and age stages. Natal dispersal is more common than dispersal between breeding attempts, but breeding dispersal may be promoted by resource availability and competition. Here, we utilize mark–recapture data on the nest-box population of Siberian flying squirrels to analyze lifetime dispersal patterns. Natal dispersal means the distance between the natal nest and the nest used the following year, whereas breeding movements refer to the nest site changes between breeding attempts. The movement distances observed here were comparable to distances reported earlier from radio-telemetry studies. Breeding movements did not contribute to lifetime dispersal distance and were not related to variation in food abundance or habitat patch size. Breeding movements of males were negatively, albeit not strongly, related to male population size. In females, breeding movement activity was low and was not related to previous breeding success or to competition between females for territories. Natal philopatry was linked to apparent death of a mother; that is, we did not find evidence for mothers bequeathing territories for offspring, like observed in some other rodent species. Our results give an example of a species in which breeding movements are not driven by environmental variability or nest site quality. Different evolutionary forces often operate in natal and breeding movements, and our study supports the view that juveniles are responsible for redistributing individuals within and between populations. This emphasizes the importance of knowledge on natal dispersal, if we want to understand consequences of movement ecology of the species at the population level. © 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.


Portin P.,University of Turku
Recent Advances in DNA and Gene Sequences | Year: 2016

The concept of a paradigm is in the key position in Thomas Kuhn’s theory of scientific revolutions. A paradigm is the framework within which the results, concepts, hypotheses and theories of scientific research work are understood. According to Kuhn, a paradigm guides the working and efforts of scientists during the time period which he calls the period of normal science. Before long, however, normal science leads to unexplained matters, a situation that then leads the development of the scientific discipline in question to a paradigm shift – a scientific revolution. When a new theory is born, it has either gradually emerged as an extension of the past theory, or the old theory has become a borderline case in the new theory. In the former case, one can speak of a paradigm extension. According to the present author, the development of modern genetics has, until very recent years, been guided by a single paradigm, the Mendelian paradigm which Gregor Mendel launched 150 years ago, and under the guidance of this paradigm the development of genetics has proceeded in a normal fashion in the spirit of logical positivism. Modern discoveries in genetics have, however, created a situation which seems to be leading toward a paradigm shift. The most significant of these discoveries are the findings of adaptive mutations, the phenomenon of transgenerational epigenetic inheritance, and, above all, the present deeply critical state of the concept of the gene. © 2015 Bentham Science Publishers.


Koskenniemi J.J.,University of Turku
Current Opinion in Endocrinology, Diabetes and Obesity | Year: 2017

PURPOSE OF REVIEW: To describe pubertal testicular growth in humans, changes in testicular cell populations that result in testicular growth, and the role of testosterone and gonadotrophins follicle-stimulating hormone (FSH) and luteinizing hormone (LH) in testicular growth. When human data were not available, studies in nonhuman primates and/or rodents were used as surrogates. RECENT FINDINGS: Testicular growth in puberty follows a sigmoidal growth curve, with a large variation in timing of testicular growth and adult testicular volume. Testicular growth early in puberty is due to increase in Sertoli cell number and length of seminiferous tubules, whereas the largest and fastest growth results from the increase in the diameter of the seminiferous tubules first due to spermatogonial proliferation and then due to the expansion of meiotic and haploid germ cells. FSH stimulates Sertoli cell and spermatogonial proliferation, whereas LH/testosterone is mandatory to complete spermatogenesis. However, FSH and LH/testosterone work in synergy and are both needed for normal spermatogenesis. SUMMARY: Testicular growth during puberty is rapid, and mostly due to germ cell expansion and growth in seminiferous tubule diameter triggered by androgens. Pre-treatment with FSH before the induction of puberty may improve the treatment of hypogonadotropic hypogonadism, but remains to be proven. Copyright © 2017 Wolters Kluwer Health, Inc. All rights reserved.


News Article | May 2, 2017
Site: www.gizmag.com

Scientists have recently confirmed that a unique species of monitor lizard, initially described in the early 19th century, is still alive and well on the island of New Ireland in northern Papua New Guinea. It is said to be "the only large-growing animal endemic to the island that has survived until modern times." The lizard was first discovered by French naturalist René Lesson, when he was visiting the island with the La Coquille exploration ship in 1823. He subsequently named the species Varanus douarrha. Unfortunately, however, the specimen that he collected was most likely lost on its way to France, when the ship that was carrying it was wrecked at the Cape of Good Hope in 1824. As a result, scientists didn't have a holotype (a name-bearing specimen), so the animal's status was left somewhat ambiguous. Since then, although it was known that monitors existed on the island, it was suspected that they belonged to the species Varanus indicus – it's the common mangrove monitor, which is found throughout northern Australia, New Guinea and surrounding islands. Recently, however, Valter Weijola from the University of Turku, Finland, spent several months surveying monitor lizards on the Bismarck Islands, of which New Ireland is one. He claims that based upon new morphological and genetic studies, the island's resident monitors have existed in isolation long enough to form a distinct species – the originally-described Varanus douarrha. Such a discovery actually isn't all that unusual. Because monitor lizards tend to inhabit remote areas where they're difficult to study, new species are uncovered with some regularity. A paper on the research was recently published in the Australian Journal of Zoology.


News Article | April 25, 2017
Site: www.eurekalert.org

The brain works most efficiently when it can focus on a single task for a longer period of time The brain works most efficiently when it can focus on a single task for a longer period of time. Previous research shows that multitasking, which means performing several tasks at the same time, reduces productivity by as much as 40%. Now a group of researchers specialising in brain imaging has found that changing tasks too frequently interferes with brain activity. This may explain why the end result is worse than when a person focuses on one task at a time. 'We used functional magnetic resonance imaging to measure different brain areas of our research subjects while they watched short segments of the Star Wars, Indiana Jones and James Bond movies,' explains Aalto University Associate Professor Iiro Jääskeläinen. Cutting the films into segments of approximately 50 seconds fragmented their continuity. In the study, the subjects' brain areas functioned more smoothly when they watched the films in segments of 6.5 minutes. The posterior temporal and dorsomedial prefrontal cortices, the cerebellum and dorsal precuneus are the most important areas of the brain in terms of combining individual events into coherent event sequences. These areas of the brain make it possible to turn fragments into complete entities. According to the study, these brain regions work more efficiently when it can deal with one task at a time. Jääskeläinen recommends completing one task each day rather than working on a dozen of different tasks simultaneously. 'It's easy to fall into the trap of multitasking. In that case, it seems like there is little real progress and this leads to a feeling of inadequacy. Concentration decreases, which causes stress. Prolonged stress hinders thinking and memory,' says Jääskeläinen. The neuroscientist also sees social media as a challenge. 'Social media is really nothing but multitasking, with several parallel plots and issues. You might end up reading the news or playing a game recommended by a friend. From the brain's perspective, social media only increases the load.' In addition to Jääskeläinen, Juha Lahnakoski from Max Planck Institute, Mikko Sams from Aalto University and Lauri Nummenmaa from the University of Turku participated in the research.


News Article | May 3, 2017
Site: www.eurekalert.org

According to a new Finnish study, cardiorespiratory fitness is inversely related to risk of fatty liver. The research was conducted at the University of Turku, Finland, and shows that, despite the person's weight, achieving moderate cardiorespiratory fitness can protect from fatty liver. In the national Cardiovascular Risk in Young Finns Study, researchers measured the cardiorespiratory fitness of 463 Finns with a cycle ergometer exercise test and determined fatty liver with an ultrasound. The participants were 30-47 years of age. -The study revealed that cardiorespiratory fitness is inversely related to the risk of fatty liver - despite physical activity, smoking, alcohol use, serum lipids, insulin, glucose, and C-reactive protein. Importantly, the same results could be seen in participants who were obese, says Researcher Kristiina Pälve from Research Centre of Applied and Preventive Cardiovascular Medicine of the University of Turku. The research results are significant for public health: despite the person's weight, achieving a moderate level of cardiorespiratory fitness can protect from fatty liver. Fatty liver is a significant and expanding public health concern. It is related to several metabolic disturbances, increased risk of cardiovascular disease and type 2 diabetes. The research article was published in April in the Medicine & Science in Sports & Exercise journal. Pälve KS, Pahkala K, Suomela E, Aatola H, Hulkkonen J, Juonala M, Lehtimäki T, Rönnemaa T, Viikari JS, Kähönen M, Hutri-Kähönen N, Telama R, Tammelin T, Raitakari OT.: Cardiorespiratory Fitness and Risk of Fatty Liver. The Young Finns Study. Medicine & Science in Sports & Exercise. 2017 Apr 11. doi: 10.1111/MSS.0000000000001288. https:/ MD Kristiina Pälve, Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku tel. +358 2 333 7220, krsoma@utu.fi


News Article | May 2, 2017
Site: www.eurekalert.org

Scientists have recently found and re-described a monitor lizard species from the island of New Ireland in northern Papua New Guinea. It is the only large-growing animal endemic to the island that has survived until modern times. The lizard, Varanus douarrha, was already discovered in the early 19th century, but the type specimen never reached the museum where it was destined as it appears to have been lost in a shipwreck. The discovery is particularly interesting as most of the endemic species to New Ireland disappeared thousands of years ago as humans colonized the island. The monitor was discovered during fieldwork by Valter Weijola from the Biodiversity Unit of the University of Turku, Finland, who spent several months surveying the monitor lizards of the Bismarck Islands. It can grow to over 1.3 metres in length and, according to current information, it is the only surviving large species endemic to the island. Based on bone discoveries, scientists now know that at least a large rat species and several flightless birds have lived in the area. - In that way it can be considered a relic of the historically richer fauna that inhabited the Pacific islands. These medium-sized Pacific monitors are clearly much better at co-existing with humans than many of the birds and mammals have been, says Weijola. Scientists have known for a long time that there are monitor lizards on the island but it has been unclear which species they belong to. French naturalist René Lesson discovered the monitor lizard when visiting the island with the La Coquille exploration ship in 1823, and later named the species Varanus douarrha which, according to Lesson, means monitor lizard in the local Siar-Lak language. However, it seems likely that Lesson's specimen was destroyed on the way to France as the ship that was carrying it shipwrecked at the Cape of Good Hope in 1824. Therefore, biologist never had a chance to study the so called holotype - or name-bearing specimen. - Since then, it has been believed that the monitor lizards on New Ireland belong to the common mangrove monitor (Varanus indicus) that occurs widely in northern Australia, New Guinea and surrounding islands. However, new morphological and genetic studies confirmed that the monitor lizards of New Ireland have lived in isolation for a long time and developed into a separate species, says Weijola. The discovery was published in the Australian Journal of Zoology and where Varanus douarrha was re-described in detail, and given a new name bearing specimen. Another monitor lizard, Varanus semotus, was described from Mussau Island last year by the same team of scientists. - Together, these two species have doubled the number of monitor lizard species known to occur in the Bismarck Archipelago and proved that there are more endemic vertebrates on these islands than previously believed, says Weijola. Monitor lizards are important predators and altogether approximately 90 different species are known to live in Africa, Asia, Australia and the Pacific islands. Most monitor lizards occur in Australia and on the Pacific islands where there are few mammalian predators. Despite their large size, many of the species are poorly known and new ones are regularly discovered. Most of them stay out of sight and inhabit remote areas which are difficult to access. The research was published in the Australian Journal of Zoology: http://www.


News Article | May 8, 2017
Site: news.yahoo.com

A monitor lizard lost to science in an 1800s shipwreck has been rediscovered on an island in Papua New Guinea. The medium-size monitor, Varanus douarrha, was first identified by French naturalist René Lesson in 1823. The scientific name was inspired by the pronunciation of the lizard's name in Siar, the language of the people who share the lizard's home of New Ireland island. [Album: Bizarre Frogs, Lizards and Salamanders] The specimen of the lizard collected by Lesson went down in a shipwreck off the Cape of Good Hope in 1824, however, so the monitor lizard was never systematically studied. Scientists knew monitor lizards roamed New Ireland, but figured they were the common mangrove monitor species (Varanus indicus) found all over New Guinea. (There are about 90 species of monitor lizard worldwide.) Not so, new research finds. Valter Weijola, a zoologist at the University of Turku in Finland, did fieldwork on the island in an effort to survey the monitor lizards there. He and his colleagues found that the monitor lizards there are both morphologically and genetically different from Varanus indicus. In fact, V. douarrha has been present on the Bismarck Islands, of which New Ireland is a part, for longer that V. indicus, the researchers reported April 26 in the Australian Journal of Zoology. V. douarrha is black with yellow speckles that are concentrated more densely on its underbelly. It grows to about 4.3 feet (1.3 meters) in length. For comparison, the largest monitor lizard — the Komodo dragon — can grow to 10 feet (3 m) long. V. douarrha is the only large native animal known to live on New Ireland, though fossils have been found of large flightless birds and rodents. Last year, Weijola and his colleagues discovered another new monitor lizard, V. semotus, on Mussau Island, which is in the northern part of Papua New Guinea. The discoveries show that there are more endemic species, or native animals found nowhere else, on the islands than previously realized, Weijola said in a statement.


News Article | May 2, 2017
Site: phys.org

Scientists have recently found and re-described a monitor lizard species from the island of New Ireland in northern Papua New Guinea. It is the only large-growing animal endemic to the island that has survived until modern times. The lizard, Varanus douarrha, was already discovered in the early 19th century, but the type specimen never reached the museum where it was destined as it appears to have been lost in a shipwreck. The discovery is particularly interesting as most of the endemic species to New Ireland disappeared thousands of years ago as humans colonized the island. The monitor was discovered during fieldwork by Valter Weijola from the Biodiversity Unit of the University of Turku, Finland, who spent several months surveying the monitor lizards of the Bismarck Islands. It can grow to over 1.3 metres in length and, according to current information, it is the only surviving large species endemic to the island. Based on bone discoveries, scientists now know that at least a large rat species and several flightless birds have lived in the area. - In that way it can be considered a relic of the historically richer fauna that inhabited the Pacific islands. These medium-sized Pacific monitors are clearly much better at co-existing with humans than many of the birds and mammals have been, says Weijola. French Naturalist Discovered the Species in 1823 - Lost in Shipwreck Scientists have known for a long time that there are monitor lizards on the island but it has been unclear which species they belong to. French naturalist René Lesson discovered the monitor lizard when visiting the island with the La Coquille exploration ship in 1823, and later named the species Varanus douarrha which, according to Lesson, means monitor lizard in the local Siar-Lak language. However, it seems likely that Lesson's specimen was destroyed on the way to France as the ship that was carrying it shipwrecked at the Cape of Good Hope in 1824. Therefore, biologist never had a chance to study the so called holotype - or name-bearing specimen. - Since then, it has been believed that the monitor lizards on New Ireland belong to the common mangrove monitor (Varanus indicus) that occurs widely in northern Australia, New Guinea and surrounding islands. However, new morphological and genetic studies confirmed that the monitor lizards of New Ireland have lived in isolation for a long time and developed into a separate species, says Weijola. The discovery was published in the Australian Journal of Zoology and where Varanus douarrha was re-described in detail, and given a new name bearing specimen. Another monitor lizard, Varanus semotus, was described from Mussau Island last year by the same team of scientists. - Together, these two species have doubled the number of monitor lizard species known to occur in the Bismarck Archipelago and proved that there are more endemic vertebrates on these islands than previously believed, says Weijola. Monitor lizards are important predators and altogether approximately 90 different species are known to live in Africa, Asia, Australia and the Pacific islands. Most monitor lizards occur in Australia and on the Pacific islands where there are few mammalian predators. Despite their large size, many of the species are poorly known and new ones are regularly discovered. Most of them stay out of sight and inhabit remote areas which are difficult to access. Explore further: The castaway: New monitor lizard fills top-order predator role on remote Pacific island More information: Valter Weijola et al, Reinstatement of Varanus douarrha Lesson, 1830 as a valid species with comments on the zoogeography of monitor lizards (Squamata:Varanidae) in the Bismarck Archipelago, Papua New Guinea, Australian Journal of Zoology (2017). DOI: 10.1071/ZO16038


A Finnish study coordinated by the Research Centre of Applied and Preventive Cardiovascular Medicine at the University of Turku shows that exposure to cardiovascular risk factors, such as high blood pressure, elevated serum LDL-cholesterol and smoking in childhood and adolescence, is associated with poorer learning ability and memory in middle age. With the aging population, cognitive deficits, such as difficulties in learning and memory, are becoming more common. Cardiovascular risk factors contribute to the occurrence of these deficits. Results from a longitudinal Finnish study show that the effects of cardiovascular risk factors on the brain begin already long before the occurrence of visible changes in cognitive performance. - Previous studies have focused on adulthood and old age, whereas this study brings novel information on the associations between cardiovascular risk factors and cognitive performance throughout the whole lifespan, says Senior Researcher Suvi Rovio from the Research Centre of Applied and Preventive Cardiovascular Medicine at the University of Turku. The results of this study can be exploited by turning the focus of prevention of the cardiovascular risk factors actively to children and adolescence in order to promote brain health in adulthood. High blood pressure, elevated serum cholesterol levels and smoking can be regulated through healthy lifestyle choices. The cognitive performance of over 2,000 participants was measured at the age of 34-49 years. The results showed that high blood pressure and serum LDL-cholesterol level measured in childhood and adolescence as well as smoking in adolescence were associated with poorer cognitive performance in midlife. This association remained regardless of the presence of such risk factors in adulthood. The difference in cognitive performance between those participants whose risk factor levels often exceeded the guideline values for cardiovascular risk factors and those always remaining within the guideline values was equivalent to the difference caused by six years of aging. This study is part of the ongoing national Cardiovascular Risk in Young Finns Study coordinated by the Research Centre of Applied and Preventive Cardiovascular Medicine at the University of Turku. Initially, 3,596 participants have been followed up repeatedly for 31 years for their cardiovascular risk factors from childhood to adulthood. The results were published in the Journal of the American College of Cardiology in May 2017. Cardiovascular Risk Factors From Childhood and Midlife Cognitive Performance The Young Finns Study Suvi P. Rovio et al. Journal of the American College of Cardiology Volume 69, Issue 18, May 2017 DOI: 10.1016/j.jacc.2017.02.060


Jenkins J.S.,University of Chile | Tuomi M.,University of Chile | Tuomi M.,University of Hertfordshire | Tuomi M.,University of Turku
Astrophysical Journal | Year: 2014

Gaining a better understanding of the effects of stellar-induced radial velocity noise is critical for the future of exoplanet studies since the discovery of the lowest-mass planets using this method will require us to go below the intrinsic stellar noise limit. An interesting test case in this respect is that of the southern solar analog HD 41248. The radial velocity time series of this star has been proposed to contain either a pair of signals with periods of around 18 and 25 days, which could be due to a pair of resonant super-Earths, or a single and varying 25 day signal that could arise due to a complex interplay between differential rotation and modulated activity. In this work, we build up more evidence for the former scenario, showing that the signals are still clearly significant, even after more than 10 yr of observations, and they likely do not change in period, amplitude, or phase as a function of time, the hallmarks of static Doppler signals. We show that over the last two observing seasons, this star was more intrinsically active and the noise reddened, highlighting why better noise models are needed to find the lowest amplitude signals, in particular, models that consider noise correlations. This analysis shows that there is still sufficient evidence for the existence of two super-Earths on the edge of, or locked into, a 7:5 mean motion resonance orbiting HD 41248. © 2014. The American Astronomical Society. All rights reserved..


Tuomi M.,University of Hertfordshire | Tuomi M.,University of Turku | Jones H.R.A.,University of Hertfordshire | Barnes J.R.,University of Hertfordshire | And 2 more authors.
Monthly Notices of the Royal Astronomical Society | Year: 2014

Due to their higher planet-star mass ratios, M dwarfs are the easiest targets for detection of low-mass planets orbiting nearby stars using Doppler spectroscopy. Furthermore, because of their low masses and luminosities, Doppler measurements enable the detection of lowmass planets in their habitable zones that correspond to closer orbits than for solar-type stars. We re-analyse literature Ultraviolet and Visual Echelle Spectrograph (UVES) radial velocities of 41 nearby Mdwarfs in a combination with new velocities obtained from publicly available spectra from the HARPS-ESO spectrograph of these stars in an attempt to constrain any low-amplitude Keplerian signals. We apply Bayesian signal detection criteria, together with posterior sampling techniques, in combination with noise models that take into account correlations in the data and obtain estimates for the number of planet candidates in the sample. More generally, we use the estimated detection probability function to calculate the occurrence rate of low-mass planets around nearby M dwarfs. We report eight new planet candidates in the sample (orbiting GJ 27.1, GJ 160.2, GJ 180, GJ 229, GJ 422, and GJ 682), including two new multiplanet systems, and confirm two previously known candidates in the GJ 433 system based on detections of Keplerian signals in the combined UVES and High Accuracy Radial velocity Planet Searcher (HARPS) radial velocity data that cannot be explained by periodic and/or quasi-periodic phenomena related to stellar activities. Finally, we use the estimated detection probability function to calculate the occurrence rate of low-mass planets around nearby M dwarfs. According to our results, M dwarfs are hosts to an abundance of low-mass planets and the occurrence rate of planets less massive than 10M? is of the order of one planet per star, possibly even greater. Our results also indicate that planets with masses between 3 and 10 M⊕ are common in the stellar habitable zones of M dwarfs with an estimated occurrence rate of 0.21+0.03 -0.05 planets per star. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Tuomi M.,University of Hertfordshire | Tuomi M.,University of Turku
Monthly Notices of the Royal Astronomical Society: Letters | Year: 2014

We re-analyse the recently published High-AccuracyRadial velocity Planet Searcher (HARPS) and Planet Finder Spectrograph (PFS) velocities of the nearby K dwarf GJ 221 that have been reported to contain the signatures of two planets orbiting the star. Our goal is to see whether the earlier studies discussing the system fell victims of false negative detections. We perform the analyses by using an independent statistical method based on posterior samplings and model comparisons in the Bayesian framework that is known to be more sensitive to weak signals of low-mass planets. According to our analyses, we find strong evidence in favour of a third candidate planet in the system corresponding to a cold sub-Saturnian planet with an orbital period of 500 d and a minimum mass of 29M⊕. Application of sub-optimal signal detection methods can leave low-amplitude signals undetected in radial velocity time series. Our results suggest that the estimated statistical properties of low-mass planets can thus be biased because several signals corresponding to low-mass candidate planets may have gone unnoticed. This also suggests that the occurrence rates of such planets based on radial velocity surveys might be underestimated. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Gollan P.J.,Swinburne University of Technology | Gollan P.J.,University of Turku | Bhave M.,Swinburne University of Technology | Aro E.-M.,University of Turku
FEBS Letters | Year: 2012

The FK506-binding proteins (FKBPs) are known both as the receptors for immunosuppressant drugs and as prolyl isomerase (PPIase) enzymes that catalyse rotation of prolyl bonds. FKBPs are characterised by the inclusion of at least one FK506-binding domain (FKBd), the receptor site for proline and the active site for PPIase catalysis. The FKBPs form large and diverse families in most organisms, with the largest FKBP families occurring in higher plants. Plant FKBPs are molecular chaperones that interact with specific protein partners to regulate a diversity of cellular processes. Recent studies have found that plant FKBPs operate in intricate and coordinated mechanisms for regulating stress response and development processes, and discoveries of new interaction partners expand their cellular influences to gene expression and photosynthetic adaptations. This review presents an examination of the molecular and structural features and functional roles of the higher plant FKBP family within the context of these recent findings, and discusses the significance of domain conservation and variation for the development of a diverse, versatile and complex chaperone family. © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.


Tuomi M.,University of Hertfordshire | Tuomi M.,University of Turku
Astronomy and Astrophysics | Year: 2012

Aims. We re-analyse the HARPS radial velocities of HD 10180 and calculate the probabilities of models with differing numbers of periodic signals in the data. We test the significance of the seven signals, corresponding to seven exoplanets orbiting the star, in the Bayesian framework and perform comparisons of models with up to nine periodicities. Methods. We used posterior samplings and Bayesian model probabilities in our analyses together with suitable prior probability densities and prior model probabilities to extract all significant signals from the data and to receive reliable uncertainties for the orbital parameters of the six, possibly seven, known exoplanets in the system. Results. According to our results, there is evidence for up to nine planets orbiting HD 10180, which would make this star a record holder with more planets in its orbits than there are in the solar system. We revise the uncertainties of the previously reported six planets in the system, verify the existence of the seventh signal, and announce the detection of two additional statistically significant signals in the data. If these are of planetary origin, they would correspond to planets with minimum masses of 5.1 -3.2 +3.1 and 1.9 -1.8 +1.6 M on orbits with 67.55 -0.88 +0.68 and 9.655 -0.072 +0.022 day periods (denoted using the 99% credibility intervals), respectively. © 2012 ESO.


Tuomi M.,University of Hertfordshire | Tuomi M.,University of Turku | Jones H.R.A.,University of Hertfordshire
Astronomy and Astrophysics | Year: 2012

Aims. Estimating the marginal likelihoods is an essential feature of model selection in the Bayesian context. It is especially crucial to have good estimates when assessing the number of planets orbiting stars and different models explain the noisy data with different numbers of Keplerian signals. We introduce a simple method for approximating the marginal likelihoods in practice when a statistically representative sample from the parameter posterior density is available. Methods. We use our truncated posterior mixture estimate to receive accurate model probabilities for models with different numbers of Keplerian signals in radial velocity data. We test this estimate in simple scenarios to assess its accuracy and rate of convergence in practice when the corresponding estimates calculated using the deviance information criterion can be applied to obtain trustworthy model comparison results. As a test case, we determine the posterior probability of a planet orbiting HD 3651 given Lick and Keck radial velocity data. Results. The posterior mixture estimate appears to be a simple and an accurate way of calculating marginal integrals from posterior samples. We show that it can be used in practice to estimate the marginal integrals reliably, given a suitable selection of the parameter λ, which controls the estimate's accuracy and convergence rate. It is also more accurate than the one-block Metropolis-Hastings estimate, and can be used in any application because it is based on assumptions about neither the nature of the posterior density nor the amount of either data or parameters in the statistical model. © 2012 ESO.


Anglada-Escude G.,University of Gottingen | Tuomi M.,University of Hertfordshire | Tuomi M.,University of Turku
Astronomy and Astrophysics | Year: 2012

Context. Several M dwarfs are targets of systematical monitoring in searches for Doppler signals caused by low-mass exoplanet companions. As a result, an emerging population of high-multiplicity planetary systems around low-mass stars are being detected as well. Aims. We optimize classic data analysis methods and develop new ones to enhance the sensitivity towards lower amplitude planets in high-multiplicity systems. We apply these methods to the public HARPS observations of GJ≠676A, a nearby and relatively quiet M dwarf with one reported gas giant companion. Methods. We rederived Doppler measurements from public HARPS spectra using the recently developed template matching method (HARPS-TERRA software). We used refined versions of periodograms to assess the presence of additional low-mass companions. We also analysed the same dataset with Bayesian statistics tools and compared the performance of both approaches. Results. We confirm the already reported massive gas giant candidate and a long period trend in the Doppler measurements. In addition to that, we find very secure evidence in favour of two new candidates in close-in orbits and masses in the super-Earth mass regime. Also, the increased time-span of the observations allows the detection of curvature in the long-period trend. suggesting the presence of a massive outer companion whose nature is still unclear. Conclusions. Despite the increased sensitivity of our new periodogram tools, we find that Bayesian methods are significantly more sensitive and reliable in the early detection of candidate signals, but more work is needed to quantify their robustness against false positives. While hardware development is important in increasing the Doppler precision, development of data analysis techniques can help to reveal new results from existing data sets with significantly fewer resources. This new system holds the record of minimum-mass range (from Msini ~ 4.5 M⊕ to 5 Mjup) and period range (from P ~ 3.6 days to more than 10 years). Although all planet candidates are substantially more massive, it is the first exoplanetary system with a general architecture similar to our solar system. GJ 676A can be happily added to the family of high-multiplicity planetary systems around M dwarfs. © ESO 2012.


Haltia-Hovi E.,University of Turku | Haltia-Hovi E.,German Research Center for Geosciences | Nowaczyk N.,German Research Center for Geosciences | Saarinen T.,University of Turku
Geophysical Journal International | Year: 2010

Holocene palaeomagnetic secular variation (PSV) in inclination and declination recorded in the sediment remanent magnetization of two small lakes, Lake Lehmilampi (63°37′N, 29°06′E) and Lake Kortejärvi (63°37′N, 28°56′E) in eastern Finland is presented. As an outcome of systematic coring, eight cores, 300-753 cm in length, were investigated. All samples (Lehmilampi n= 1320, Kortejärvi n= 943) were subjected to palaeo- and mineral magnetic analyses. The directions of the characteristic remanent magnetization (ChRM) were obtained from progressive alternating field demagnetization of the natural remanent magnetization (NRM) followed by principle component analysis. The younger sections of the sediment columns in the studied lakes are annually laminated, providing detailed chronologies for dating PSV features back to 5100 cal. BP. The underlying older sections of the cores were dated by palaeomagnetic pattern matching in respect to varve-dated Lake Nautajärvi PSV data (Ojala & Saarinen 2002), thus yielding a composite age model covering nearly the whole Holocene epoch. Average sedimentation rates ranging from ∼0.68 to 0.74 mm yr-1 enabled recording of changes in the geomagnetic field at decadal resolution. The carriers of remanence are dominantly magnetite of stable single-domain to pseudo-single-domain grain size, accompanied by magnetic minerals of harder coercivity. The sediments from both lakes exhibit strong and stable single-component magnetizations nearly throughout the whole cores. The sediment magnetization lock-in delay is estimated to range between 80 and 100 yr. PSV data were transformed into time-series and subsequently stacked to comprise North Karelian stack, and Fisher statistics were used to calculate mean directions together with the 95 per cent confidence level (α95). A comparison of declination and inclination features of the North Karelian stack with previously published data expresses remarkable similarity, therefore confirming the similar source behind the changes in the NRM directional records. The high quality of the PSV data extracted from Lehmilampi and Kortejärvi, in terms of dating as well as amplitude reconstruction, have a high potential to improve existing and future geomagnetic field models. © 2009 The Authors Journal compilation © 2009 RAS.


Juonala M.,University of Turku | Raitakari O.T.,University of Turku
Current Opinion in Lipidology | Year: 2013

PURPOSE OF REVIEW: To provide a comprehensive overview on the main findings from the Cardiovascular Risk in Young Finns Study. This prospective multicenter study initiated in 1980 (N=3596, baseline age 3-18 years) has followed up study participants over 30 years to investigate childhood risk factors for cardiometabolic outcomes in adulthood. RECENT FINDINGS: Childhood BMI, socioeconomic status, parental risk factor status, as well as genetic polymorphisms are independent predictors of adult obesity, hypertension, and dyslipidemia. Results from the Young Finns Study and other follow-up studies have shown that conventional childhood risk factors, such as dyslipidemia, obesity, elevated blood pressure and smoking, are predictive of subclinical atherosclerosis in young adults. Recent findings suggest that childhood lifestyle (diet, physical activity) is associated with subclinical atherosclerosis and its progression in adulthood. Concerning the timing of risk factor measurements, they seem to be predictive of adult atherosclerosis from the age of 9 onwards. From a clinical point of view, a recent observation suggesting that the adverse cardiometabolic effects of childhood overweight/obesity are reversed among those who become nonobese adults, provides optimism during the days of obesity epidemic. SUMMARY: Current data suggest that childhood risk factors are associated with higher risk of subclinical atherosclerosis in adulthood. Future studies among aging cohorts followed since childhood will provide data on their influence on clinical cardiovascular outcomes. © 2013 Wolters Kluwer Health | Lippincott Williams & Wilkins.


Lu H.-F.,National Chiao Tung University | Hollanti C.,University of Turku | Hollanti C.,University of Tampere
IEEE Transactions on Information Theory | Year: 2010

In multiple-inputmultiple-output (MIMO) communications, the notion of asymmetric channel refers to the situation when the number of transmit antennas is strictly larger than the number of receive antennas. Such channels can often be found in MIMO downlink transmissions. While existing cyclic-division-algebra (CDA)-based codes can still be employed to achieve the optimal diversitymultiplexing tradeoff (DMT) at high signal-to-noise ratio (SNR) regime, such codes cannot be directly decoded using, for example, the pure sphere decoding method. Although other means of decoding methods such as minimum mean square error generalized decision feedback equalizer (MMSE-GDFE) with lattice search and regularized lattice decoding are available, an alternative approach is to constrain the number of active transmit antennas in each channel use to be no larger than the number of receive antennas. The resulting system is coined constrained asymmetric MIMO system. Two general types of asymmetrical channels are considered in this paper, namely, 1) when there are two receive antennas and the number of transmit antennas is arbitrary, and 2) when the number of transmit antennas is one larger than the number of receive antennas. Explicit optimal transmission schemes as well as the corresponding code constructions for such constrained asymmetric MIMO channels are presented, and are shown to achieve the same DMT performance as their unconstrained counterparts. © 2010 IEEE.


Ferris H.,University of California at Davis | Tuomisto H.,University of Turku
Soil Biology and Biochemistry | Year: 2015

The soil provides a great variety of microhabitats for myriad organisms of different size, physiological activity, behavior and ecosystem function. Besides abundance of participating soil organisms, their species diversity facilitates maximum exploitation of the resources available in the different habitats. At various levels of resolution, species can be categorized into classes performing ecosystem functions and, within each functional class, into guilds of species with similar life course characteristics. Measurement of the diversity and abundance of species within a functional class provides insights into the nature of ecosystem functions and services and to the health of the soil. At higher resolution, species diversity within guilds of a functional class may infer the degree of exploitation of available resources and the complementarity of an ecosystem service; diversity among the guilds of a functional class may indicate successional complementarity of the services. A diversity of guilds within a functional class expands the range of conditions over which ecosystem services are performed while species diversity within a functional class and its guilds contributes to the magnitude of the services. Consequently, diversity of species within functional classes is a key element of the biological component of soil health. In the context of ecosystem services and soil health, the biomass or metabolic activity of species are more useful measures of their abundance than numbers of individuals. Thus, understanding of soil health and ecosystem function requires, besides knowledge of species diversity within functional classes, assessment of the range of functions currently performed in the system and the abundances of organisms by which they are performed. We propose a diversity-weighted abundance product for comparison of the functional magnitude of different assemblages of like organisms. © 2015 Elsevier Ltd.


Eskelinen A.,University of Oulu | Eskelinen A.,University of California at Davis | Harrison S.,University of California at Davis | Tuomi M.,University of Helsinki | Tuomi M.,University of Turku
Ecology | Year: 2012

The interactive effects of consumers and nutrients on terrestrial plant communities, and the role of plant functional traits in mediating these responses, are poorly known. We carried out a six-year full-factorial field experiment using mammalian herbivore exclusion and fertilization in two habitat types (fertile and infertile alpine tundra heaths) that differed in plant functional traits related to resource acquisition and palatability. Infertile habitats were dominated by species with traits indicative of a slow-growing strategy: high C:N ratio, low specific leaf area, and high condensed tannins. We found that herbivory counteracted the effect of fertilization on biomass, and that this response differed between the two habitats and was correlated with plant functional traits. Live biomass dominated the treatment responses in infertile habitats, whereas litter accumulation dominated the treatment responses in fertile habitats and was strongly negatively associated with resident community tannin concentration. Species richness declined under herbivore exclusion and fertilization in fertile habitats, where litter accumulation was greatest. Community means of plant C:N ratio predicted treatment effects on diversity: fertilization decreased and herbivory increased dominance in communities originally dominated by plants with high C:N, while fertilization increased and herbivory diminished dominance in communities where low C:N species were abundant. Our results highlight the close interdependence between consumer effects, soil nutrients, and plant functional traits and suggest that plant traits may provide an improved understanding of how consumers and nutrients influence plant community productivity and diversity. © 2012 by the Ecological Society of America.


Mazya M.V.,Karolinska University Hospital | Lees K.R.,University of Glasgow | Markus R.,St Vincents Hospital | Roine R.O.,University of Turku | And 3 more authors.
Annals of Neurology | Year: 2013

Objective Controversy surrounds the safety of intravenous (IV) tissue plasminogen activator (tPA) in ischemic stroke patients treated with warfarin. The European tPA license precludes its use in anticoagulated patients altogether. American guidelines accept IV tPA use with an international normalized ratio (INR) ≤ 1.7. The influence of warfarin on symptomatic intracerebral hemorrhage (SICH), arterial recanalization, and long-term functional outcome in stroke thrombolysis remains unclear. Methods We analyzed data from 45,074 patients treated with IV tPA enrolled in the Safe Implementation of Thrombolysis in Stroke (SITS) International Stroke Thrombolysis Register. A total of 768 patients had baseline warfarin treatment with INR ≤ 1.7. Outcome measures were SICH, arterial recanalization, mortality, and functional independence at 3 months. Results Patients on warfarin with INR ≤ 1.7 were older, had more comorbidities, and had more severe strokes compared to patients without warfarin. There were no significant differences between patients with and without warfarin in SICH rates (adjusted odds ratio [aOR] = 1.23, 95% confidence interval [CI] = 0.72-2.11 per SITS-MOST; aOR = 1.26, 95% CI = 0.82-1.70 per European Cooperative Acute Stroke Study II) after adjustment for age, stroke severity, and comorbidities. Neither did warfarin independently influence mortality (aOR = 1.05, 95% CI = 0.83-1.35) or functional independence at 3 months (aOR = 1.01, 95% CI = 0.81-1.24). Arterial recanalization by computed tomography/magnetic resonance angiography trended higher in warfarin patients (62% [37 of 59] vs 55% [776/1,475], p = 0.066). Recanalization approximated by disappearance at 22 to 36 hours of a baseline hyperdense middle cerebral artery sign was increased (63% [124 of 196] vs 55% [3,901 of 7,099], p = 0.022). Interpretation Warfarin treatment with INR ≤ 1.7 did not increase the risk for SICH or death, and had no impact on long-term functional outcome in patients treated with IV tPA for acute ischemic stroke. © 2013 American Neurological Association.


Roivainen A.,University of Turku | Jalkanen S.,University of Turku | Nanni C.,UO Medicina Nucleare
European Journal of Nuclear Medicine and Molecular Imaging | Year: 2012

Inflammation plays a major role in the development of many diseases. This review article summarizes recent research in the field of in vivo imaging of inflammation. Novel methodologies using PET with 68Ga peptides targeting, for example, vascular adhesion protein 1 are discussed. © 2012 Springer-Verlag.


Engstrom-Ost J.,Novia University of Applied Sciences | Repka S.,University of Turku | Mikkonen M.,University of Swansea
Harmful Algae | Year: 2011

The aim of the study was to measure toxin production and growth of the cyanobacterium Anabaena sp. in the presence of competitor algae and grazers. The study was comparative, as it was repeated at two sites in the Baltic Sea. The results showed that growth and intracellular microcystin concentrations of Anabaena were significantly higher at the Bothnian Sea site than at the Gulf of Finland. Toxin concentrations of Anabaena were higher in the presence of chlorophyte Brachiomonas submarina than in incubations with cryptophyte Rhodomonas salina or copepod Eurytemora affinis. Chlorophyll content was higher in the presence of copepods. The results suggest that both growth and toxin production of Anabaena may be controlled by salinity, because salinity is lower at the Bothnian Sea site, whereas also other factors could have influenced the results. Our data are also in line with the hypothesis that possible allelopathic interactions (here measured as toxicity) are more probable in the presence of foreign species. © 2011 Elsevier B.V.


Louvanto K.,University of Turku | Syrjanen K.J.,University of Turku | Syrjanen S.M.,University of Turku
Journal of Infectious Diseases | Year: 2010

Background. Persistent human papillomavirus (HPV) infection is the most important risk factor for cervical cancer, and understanding genotype-specific HPV persistence is essential for elucidating the natural history of HPV infections. Methods. In the Finnish Family HPV Study, 329 pregnant women (mean age, 25.5 years) were recruited during the third trimester of pregnancy and were followed up for 6 years. Multiplex HPV genotyping for 27 low- and high-risk HPV types was used to define genotype-specific prevalence at each visit. Generalized estimating equation models were constructed to estimate predictors of type-specific persistence (positive results at 2 consecutive visits) of species 7 and 9 HPV genotypes. Results. HPV16 was the most common type, followed by HPV types 18, 31, 35, 45, 58, 70, and 6. Prevalence of multiple infections ranged from 21% to 45%. Persistence was most prolonged for HPV types 35, 58, and 52, with durations of 38.7, 32.1, and 24.2 months, respectively, and was equal for multiple-type infections and HPV16, with durations of 21 and 24 months, respectively. Independent predictors of type-specific persistence of species 7 and 9 HPV genotypes were age (odds ratio, 1.13 [95% confidence interval, 1.02-1.25]; ), oral sex Pp.017 (odds ratio, 0.37 [95% confidence interval, 0.17-0.81]; Pp.013), and young age (!13 years) at initiation of smoking (odds ratio, 0.51 [95% confidence interval, 0.27-0.98]; Pp.046). Conclusion. HPV16 was the most frequent persisting HPV genotype followed by multiple infections. Early initiation of smoking, practicing oral sex and older age increase the risk for persistence of species 7 and 9 HPV genotypes. © 2010 by the Infectious Diseases Society of America.


Virta L.,Social Insurance Institution | Auvinen A.,University of Tampere | Helenius H.,University of Turku | Huovinen P.,University of Turku | And 2 more authors.
American Journal of Epidemiology | Year: 2012

To determine whether childhood exposure to antibiotics is associated with the risk of developing inflammatory bowel disease (IBD), the authors conducted a national, register-based study comprising all children born in 1994-2008 in Finland and diagnosed with IBD by October 2010. The authors identified 595 children with IBD (233 with Crohn's disease and 362 with ulcerative colitis) and 2,380 controls matched for age, gender, and place of residence. The risk of pediatric Crohn's disease increased with the number of antibiotic purchases from birth to the index date and persisted when the 6 months preceding the case's diagnosis were excluded (for 7-10 purchases vs. none, odds ratio = 3.48, 95% confidence interval: 1.57, 7.34; conditional logistic regression). The association between Crohn's disease and antibiotic use was stronger in boys than in girls (P = 0.01). Cephalosporins showed the strongest association with Crohn's disease (for 3 purchases vs. nonuse, odds ratio = 2.82, 95% confidence interval: 1.65, 4.81). Antibiotic exposure was not associated with the development of pediatric ulcerative colitis. Repeated use of antibiotics may reflect shared susceptibility to childhood infections and pediatric Crohn's disease or alternatively may trigger disease development. © The Author 2012. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved.


Tuomi M.,University of Hertfordshire | Tuomi M.,University of Turku
Astronomy and Astrophysics | Year: 2011

Aims: The Gliese 581 planetary system has received attention because it has been proposed to host a low-mass planet in its habitable zone. We re-analyse the radial velocity measurements reported to contain six planetary signals to see whether these conclusions remain valid when the analyses are made using Bayesian tools instead of the common periodogram analyses. Methods. We analyse the combined radial velocity data set obtained using the HARPS and HIRES spectrographs using posterior sampling techniques and computation of the posterior probabilities of models with differing numbers of Keplerian signals. We do not fix the orbital eccentricities and stellar jitter to certain values but treat these as free parameters of our statistical models. Hence, we can take the uncertainties of these parameters into account when assessing the number of planetary signals present in the data, the point estimates of all of the model parameters, and the uncertainties of these parameters. Results. We conclude that based on the Bayesian model probabilities and the nature of the posterior densities of the different models, there is evidence in favour of four planets orbiting GJ 581. The HARPS and HIRES data do not imply the conclusion that there are two additional companions orbiting GJ 581. We also revise the orbital parameters of the four companions in the system. Especially, according to our results, the eccentricities of all the companions in the system are consistent with zero. © ESO, 2011.


Tuomi M.,University of Hertfordshire | Tuomi M.,University of Turku | Anglada-Escude G.,University of Gottingen
Astronomy and Astrophysics | Year: 2013

Context. Exoplanet Doppler surveys are currently the most efficient means to detect low-mass companions to nearby stars. Among these stars, the light M dwarfs provide the highest sensitivity to detect low-mass exoplanet candidates. Evidence is accumulating that a substantial fraction of these low-mass planets are found in high-multiplicity planetary systems. GJ 163 is a nearby inactive M dwarf with abundant public observations obtained using the HARPS spectrograph. Aims. We obtain and analyse radial velocities from the HARPS public spectra of GJ 163 and investigate the presence of a planetary companions orbiting it. The number of planet candidates detected might depend on some prior assumptions. Since the impact of prior choice has not been investigated throughly previously, we study the effects of different prior densities on the detectability of planet candidates around GJ 163. Methods. We use Bayesian tools, i.e. posterior samplings and model comparisons, when analysing the GJ 163 velocities. We consider models accounting for the possible correlations of subsequent measurements. We also search for activity-related counterparts of the signals we observe and test the dynamical stability of the planetary systems corresponding to our solutions using direct numerical integrations of the orbits. Results. We find that there are at least three planet candidates orbiting GJ 163. The existence of a fourth planet is supported by the data but the evidence in favor of the corresponding model is not yet conclusive. The second innermost planet candidate in the system with an orbital period of 25.6 days and a minimum mass of 8.7 M· is inside the liquid-water habitable zone of the star. Conclusions. The architecture of GJ 163 system resembles a scaled-down Solar System in the sense that there are two low-mass planets on orbital periods of 8.7 and 25.6 days in the inner system, a possible slightly more massive companion on an intermediate orbit, and an outer sub-Saturnian companion at roughly 1 AU. The discovery of (yet) another planetary system with several low-mass companions around a nearby M-dwarf indicates that the high-multiplicity planetary systems found by the NASA Kepler mission around G and K dwarfs is also present (possibly even reinforced) around low-mass stars. © 2013 ESO.


Lahdenpera M.,University of Turku | Gillespie D.O.S.,Stanford University | Gillespie D.O.S.,French National Center for Scientific Research | Lummaa V.,University of Sheffield | And 3 more authors.
Ecology Letters | Year: 2012

Human menopause is ubiquitous among women and is uninfluenced by modernity. In addition, it remains an evolutionary puzzle: studies have largely failed to account for diminishing selection on reproduction beyond 50 years. Using a 200-year dataset on pre-industrial Finns, we show that an important component is between-generation reproductive conflict among unrelated women. Simultaneous reproduction by successive generations of in-laws was associated with declines in offspring survivorship of up to 66%. An inclusive fitness model revealed that incorporation of the fitness consequences of simultaneous intergenerational reproduction between in-laws, with those of grandmothering and risks of dying in childbirth, were sufficient to generate selection against continued reproduction beyond 51 years. Decomposition of model estimates suggested that the former two were most influential in generating selection against continued reproduction. We propose that menopause evolved, in part, because of age-specific increases in opportunities for intergenerational cooperation and reproductive competition under ecological scarcity. © 2012 Blackwell Publishing Ltd/CNRS.


Valtonen T.M.,University of Turku | Roff D.A.,University of California at Riverside | Rantala M.J.,University of Turku
Journal of Evolutionary Biology | Year: 2011

The impact of nutritional deficiencies early in life in determining life-history variation in organisms is well recognized. The negative effects of inbreeding on fitness are also well known. Contrary to studies on vertebrates, studies on invertebrates are not consistent with the observation that inbreeding compromises resistance to parasites and pathogens. In this study, we investigated the effect of early nutrition on the magnitude of inbreeding depression in development time, adult body size and adult resistance to the bacterium Serratia marcescens in Drosophila melanogaster. We found that early nutritional environment had no effect on the magnitude of inbreeding depression in development time or adult body size but may have played a small role in adult resistance to the bacterial infection. Estimates of heritabilities for development time under the poor nutritional environment were larger than those measured under the standard nutritional conditions. © 2010 The Authors. Journal of Evolutionary Biology © 2010 European Society For Evolutionary Biology.


Vehkalahti R.,University of Turku | Francis Lu H.-F.,National Chiao Tung University | Luzzi L.,Cergy-Pontoise University
IEEE Transactions on Information Theory | Year: 2013

This work considers inverse determinant sums, which arise from the union bound on the error probability, as a tool for designing and analyzing algebraic space-time block codes. A general framework to study these sums is established, and the connection between asymptotic growth of inverse determinant sums and the diversity-multiplexing gain tradeoff is investigated. It is proven that the growth of the inverse determinant sum of a division algebra-based space-time code is completely determined by the growth of the unit group. This reduces the inverse determinant sum analysis to studying certain asymptotic integrals in Lie groups. Using recent methods from ergodic theory, a complete classification of the inverse determinant sums of the most well-known algebraic space-time codes is provided. The approach reveals an interesting and tight relation between diversity-multiplexing gain tradeoff and point counting in Lie groups. © 1963-2012 IEEE.


Liu Y.,University of Oulu | Li H.,University of Turku | Hu F.,Zhejiang Normal University
Decision Support Systems | Year: 2013

A multitude of evidences show that impulse purchase is prevalent online, yet relatively limited knowledge is available on this phenomenon. The study borrows marketing wisdom to information systems space to quantify how the website cues (products availability, website ease of use and visual appeal) affect personality traits (instant gratification, normative evaluation and impulsiveness) to urge the impulse purchase online. Structural equation modeling technologies are employed to evaluate the research model based on a survey questionnaire. The results show that personality factors of instant gratification, normative evaluation and impulsiveness are key determinants of urge to buy impulsively, while perceived website cues of visual appeal, website ease of use and product availability are important precursors. Through combining marketing and IS wisdom, a number of new insights are offered which enrich our understanding on the determinants of online impulse purchase decision as well as on how a proper IS design alters consumer shopping experience to engender more online impulse purchase. © 2013 Elsevier B.V.


Valtonen T.M.,University of Turku | Roff D.A.,University of California at Riverside | Rantala M.J.,University of Turku
Behavior Genetics | Year: 2014

In order for the male courtship traits to honestly signal quality they need to be condition-dependent. Moreover, if these traits capture genetic variation in condition they should resemble life-history traits in being subject to strong directional selection and, consequently, suffer strong inbreeding depression. In this study we investigated the effect of high inbreeding on male attractiveness by assessing mating success, mating speed and copulation duration of inbred, outbred and crossbred (constructed by crossing separate, randomly chosen inbred lines) males of Drosophila melanogaster. When set to compete against a standardized competitor and compared to the success rate of the crossbred lines, inbreeding significantly reduced male mating success. Under competition, outbred males initiated copulation significantly sooner than crossbred and inbred males. Under non-competitive conditions, no effect of inbreeding was found on either mating speed or copulation duration. Both mating success and mating speed showed much higher inbreeding depression than male size. © 2014 Springer Science+Business Media New York.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2010-ITN | Award Amount: 5.76M | Year: 2010

Chemical Bioanalysis aims for retrieving selective information out of complex biological systems. Sensors, probes and devices are the future tools of medicinal diagnostics, environmental monitoring, food analysis and molecular biology. The ITN CHEBANA provides interdisciplinary research training for early stage and experienced researchers and focuses on the most important techniques in the field. These are based on fluorescence, electrochemistry and mass spectrometry. Eleven excellently qualified academic partners (with well documented expertise) along with one of Europes leading industrial companies in the diagnostic area will provide a network of research activities, short courses and classes that are complemented by skill training and career development events. In fact, we believe that we have unified Europes leading experts in these fields, many of which outperform their American and other colleagues. Moreover, joint research projects between the partners build the foundation of the training network. The research activities are divided into four overlapping areas: * sensor development for the detection of small analytes, * monitoring of biomolecular interactions, * analysis of cellular function, and * development of diagnostic tools. Interdisciplinary expertise and specialized techniques are mandatory in order to accomplish these challenges, and this cannot be provided at a single institution at the required level. Therefore, a European hub for research and training in the fast developing field of Chemical Bioanalysis is assembled by co-supervised PhD theses, postdoctoral training, workshops and summer schools bringing together the individual expertise of the partners from academia and industry. Eventually, this ITN will provide highly specialized experts that are urgently looked for by the respective European industry.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-CSA-Infra-PP | Phase: INFRA-2010-2.2.10 | Award Amount: 8.01M | Year: 2010

The Cherenkov Telescope Array CTA will be the first open facility for gamma-ray astronomy in the very-high-energy domain, with a performance which is dramatically improved over existing instruments in terms of sensitivity, energy coverage, survey capability and flexibility. CTA will probe non-thermal phenomena in the Universe known to have comparable energy content to other forms of energy such as thermal radiation both in our own Galaxy and at cosmological distances, addressing questions in astrophysics, astroparticle physics, particle physics, plasma physics, cosmology, and fundamental physics. The CTA preparatory phase CTA-PP will address a number of crucial prerequisites for the approval, construction and operation of CTA: > the set-up of a Project Office offering means for electronic communication as well as data storage and handling for documents of the whole consortium > the legal framework, governance schemes, and financial regulations for the following phases of CTA (pre-construction, construction and operation) > assuring funding for the pre-construction phase after termination of CTA-PP > the preparation of funding agreements between potential funding agencies > the preparation of negotiations with potential host countries for the CTA instrument > the detailed technical design and costing of the CTA observatory > the selection of sites for deployment negotiations, and detailing and cost-estimation of the required site infrastructure > the schemes for procurement and industry involvement in the technical design and construction of CTA > the required linking with relevant science communities regarding the detailed definition of the science program, the corresponding final optimisation of the observatory layout, and the definition of user services and data access. For CTA-PP, support is sought primarily for work on the legal, governance and financial issues, for the installation of a project office coordinating and supporting management of CTA-PP as well as the design of CTA and the planning of the implementation, and for studies regarding the optimisation and production of CTA components by industry. The ultimate delivery of CTA-PP will be a detailed implementation plan for the CTA infrastructure.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-ITN-2008 | Award Amount: 5.18M | Year: 2009

New and recent developments have revolutionized the prostate cancer research and clinical arenas, requiring the next generation scientists to have comprehensive knowledge and expertise in basic, clinical and applied research. PRO-NEST offers young researchers a European integrated, multi-disciplinary training programme to become an independent and all-round scientist and team leader in (prostate) cancer research. This network is driven by recognised and experienced scientists from 17 academic and industrial partners. The joint PRO-NEST research programme focuses on the understanding of the molecular events responsible for the initiation and progression of prostate cancer as well as on the development of novel biomarkers and therapeutic targets, with the ultimate goal to improve the diagnosis, prognosis, treatment and prevention of this major European health problem. The fellows will strongly contribute to this programme by their individual research projects that will be carried out in a high standard and collaborative scientific infrastructure under the supervision of experts in the field. In this way, they will become technical specialists in a dedicated area of cancer research. The scientific and complementary skills of the fellows will be expanded and deepened by secondments and by theoretical and practical network-wide training courses on basic and clinical aspects of prostate cancer, biomarkers, technology, valorisation, scientific writing and presentation, project management, communication skills and job application skills. In an international conference entitled The European prostate cancer research floor on stage organised at the end of PRO-NEST, the fellows are given the opportunity to present themselves to potential coming academic and industrial employers. The expertise, state of the art tools and technological skills provided by each of the partners are competitive at the world scale, and form the comprehensive basis of top-level research and training in PRO-NEST. The available support from professional organizations and the existing collaborations in large research consortia ensures the successful realization of the PRO-NEST goals.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2011-ITN | Award Amount: 3.89M | Year: 2012

The objectives of the proposal are: - To introduce ESRs and ERsto a range of astrodynamical concepts and problems and the relevant new mathematical theories and techniques. To develop their expertise in a number of these fields and to train them to conduct research, collaborate, and communicate their results. - To deepen and and broaden the knowledge and skills of ERs working in the areas of astrodynamics and dynamical systems theory. To encourage the more mathematical scientists to apply their skills to spacecraft dynamics and control, and the more applied scientists to apply new ideas and theories from mathematics to their problems - To provide both ESRs and ERs with the complementary communications and project management skills that are needed, in addition to scientific skills, for a successful career in either an academic or a non-academic enviroment.


Grant
Agency: GTR | Branch: NERC | Program: | Phase: Research Grant | Award Amount: 401.39K | Year: 2011

Future climate change is one of the most challenging issues facing humankind and an enormous research effort is directed at attempting to construct realistic projections of 21st century climate based on underlying assumptions about greenhouse gas emissions. Climate models now include many of the components of the earth system that influence climate over a range of timescales. Understanding and quantifying earth system processes is vital to projections of future climate change because many processes provide feedbacks to climate change, either reinforcing upward trends in greenhouse gas concentrations and temperature (positive feedbacks) or sometimes damping them (negative feedbacks). One key feedback loop is formed by the global carbon cycle, part of which is the terrestrial carbon cycle. As carbon dioxide concentrations and temperatures rise, carbon sequestration by plants increases but at the same time, increasing temperatures lead to increased decay of dead plant material in soils. Carbon cycle models suggest that the balance between these two effects will lead to a strong positive feedback, but there is a very large uncertainty associated with this finding and this process represents one of the biggest unknowns in future climate change projections. In order to reduce these uncertainties, models need to be validated against data such as records for the past millennium. Furthermore, it is extremely important to make sure that the models are providing a realistic representation of the global carbon cycle and include all its major component parts. Current models exclude any consideration of the reaction of peatlands to climate change, even though these ecosystems contain almost as much carbon as the global atmosphere and are potentially sensitive to climate variability. On the one hand, increased warmth may increase respiration and decay of peat and on the other hand, even quite small increases in productivity may compensate for this or even exceed it in high latitude peatlands. A further complication is that peatlands emit quite large quantities of methane, another powerful greenhouse gas. Our proposed project aims to assess the contribution of peatlands to the global carbon cycle over the past 1000 years by linking together climate data and climate model output with models that simulate the distribution and growth of peatlands on a global scale. The models will also estimate changes in methane emissions from peatlands. In particular, we will test the hypotheses that warmth leads to lower rates of carbon accumulation and that this means that globally, peatlands will sequester less carbon in future than they do now. We will also test whether future climate changes lead to a positive or negative feedback from peatland methane emissions. To determine how well our models can simulate the peatland-climate links, we will test the model output for the last millennium against fossil data of peat growth rates and hydrological changes (related to methane emissions). To do this, we will assemble a large database of published information but also new data acquired in collaboration with partners from other research organisations around the world who are involved in collecting information and samples that we can make use of once we undertake some additional dating and analyses. Once the model has been evaluated against the last millennium data, we will make projections of the future changes in the global carbon cycle that may occur as a result of future climate change. This will provide a strong basis for making a decision on the need to incorporate peatland dynamics into the next generation of climate models. Ultimately we expect this to reduce uncertainty in future climate change predictions.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-ITN-2008 | Award Amount: 4.68M | Year: 2009

Photoprotection against excess absorbed light energy is an essential and universal attribute of oxygenic photosynthetic organisms. This requirement has been a strong force in the evolution of plants and micro-organisms, and a diverse range of solutions have arisen. It has determined survival, productivity and habitat preference, and it determines the ceiling on the efficiency of energy conversion in photosynthesis in natural environment. Its investigation also provides insights into unique nanoscale switching processes. Understanding the molecular mechanisms of biological light adaptation will therefore have implication for many aspects of life, such as agriculture and food security, biodiversity and global climate change, biosolar energy and biofuels. This network brings together major high-quality EU centres with expertise in a wide range of disciplines from plant physiology to molecular biology, structural biology and photophysics and with great interest in interdisciplinary collaborative research. The network will thus provide a unique training opportunity for young researchers in key aspects of molecular biosciences and biophysical sciences in the context of practical applications in instrument development, agronomy, ecology and biotechnology. Researchers from within and outside this network will receive key research skills from several disciplines combined in a high-level and intrinsically collaborative research project, key transferable skills on information technology, written and oral communication and critical assessment, and key business and commercial skills on commercial exploitation and product development.


Grant
Agency: European Commission | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2015-ETN | Award Amount: 3.87M | Year: 2016

In the face of the increasing global consumption of fossil resources, photosynthetic organisms offer an attractive alternative that could meet our rising future needs as clean, renewable, sources of energy and for the production of fine chemicals. Key to the efficient exploitation of these organisms is to optimise the conversion of Solar Energy into Biomass (SE2B). The SE2B network deals with this optimisation in an interdisciplinary approach including molecular biology, biochemistry, biophysics and biotechnology. Regulation processes at the level of the photosynthetic membranes, integrating molecular processes within individual proteins up to flexible re-arrangements of the membranes, will be analysed as a dynamic network of interacting regulations. SE2B will yield information about the similarities and differences between cyanobacteria, green algae, diatoms and higher plants, the organisms most commonly employed in biotechnological approaches exploiting photosynthetic organisms, as well as in agriculture. The knowledge gained from understanding these phenomena will be directly transferred to increase the productivity of algal mass cultures for valuable products, and for the development of sophisticated analytic devices that are used to optimise this production. In future, the knowledge created can also be applicable to the design of synthetic cell factories with efficient light harvesting and energy conversion systems. The SE2B network will train young researchers to work at the forefront of innovations that shape the bio-based economy. SE2B will develop a training program based on individual and network-wide training on key research and transferable skills, and will furthermore disseminate these results by open online courses prepared by the young researchers themselves.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-SA | Phase: SEC-2007-6.3-01;SEC-2007-6.4-02 | Award Amount: 971.80K | Year: 2009

The FESTOS goal is to identify and assess evolving security threats posed by abuse or inadequate use of emerging technologies and new S&T knowledge, and to propose means to reduce their likelihood. Almost all such knowledge can be abused or cause damage through inadequate use. In a free society this should not hinder free generation and exchange of knowledge. As the pace of science-based development accelerates, there is a pressing need for continual scanning of the unfolding technology landscape for potential security threats. Looking ahead to 2030, the foresight study will identify and assess security threats that could stem from future technologies. Robotics, Cognition, New Materials, Nano and Biotechnologies are some of the fields to be scanned. FESTOS will stimulate an out of the box anticipatory thinking and construct threat scenarios by analysing the impact of the identified threats on the background of envisioned security climates (societal context of security issues). The threat scenarios will be evaluated in terms of their levels of impact and uncertainty. In conjunction with each scenarios critical early-warning indicators will be identified, namely signals that hint at a growing likelihood of specific scenarios and thus provide basis for possible prevention means. Societal issues will be discussed, as well as the controversial issue of controlled dissemination of scientific knowledge in the context of necessary trade-offs between security and the freedom of research and knowledge. Finally policy recommendations will be derived, aiming at novel means of preparedness. Adequate mix of Foresight methods will be employed, e.g. horizon scanning, weak signals analysis, expert surveys, brainstormings, futures wheel, interactive scenario building, STEEPV analysis. Key European stakeholders are addressed in the projects dissemination plan. The impact of successful foresight in FESTOS could be the initiation of a continuous anticipatory process in Europe.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-2.4.1-3 | Award Amount: 4.84M | Year: 2008

Genomic instability is a characteristic of practically all human cancers. Recent results generated by members of this Consortium suggest that signs of genomic instability are evident from the very beginning of human cancer development, even in precancerous lesions. In these early lesions, the genomic instability affects primarily specific genomic loci, called common fragile sites. Because common fragile sites are very sensitive to perturbations in DNA replication, we proposed that cancer development from its very beginning is associated with DNA replication stress. A separate set of observations focused on telomeres and showed that short telomeres mimick DNA ends, activate the DNA damage checkpoint and promote genomic instability and cancer development. We propose here to study the role of DNA replication stress and short telomeres on driving genomic instability particularly in human precancerous lesions. Our studies will investigate the most common forms of cancer in the EU and will benefit from access to some of the largest databases of cancerous and precancerous lesions in Europe. Genomic instability will be explored using high resolution genomic arrays and the data will be correlated to clinical information on tumor progression. Further, analysis of proteins and genes involved in the cellular response to DNA replication stress and short telomeres will be explored using high throughput and targeted approaches and will be used to identify novel targets for cancer therapy.


Grant
Agency: European Commission | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2016 | Award Amount: 3.97M | Year: 2017

MMbio will bridge the classically separate disciplines of Chemistry and Biology by assembling leading experts from academia and non-academic partners (industry, technology transfer & science communication) to bring about systems designed to interfere therapeutically with gene expression in living cells. Expertise in nucleic acid synthesis, its molecular recognition and chemical reactivity is combined with drug delivery, cellular biology and experimental medicine. This project represents a concerted effort to make use of a basic and quantitative understanding of chemical interactions to develop and deliver oligonucleotide molecules of utility for therapy. Our chemical biology approach to this field is ambitious in its breadth and represents a unqiues opportunity to educate young scientists across sectorial and disciplinary barriers. Training will naturally encompass a wide range of skills, requiring a joint effort of chemists and biologists to introduce young researchers in a structured way to and array of research methodologies that no single research grouping could provide. The incorporation of early-stage and later stag ebiotechnology enterprises ensures that commercialisation of methodologies as well as the drug development process is covered in this ITN. We hope that MMBio will train scientists able to understand both the biological problem and the chemistry that holds the possible solution and develop original experimental approaches to stimulate European academic and commercial success in this area.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: PHC-30-2015 | Award Amount: 5.01M | Year: 2016

SMARTool aims at developing a platform based on cloud technology, for the management of patients with coronary artery disease (CAD) by standardizing and integrating heterogeneous health data, including those from key enabling technologies. The platform includes existing multiscale and multilevel ARTreat (FP7-224297) models of coronary plaque progression based on non-invasive coronary CT angiography (CCTA) and fractional flow reserve computation, refined by heterogeneous patient-specific non-imaging data (history, lifestyle, exposome, biohumoral data, genotyping) and cellular/molecular markers derivable from a microfluidic device for on-chip blood analysis. SMARTool models will be applied and validated by historical and newly acquired CCTA imaging plus non-imaging health data from the EVINCI project (FP7-222915) population. SMARTool cloud-based platform, through Human Computer Interaction techniques, 3D visual representation and artery models, will use heterogeneous data in a standardized format as input, providing as output a CDSS - assisted by a microfluidic device as a point of care testing of inflammatory markers for: i) Patient specific CAD stratification - existing models, based on clinical risk factors, will be implemented by patient genotyping and phenotyping to stratify patients with non-obstructive CAD, obstructive CAD and those without CAD, ii) site specific plaque progression prediction - existing multiscale and multilevel ARTreat tools of CAD progression prediction will be refined by genotyping and phenotyping parameters and tested by baseline and follow CCTA and integrated by non-imaging patient-specific data, iii) patient-specific CAD diagnosis and treatment - life style changes, standard or high intensity medical therapy and a virtual angioplasty tool to provide the optimal stent type(s) and site(s) for appropriate deployment.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: INFRAIA-01-2016-2017 | Award Amount: 10.51M | Year: 2017

RadioNet is a consortium of 28 institutions in Europe, Republic of Korea and South Africa, integrating at European level world-class infrastructures for research in radio astronomy. These include radio telescopes, telescope arrays, data archives and the globally operating European Network for Very Long Baseline Interferometry (EVN). RadioNet is de facto widely regarded to represent the interests of radio astronomy in Europe. A comprehensive, innovative and ambitious suite of actions is proposed that fosters a sustainable research environment. Building on national investments and commitments to operate these facilities, this specific EC program leverages the capabilities on a European scale. The proposed actions include: - Merit-based trans-national access to the RadioNet facilities for European and for the first time also for third country users; and integrated and professional user support that fosters continued widening of the community of users. - Innovative R&D, substantially enhancing the RadioNet facilities and taking leaps forward towards harmonization, efficiency and quality of exploitation at lower overall cost; development and delivery of prototypes of specialized hardware, ready for production in SME industries. - Comprehensive networking measures for training, scientific exchange, industry cooperation, dissemination of scientific and technical results; and policy development to ensure long-term sustainability of excellence for European radio astronomy. RadioNet is relevant now, it enables cutting-edge science, top-level R&D and excellent training for its European facilities; with the Atacama Large Millimetre Array (ALMA) and the ESFRI-listed Square Kilometre Array (SKA) defined as global radio telescopes, RadioNet assures that European radio astronomy maintains its leading role into the era of these next-generation facilities by involving scientists and engineers in the scientific use and innovation of the outstanding European facilities.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2011-ITN | Award Amount: 4.10M | Year: 2012

Europe must face the Grand Challenges of climate change and global warming, which will seriously affect the production of foods, including animal feeds. Tightening supplies of energy, foods and feeds will further impact on food security. Feeding animals in Europe with large quantities of imported soyabeans is not sustainable. Home-grown protein sources, such as forage legumes, offer a valuable alternative, but ruminant animals make inefficient use of protein from most forage legumes. LegumePlus proposes to investigate alternative forage legumes, which increase feed use efficiency through their bioactive polyphenols. In addition to tackling such sustainability issues, they will also contribute to livestock health, welfare and reduce environmental emissions. LegumePlus will study the efficacy of bioactive legumes to i) optimise ruminant nutrition, ii) reduce greenhouse gas emissions and iii) improve milk, cheese and meat quality. It will also investigate how bioactive legumes can control parasitic worms in animals. This network will enable integrated multidisciplinary and intersectoral research training. New tools for comparative genomics in plant breeding will be harnessed and exploited to benefit ruminants and the environment. A new generation of agricultural biotechnologists will be trained to work across disciplines and solve sustainability and bioresource issues. Young researchers will acquire a thorough understanding of ruminant nutrition and parasitology, analytical chemistry and plant breeding and excellent training in state-of-the-art and industrially relevant scientific skills. Close collaboration between participants from the public and private sectors will ensure that the training programme will enhance the employability of young researchers and meet employers requirements for interdisciplinary and transferrable skills. This will contribute to the EU policy aim of transforming Europe into an eco-efficient, knowledge based bio-economy.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2012-2.2.4. | Award Amount: 6.56M | Year: 2012

The Infrastructure for Systems Biology in Europe (ISBE) programme comprises an infrastructure that is designed to meet the needs of European systems biology, in terms of development, applications and training. In order to address this requirement, we are proposing a distributed, interconnected infrastructure which primarily comprises three types of centres: Data Integration Centres (DICs), and systems biology dedicated Data Generation Centres (DGCs), and Data Stewardship Centres (DSCs). DICs are research centres that apply and develop expertise in model-driven data integration and make this expertise available to the community. DGCs are technology-based centres that make available a wide range of high, medium and low throughput technologies that are essential for the acquisition of quantitative datasets under standardised conditions. DSCs are centres that are responsible for data processing, curation and analysis they store data, models and simulations. Each type of centre will be functionally different, but organisationally similar. Within participating universities and other organisations across Europe there will be foci of expertise and facilities which fit the requirements for a DIC, DGC or DSC. Such foci will be evaluated and then designated as local centres of a particular type. Each focus will then form a component of a particular type of DIC, DGC or DSC centre. ISBE centres may be single institutions or can be distributed. Large institutions, such as leading universities, may well contribute facilities and expertise across different types of centres. A particular distributed centre may focus on an area of Systems Biology; for example, a model organism, a disease, or, alternatively an area such as biotechnology, ecology or green biology. Importantly, the ISBE will include technological expertise; for example, stochastic computation, algorithmic modelling, multi-scale modelling integration of diverse high-and low-throughput datasets.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2007-2.2-01 | Award Amount: 7.16M | Year: 2008

The Preparatory Phase for a pan-European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) will focus on technical, legal, governance, and financial issues to prepare to construct BBMRI, building on existing biobanks, resources and technologies, specifically complemented with innovative components and properly embedded into European scientific, ethical, legal and societal frameworks, provide the concept for a key resource to increase excellence and efficacy in biomedical sciences, drug development and public health, expand and secure competitiveness of European research and industry in a global context, develop a sustainable financial framework. Biomedical quality-assessed samples and data as well as biomolecular resources and molecular analysis tools are essential for academic and industry-driven research to treat and prevent human diseases. Although currently established national biobanks and biomolecular resources are a unique European strength, valuable collections typically suffer from fragmentation of the European biobanking-related research community. This hampers the collation of biological samples and data from different biobanks required to achieve sufficient statistical power. Moreover, it results in duplication of effort and jeopardises sustainability due to the lack of long-term funding. BBMRI will comprise: biobanks of different formats (collections of blood, DNA, tissue, etc., together with medical, environmental, life-style and follow-up data), biomolecular resources (antibody and affinity binder collections, ORF clone collections, siRNA libraries, proteins, cellular resources etc.), enabling technologies and high-throughput analysis platforms and molecular tools to decipher gene, protein and metabolite functions and their interactions, harmonized standards for sample collection, storage, preanalytics and analysis harmonized databases and biocomputing infrastructure, ethical, legal and societal


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-CA | Phase: REGIONS-2012-2013-1 | Award Amount: 2.95M | Year: 2013

The proposed BALTIC-FLOWS project concerns rainwater monitoring and management in Baltic Sea catchment areas. Rainwater forms streams and rivers, and in urban environments, heavy rainfall can amount to stormwater and floods. Over the years, much of this rainwater ends up in the sea. In Northern Europe, the Baltic Sea conceals a history of water quality from streams, rivers and urban runoff in catchment areas. Encircled by a mix of Nordic, Central and Eastern European countries, the Baltic Sea is at the mercy of a diversity of national practices and policies. The project shall lay the foundation for development of new capacities and policies for effectively monitoring and managing the quality and quantities of rainwater moving from one place to the next. The project focuses on streams, rivers and cities in Baltic Sea catchment areas, not on the sea itself. The strategies, knowledge and expertise created during the project can be exploited elsewhere in the Union and in other global regions. The project will support the development of research-driven clusters in each region; enhanced capacities in diffuse load monitoring and urban stormwater management will lead to new business opportunities in the global market for water monitoring and management know-how and solutions. A total of 47 organisations will be participating in the project: 16 project partners in five European regions - Estonia, Finland, Germany, Latvia and Sweden, one project partner from the UK specialised in the Chinese environmental sector, and 30 supporting partners, including entities in participating regions, entities in the international regions of Russia, China, Vietnam and Brazil, inter-regional financing entities operating in the Baltic Sea region, and a Russian-Belarus collaboration forum. The project primarily addresses domain b) of the REGIONS-2012-2013-1 topic, but is also strongly related to themes in domain a).


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: ENV.2007.2.2.1.2. | Award Amount: 5.62M | Year: 2008

Over the past two decades, an increasing proportion of North Atlantic salmon are dying at sea during their oceanic feeding migration. The specific reasons for the decline in this important species are as yet unknown, however, climate change is likely to be an important factor. In some rivers in the southern part of the salmons range, wild salmon now face extinction. This is in spite of unprecedented management measures to halt this decline. Arguably the greatest challenge in salmon conservation is to gain insight into the spatial and ecological use of the marine environment by different regional and river stocks, which are known to show variation in marine growth, condition, and survival. Salmon populations may migrate to different marine zones, whose environmental conditions may vary. To date it has been impossible to sample and identify the origin of sufficient numbers of wild salmon at sea to enable this vital question to be addressed. SALSEA-Merge will provide the basis for advancing our understanding of oceanic-scale, ecological and ecosystem processes. Such knowledge is fundamental to the future sustainable management of this key marine species. Through a partnership of 9 European nations the programme will deliver innovation in the areas of: genetic stock identification techniques, new genetic marker development, fine scale estimates of growth on a weekly and monthly basis, the use of novel high seas pelagic trawling technology and individual stock linked estimates of food and feeding patterns. In addition, the use of the three-dimensional Regional Ocean Modelling System, merging hydrography, oceanographic, genetic and ecological data, will deliver novel stock specific migration and distribution models. This widely supported project, provides the basis for a comprehensive investigation into the problems facing salmon at sea. It will also act as an important model for understanding the factors affecting survival of many other important marine species.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2010.2.4.5-2 | Award Amount: 7.90M | Year: 2011

Type 1 diabetes is caused by an inflammatory process which damage insulin-producing beta-cells in the pancreas. It is one of the most common chronic diseases and its incidence is rapidly increasing. Due to its complications it causes a significant medical and economic burden to European society. A causal association between enterovirus and type 1 diabetes has become more and more likely. The aim of the present research programme is to create a new research strategy aligned to a concerted scientific research effort and creation of a network of unique resources which makes it possible to achieve a significant breakthrough in this field. The main focus is in the detection of persistent enterovirus infection leading to inflammation and tissue damage in the pancreas and its role in mediating the inflammatory response that causes type 1 diabetes. The goal is to take the critical steps towards therapeutic translation of research findings by employing a novel research design and synergistic networks of excellence based on the combination of a multidisciplinary research strategy and availability of unique biobanks existing in Europe. This research programme will also create a completely new type of biobank which facilitates a wide range of new analyses of fresh tissues. The programme includes a strong translational component which facilitates the ongoing efforts to develop vaccines against diabetogenic enteroviruses and other targeted therapies. The program also has a wider impact on the entire field of research on pathogen-disease associations, since the same innovative research strategy can be applied to other diseases as well. Altogether, this research program will take full advantage of the excellent biobank networks and a long tradition in biomedical and clinical research in Europe and creates an exceptional opportunity to take the final steps towards proving causality in the enterovirus-diabetes association.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: ENERGY-2007-3.5-01 | Award Amount: 5.53M | Year: 2008

SOLAR-H2 brings together 12 world-leading European laboratories to carry out integrated, basic research aimed at achieving renewable hydrogen (H2) production from environmentally safe resources. The vision is to develop novel routes for the production of a Solar-fuel, in our case H2, from the very abundant, effectively inexhaustible resources, solar energy and water. Our multidisciplinary expertise spans from molecular biology, biotechnology, via biochemistry and biophysics to organo-metallic and physical chemistry. The project integrates two frontline research topics: artificial photosynthesis in man-made biomimetic systems, and photobiological H2 production in living organisms. H2 production by these methods on a relevant scale is still distant but has a vast potential and is of utmost importance for the future European economy. The scientific risk is high - the research is very demanding. Thus, our overall objective now, is to explore, integrate and provide the basic science necessary to develop these novel routes and advance them toward new horizons. Along the first track, the knowledge gained from biochemical/biophysical studies of efficient enzymes will be exploited by organometallic chemists to design and synthesize bio-mimetic compounds for artificial photosynthesis. The design of these molecules is based on molecular knowledge about how natural photosynthesis works and how hydrogenase enzymes form H2. Along the second track, we perform research and development on the genetic level to increase our understanding of critical H2 forming reactions in photosynthetic alga and cyanobacteria. These studies are directly aimed at the improvement of the H2 producing capability of the organisms using novel genetic and metabolic engineering. The project also involves research aimed at demonstrating the concept of photobiological H2 production in photobioreactors.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-1.2-2;HEALTH-2007-2.4.1-4 | Award Amount: 5.54M | Year: 2008

The overall objective of this proposal is to develop and validate a quantitative, minimally invasive diagnostic tool for early and conclusive detection, diagnosis and monitoring of disease and disease progression of breast and prostate cancer. A methodology will be developed making use of a combination of the probably most exciting recent advances in the field of light microscopy, for fluorescence-based optical imaging of individual sample cells. It includes advances which will take the spatial resolution far beyond the fundamental limits of optical resolution, the sensitivity down to an ultimate single-molecule level, and multi-parameter detection schemes significantly increasing the fluorescence information by which these cellular images can be analysed. Apart from detecting and identifying tumour markers in the samples, tumour-specific spatio-temporal molecular distributions within the intact sample cells will be exploited. This is to date an almost unexploited dimension of diagnostic information. By combining and supporting these novel optical methods with state-of-the-art affinity molecule biotechnology, , tumor biomarkers, fluorophore chemistry, and bioinformatic validation tools, all possible means will be exploited to extract a maximum amount of information out of very small amounts of sample material. We thereby expect that an improved, early and reliable diagnosis of breast and prostate cancer will be possible, from amounts of sample material small enough that a minimally invasive procedure such as Fine-needle aspiration (FNA) can be used. In addition, by the minimally invasive FNA-based sampling, serious sampling-related side-effects, such as seeding and spread of cancer cells can be completely avoided. Given the high incidence of breast and prostate cancer, and the utmost importance of an early and conclusive diagnosis for the prognosis of these diseases, the relevance of this project can not be overestimated.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2013.1.2-1 | Award Amount: 7.83M | Year: 2014

Background: Hyperinsulinaemic hypoglycaemia (HH) is a potentially lethal disease caused by over functioning beta cells derived from the pancreatic islets of Langerhans. Lethal HH and brain damage is a problem especially in infants with congenital HH. Current therapeutic approaches are associated with severe side effects/morbidity (diabetes, exocrine pancreas insufficiency etc.) considered acceptable in relation to the lethal outcome of HH although massively reducing quality of life and also life expectancy. Aims and objectives: In order to significantly improve therapy of this awful disorder, we propose to develop a simultaneous imaging/therapy platform allowing diagnostic imaging as well as image guided surgical, photodynamic or radiopeptide therapy to selectively resect/destroy diseased beta cells. This platform will enable delivery of patient-individual tailored therapy, increasing cure rate while significantly reducing or even avoiding side effects. The platform will integrate information from pre-clinical imaging for optimal therapy planning with intra-operative imaging for image guided surgery. By implementation of extended field optical coherence tomography, information on a histopathological level will allow increased precision of therapy. Highly innovative photodynamic therapy will enable selective (endoscopic) destruction of diseased beta cells without resection of pancreatic tissue. Outcome: Our highly-innovative integrated imaging/therapy (theranostic) platform will allow diagnosis and monitoring of disease, support and guide therapeutic intervention, predict outcome of intervention and individual prognosis. This technology will massively improve therapy, especially in infants, by improving cure rates while significantly reducing morbidity for improved quality of life and increased life expectancy. We will contribute to the goals of the International Rare Diseases Research Consortium (IRDiRC): 200 new therapies.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: SSH-2007-2.1-02 | Award Amount: 1.51M | Year: 2008

The consortium participants have developed tools for analysing the different dimensions of sustainability in a FP6 project DECOIN (Development and Comparison of Sustainability Indicators). The objective of the proposed SMILE project is to apply and further develop these tools to analyse the trade-offs and synergies between different aspects of sustainable development. A number of case studies will be carried out to assess the use of the toolkit in different socio-economic, environmental and cultural contexts and at different levels. The project analyses the trade-offs and synergies that exist between the different objectives related to sustainable development by utilising the different indicators developed within the European Sustainable Development Indicator (SDI) Working Group as well as new types of indicators provided by the tools developed by the consortium partners in previous projects. The assessment takes place (i) between economic and environmental aspects, (ii) between economic and social aspect, (iii) between social and environmental aspects and (iv) between all the three objectives. In addition, interfacing the scientific results with societal/policy processes (stakeholder participation, sustainable consumption and production patterns) will be assessed and policy recommendations will be formulated. The assessment of the interlinkages of the different dimensions will form the basis for policy recommendations on improvement of sustainability conditions at various geographical scales. The futures oriented approach of the project, including construction of different scenarios of future development paths relating to the synergies and trade-offs, will provide knowledge that will be relevant for economic, social and environmental policies and their combination in the longer term.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: SSH-2007-3.1-01 | Award Amount: 1.65M | Year: 2008

DEMHOW will investigate links between demographic change and housing wealth. Whereas those who rent their homes may have no housing wealth at all, for many older Europeans - perhaps 75% of the total - housing is their single largest item of wealth But, increasing numbers do not have children to whom their wealth might be bequeathed. The potential of housing assets is that they offer: older households a way of increasing their consumption; governments a way to respond to the pension crisis;and financial institutions a way to increase business. DEMHOW will investigate the ways in which, across member states, ageing populations and housing wealth are linked, how housing wealth has been used in the past and how attitudes to its use in old age are changing. In addition, it will investigate developments in policy and in financial markets that may encourage its use as a form of pension, and assess the characteristics of housing assets as a form of pension.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: HEALTH-2007-2.1.2-2 | Award Amount: 14.64M | Year: 2008

T-cell activation, whether induced by pathogens or auto-antigens, is a complex process relying on multiple layers of tightly controlled intracellular signalling modules that form an intricate network. Defects in this network can cause severe and chronic disorders such as autoimmune diseases. Although 5% of the population suffer from these diseases, only a few therapeutic treatments are available. To a large extent this is attributed to the lack of systems-level insights, which would provide concepts of how to modulate T-cell activation. The SYBILLA project groups 14 partners from 9 different EU countries, including 3 SMEs. Through a multidisciplinary effort it aims to understand at the systems level, how T-cells discriminate foreign from auto-antigens. Towards this goal, a transgenic mouse system will be used as a tractable physiological model. Data will be validated in human T-cells and a humanised mouse model for multiple sclerosis. SYBILLA will develop technological and mathematical tools to generate and integrate high-density quantitative data describing T-cell activation. Proteomics, transcriptomics, metabolomics, imaging and multiplexed biochemical techniques will be applied to obtain holistic maps of T-cell signalling networks and to achieve a quantitative understanding of the network and its regulation in response to different inputs. Building upon our existing network model, constant iterations will be used to develop more robust dynamic models to describe the networks response to perturbations. This will culminate in the generation of a Virtual T-Cell, allowing computer simulation to refine the predictability of physiological and pathophysiological reactions. SYBILLAs impact on EU biopharmaceutical competitiveness will be enormous through identification of new pharmacologic targets, optimised prediction of immunomodulatory drug efficacy, discovery of new concerted biomarkers and improvement of personalised medication for treating autoimmune diseases.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: SSH.2011.2.1-2 | Award Amount: 3.46M | Year: 2012

This research proposal takes as its starting points: (a) the long standstill in poverty reduction, especially for people of working age, (b) the complementarity between employment, economic growth and social inclusion that is focal in the EU 2020 strategy, and, (c) the emergence of socially innovative policies and actions in the margins of the European welfare states. It aims at the evaluation of the Lisbon decade in terms of policies and actions against poverty at European, national and sub-national level and at improving the understanding of the interrelationships between employment, social protection and social inclusion and between institutionalised macro level social policies and innovative local action. The proposal views sustainable growth strategies, effective employment policies and adequate social designs as the drivers of every strategy to reduce and eliminate poverty and social exclusion. It considers local socially innovative practices as laboratories to complement and modify these macro-level policies. The quantitative analysis of poverty trends in the past, the adequacy of existing policies and the implications of alternative scenarios for employment and tax-benefit-services schemes to meet the 2020 poverty targets will therefore be complemented with in-depth studies of selected cases of local social policies. The research will develop new tools for monitoring poverty, social policy and social innovative practices. For the first time reference budgets will be computed for several member states. The research consortium together with the support from well-known associates and two outstanding Advisory Boards, involving academics, policy makers and civil society organisations and the broad dissemination plan, will allow the highly experienced multidisciplinary research team to deliver important new answers to questions of great importance to European societies.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 3.31M | Year: 2012

Aim of the CAFFEIN network is to provide 10 early stage researchers (ESRs) and 2 exprerienced researchers (ERs) with excellent training in an industry relevant area of cancer research, complementary skills required for pharmaceutical industry, and knowledge in setting up biomedical start-up companies. To this end, the network comprises two full industrial partners: the established pharmaceutical company Medimmune, a global leader in immunopharmaceuticals, and the small biotech company Gimmune, which used breakthrough results in nanotechnology to establish a new enterprise. The research focus of CAFFEIN, which stands for Cancer Associated Fibroblasts (CAF) Function in Tumor Expansion and Invasion, is to understand the mechanisms, how fibroblastoid cells support tumor progression and metastasis formation. CAF biology is therefore rather complex, but the research groups of the CAFFEIN network cover many different aspects of it, thus having a critical mass to provide relevant training in this area. Training in complementary skills important for work in the pharmaceutical industry is provided by the industrial partner MedImmune, where communication with management, industrial project planning, IPR, etc. will be taught. Entrepreneurial skills, business plans, funding by venture capitalists, and patentability of research findings are highlights of the training provided by the industrial partner Gimmune. All this training is transmitted to the ESRs/ERs by networkwide events, secondments and tight research collaboration. Taken together, the CAFFEIN research training network combines the acquisition of excellent scientific knowledge in an area highly attractive for pharmaceutical industry with special education in relevant complementary skills that increase employment chances of the trained researchers in industry and that encourage them to translate their scientific results into products, thus improving health and economic welfare of European citizens.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: SSH-2009-1.1.1. | Award Amount: 3.52M | Year: 2010

The GOETE project will analyse the role of school in re-conceptualising education in terms of lifelong learning by combining a life course and a governance perspective. In European knowledge societies adequacy of education means a balance of individual, social and economic aspects. This is operationalised by exploring how educational institutions conceptualise and organise individual educational trajectories. The study covers the period from transition into lower secondary education to transition into upper secondary education/vocational education and training, i.e. the age group between 10 and 16 years. Comparative analysis will focus on the regulation of access to education, of support measures for coping with education and of securing the relevance of education for social integration and the labour market. In 8 EU countries the mixed-method study involves surveys with students, parents and school principals; comparison of teacher training; case studies of local school spaces; discourse analysis; expert interviews with policy makers and stakeholders. On a scientific level, the comparison of the regulation of educational trajectories involves re-conceptualising the social aspects of learning and education under conditions of late modern knowledge societies. It reflects the need for formal education to be embedded in social life worlds, enabled by social support, and complemented by informal and non-formal learning. On a practice and policy level, it will provide information about alternative means of providing children and young people with access to education; of supporting them in coping with education and ensuring the relevance of education by communication and cooperation between school, labour market, other educational actors, students and parents. The communication of findings will include a dialogic model of educational policy planning at local level, training workshops with teachers, youth workers and policy makers, and a European policy seminar.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: SSH-2007-2.1-04 | Award Amount: 1.80M | Year: 2008

Most business-as-usual scenarios built up till now have shown that hydrocarbon resources scarcity and the growing release of greenhouse gases will bring the world far away from sustainability over the next decades. Then, deep changes in behaviours away from BAU are unavoidable long before the turn of the century in a move towards a post-carbon society. Urbanisation and mobility are probably the domains where these changes might be the most important and they will be necessarily driven and limited by socio-economic and cultural forces that will dominate the century. They will induce further deep changes in behaviours of consumers and producers and are likely to deeply impact the use and production of bulk materials, large energy consumers and GHG emitters. To address these challenges, key milestones were defined by the EU : - A 20% reduction (minimum) of CO2 emissions by 2020 (compared to 1990) in Europe - A reduction of the GHG emissions by 2050 and after, so as to limit the increase of the temperature due to climatic change within 2C. In this framework, the PACT project objective is to provide strategic decision-support information to decision makers to achieve these milestones. It will focus on 3 themes : - What shape the energy demand, and how this should evolve towards post-carbon concept, from the infrastructures viewpoint, in relation to urbanisation and land-use schemes, and that of the life-styles and behaviours, in relation to the available technologies. - The question of urbanisation and land-use from the renewable energy perspective, including that of the systems. - The role of social forces, actors, stakeholders in the transition process. PACT will address these issues in two phases: first, by developing the necessary analytical and conceptual framework, second in attempting to quantify scenarios of post-carbon societies at EU and world level by 2050 and beyond, using enhanced versions of the VLEEM and POLES models.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-2.4.3-9 | Award Amount: 7.09M | Year: 2008

The development of sensitive, non-invasive methods for the characterisation and quantification of beta-cell mass would greatly enhance our means for gaining understanding of the pathophysiology of diabetes and allow the development of novel therapies to prevent, halt and reverse the disease. The aim of this project is to develop and apply innovative approaches for beta-cell imaging, the emphasis being on beta-cell mass regulation (loss and neogenesis) with the perspective of entering initial clinical trials. For this purpose, our approach is to: (1) Focus on imaging technologies offering the potential to enter clinical trials during the runtime of the project. Since beta cells contribute only marginally (1-2%) to the total mass of the pancreas, a highly sensitive method for clinical imaging is required. BETA IMAGE will focus on positron emission tomography (PET) relying on chemical resolution, i.e. the specificity of a radiolabelled tracer molecule. The lead compound will be radiolabelled Exendin 4, developed in the consortium for GLP-1 receptor imaging. (2) Devise novel imaging strategies by generating labelled design molecules/peptides/nanobody molecules targeting newly identified beta-cell surface proteins. These targets will be identified using a Systems Biology approach. For high-throughput tracer development, a stream-lined methodology will be established based on in vitro model systems and micro-/macroscopic in vivo real time dynamic imaging of tracer distribution by optical coherence tomography and complementary small animal PET and MRI. (3) Build on European excellence in tracer development using peptides, peptide-like and organic molecules for different imaging modalities. To achieve these ambitious goals, we have established a highly interdisciplinary and interactive project combining leading European research groups. In this way, a unique expertise is achieved regarding tracer development and imaging, beta-cells/diabetes and target definition.


HELSINKI, Finland--(BUSINESS WIRE)--Transitioning to a fully renewable electricity system is possible for South America by 2030. A study by Lappeenranta University of Technology (LUT) and VTT Technical Research Centre of Finland Ltd. also shows that a 100 percent renewable system (100% RE) is the cheapest electricity production option and can be achieved with very few energy storages. “South America has a unique renewable energy resource base since one of the best wind sites globally is in Patagonia, the best solar energy sites are in the Atacama Desert, hydro power is already used in large amounts and the sustainable biomass potential is significant. For these reasons, South America is one of the most favourable regions globally to shift to a 100% RE system,” explains Professor Christian Breyer. The cost of electricity in a 100% RE system ranges between 47 to 62 euros per megawatt hour, depending on the applied assumptions. In comparison, other options, including new nuclear and carbon capture and storage (CCS), are 75-150 percent higher in cost than the 100% RE. The total installed capacity of renewable electricity in the fully renewable system is composed of 415 gigawatts of solar photovoltaics, 144 gigawatts of hydro dams, 39 gigawatts of hydro run-of-river, 17 gigawatts of biogas, 4 gigawatts of biomass and 69 gigawatts of wind power. The abundance of solar and wind power in South America as well as the high capacity of hydro dams means that the region does not need many energy storages. Hydro dams can be used as a virtual battery for solar and wind electricity storage, balancing generation and demand in times of lacking solar of wind electricity during the course of the year. In other parts of the world, this would require power-to-gas technology, in which electricity is converted into gases, such as hydrogen and synthetic natural gas, and converting them again back to power. The study also showed that if the current industrial natural gas demand in South America is replaced by power-to-gas technology, the need for energy storages will plummet. This is called system integration in which power-to-gas, but also other technologies, increase the flexibility of the electricity system without the need for large energy storages. This flexibility lowers the cost of electricity. This integration is estimated to save up to 13 billion euros. The research is one of several similar studies the researchers have conducted on other regions of the world. Results have already been published for North America , Northeast Asia , Southeast Asia , Central Asia and Russia , the Middle East and Northern Africa , Sub-Saharan Africa and Europe. These studies have allowed the researchers to highlight regional issues. South America has a competitive advantage over other parts of the world to develop a 100% RE system. The study was done as part of the Neo-Carbon Energy research, which is funded by the Finnish Funding Agency for Innovation, Tekes, and is carried out in cooperation with Lappeenranta University of Technology (LUT), VTT Technical Research Centre of Finland Ltd. and the University of Turku, Finland Futures Research Centre. Publications: Complementary of hydro, wind and solar power as a base for a 100% Renewable Energy supply for South and Central America Hydropower and Power-to-Gas Storage Options: The Brazilian Energy System Case This information was brought to you by Cision http://news.cision.com


News Article | December 12, 2016
Site: www.eurekalert.org

In 2015, the All Sky Automated Survey for SuperNovae (ASAS-SN) detected an event, named ASASSN-15lh, that was recorded as the brightest supernova ever -- and categorised as a superluminous supernova, the explosion of an extremely massive star at the end of its life. It was twice as bright as the previous record holder, and at its peak was 20 times brighter than the total light output of the entire Milky Way. An international team, led by Giorgos Leloudas at the Weizmann Institute of Science, Israel, and the Dark Cosmology Centre, Denmark, has now made additional observations of the distant galaxy, about 4 billion light-years from Earth, where the explosion took place and they have proposed a new explanation for this extraordinary event. "We observed the source for 10 months following the event and have concluded that the explanation is unlikely to lie with an extraordinarily bright supernova. Our results indicate that the event was probably caused by a rapidly spinning supermassive black hole as it destroyed a low-mass star," explains Leloudas. In this scenario, the extreme gravitational forces of a supermassive black hole, located in the centre of the host galaxy, ripped apart a Sun-like star that wandered too close -- a so-called tidal disruption event, something so far only observed about 10 times. In the process, the star was "spaghettified" and shocks in the colliding debris as well as heat generated in accretion led to a burst of light. This gave the event the appearance of a very bright supernova explosion, even though the star would not have become a supernova on its own as it did not have enough mass. The team based their new conclusions on observations from a selection of telescopes, both on the ground and in space. Among them was the Very Large Telescope at ESO's Paranal Observatory, the New Technology Telescope at ESO's La Silla Observatory and the NASA/ESA Hubble Space Telescope [1]. The observations with the NTT were made as part of the Public ESO Spectroscopic Survey of Transient Objects (PESSTO). "There are several independent aspects to the observations that suggest that this event was indeed a tidal disruption and not a superluminous supernova," explains coauthor Morgan Fraser from the University of Cambridge, UK (now at University College Dublin, Ireland). In particular, the data revealed that the event went through three distinct phases over the 10 months of follow-up observations. These data overall more closely resemble what is expected for a tidal disruption than a superluminous supernova. An observed re-brightening in ultraviolet light as well as a temperature increase further reduce the likelihood of a supernova event. Furthermore, the location of the event -- a red, massive and passive galaxy -- is not the usual home for a superluminous supernova explosion, which normally occur in blue, star-forming dwarf galaxies. Although the team say a supernova source is therefore very unlikely, they accept that a classical tidal disruption event would not be an adequate explanation for the event either. Team member Nicholas Stone from Columbia University, USA, elaborates: "The tidal disruption event we propose cannot be explained with a non-spinning supermassive black hole. We argue that ASASSN-15lh was a tidal disruption event arising from a very particular kind of black hole." The mass of the host galaxy implies that the supermassive black hole at its centre has a mass of at least 100 million times that of the Sun. A black hole of this mass would normally be unable to disrupt stars outside of its event horizon -- the boundary within which nothing is able to escape its gravitational pull. However, if the black hole is a particular kind that happens to be rapidly spinning -- a so-called Kerr black hole -- the situation changes and this limit no longer applies. "Even with all the collected data we cannot say with 100% certainty that the ASASSN-15lh event was a tidal disruption event," concludes Leloudas. "But it is by far the most likely explanation." [1] As well as the data from ESO's Very Large Telescope, the New Technology Telescope and the NASA/ESA Hubble Space Telescope the team used observations from NASA's Swift telescope, the Las Cumbres Observatory Global Telescope (LCOGT), the Australia Telescope Compact Array, ESA's XMM-Newton, the Wide-Field Spectrograph (WiFeS and the Magellan Telescope. This research was presented in a paper entitled "The Superluminous Transient ASASSN-15lh as a Tidal Disruption Event from a Kerr Black Hole", by G. Leloudas et al. to appear in the new Nature Astronomy magazine. The team is composed of G. Leloudas (Weizmann Institute of Science, Rehovot, Israel; Niels Bohr Institute, Copenhagen, Denmark), M. Fraser (University of Cambridge, Cambridge, UK), N. C. Stone (Columbia University, New York, USA), S. van Velzen (The Johns Hopkins University, Baltimore, USA), P. G. Jonker (Netherlands Institute for Space Research, Utrecht, the Netherlands; Radboud University Nijmegen, Nijmegen, the Netherlands), I. Arcavi (Las Cumbres Observatory Global Telescope Network, Goleta, USA; University of California, Santa Barbara, USA), C. Fremling (Stockholm University, Stockholm, Sweden), J. R. Maund (University of Sheffield, Sheffield, UK), S. J. Smartt (Queen's University Belfast, Belfast, UK), T. Krühler (Max-Planck-Institut für extraterrestrische Physik, Garching b. München, Germany), J. C. A. Miller-Jones (ICRAR - Curtin University, Perth, Australia), P. M. Vreeswijk (Weizmann Institute of Science, Rehovot, Israel), A. Gal-Yam (Weizmann Institute of Science, Rehovot, Israel), P. A. Mazzali (Liverpool John Moores University, Liverpool, UK; Max-Planck-Institut für Astrophysik, Garching b. München, Germany), A. De Cia (European Southern Observatory, Garching b. München, Germany), D. A. Howell (Las Cumbres Observatory Global Telescope Network, Goleta, USA; University of California Santa Barbara, Santa Barbara, USA), C. Inserra (Queen's University Belfast, Belfast, UK), F. Patat (European Southern Observatory, Garching b. München, Germany), A. de Ugarte Postigo (Instituto de Astrofisica de Andalucia, Granada, Spain; Niels Bohr Institute, Copenhagen, Denmark), O. Yaron (Weizmann Institute of Science, Rehovot, Israel), C. Ashall (Liverpool John Moores University, Liverpool, UK), I. Bar (Weizmann Institute of Science, Rehovot, Israel), H. Campbell (University of Cambridge, Cambridge, UK; University of Surrey, Guildford, UK), T.-W. Chen (Max-Planck-Institut für extraterrestrische Physik, Garching b. München, Germany), M. Childress (University of Southampton, Southampton, UK), N. Elias-Rosa (Osservatoria Astronomico di Padova, Padova, Italy), J. Harmanen (University of Turku, Piikkiö, Finland), G. Hosseinzadeh (Las Cumbres Observatory Global Telescope Network, Goleta, USA; University of California Santa Barbara, Santa Barbara, USA), J. Johansson (Weizmann Institute of Science, Rehovot, Israel), T. Kangas (University of Turku, Piikkiö, Finland), E. Kankare (Queen's University Belfast, Belfast, UK), S. Kim (Pontificia Universidad Católica de Chile, Santiago, Chile), H. Kuncarayakti (Millennium Institute of Astrophysics, Santiago, Chile; Universidad de Chile, Santiago, Chile), J. Lyman (University of Warwick, Coventry, UK), M. R. Magee (Queen's University Belfast, Belfast, UK), K. Maguire (Queen's University Belfast, Belfast, UK), D. Malesani (University of Copenhagen, Copenhagen, Denmark; DTU Space, Denmark), S. Mattila (University of Turku, Piikkiö, Finland; Finnish Centre for Astronomy with ESO (FINCA), University of Turku, Piikkiö, Finland; University of Cambridge, Cambridge, UK), C. V. McCully (Las Cumbres Observatory Global Telescope Network, Goleta, USA; University of California Santa Barbara, Santa Barbara, USA), M. Nicholl (Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, USA), S. Prentice (Liverpool John Moores University, Liverpool, UK), C. Romero-Ca[ñ] - https:/ izales (Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute of Astrophysics, Santiago, Chile), S. Schulze (Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute of Astrophysics, Santiago, Chile), K. W. Smith (Queen's University Belfast, Belfast, UK), J. Sollerman (Stockholm University, Stockholm, Sweden), M. Sullivan (University of Southampton, Southampton, UK), B. E. Tucker (Australian National University, Canberra, Australia; ARC Centre of Excellence for All-sky Astrophysics (CAASTRO), Australia), S. Valenti (University of California, Davis, USA), J. C. Wheeler (University of Texas at Austin, Austin, USA), and D. R. Young (Queen's University Belfast, Belfast, UK). ESO is the foremost intergovernmental astronomy organisation in Europe and the world's most productive ground-based astronomical observatory by far. It is supported by 16 countries: Austria, Belgium, Brazil, the Czech Republic, Denmark, France, Finland, Germany, Italy, the Netherlands, Poland, Portugal, Spain, Sweden, Switzerland and the United Kingdom, along with the host state of Chile. ESO carries out an ambitious programme focused on the design, construction and operation of powerful ground-based observing facilities enabling astronomers to make important scientific discoveries. ESO also plays a leading role in promoting and organising cooperation in astronomical research. ESO operates three unique world-class observing sites in Chile: La Silla, Paranal and Chajnantor. At Paranal, ESO operates the Very Large Telescope, the world's most advanced visible-light astronomical observatory and two survey telescopes. VISTA works in the infrared and is the world's largest survey telescope and the VLT Survey Telescope is the largest telescope designed to exclusively survey the skies in visible light. ESO is a major partner in ALMA, the largest astronomical project in existence. And on Cerro Armazones, close to Paranal, ESO is building the 39-metre European Extremely Large Telescope, the E-ELT, which will become "the world's biggest eye on the sky".


News Article | November 14, 2016
Site: www.greencarcongress.com

« Samsung Electronics to acquire HARMAN for ~$8B, accelerating growth in automotive and connected technologies | Main | Siemens to acquire Mentor Graphics for $4.5B » Rolls-Royce and VTT Technical Research Centre of Finland Ltd have formed a strategic partnership to design, to test and to validate the first generation of remote and autonomous ships. The new partnership will combine and integrate the two companies’ unique expertise to make such vessels a commercial reality. (Earlier post.) Rolls-Royce is pioneering the development of remote-controlled and autonomous ships and believes a remote-controlled ship will be in commercial use by the end of the decade. The company is applying technology, skills and experience from across its businesses to this development. VTT has deep knowledge of ship simulation and extensive expertise in the development and management of safety-critical and complex systems in demanding environments such as nuclear safety. VTT combines physical tests such as model and tank testing, with digital technologies, such as data analytics and computer visualisation. VTT will also use field research to incorporate human factors into safe ship design. As a result of working with the Finnish telecommunications sector, VTT has extensive experience of working with 5G mobile phone technology and wi-fi mesh networks. VTT has the first 5G test network in Finland. Working with VTT will allow Rolls-Royce to assess the performance of remote and autonomous designs through the use of both traditional model tank tests and digital simulation, allowing the company to develop functional, safe and reliable prototypes. Rolls-Royce has experience in secure data analytics across civil aerospace, defence, nuclear power and marine; coupled with its ship intelligence capabilities, design, propulsion and machinery expertise, this base means it is ideally placed to take the lead in defining the future of shipping, in collaboration with industry, academia and Government. Rolls-Royce is leading the Advanced Autonomous Waterborne Applications Initiative (AAWA). Funded by Tekes (Finnish Funding Agency for Technology and Innovation), AAWA brings together universities, ship designers, equipment manufacturers, and classification societies to explore the economic, social, legal, regulatory and technological factors which need to be addressed to make autonomous ships a reality. It combines the expertise of some of Finland’s top academic researchers from Tampere University of Technology; VTT Technical Research Centre of Finland Ltd; Åbo Akademi University; Aalto University; the University of Turku; and leading members of the maritime cluster including Rolls-Royce, NAPA, Deltamarin, DNV GL and Inmarsat. Rolls-Royce is also a member of the Norwegian Forum for Autonomous Ships (NFAS) which has the backing of the Norwegian Maritime Administration, The Norwegian Coastal Administration, the Federation of Norwegian Industries and MARINTEK. Its objectives are to strengthen the cooperation between users, researchers, authorities and others that are interested in autonomous ships and their use; contribute to the development of common Norwegian strategies for development and use of autonomous ships and co-operate with other international and national bodies interested in autonomous shipping. Rolls-Royce is also a founding member of the Finnish ecosystem for autonomous marine transport (DIMECC). Supported by the Finnish Marine Industries Association, the Ministry of Transport and Communications, Tekes (the Finnish Funding Agency for Innovation) and leading companies including Rolls-Royce, Cargotec, Ericsson, Meyer Turku, Tieto, and Wärtsilä, it aims to create the world’s first autonomous marine transport system in the Baltic Sea.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: INT-04-2015 | Award Amount: 3.72M | Year: 2016

This Project aims to address an increasingly pressing global challenge: How to achieve the EUs development goals and the UNs Sustainable Development Goals, while meeting the global target of staying within two degrees global warming and avoid transgressing other planetary boundaries. EU policies must align with sustainable development goals (Article 11 TFEU). The impacts of climate change and global loss of natural habitat undermine the progress achieved by pursuing the Millennium Development Goals and threaten the realisation of EU development policy goals. Our focus is the role of EUs public and private market actors. They have a high level of interaction with actors in emerging and developing economies, and are therefore crucial to achieving the EUs development goals. However, science does not yet cater for insights in how the regulatory environment influences their decision-making, nor in how we can stimulate them to make development-friendly, environmentally and socially sustainable decisions. Comprehensive, ground-breaking research is necessary into the regulatory complexity in which EU private and public market actors operate, in particular concerning their interactions with private and public actors in developing countries. Our Consortium, leading experts in law, economics, and applied environmental and social science, is able to analyse this regulatory complexity in a transdisciplinary and comprehensive perspective, both on an overarching level and in depth, in the form of specific product life-cycles: ready-made garments and mobile phones. We bring significant new evidence-based insights into the factors that enable or hinder coherence in EU development policy; we will advance the understanding of how development concerns can be successfully integrated in non-development policies and regulations concerning market actors; and we provide tools for improved PCD impact assessment as well as for better corporate sustainability assessment.


News Article | November 14, 2016
Site: www.eurekalert.org

Rolls-Royce and VTT Technical Research Centre of Finland Ltd have announced a strategic partnership to design, test and validate the first generation of remote and autonomous ships. The new partnership will combine and integrate the two company's unique expertise to make such vessels a commercial reality. Rolls-Royce is pioneering the development of remote controlled and autonomous ships and believes a remote controlled ship will be in commercial use by the end of the decade. The company is applying technology, skills and experience from across its businesses to this development. VTT has deep knowledge of ship simulation and extensive expertise in the development and management of safety-critical and complex systems in demanding environments such as nuclear safety. They combine physical tests such as model and tank testing, with digital technologies, such as data analytics and computer visualisation. They will also use field research to incorporate human factors into safe ship design. As a result of working with the Finnish telecommunications sector, VTT has extensive experience of working with 5G mobile phone technology and wi-fi mesh networks. VTT has the first 5G test network in Finland. Working with VTT will allow Rolls-Royce to assess the performance of remote and autonomous designs through the use of both traditional model tank tests and digital simulation, allowing the company to develop functional, safe and reliable prototypes. Karno Tenovuo, Rolls-Royce, Vice President Ship Intelligence, said: "Remotely operated ships are a key development project for Rolls-Royce Marine, and VTT is a reliable and innovative partner for the development of a smart ship concept. This collaboration is a natural continuation of the earlier User Experience for Complex systems (UXUS) project, where we developed totally new bridge and remote control systems for shipping." Erja Turunen, Executive Vice President at VTT, said: "Rolls-Royce is a pioneer in remotely controlled and autonomous shipping. Our collaboration strengthens the way we can integrate and leverage VTT's expertise in simulation and safety validation, including the industrial Internet of Things, to develop new products and in the future, enable us to develop new solutions for new areas of application as well." Rolls-Royce is pioneering the development of remote controlled and autonomous ships, applying technology, skills and experience from across its businesses with the ambition of seeing a remote controlled ship in commercial use by the end of the decade. Rolls-Royce's experience in secure data analytics across civil aerospace, defence, nuclear power and marine; coupled with its ship intelligence capabilities, design, propulsion and machinery expertise means it is ideally placed to take the lead in defining the future of shipping, in collaboration with industry, academia and Government. Rolls-Royce is leading the Advanced Autonomous Waterborne Applications Initiative (AAWA). Funded by Tekes (Finnish Funding Agency for Technology and Innovation), AAWA brings together universities, ship designers, equipment manufacturers, and classification societies to explore the economic, social, legal, regulatory and technological factors which need to be addressed to make autonomous ships a reality. It combines the expertise of some of Finland's top academic researchers from Tampere University of Technology; VTT Technical Research Centre of Finland Ltd; Åbo Akademi University; Aalto University; the University of Turku; and leading members of the maritime cluster including Rolls-Royce, NAPA, Deltamarin, DNV GL and Inmarsat. Rolls-Royce is also a member of the Norwegian Forum for Autonomous Ships (NFAS) which has the backing of the Norwegian Maritime Administration, The Norwegian Coastal Administration, the Federation of Norwegian Industries and MARINTEK. Its objectives are to strengthen the cooperation between users, researchers, authorities and others that are interested in autonomous ships and their use; contribute to the development of common Norwegian strategies for development and use of autonomous ships and co-operate with other international and national bodies interested in autonomous shipping. Rolls-Royce is a founder member of the Finnish ecosystem for autonomous marine transport (DIMECC). Supported by the Finnish Marine Industries Association, the Ministry of Transport and Communications, Tekes - the Finnish Funding Agency for Innovation and leading companies including: Rolls-Royce, Cargotec, Ericsson, Meyer Turku, Tieto, and Wärtsilä it aims to create the world's first autonomous marine transport system in the Baltic Sea. More information on VTT's ship model and propulsion device test facilities: http://www. Ship Intelligence press photos are available for download at: https:/ For further information, please contact: Erja Turunen Executive Vice President VTT Technical Research Centre of Finland Ltd +358 50 380 9671, erja.turunen@vtt.fi 1. Rolls-Royce's vision is to be the market-leader in high performance power systems where our engineering expertise, global reach and deep industry knowledge deliver outstanding customer relationships and solutions. We operate across five businesses: Civil Aerospace, Defence Aerospace, Marine, Nuclear and Power Systems. 2. Rolls-Royce has customers in more than 120 countries, comprising more than 400 airlines and leasing customers, 160 armed forces, 4,000 marine customers including 70 navies, and more than 5,000 power and nuclear customers. 3. We have three common themes across all our businesses: 4. Annual underlying revenue was £13.4 billion in 2015, around half of which came from the provision of aftermarket services. The firm and announced order book stood at £76.4 billion at the end of 2015. 5. In 2015, Rolls-Royce invested £1.2 billion on research and development. We also support a global network of 31 University Technology Centres, which position Rolls-Royce engineers at the forefront of scientific research. 6. Rolls-Royce employs over 50,000 people in more than 46 countries. Nearly 15,700 of these are engineers. 7. The Group has a strong commitment to apprentice and graduate recruitment and to further developing employee skills. In 2015 we employed 228 graduates and 277 apprentices through our worldwide training programmes. VTT Technical Research Centre of Finland Ltd is the leading research and technology company in the Nordic countries. We use our research and knowledge to provide expert services for our domestic and international customers and partners, and for both private and public sectors. We use 4,000,000 hours of brainpower a year to develop new technological solutions. VTT in social media: Facebook, LinkedIn, YouTube and Twitter @VTTFinland.


News Article | November 16, 2016
Site: www.prweb.com

Knowing the likely course of cancer can influence treatment decisions. Now a new prediction model published today in Lancet Oncology offers a more accurate prognosis for a patient's metastatic castration-resistant prostate cancer. The approach was as novel as the result – while researchers commonly work in small groups, intentionally isolating their data, the current study embraces the call in Joe Biden's "Cancer Moonshot" to open their question and their data, collecting previously published clinical trial data and calling for worldwide collaboration to evaluate its predictive power. That is, researchers crowdsourced the question of prostate cancer prognosis, eventually involving over 550 international researchers and resulting in 50 computational models from 50 different teams. The approach was intentionally controversial. "Scientists like me who mine open data have been called 'research parasites'. While not the most flattering name, the idea of leveraging existing data to gain new insights is a very important part of modern biomedical research. This project shows the power of the parasites," says James Costello, PhD, senior author of the paper, investigator at the University of Colorado Cancer Center, assistant professor in the Department of Pharmacology at the CU School of Medicine, and director of Computational and Systems Biology Challenges within the Sage Bionetworks/DREAM organization. The project was overseen as a collaborative effort between 16 institutions, led by academic research institutions including CU Cancer Center, open-data initiatives including Project Data Sphere, Sage Bionetworks, and the National Cancer Institute's DREAM Challenges, and industry and research partners including Sanofi, AstraZeneca, and the Prostate Cancer Foundation. Challenge organizers made available the results from five completed clinical trials. Teams were challenged to connect a deep set of clinical measurements to overall patient survival, organizing their insights into novel computational models to better predict patient survival based on clinical data. "The idea is that if a patient comes into the clinic and has these measurements and test results, can we put this data in a model to say if this patient will progress slowly or quickly. If we know the features of patients at the greatest risk, we can know who should receive standard treatment and who might benefit more from a clinical trial," Costello says. The most successful of the 50 models was submitted by a team led by Tero Aittokallio, PhD, from the Institute for Molecular Medicine Finland, FIMM, at University of Helsinki, and professor in the Department of Mathematics and Statistics at University of Turku, Finland. "My group has a long-term expertise in developing multivariate machine learning models for various biomedical applications, but this Challenge provided the unique opportunity to work on clinical trial data, with the eventual aim to help patients with metastatic castration-resistant prostate cancer," Aittokallio says. Basically, the model depended on not only groups of single patient measurements to predict outcomes, but on exploring which interactions between measurements were most predictive – for example, data describing a patient's blood system composition and immune function were only weakly predictive of survival on their own, but when combined became an important part of the winning model. The model used a computational learning strategy technically referred to as an ensemble of penalized Cox regression models, hence the model's name ePCR. This model then competed with 49 other entries, submitted by other teams working independently around the world. "Having 50 independent models allowed us to do two very important things. First when a single clinical feature known to be predictive of patient survival is picked out by 40 of the 50 teams, this greatly strengthens our overall confidence. Second, we were able to discover important clinical features we hadn't fully appreciated before," Costello says. In this case, many models found that in addition to factors like prostate-specific antigen (PSA) and lactate dehydrogenase (LDH) that have long been known to predict prostate cancer performance, blood levels of an enzyme called asparate aminotransferease (AST) is an important predictor of patient survival. This AST is an indirect measure of liver function and the fact that disturbed levels of AST are associated with poor patient performance implies that studies could evaluate the role of AST in prostate cancer. "The benefits of a DREAM Challenge are the ability to attract talented individuals and teams from around the world, and a rigorous framework for the assessment of methods. These two ingredients came together for our Challenge, leading to a new benchmark in metastatic prostate cancer," says paper first author, Justin Guinney, PhD, director of Computational Oncology for Sage Bionetworks located at Fred Hutchinson Cancer Research Center. “A goal of the Project Data Sphere initiative is to spark innovation – to unlock the potential of valuable data by generating new insights and opening up a new world of research possibilities. Prostate Cancer DREAM Challenge did just that. To witness cancer clinical trial data from Project Data Sphere be used in research collaboration and ultimately help improve patient care in the future is extremely rewarding!” says Liz Zhou, MD, MS, director of Global Health Outcome Research at Sanofi. The goal now is to make the ePCR model publicly accessible through an online tool with an eye towards clinical application. In fact, the National Cancer Institute (NCI) has contracted the winning team to do exactly this. Soon, when patients face difficult decisions about the best treatment for metastatic castration-resistant prostate cancer, ePCR tool could be an important piece of the decision-making process. Challenge winners and results can be found on the Prostate Cancer DREAM Challenge homepage. The clinical trial data can be found at Project Data Sphere. The research article describing this work can be found at The Lancet Oncology. Additional papers that describe individual team methods can be found in the DREAM Channel at F1000Research. About University of Colorado Cancer Center The University of Colorado Cancer Center, located at the Anschutz Medical Campus, is Colorado’s only National Cancer Institute-designated comprehensive cancer center, a distinction recognizing its outstanding contributions to research, clinical trials, prevention and cancer control. CU Cancer Center’s clinical partner University of Colorado Hospital is ranked 15th by US News and World Report for Cancer and the CU Cancer Center is a member of the prestigious National Comprehensive Cancer Network®, an alliance of the nation’s leading cancer centers working to establish and deliver the gold standard in cancer clinical guidelines. CU Cancer Center is a consortium of more than 400 researchers and physicians at three state universities and three institutions, all working toward one goal: Translating science into life. For more information visit Coloradocancercenter.org and follow CU Cancer Center on Facebook and Twitter. About the DREAM Challenges Initiative Founded in 2006 by A. Califano (Columbia University) and Gustavo Stolovitzky (IBM Research) the Dialogue on Reverse Engineering Assessment and Methods (DREAM) Challenges Initiative poses fundamental questions about systems biology and translational medicine. Designed and run by a community of researchers from a variety of organizations, the DREAM challenges invite participants to propose solutions — fostering collaboration and building communities in the process. Expertise and institutional support are provided by Sage Bionetworks, along with the infrastructure to host challenges via their Synapse platform. Together, the leaders of the DREAM Challenges Initiative share a vision allowing individuals and groups to collaborate openly so that the “wisdom of the crowd” provides the greatest impact on science and human health. More information is available at: http://dreamchallenges.org/. About the Project Data Sphere Initiative Project Data Sphere, LLC, an independent, not-for-profit initiative of the CEO Roundtable on Cancer's Life Sciences Consortium (LSC), operates the Project Data Sphere® platform (http://www.ProjectDataSphere.org). Launched in April 2014, the Project Data Sphere platform provides one place where the cancer community can broadly share, integrate, analyze and discuss historical patient-level comparator arm data sets (historical patient-level cancer phase III) from multiple providers, with the goal of advancing research. With its broad-access approach, the initiative brings diverse minds and technology together to help unleash the full potential of existing clinical trial data and speed innovation by generating collective insights that may lead to improved trial design, disease modeling and beyond. The platform currently contains 27,600 patient lives of data; 9,400 of those are across a wide spectrum of prostate cancer populations. In order to ensure that researchers can realize the full potential of this data, PDS teamed with CEO Roundtable on Cancer Member, SAS Institute Inc. SAS, a leader in data and health analytics, developed and hosts the site and provides free state-of-the-art analytic tools to authorized users within the Project Data Sphere environment. About Sage Bionetworks Sage Bionetworks is a nonprofit biomedical research organization, founded in 2009, with a vision to promote innovations in personalized medicine by enabling a community-based approach to scientific inquiries and discoveries. Sage Bionetworks strives to activate patients and to incentivize scientists, funders and researchers to work in fundamentally new ways in order to shape research, accelerate access to knowledge and transform human health. It is located on the campus of the Fred Hutchinson Cancer Research Center in Seattle, Washington and is supported through a portfolio of philanthropic donations, competitive research grants, and commercial partnerships. More information is available at http://www.sagebase.org.


News Article | November 30, 2016
Site: www.eurekalert.org

An international group of researchers report success in mice of a method of using positron emission tomography (PET) scans to track, in real time, an antibody targeting a hormone receptor pathway specifically involved in prostate cancer. This androgen receptor pathway drives development and progression of the vast majority of prostate cancers. The technique shows promise, the investigators say, as a novel way to use such an antibody to detect and monitor prostate and other hormone-sensitive cancers, as well as to guide therapy in real time. "The findings show that individually tailored imaging agents can provide a unique way of looking at disease progression in real time and in a noninvasive manner," says Daniel Thorek, Ph.D., assistant professor of radiology and radiological science at the Johns Hopkins University School of Medicine, and the paper's first author. "Perhaps someday we can put a personalized antibody such as the one we created in our study on a therapeutic agent and conduct cancer treatment using imaging with very high specificity." A summary of the findings was published in Science Translational Medicine on Nov. 30. Thorek says the success is especially important given the challenges of working with small-animal models. "We managed to very accurately and precisely monitor the mouse prostate, and that leads us to hope that a similar approach can be used to guide treatment in people," he adds. Current clinical practice detects prostate cancer by tracking the androgen receptor pathway -- a marker for the cancer -- by testing blood for prostate-specific antigen (PSA). Presence of elevated PSA indicates that the androgen receptor pathway is active and may indicate prostate cancer is present. PSA concentration in the blood, however, is affected by numerous factors, such as age and type of tumor, making it difficult to determine true androgen receptor pathway activation. Furthermore, attempts to target PSA with an antibody is complicated by the "washing out" of the antibody-PSA complex, a process in which the complex is formed but does not remain near the disease site, thus making it difficult to definitively identify and measure disease sites. In the new study, the investigators developed a new antibody called 11B6 to target human kallikrein-related peptidase 2 (hK2), another antigen that indicates androgen receptor pathway activation. Unlike PSA, hK2 is specifically active only in the prostate and an aggressive type of breast cancer. By binding free, unbound hK2 to 11B6, the research team found that the newly formed 11B6-hK2 complex is taken directly back into the cancerous cell rather than washed out. This biological process relies on a transport mechanism involving the neonatal Fc receptor, in which cells are able to recognize and take in antibodies. The Fc receptor is most well-known for how antibodies in mothers' milk are able to pass from the gut of the baby into newborns' bloodstream to provide them with immunity. As far as the research team is aware, this is the first study to exploit the biological mechanism for imaging purposes, Thorek says. In the next phase of their experiments, the team made 11B6 "light up" during PET and fluorescence imaging by binding it to zirconium-89, creating a traceable radiochemical compound called 89Zr-11B6. By imaging the 89Zr-11B6 using PET, the team showed that binding 11B6 to hK2 can measure activity of cancerous lesions robustly, in both soft tissue and bone. Prostate and breast cancer often metastasize to bone, therefore detection of lesions in all areas of the body is critical. To further demonstrate the potential value of 89Zr-11B6 imaging, the team tested the imaging agent in disease models under standard treatment regimens. In one such case, disease activity was imaged and quantified in mice treated with saline and a second group with enzalutamide, a drug used to treat prostate cancer by inhibiting the androgen receptor hormone activity. All of the mice had prostate cancer. Following initial castration, imaging of 89Zr-11B6 allowed the research team to see lower androgen receptor pathway activity, as one might expect. This effect was augmented in the animals with adjuvant enzalutamide treatment. This may inform current clinical practice as the use of adjuvant enzalutamide after castration may show benefit to patients with prostate cancer. By tracking the antibody localization to disease sites in real time, the team hopes this may be a way to determine optimal dosages that don't compromise efficacy while avoiding negative side effects. Imaging of the antibody uptake before and after treatment could, in theory, aid in the decision of whether to keep a patient on chosen drug. If a response is seen, the imaging agent could be used to choose the right dose, balancing the therapeutic effect and minimizing adverse effects. And if there is not an imaging change with a particular drug, this tool would provide a caregiver with rapid information to discontinue ineffective treatments, saving time and cost. The team is currently conducting preliminary nonhuman primate toxicity tests, the final step before applying for human clinical trials, and has thus far found no adverse effects. Other authors on this paper include Diane S. Abou and Marise R.H. van Voss of the Johns Hopkins University School of Medicine; Philip A. Watson, Sang-Gyu Lee, Anson T. Ku, Kwanghee Kim, Michael G. Doran, Elmer Santos, Darren Veach, Mesruh Turkekul, Emily Casey, Jason S. Lewis, Howard I. Scher, Hans Lilja, Steven M. Larson and David Ulmert of Memorial Sloan Kettering Cancer Center; Stylianos Bournazos of Rockefeller University; Katharina Braun of the University of Bochum; Kjell Sjöström of Innovagen AB; Urpo Lamminmäki of the University of Turku; Sven-Erik Strand of Lund University; and Mary L. Alpaugh of Rowan University. Funding for this study was provided by the National Cancer Institute of the National Institutes of Health (P30 CA008748, P30 CA006973, P30 CA008748-48, S10 RR020892-01, S10 RR028889-01, R33 CA127768-02, P50-CA86438), the National Institutes of Health Molecular Imaging Fellowship Program (5R25CA096945-07), the Geoffrey Beene Cancer Research Center, the W.H. Goodwin and A. Goodwin and their Commonwealth Foundation for Cancer Research, the Experimental Therapeutics Center, the Radiochemistry and Molecular Imaging Probe Core (P50-CA086438), the Steve Wynn Prostate Cancer Foundation Young Investigator Award, the Knut and Alice Wallenberg Foundation, the Bertha Kamprad Foundation and the David H. Koch Fund of the Prostate Cancer Foundation, the Ludwig Center for Cancer Immunotherapy, the Swedish Cancer Society, the Swedish National Health Foundation, the Swedish Research Council (Medicine- 20095), the Memorial Sloan Kettering Cancer Center Specialized Programs of Research Excellence in Prostate Cancer (P50 CA92629), the Sidney Kimmel Center for Prostate and Urologic Cancers and the Hascoe Charitable Foundation. D.L.J.T., D.U., U.L., S.-E.S., and H.L. are shareholders of Diaprost Inc. D.L.J.T., S.-E.S., and D.U. currently serve as board members of Diaprost Inc. D.L.J.T., A.K., S.-E.S., S.M.L., and D.U. are inventors on a patent (62257179) submitted by the MSKCC that covers systems, methods and compositions for imaging AR axis activity in carcinoma. D.U. is also the inventor on a patent (20060182682) held by Diaprost Inc. that covers diagnostic imaging of PCa using 11B6. S.-E.S. and U.L. are inventors on a patent application (WO2015075445) submitted by Diaprost Inc. that covers the humanized anti-hK2 antibody.


News Article | November 15, 2016
Site: www.eurekalert.org

Knowing the likely course of cancer can influence treatment decisions. Now a new prediction model published today in Lancet Oncology offers a more accurate prognosis for a patient's metastatic castration-resistant prostate cancer. The approach was as novel as the result - while researchers commonly work in small groups, intentionally isolating their data, the current study embraces the call in Joe Biden's "Cancer Moonshot" to open their question and their data, collecting previously published clinical trial data and calling for worldwide collaboration to evaluate its predictive power. That is, researchers crowdsourced the question of prostate cancer prognosis, eventually involving over 550 international researchers and resulting in 50 computational models from 50 different teams. The approach was intentionally controversial. "Scientists like me who mine open data have been called 'research parasites'. While not the most flattering name, the idea of leveraging existing data to gain new insights is a very important part of modern biomedical research. This project shows the power of the parasites," says James Costello, PhD, senior author of the paper, investigator at the University of Colorado Cancer Center, assistant professor in the Department of Pharmacology at the CU School of Medicine, and director of Computational and Systems Biology Challenges within the Sage Bionetworks/DREAM organization. The project was overseen as a collaborative effort between 16 institutions, led by academic research institutions including CU Cancer Center, open-data initiatives including Project Data Sphere, Sage Bionetworks, and the National Cancer Institute's DREAM Challenges, and industry and research partners including Sanofi, AstraZeneca, and the Prostate Cancer Foundation. Challenge organizers made available the results from five completed clinical trials. Teams were challenged to connect a deep set of clinical measurements to overall patient survival, organizing their insights into novel computational models to better predict patient survival based on clinical data. "The idea is that if a patient comes into the clinic and has these measurements and test results, can we put this data in a model to say if this patient will progress slowly or quickly. If we know the features of patients at the greatest risk, we can know who should receive standard treatment and who might benefit more from a clinical trial," Costello says. The most successful of the 50 models was submitted by a team led by Tero Aittokallio, PhD, from the Institute for Molecular Medicine Finland, FIMM, at University of Helsinki, and professor in the Department of Mathematics and Statistics at University of Turku, Finland. "My group has a long-term expertise in developing multivariate machine learning models for various biomedical applications, but this Challenge provided the unique opportunity to work on clinical trial data, with the eventual aim to help patients with metastatic castration-resistant prostate cancer," Aittokallio says. Basically, the model depended on not only groups of single patient measurements to predict outcomes, but on exploring which interactions between measurements were most predictive - for example, data describing a patient's blood system composition and immune function were only weakly predictive of survival on their own, but when combined became an important part of the winning model. The model used a computational learning strategy technically referred to as an ensemble of penalized Cox regression models, hence the model's name ePCR. This model then competed with 49 other entries, submitted by other teams working independently around the world. "Having 50 independent models allowed us to do two very important things. First when a single clinical feature known to be predictive of patient survival is picked out by 40 of the 50 teams, this greatly strengthens our overall confidence. Second, we were able to discover important clinical features we hadn't fully appreciated before," Costello says. In this case, many models found that in addition to factors like prostate-specific antigen (PSA) and lactate dehydrogenase (LDH) that have long been known to predict prostate cancer performance, blood levels of an enzyme called asparate aminotransferease (AST) is an important predictor of patient survival. This AST is an indirect measure of liver function and the fact that disturbed levels of AST are associated with poor patient performance implies that studies could evaluate the role of AST in prostate cancer. "The benefits of a DREAM Challenge are the ability to attract talented individuals and teams from around the world, and a rigorous framework for the assessment of methods. These two ingredients came together for our Challenge, leading to a new benchmark in metastatic prostate cancer," says paper first author, Justin Guinney, PhD, director of Computational Oncology for Sage Bionetworks located at Fred Hutchinson Cancer Research Center. "A goal of the Project Data Sphere initiative is to spark innovation - to unlock the potential of valuable data by generating new insights and opening up a new world of research possibilities. Prostate Cancer DREAM Challenge did just that. To witness cancer clinical trial data from Project Data Sphere be used in research collaboration and ultimately help improve patient care in the future is extremely rewarding!" says Liz Zhou, MD, MS, director of Global Health Outcome Research at Sanofi. The goal now is to make the ePCR model publicly accessible through an online tool with an eye towards clinical application. In fact, the National Cancer Institute (NCI) has contracted the winning team to do exactly this. Soon, when patients face difficult decisions about the best treatment for metastatic castration-resistant prostate cancer, ePCR tool could be an important piece of the decision-making process. Challenge winners and results can be found on the Prostate Cancer DREAM Challenge homepage. The clinical trial data can be found at Project Data Sphere. The research article describing this work can be found at The Lancet Oncology. Additional papers that describe individual team methods can be found in the DREAM Channel at F1000Research. The University of Colorado Cancer Center, located at the Anschutz Medical Campus, is Colorado's only National Cancer Institute-designated comprehensive cancer center, a distinction recognizing its outstanding contributions to research, clinical trials, prevention and cancer control. CU Cancer Center's clinical partner University of Colorado Hospital is ranked 15th by US News and World Report for Cancer and the CU Cancer Center is a member of the prestigious National Comprehensive Cancer Network®, an alliance of the nation's leading cancer centers working to establish and deliver the gold standard in cancer clinical guidelines. CU Cancer Center is a consortium of more than 400 researchers and physicians at three state universities and three institutions, all working toward one goal: Translating science into life. For more information visit Coloradocancercenter.org and follow CU Cancer Center on Facebook and Twitter. Founded in 2006 by A. Califano (Columbia University) and Gustavo Stolovitzky (IBM Research) the Dialogue on Reverse Engineering Assessment and Methods (DREAM) Challenges Initiative poses fundamental questions about systems biology and translational medicine. Designed and run by a community of researchers from a variety of organizations, the DREAM challenges invite participants to propose solutions -- fostering collaboration and building communities in the process. Expertise and institutional support are provided by Sage Bionetworks, along with the infrastructure to host challenges via their Synapse platform. Together, the leaders of the DREAM Challenges Initiative share a vision allowing individuals and groups to collaborate openly so that the "wisdom of the crowd" provides the greatest impact on science and human health. More information is available at: http://dreamchallenges. . Project Data Sphere, LLC, an independent, not-for-profit initiative of the CEO Roundtable on Cancer's Life Sciences Consortium (LSC), operates the Project Data Sphere® platform. Launched in April 2014, the Project Data Sphere platform provides one place where the cancer community can broadly share, integrate, analyze and discuss historical patient-level comparator arm data sets (historical patient-level cancer phase III) from multiple providers, with the goal of advancing research. With its broad-access approach, the initiative brings diverse minds and technology together to help unleash the full potential of existing clinical trial data and speed innovation by generating collective insights that may lead to improved trial design, disease modeling and beyond. The platform currently contains 27,600 patient lives of data; 9,400 of those are across a wide spectrum of prostate cancer populations. In order to ensure that researchers can realize the full potential of this data, PDS teamed with CEO Roundtable on Cancer Member, SAS Institute Inc. SAS, a leader in data and health analytics, developed and hosts the site and provides free state-of-the-art analytic tools to authorized users within the Project Data Sphere environment. Sage Bionetworks is a nonprofit biomedical research organization, founded in 2009, with a vision to promote innovations in personalized medicine by enabling a community-based approach to scientific inquiries and discoveries. Sage Bionetworks strives to activate patients and to incentivize scientists, funders and researchers to work in fundamentally new ways in order to shape research, accelerate access to knowledge and transform human health. It is located on the campus of the Fred Hutchinson Cancer Research Center in Seattle, Washington and is supported through a portfolio of philanthropic donations, competitive research grants, and commercial partnerships. More information is available at http://www. .


Grant
Agency: European Commission | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2010-1.1.19 | Award Amount: 9.36M | Year: 2011

Environmental change and particularly amplified global climate change are accelerating in the Arctic. These changes already affect local residents and feedback from the Arctics land surface to the climate system, will have global implications. However, climate change and its impacts are variable throughout the wide environmental and land use envelopes of the Arctic. Unfortunately, the Arctic is generally remote, sparsely populated and research and monitoring activities are more restricted in time and space than elsewhere. This limitation comes when there is a rapidly expanding need for knowledge as well as increasing technological opportunities to make data collection in the field and accessibility more efficient. INTERACT is a network under the auspices of SCANNET, a circumarctic network of terrestrial field bases. INTERACT specifically seeks to build capacity for research and monitoring in the European Arctic and beyond. Partnerships will be established between Station Managers and researchers within Joint Research Activities that will develop more efficient networks of sensors to measure changing environmental conditions and make data storage and accessibility more efficient through a single portal. New communities of researchers will be offered access to Arctic terrestrial infrastructures while local stakeholders as well as major international organisations will be involved in interactions with the infrastructures. This will lead to increased public awareness of environmental change and methods to adapt to them, increased access to information for education at all levels, and input to major international research and assessment programmes.The whole consortium will form a coherent and integrated unit working within a concept of a wide environmental and land use envelopes in which local conditions determine the directions and magnitudes of environmental change whereas the balance and synergies of processes integrated across the whole region have global impacts.


Grant
Agency: European Commission | Branch: FP7 | Program: CP | Phase: SEC-2009-1.3-02 | Award Amount: 5.30M | Year: 2010

A large number of techniques have been developed in the latest decades, which are able to screen and identify specific molecules for drug precursors detection even at very low concentration in lab testing.Nevertheless the objective to build up a system which proves to be easy to use, compact, able to provide screening over a large number of compounds and discriminate them with low false alarm (FA) and high probability of detection (POD) is still an open issue.The project will focus on employing multiple techniques, integrating them in a complex system which employs them in a complimentary approach in order to identify an optimum trade-off between opposite requirements: compactness, simplicity, low cost vs. sensitivity low false alarm rate, selectivity. Known techniques, as fluorescence will be improved by mean of novel proteins, as antibodies to extend Probability of Detection (PoD). The techniques are: 1. A low cost, high data throughput sensing technique, based on UV-Vis-NIR fluorescence. Fluorescence will be enhanced by development of Organic macro-molecules sensitive to specific classes of compounds of interest (ephedrine, pseudoephedryne, P2P, ) in the domain of drug detection. The fluorescence analysis will be based on an opto-chip which can incorporate an array of different properly engineered fluorescent chemical protein able to bind to the analytes with an immuno-type reaction. An array of classes of compounds can be thus very fast discriminated by one-shot measurement. 2. A high sensitivity and selectivity, but compact and low weight, spectroscopic sensing technique in MIRIR optical range, based on Laser PhotoAcoustic Sensor (LPAS). Detection of drug precursors based on spectroscopic techniques can guarantee a good selectivity, a low Probability of False Alarm and a suitable operation speed. The size of the photo-acoustic cell can be made as small as possible for a compact sensor and, depending on the performances, it can cost down to 1000.


Korhonen H.J.,Durham University | Korhonen H.J.,University of Turku | Conway L.P.,Durham University | Hodgson D.R.W.,Durham University
Current Opinion in Chemical Biology | Year: 2014

Phosphoryl group transfer is central to genetic replication, cellular signalling and many metabolic processes. Understanding the mechanisms of phosphorylation and phosphate ester and anhydride cleavage is key to efforts towards biotechnological and biomedical exploitation of phosphate-handling enzymes. Analogues of phosphate esters and anhydrides are indispensable tools, alongside protein mutagenesis and computational methods, for the dissection of phosphoryl transfer mechanisms. Hydrolysable and non-hydrolysable phosphate analogues have provided insight into the nature and sites of phosphoryl transfer processes. Kinetic isotope effects and crystallography using transition state analogues have painted more detailed pictures of transition states and how enzymes work to stabilise them. © 2014 The Authors.


Lopez M.,University of Santiago de Compostela | Lopez M.,CIBER ISCIII | Tena-Sempere M.,CIBER ISCIII | Tena-Sempere M.,University of Cordoba, Spain | Tena-Sempere M.,University of Turku
Trends in Endocrinology and Metabolism | Year: 2015

Despite their prominent roles in the control of reproduction, estrogens pervade many other bodily functions. Key metabolic pathways display marked sexual differences, and estrogens are potent modulators of energy balance, as evidenced in extreme conditions of estrogen deficiency characterized by hyperphagia and decreased energy expenditure, and leading to obesity. Compelling evidence has recently demonstrated that, in addition to their peripheral effects, the actions of estrogens on energy homeostasis are exerted at central levels, to regulate almost every key aspect of metabolic homeostasis, from feeding to energy expenditure, to glucose and lipid metabolism. We review herein the state-of-the-art of the role of estrogens in the regulation of energy balance, with a focus on their central effects and modes of action. © 2015 Elsevier Ltd.


Kangasjarvi S.,University of Turku | Neukermans J.,University Paris - Sud | Li S.,University Paris - Sud | Aro E.-M.,University of Turku | Noctor G.,University Paris - Sud
Journal of Experimental Botany | Year: 2012

Visible light is the basic energetic driver of plant biomass production through photosynthesis. The constantly fluctuating availability of light and other environmental factors means that the photosynthetic apparatus must be able to operate in a dynamic fashion appropriate to the prevailing conditions. Dynamic regulation is achieved through an array of homeostatic control mechanisms that both respond to and influence cellular energy and reductant status. In addition, light availability and quality are continuously monitored by plants through photoreceptors. Outside the laboratory growth room, it is within the context of complex changes in energy and signalling status that plants must regulate pathways to deal with biotic challenges, and this can be influenced by changes in the highly energetic photosynthetic pathways and in the turnover of the photosynthetic machinery. Because of this, defence responses are neither simple nor easily predictable, but rather conditioned by the nutritional and signalling status of the plant cell. This review discusses recent data and emerging concepts of how recognized defence pathways interact with and are influenced by light-dependent processes. Particular emphasis is placed on the potential roles of the chloroplast, photorespiration, and photoreceptor-associated pathways in regulating the outcome of interactions between plants and pathogenic organisms. © 2011 The Author.


Ivaska J.,VTT Technical Research Center of Finland | Ivaska J.,Center for Biotechnology | Ivaska J.,University of Turku | Heino J.,University of Turku
Annual Review of Cell and Developmental Biology | Year: 2011

All multicellular animals express receptors for growth factors (GFs) and extracellular matrix (ECM) molecules. Integrin-type ECM receptors anchor cells to their surroundings and concomitantly activate intracellular signal transduction pathways. The same signaling mechanisms are regulated by GF receptors (GFRs). Recently, intensive research efforts have revealed novel mechanisms describing how the two receptor systems collaborate at many different levels. Integrins can directly bind to GFs and promote their activation. Adhesion receptors also organize signaling platforms and assist GFRs or even activate them via ligand-independent mechanisms. Furthermore, integrins can orchestrate endocytosis and recycling of GFRs. Here, we review the present knowledge about the interplay between integrins and GFRs and discuss recent ideas of how this collaboration may explain some previous controversies in integrin research. © 2011 by Annual Reviews. All rights reserved.


Heikkinen T.,University of Turku | Tsolia M.,National and Kapodistrian University of Athens | Finn A.,University of Bristol
Pediatric Infectious Disease Journal | Year: 2013

Despite ample evidence for the great burden that annual influenza epidemics place on children and society in general, few European countries currently recommend influenza vaccination of healthy children of any age. The most frequently cited reasons for reluctance to extend general vaccine recommendations to children include the view that influenza is a mild illness of limited clinical importance, lack of country-specific data on disease burden, uncertainty about the efficacy and safety of influenza vaccines in children and inadequate evidence of cost-effectiveness of vaccinating children. In recent years, several clinical studies have provided new and important information that help address many of these areas of question and concern. In light of this newly available scientific evidence, influenza vaccine recommendations for children should be properly reevaluated in all European countries. Furthermore, to allow for variation in costs and patterns of healthcare delivery between different countries, cost-effectiveness analyses of influenza vaccination of healthy children should be performed in each country or region. Finally, increased efforts should be made to educate both healthcare professionals and the great public about recent findings and advances in the field of pediatric influenza. Copyright © 2013 Lippincott Williams &Wilkins.


Salmivalli C.,University of Turku | Salmivalli C.,University of Stavanger
Aggression and Violent Behavior | Year: 2010

It is often stated that bullying is a "group process", and many researchers and policymakers share the belief that interventions against bullying should be targeted at the peer-group level rather than at individual bullies and victims. There is less insight into what in the group level should be changed and how, as the group processes taking place at the level of the peer clusters or school classes have not been much elaborated. This paper reviews the literature on the group involvement in bullying, thus providing insight into the individuals' motives for participation in bullying, the persistence of bullying, and the adjustment of victims across different peer contexts. Interventions targeting the peer group are briefly discussed and future directions for research on peer processes in bullying are suggested. © 2009 Elsevier Ltd. All rights reserved.


Nummenmaa L.,Aalto University | Nummenmaa L.,University of Turku | Calvo M.G.,University of La Laguna
Emotion | Year: 2015

Happy facial expressions are recognized faster and more accurately than other expressions in categorization tasks, whereas detection in visual search tasks is widely believed to be faster for angry than happy faces. We used meta-analytic techniques for resolving this categorization versus detection advantage discrepancy for positive versus negative facial expressions. Effect sizes were computed on the basis of the r statistic for a total of 34 recognition studies with 3,561 participants and 37 visual search studies with 2,455 participants, yielding a total of 41 effect sizes for recognition accuracy, 25 for recognition speed, and 125 for visual search speed. Random effects meta-analysis was conducted to estimate effect sizes at population level. For recognition tasks, an advantage in recognition accuracy and speed for happy expressions was found for all stimulus types. In contrast, for visual search tasks, moderator analysis revealed that a happy face detection advantage was restricted to photographic faces, whereas a clear angry face advantage was found for schematic and "smiley" faces. Robust detection advantage for nonhappy faces was observed even when stimulus emotionality was distorted by inversion or rearrangement of the facial features, suggesting that visual features primarily drive the search. We conclude that the recognition advantage for happy faces is a genuine phenomenon related to processing of facial expression category and affective valence. In contrast, detection advantages toward either happy (photographic stimuli) or nonhappy (schematic) faces is contingent on visual stimulus features rather than facial expression, and may not involve categorical or affective processing. © 2015 American Psychological Association.


Lu S.,University of Turku | Lu S.,KTH Royal Institute of Technology
Acta Materialia | Year: 2016

First-principles calculations have been performed to study the effects of point defects on the tetragonality of martensites in ferrous shape memory alloy Fe3Pt. By computing the Bain path, I show that by considering point defects, all the face-centered cubic (fct) and body-centered cubic (bct) phases with c/a values close to the experimental observations are predicted. Atomic structure analysis gives evidence about the proposed "antiferrodistortive transformation" which was previously derived from the softened phonon mode of Fe3Pt. We discuss the dependence of the Bain path on the concentration of defects and show that the observed bct structures are closely related to the particular shape of the L12 Bain path. Magnetism is identified as the origin of the extremely flat Bain path. The role of the enhanced band Jahn-Teller effect in stabilizing the fct phases is discussed. © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.


Okhotin A.,University of Turku | Rondogiannis P.,National and Kapodistrian University of Athens
Information and Computation | Year: 2012

Equations of the form X=φ(X) are considered, where the unknown X is a set of natural numbers. The expression φ(X) may contain the operations of set addition, defined as S+T={m+n|m ∑ S,n ∑ T}, union, intersection, as well as ultimately periodic constants. An equation with a non-periodic solution of exponential growth rate is constructed. At the same time it is demonstrated that no sets with super-exponential growth rate can be represented. It is also shown that restricted classes of these equations cannot represent sets with super-linearly growing complements nor sets that are additive bases of order 2. The results have direct implications on the power of unary conjunctive grammars with one nonterminal symbol. © 2012 Elsevier Inc.


Grieco M.,University of Turku | Grieco M.,University of Vienna | Suorsa M.,University of Turku | Jajoo A.,Devi Ahilya University | And 2 more authors.
Biochimica et Biophysica Acta - Bioenergetics | Year: 2015

In plant chloroplasts, the two photosystems (PSII and PSI) are enriched in different thylakoid domains and, according to the established view, are regarded as energetically segregated from each other. A specific fraction of the light harvesting complex II (LHCII) has been postulated to get phosphorylated by the STN7 kinase and subsequently to migrate from PSII to PSI as part of a process called 'state transition'. Nevertheless, the thylakoid membrane incorporates a large excess of LHCII not present in the isolatable PSII-LHCII and PSI-LHCII complexes. Moreover, LHCII phosphorylation is not limited to a specific LHCII pool and "state 2" condition, but is found in all thylakoid domains in any constant light condition. Here, using a targeted solubilization of pigment-protein complexes from different thylakoid domains, we demonstrate that even a minor detachment of LHCII leads to markedly increased fluorescence emission from LHCII and PSII both in grana core and non-appressed thylakoid membranes and the effect of the detergent to detach LHCII is enhanced in the absence of LHCII phosphorylation. These findings provide evidence that PSII and PSI are energy traps embedded in the same energetically connected LHCII lake. In the lake, PSI and LHCII are energetically connected even in the absence of LHCII phosphorylation, yet the phosphorylation enhances the interaction required for efficient energy transfer to PSI in the grana margin regions. © 2015 Elsevier B.V. All rights reserved.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2013-ITN | Award Amount: 3.41M | Year: 2013

CALIPSO is a genuine interdisciplinary and intersectorial research network composed of nine academic research institutions and three industrial partners, thus presenting an example of true translational research and training of young researchers in communicating and transferring achievements from different model organisms directly to industrial partners. CALIPSO aims at identifying environmentally triggered regulatory calcium signals and protein phosphorylation events that control photosynthesis and metabolism. CALIPSO partners work with a wide range of different organisms covering the full phylogenetic spectrum from algae to higher plants including economically important crops. They combine a wide spectrum of newest technologies in molecular biology, biochemistry, proteomics, metabolomics, genetics, bioinformatics and systems biology to uncover how photosynthetic organisms acclimate to changing environmental conditions or stress. This novel combination of scientific expertise combined with industrial applications is one of the major strengths of CALIPSO, exposing the participating researchers to different schools of thought. The active participation of Bayer CropScience Gent and Ecoduna as full network partners, and Photon Systems Instruments as associated partner, will enable intersectorial industry-academia cooperation with the long term objectives of (i) improving yield and stress robustness of crops and (ii) developing microalgal-biotechnology. The integrated systematic training programme of CALIPSO will boost the future employability of the young researchers by acquisition of technical skills for their work in academia or the private sector and also essential complementary skills for their future career. The training programme comprises three workshops on state-of-the art techniques - and one on industrial-relevant skills. This is completed by secondments to partner laboratories and industry and network-wide training events in further complementary skills.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 3.93M | Year: 2012

The generation of young biotechnologists is of paramount importance for Europes future. PHOTO.COMM will train primarily early stage researchers who have demonstrated high ambitions and talents in a unique platform based on emerging technology and science that would shape the forefront of future European biotechnology. PHOTO.COMM involves the utilization of microalgae for the conversion of carbon dioxide and water into chemicals and fuels, to directly replace finite fossil fuels and products. Although this is a rapidly growing industry, true societal impact cannot be expected until larger-scale production of low value end-products becomes a commercial reality. PHOTO.COMM has the primary objective of generating the next-generation scientists that will make a substantial and potentially game-changing contribution towards this global challenge. The young researchers will be trained in multidisciplinary science and innovation-based business creation to foster a new approach to microalgae based production and the use of synthetic photobiological communities. The researchers will also strengthen the core of photobiological metabolism by innovative approaches to enhance photosynthesis and carbon-assimilation and deliver new approaches to create valuable end-products. PHOTO.COMM will provide an exciting environment where the young researchers will absorb and implement state-of-the-art analytical methods, intellectual property and business principles and obtain extensive training and practical experience in close collaboration between universities and companies. Altogether, the educated next-generation scientists and their technologies are expected to make a strong contribution towards a future Europe in which both economically and environmentally sustainable photosynthetic biotechnology is a main supply of commodities and energy.


Patent
University of Turku and Genentech | Date: 2015-11-19

Compositions and methods useful for detecting and treating cancers which express the HER4 JM-a isoform are disclosed.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-IRSES | Phase: FP7-PEOPLE-2011-IRSES | Award Amount: 391.30K | Year: 2012

The proposed International Foresight Academy is the first organization to bind together Foresight activities around the globe and from contrasting cultural and political contexts. As the Mapping Report of the European Foresight Monitoring Network (2009) has documented, Foresight is used differently in various regions of the world. Foresight activities vary according to sponsors and customers, methods used, topics explored, actors involved etc. They vary also with regard to their functions in political strategy formulation of modern democracies. During the past 30 years in Europe, Foresight has become an unconventional means of political priority setting and strategic decision making that affect a wide set of societal stakeholders. The added value of foresight is seen in the shared goals and visions among a group of participating actors from different sectors, the development of networks, and the combination of relevant information on current trends and future developments with actor-based information and attitudes. Many foresight practitioners value the possibility granted by foresight exercises to bring topics on the political agenda that need to be discussed not behind closed doors but with broad public involvement. The proposal for the IFA consists two parts: a research part dedicated to the issue of FS as a format of participation in different democratic traditions; and a second part that manages the networking of the partners doing research on the FS field with regard to democracy and participation. The network will involve activities such as mutual exchange among the partners, summer/winter schools for early stage researchers, seminars and academic workshops. The outreach of some of these activities will address additional actors as well, e.g. stakeholders, organizers, practitioners of FS exchanging knowledge in the envisaged conferences.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-CSA-Infra | Phase: INFRA-2011-1.1.21. | Award Amount: 11.58M | Year: 2012

RadioNet is an I3 that coordinates all of Europes leading radio astronomy facilities in an integrated cooperation to achieve transformational improvement in the quality and quantity of the scientific research of European astronomers. RadioNet3 includes 27 partners operating world-class radio telescopes and/or performing cutting-edge R&D in a wide range of technology fields important for radio astronomy. RadioNet3 proposes a work plan that is structured into 6 NAs, 7 TNAs and 4 JRAs with the aim to integrate and optimise the use and development of European radio astronomy infrastructures. The general goals of RadioNet3 are to: - facilitate, for a growing community of European researchers, access to the complete range of Europes world-leading radio-astronomical facilities, including the ALMA telescope; - secure a long-term perspective on scientific and technical developments in radio astronomy, pooling resources and expertise that exist among the partners; - stimulate new R&D activities for the existing radio infrastructures in synergy with ALMA and the SKA; - contribute to the implementation of the vision of the ASTRONET Strategic Plan for European Astronomy by building a sustainable and world leading radio astronomical research community. RadioNet3 builds on the success of two preceeding I3s under FP6 and FP7, but it also takes a leap forward as it includes facilitation of research with ALMA via a dedicated NA, and 4 pathfinders for the SKA in its TNA Program. It has a transparent and efficient management structure designed to optimally support the implementation of the project. RadioNet is now recognized by funding agencies and international project consortia as the European entity representing radio astronomy and facilitating the access to and exploitation of excellent facilities in this field. This is of paramount importance, as a dedicated, formal European radio astronomy organisation to coordinate and serve the needs of this community does not yet exist.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: TPT-2007-0.0-02 | Award Amount: 1.25M | Year: 2008

The KOMODA proposal is presented as an answer to the research objectives launched by call TPT 2007.2 concerning the optimization of the logistics chain through co-modality. More precisely, KOMODAs objective is to produce a roadmap, with associated action plans, to nurture an integrated e-Logistics platform by and between modes of freight transport across Europe. Such platform must comply with a series of basic requirements: has to be based in open standards, usable by any concern, able to communicate freely between existing applications and allow the integration of legacy systems and future development. Several of such IT logistics platforms are currently in use, but mostly consist of private company applications not connected and not even compatible. For such developments, KOMODA will identify the industry requirements in terms of organization of the logistic chain and technical specifications of the integrated information system. Opportunities and obstacles affecting the future implementation of the e-Logistics integrated platform will be identified, resulting in the development of recommendations to empower the former and minimize the later. KOMODA will follow a bottom-up approach, with a strong involvement of freight industry stakeholders. The work will include a wide Delphi survey amongst the logistics chain stakeholders to obtain a comprehensive picture of available e-logistics applications used in transport operations, their sources, availability, functionality and use by companies. A desk research on transport and technical requirements will complement such exercise. Obstacles and opportunities will be identified for finally developing a structured and coherent action plan for innovation and change leading towards an integrated e-logistics system Europe-wide.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-2.4.2-6 | Award Amount: 3.43M | Year: 2009

The main purpose of the EVINCI-study is to test the impact of combined anatomo-functional non invasive cardiac imaging for detection and characterization of Ischemic Heart Disease (IHD). The EVINCI-study is a prospective clinical European multicenter trial performed in a cohort of 700 patients with suspected IHD. Patients with intermediate pre-test probability will undergo clinical and biohumoral characterization, including novel circulating markers of cardiovascular risk. They will be admitted to a non-invasive cardiac evaluation, consisting of anatomic imaging, by multislice computerized tomography, combined with functional tests among radionuclide, magnetic resonance and ultrasound imaging. Heart catheterization will be performed to validate non-invasive diagnosis and follow-up to assess outcome. The diagnostic accuracy of combined non-invasive anatomo-functional imaging will be tested against reference methods for diagnosing epicardial coronary lesions (coronary angiography), vessel wall atherosclerosis (intracoronary ultrasound) and impaired coronary flow reserve (intracoronary doppler/pressure wire). The individual profiles from anatomo-functional cardiac imaging and clinical-biohumoral data will be combined and tested against outcome. A cost-benefit analysis (including an estimate of procedural/radiological risks) of the new diagnostic work-up will also be performed. A relevant part of the EVINCI-study will be dedicated to the development, in cooperation with the industry, of an advanced informatics platform able to synthetically present to the end-user (patients, physicians, etc.) the integrated cardiological diagnostic profile of the individual patient as resulting from clinical-biohumoral and multi-imaging assessment. Overall results will be disseminated in cooperation with the European Society of Cardiology (ESC) and will guide the work of a dedicated ESC Commission which will release specific European Recommendations.


Grant
Agency: European Commission | Branch: FP7 | Program: ERC-AG | Phase: ERC-AG-LS6 | Award Amount: 1.24M | Year: 2009

The Aryl hydrocarbon receptor is an evolutionary conserved widely expressed transcription factor that mediates the toxicity of a substantial variety of exogenous toxins, but is also stimulated by endogenous physiological ligands. While it is known that this receptor mediates the toxicity of dioxin, this is unlikely to be its physiological function. We have recently identified selective expression of AhR in the Th17 subset of effector CD4 T cells. Ligation of AhR by a candidate endogenous ligand (FICZ) which is a UV metabolite of tryptophan causes expansion of Th17 cells and the induction of IL-22 production. As a consequence, AhR ligation will exacerbate autoimmune diseases such as experimental autoimmune encephalomyelitis. Little is known so far about the impact of AhR ligands on IL-17/IL-22 mediated immune defense functions. IL-22 is considered a pro-inflammatory Th17 cytokine, which is involved in the etiology of psoriasis, but it has also been shown to be a survival factor for epithelial cells. AhR is polymorphic and defined as high or low affinity receptor for dioxin leading to the classification of high and low responder mouse strains based on defined mutations. In humans similar polymorphisms exist and although on the whole human AhR is thought to be of low affinity in humans, there are identified mutations that confer high responder status. No correlations have been made with Th17 mediated immune responses in mice and humans. This study aims to investigate the role of AhR ligands and polymorphisms in autoimmunity as well as protective immune responses using both mouse models and human samples from normal controls as well as psoriasis patients.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-SA | Phase: ENV.2009.5.1.0.2 | Award Amount: 1.14M | Year: 2010

Genetic biodiversity is recognised by the Convention on Biological Diversity and the EC Biodiversity Strategy as one of three essential elements of living diversity, yet it is poorly represented at the policy level, compared to the two other components, species and ecosystems. The CONGRESS consortium aims to rectify this situation by delivering dissemination tools which policy makers and conservation managers can conveniently use to incorporate genetic biodiversity into their policy framework. The six work packages of this project fall into two components. The first component comprises WPs 1 5 which will provide a one-stop, community-enabled web portal, including the following components. WP1 concerns web portal design and construction. WP2 will provide databases on academics and professional end-users, publications and genetic data for key European species of conservation concern. WP3 will provide a simulation tool for biodiversity managers to assess the power of genetic data to reveal processes which may result in genetic erosion. WP4 will provide a decision matrix module to allow end-users to establish optimal policy and management options given the genetic data which have been produced. WP5 will provide a knowledge pack and information leaflets, translated into the main European languages, which can be assembled into a manual. The second component is WP6, which comprises a series of dissemination and exchange workshops carried out across the European Union, including a transborder workshop and hands-on demonstration meeting in Eastern Europe. CONGRESS will integrate and enhance these work packages by using the workshops as forums to discuss the contents of the portal and will be guided by an end-user advisory group, who will oversee the development of these tools and ensure their utility for the community who will benefit from them.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2013-ITN | Award Amount: 3.14M | Year: 2013

Euroclast proposes a research training program on osteoclast biology in the context of osteoclast-driven diseases. Osteoclasts are the complex, multinuclear cells responsible for bone breakdown. Many diseases of osteoclast malfunctioning manifest in bone loss, for example, osteoporosis, cancer-induced bone disease, periodontitis, or rheumatoid arthritis, all conditions set to increase in an ageing EU population. The Euroclast consortium (7 academic, 2 private and 1 ass. partner) focuses on osteoclast heterogeneity, a recent insight that poses new fundamental questions best tackled by a multi-partner consortium capable of assembling the sophisticated molecular, genetic and imaging tools required. We will analyze changes in gene and protein expression during osteoclast (trans)differentiation from different precursor cell pools and in various bone sites and relate this to osteoclast activity and sensitivity to therapeutics. The osteoclast resorptive apparatus will be studied using in depth and will define the key enzymatic and molecular machinery to be translated into novel site-specific drug targets or biomarkers. High throughput screening assays for therapeutics and ELISAs for biomarkers will be developed with our private partners. Our multidisciplinary and cross-sectorial approach will improve understanding and treatment of common disorders associated with osteoclast malfunction and train 11 early stage researchers (ESRs) in modern cell and bone biology. We will provide extensive training in generic skills and all ESRs will spend time with our private partners and be seconded to other academic partners to ensure they are well equipped for employment in research and industrial settings. Euroclast will produce an on-line repository for osteoclast protocols, make methodological and scientific advances in osteoclast and bone biology and create a sustainable network of ESRs and senior academics to tackle diseases of bone loss into the future.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2013.2.2.1-2 | Award Amount: 6.32M | Year: 2013

The theme of this collaborative project is development and application of neuroimaging and bioinformatics tools to study lipid metabolism as a common pathogenic link between psychotic disorders and its metabolic co-morbidities. The overall objective is to identify, prioritize and evaluate multi-modal blood and neuroimaging markers with diagnostic potential for prediction and monitoring of psychotic disorders and associated metabolic co-morbidities. We aim to (1) optimise a multidisciplinary approach for combining positron emission tomography (PET) and magnetic resonance imaging (MRI) with metabolomics approaches, (2) develop a PET-method for exploring endocannabinoid pathways in early psychosis in longitudinal study setting, and (3) develop combined PET-MRI biomarker methodology for psychiatric disorders by studying neurotransmitter interactions with multiple PET scan and MRI sequences. The balance of two or more neurotransmitter systems may function as a novel biomarker in these disorders. The expected impacts are (1) etiopathogenic understanding, (2) new validated multi-modal markers for early disease detection and monitoring, (3) new tools for the identification of subjects who may benefit from specific treatment (4) discovery of new avenues for disease prevention and therapy, and (5) new tools and processes for applying brain imaging in personalised medicine. The consortium brings together clinicians, researchers and industry partners in the domains of psychiatry, neuroimaging, metabolic research, systems biology and bioinformatics.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2010.2.4.5-2 | Award Amount: 7.86M | Year: 2010

Chronic inflammatory diseases associated with allergy, including asthma and rhinitis, constitute a major and continuously growing public health concern for Europe. However, the causative factors and mechanisms converting a physiological inflammatory reaction to a chronic response triggering allergic disease remain elusive. Viral infections, particularly those caused by human rhinoviruses (RV) are the most frequent triggers of acute asthma exacerbations. RV infections have more recently been associated with asthma initiation; there is evidence suggesting that such infections may also contribute to respiratory allergy persistence. The strategic aims of PreDicta are to evaluate the hypothesis that repeated infections reprogram the immune system towards a persistent inflammatory pattern leading to respiratory allergies by (i) dissecting the molecular and cellular mechanisms involved in the lack of resolution of inflammation in the context of a human disease, (ii) identifying specific infectious agents and underlying altered host-pathogen interactions, and develop relevant prognostic and therapeutic strategies. PreDicta follows three interconnected workflows: models, mechanisms and translational output. Models include a longitudinal cohort in children, mouse models of repeated virus infection, primary epithelial cultures from patients, viral-bacterial interaction models, and models of epithelial-T-cell-dendritic cell interactions. These will be used to look into disease persistence, inflammation patterns, dysbiosis, immune regulation and resolution of inflammation. Translational outputs include prognostic use of subtype-specific antiviral antibodies, DNAZymes for therapeutic use and delivery technologies targeted to the bronchial epithelium. This interdisciplinary Consortium with strong track record, unique resources and strong translational focus, aims to produce new knowledge and technologies that can rapidly and effectively reach clinical care.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2011.2.4.3-2 | Award Amount: 9.96M | Year: 2011

The DIABAT project will employ knowledge of the function, dysfunction and physiological regulation of brown adipocytes to develop innovative therapeutic and preventive strategies for type 2 diabetes. Brown adipose tissue (BAT) is currently a worldwide recognized target to combat obesity and diabetes due to last years re-discovery of functional BAT in adult humans by several of the members of the DIABAT network (van Marken LIchtenbelt et al., N. Engl. J. Med. 360, 1500, 2009; Virtanen, Enerbck & Nuutila, N. Engl. J. Med. 360, 1518, 2009) along with sharp rise in insight in cellular, genetic, and regulatory mechanisms from animal studies. Therefore, the DIABAT project aims at recruiting and re-activating endogenous energy-dissipating BAT as a preventive and/or remedial measure for weight and blood sugar control in obesity-related type 2 diabetes (diabesity), thereby halting or preventing destruction and facilitating recovery of pancreatic beta-cells under diabetic conditions.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-SA | Phase: SME-2009-3-01 | Award Amount: 1.87M | Year: 2009

The MaPEeR SME proposed CSA covering EU-27 Member States and Bosnia & Herzegovina, with a clear cross-sectoral approach, aims to acquire comprehensive insight into the design, implementation and impact of existing SME research and innovation support programmes and initiatives and convey it in the most appropriate way to SME stakeholders and policy-makers. The methodology adopted by MaPEeR SME brings SME needs and requirements in the centre of the development and evolution processes of programmes and initiatives, in a user-centric framework. End-users will be integral part of the process. MaPEeR SME is to identify, map and analyse all those programmes and initiatives that assist the collaboration between science and SMEs. Including purely technology-oriented and R&D programmes, but also life-long learning or applications of industrial science results. MaPEeR SME will also identify and evaluate the economic, social and environmental impact of identified support measures on SMEs to pro-actively feed in the web platform and to improve and develop recommendations for new support measures better addressing SMEs through the European SME Council. On this basis the MaPEeR SME work plan foresees the definition and refining of a (regionally-differentiated, and cross-sectoral) Strategy for the future design of new RTD and innovation policies, measures, and support services to assist research actions in favour of SMEs and fully exploit synergies between research, innovation and education activities. The approach guiding the MaPEeR SME project is to come up with a comprehensive set of practical recommendations, comparative analysis and consistently effective strategies and policies to improve performance of SMEs advance research and innovation initiatives and programmes by learning not only from best practices but also mainly from the processes by which they are achieved.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: ENV.2007.1.2.1.2. | Award Amount: 4.62M | Year: 2008

The multidisciplinary research teams in this consortium have played lead roles in establishing that fetal and childhood periods are vulnerable to environmental disruption leading to common reproductive disorders. This proposal will investigate: (1) connections between normal/abnormal perinatal reproductive development and maturation of reproductive function at puberty and in adulthood; (2) systemic gene-environment interactions underlying reproductive disorders taking account of genetic susceptibility, multiple exposures (e.g. mixtures of environmental chemicals) and their timing (perinatal, peripubertal, adult); (3) connection between perinatal reproductive development and later obesity/metabolic disorders. To achieve this we will utilize large cohorts generated in previous EU projects and collect new data from these on reproductive maturation and adult function. Existing genomic and proteomics data, exposure data for >100 potentially toxic environmental chemicals, lifestyle, dietary and medical history information will be analysed using integrative systems biology approaches to pinpoint critical (interacting) factors influencing development. Established animal models will be used to test putative mechanisms by analysing the roles of neuroendocrine regulation, intrauterine growth, time windows of reproductive development, metabolic balance and xenobiotic metabolism. Toxicogenomics, proteomics and metabolomics results from these studies will identify pathways for study in the human cohorts. The overall aim is to create new cause-effect frameworks and knowledge networks to refine research in this critical area and to identify novel biomarkers of exposure and disease. The proposed studies will facilitate prediction and prevention of reproductive disorders and provide large new datasets and exposure-outcome information to improve environmental risk assessment and risk management.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 3.92M | Year: 2012

The RADIOMI Initial Training Network (ITN) has the goal of providing training in a superbly suited academic and industrial environment uniquely equipped to conduct a scientific research program that addresses one of the key aspects of functional imaging, the underpinning radiochemistry essential for preparation of radiotracers currently difficult or not possible to access. This will be exploited for biomarkers development inclusive of preclinical investigation to maximise research and training output. The network will enhance the European knowledge economy via the provision of trained and mobile researchers equipped with the skills necessary to pursue successful careers across a wide range of employment sectors in the face of increasing global competition. Molecular imaging is a booming research field of critical importance to facilitate diagnosis of disease states, to monitor response to therapy and to streamline the process of pharmaceutical drug development. Upon completion of this ITN, a group of highly skilled radiochemists will be available to carry out cutting edge research in the field of radiotracer development and naturally enhance the global standing of European culture. From a research output point of view, a series of innovative and new concepts for radiolabeling will emerge, thereby facilitating tremendously the production of probes for molecular imaging. Novel biomarkers with preclinical evaluation will be made available upon completion of the project.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2010.1.2-1 | Award Amount: 3.75M | Year: 2010

The objective of the ACUSEP research project is to develop an integrated, dry-reagent based disposable ready-to-use cartridge enabling rapid analysis of sepsis-causing organisms and eventual identification of antibiotic resistance directly from suspected blood samples. Sepsis causes annually up to 135 000 deaths in Europe and the early diagnosis is the key to improved survival. Identification of the antibiotic resistance is further beneficial to fast initiation of proper antimicrobial treatment. The rapid diagnostics of sepsis and identification of the causative pathogens can be achieved by research utilizing the recent technological advances; combining acoustophoretic collection of the pathogens from whole blood and photoluminescent dual-tag probe-pair detection technology with nucleic acid amplification providing excellent sensitivity and speed needed in acute diagnostics. The consortium is assembled to cover all the key research areas of the project. It consists of academic research organizations with significant technical and scientific experience of acoustophoretic target organism collection and purification, nucleic acid amplification, photoluminescent reporters and multiplexed homogeneous probe detection technologies. The project will proceed in phases, divided to both parallel and serial tasks in collaboration with SME and clinical partners involved, to perform a clinical evaluation of the developed prototype consumable assay cartridge and to initiate further exploitation activities. The specific objective in FP7 HEALTH-2010 addressed to is to develop detection and analytical tools and technologies for diagnosis, monitoring and prognosis of diseases.


Grant
Agency: European Commission | Branch: FP7 | Program: CP | Phase: SST.2013.6-2. | Award Amount: 4.26M | Year: 2013

PORTOPIA aims to develop, next to extensions of existing indicators within the different perspectives of port performance, innovative approaches for the industrys stakeholders, such as: Development of a forecasting dimension in port performance management within the market trends and structure category; Development of top-down methods for harmonised socio-economic impact calculation; Development of an innovative, port-individualized tool for environmental and safety performance; Development of European port-related logistics chain connectivity indicators; Development of new governance indicators based on the changing role of port authorities, including indicators on financial capabilities and transparency; Development of a method to capture user perceptions of port performance; Development of a dedicated performance management system for the inland ports sector, including attention to the interaction between sea and inland ports; Development of a strategy map and an integrated benchmarking tool taking into account the specificities of ports. Furthermore, PORTOPIA aims to increase substantially the efficiency (user friendliness) of the data collection, to automate the calculations and the management system, and to build a solid data warehouse ensuring data confidentiality of individual contributors in all phases (collection, calculation, reporting). Also, further professionalizing of the communication and dissemination of results through a dedicated website, professional reporting, annual events on port performance, etc. belongs to PORTOPIAs objectives. The end result of PORTOPIA will be a state-of-the-art, sustainable, self-supporting European Ports Observatory, endorsed by port stakeholders, that provides superior value to the industry and its stakeholders by supplying transparent, useful and robust indicators and the contextual analysis of thereof, leading to improved resource efficiency, effectiveness and societal support for the European Port System.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: PROTEC-1-2014 | Award Amount: 1.21M | Year: 2015

HESPERIA will produce two novel operational forecasting tools based upon proven concepts (UMASEP, REleASE). At the same time it will advance our understanding of the physical mechanisms that result into high-energy solar particle events (SEPs) exploiting novel datasets (FERMI/LAT/GBM; PAMELA; AMS) and it will explore the possibility to incorporate the derived results into future innovative space weather services. In order to achieve these goals HESPERIA will exploit already available large datasets stored into databases such as the neutron monitor database (NMDB) and SEPServer that have been developed under FP7 projects from 2008 to 2013. The objectives of HESPERIA are: 1) To develop two novel SEP forecasting systems based upon proven concepts. 2) To develop SEP forecasting tools searching for electromagnetic proxies of the gamma-ray emission in order to predict large SEP events. 3) To perform systematic exploitation of the novel high-energy gamma-ray observations of the FERMI mission together with in situ SEP measurements near 1 AU. 4) To provide for the first time publicly available software to invert neutron monitor observations of relativistic SEPs to physical parameters that can be compared with the space-borne measurements at lower energies. 5) To perform examination of currently unexploited tools (radio emission) 6) To design recommendations for future SEP forecasting systems. The results will be openly accessible to the public through the dedicated web interface of HESPERIA and will further be posted in related servers such as NMDB and SEPServer. The HESPERIA consortium consists of 9 partners with complementary expertise covering all aspects of the project. HESPERIA will also collaborate with a number of institutes and individuals from US and Russia, ensuring both the in depth analysis of the novel datasets to be utilized within the project and the efficient dissemination of the results to the whole space physics/space weather community.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2009-1.2-1 | Award Amount: 5.28M | Year: 2009

6.1 million people currently live with a form of dementia in the European Union with an addition of 1.4 million new cases every year. Combination of psychological testing, brain-imaging and exclusion of other neurological disorders makes the diagnosis of Alzheimers disease complicated and time consuming (taking up to 20 months). A rapid, sensitive and specific immunoassay for protein markers inside blood would largely improve early diagnosis and lead to a better treatment of dementia. Homogeneous assays based on FRET from one dye labeled specific antibody (AB1) to another (AB2) within an AB1-biomarker-AB2 immune complex are an ideal basis to meet these diagnostic requirements. As the detection of several protein markers is obligatory for a highly sensitive and specific diagnosis an optical multiplexing approach with dyes of different colors is a smart solution. Semiconductor quantum dots (QDs) are the ideal candidates due to their size-dependent absorption and emission wavelengths. Moreover, they possess unique photophysical properties that overcome conventional fluorescence dyes. In combination with lanthanide complexes (LCs), that display long luminescence lifetimes and well separated emission bands, QDs render a powerful multiplexing tool for highly sensitive diagnostics even for large immune complexes. FRET applications using QDs are to date restricted to academic research and a profound understanding of QD-based FRET is not available. For a comprehensive analysis the use of LCs is mandatory, because they are the only known donors for efficient FRET to QD acceptors. NANOGNOSTICS strives for a profound understanding of QD-based FRET, the synthetic creation of highly efficient QD immune sensors for detection of several Alzheimer-specific protein markers and the development of a modular high-throughput-screening immuno analyzer for the integration of QD-based multiplexing immunoassays into early diagnosis for improved patient outcome in dementia therapy.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-SA | Phase: SiS.2013.2.2.1-1 | Award Amount: 2.79M | Year: 2014

The Ark of Inquiry project aims to raise youth awareness to Responsible Research and Innovation (RRI) by providing young European citizens (7 to 18-year-olds) with a pool of engaging inquiry activities to improve their inquiry skills, increase their awareness and understanding of conducting real science, and prepare them to participate in different roles in the European research and innovation process. In order to achieve these aims, the project will 1) develop a framework for identifying inquiry activities that promote pupils awareness of RRI; 2) collect existing inquiry activities and environments from various national and international projects; 3) make the activities available across Europe through the Ark of Inquiry platform in order to bring together inquiry activities, learners, and supporters (teachers, science and teacher education students, and staff of universities and science centres); 4) train at least 1 100 teachers to support pupils inquiry activities in a manner that attracts pupils interest and motivation towards RRI; and 5) implement the inquiry activities on a large-scale across a European school network. During the project at least 23 000 students will participate in the Ark of Inquiry. After completing a particular set of inquiry activities the pupils can apply for an Inquiry Award. A large community consisting of 1 100 trained teachers and at least 100 science and teacher education students and 50 researchers from universities and science centres over Europe will support learners inquiry activities and award their performance. Based on evaluation results the Ark of Inquiry platform will be made available for the whole of Europe. The platform will connect formal learning settings and curricula to centres for science and research, so that generations of scientists can meet each other. This project helps build a society skilled in RRI and related scientific communication.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: INSO-2-2014 | Award Amount: 3.10M | Year: 2015

Reaching the ambitions of the Europe 2020 and the Innovation Union requires much more than just technological innovations. In the academic community, Business Model Innovation (BMI) has for a long time been recognized as the key to improved competitiveness and innovativeness. However, BMI does not reach SMEs yet nor is there knowledge on how SMEs conduct BMI in practice. Empowering SMEs to conduct BMI requires new approaches. By leveraging existing networks and communities, we will gather examples, best practices and insights into Business Models (BM) from case studies from each and every European region or industry, complemented with insights from other leading countries worldwide. The BM vortex will thus generate an enormous and rich library of business models patterns and managerial structures, provided on a platform, to support SMEs in these communities. We will also develop innovative tooling and provide them on the platform to makes it easy for SMEs to develop, evaluate and plan new business models. The ENVISION consortium covers Northern, Western, Central, Eastern and Southern Europe. In each region a top-ranked academic institution in the field of BMI is present as well as innovative businesses that deliver smart and tailored BMI tooling and reach out to SMEs. We build on over a decade of joint work on BMI and BM tooling. We will build and maintain regional and thematic communities. In the communities, support is delivered to help SMEs transform and improve their BMs. The consortium also includes partners and associated partners that will realize our pan-European reach to SMEs: on a pan-European level (e.g., UAEPME and female entrepreneurs network), on a national and regional level (e.g., chambers of commerce, family business organizations and statistical offices). The consortium also has linkages to EIT/ICT Labs and the European Service Innovation Centre (ESIC).


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-CA | Phase: SST-2007-2.2-03 | Award Amount: 2.49M | Year: 2008

The PROPS project builds on previous EU and national activities undertaken to promote and develop short sea shipping. In particular, PROPS aims to work closely with the Short Sea Promotion Centres (SPCs) to develop a workable and replicable methodology that will enhance their practical promotion activities in the fields of legislative, technical, and operational actions and to extend their operations to encompass inter-modal and co-modal transport. The first step will be to identify, from the SPCs, the best practices aimed at improving the integration of short sea shipping with relevant inland logistics chains. Particular attention will be paid to the linkages of key supply chain stakeholders and the removal of bottlenecks. This initial activity will be followed by a comprehensive analysis of the core processes that are, or need to be, carried out by SPCs, both individually and via the SPC European Network, to develop and utilise a business networking approach to enhance the current. practical work of the SPCs. One outcome of this activity will be a set of performance indicators and benchmarks, linked to self-assessment tools and training programmes for the SPCs. Tools will be developed to assist the SPCs improve their performance and their overall integration into European logistics business networks. For instance, an e-booking system integrator, to improve access to commercial freight booking systems, will be established. Both strategic and tactical support mechanisms will be developed, and learning from past failures will be formalised as a mechanism for improving the work of the SPCs to promote short sea shipping and intermodal transport. A media campaign, run by a large, professional media company will establish and test the campaign in enhancing role of the SPCs and the perception by business of the need to increase the amount of freight transport by short sea shipping as an integral part of logistics supply chains.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP-SICA | Phase: SSH.2013.2.1-3 | Award Amount: 2.88M | Year: 2014

MNEmerge Project aims to address the issues raised in this call together with a consortium that consists of top European universities, international organisations and multinational enterprises. We wish to provide a comprehensive framework, case study methodology and policy analysis of the activities of MNE and organisations operating in- and outside of EU. We are mostly interested on activities that take part in India, Brazil and Africa. The consortium has been an active contributor to the multinationals research and it has expertise on studying societal problems in emerging markets. The research will be carried out by an international, interdisciplinary team, involving researchers from Finnish, British and Dutch institutes. The issues studied in this project are varied but there is a common thread uniting all of its sub-themes; namely they all relate to how MNE activities in terms of one of the following: FDI, business functioning, technology and innovation strategies, corporate philanthropy or socially responsible investment, can contribute to the attainment of poverty alleviation, food security, health security and environmental security, which are intimately interlinked. The objectives of the project are: 1. Development of a framework to analyse MNE impact towards socio-economic development 2. Development of a model that describes the relationship between MNE, FDI and the economy 3. Role of public policies in supporting responsible business practises and the Millennium Declaration Goals 4. Case Studies to support the methodological framework model on health, environment and energy We identify modes of MNE collaboration with other societal stakeholders including the State, which permit the business sustainability while ensuring sustainable development of society as a whole with the environment being a passive stakeholder. We will also develop tools and aids for decision making that can facilitate the implementation of the aforesaid recommendations.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: NMP-2007-4.0-4 | Award Amount: 14.37M | Year: 2008

The search for effective therapies and early detection strategies for Alzheimers Disease (AD), the major cause of dementia in Europe, is imperative. It is known that -amyloid (A) peptide plays a central role in neurodegeneration. In AD brain, A is released in a soluble form that progressively becomes insoluble forming aggregates; extracellular plaques mainly composed of A are a hallmark of post-mortem brains. These premises strongly suggest brain A as a possible target for therapy and diagnosis of AD. In addition, it is known that brain and blood A pools are in equilibrium via the blood-brain-barrier (BBB). Accordingly, it has been reported that removal of blood A may withdraw the excess of brain A by a sink effect. Thus, blood A is another potential target. The aim of this project is to utilize nanoparticles (NPs) specifically engineered for targeting brain A, for the combined diagnosis and therapy (theranostics) of AD. NPs (liposomes, solid lipid NPs, polymeric-NPs) will be multiple-functionalized with: i) a large arsenal of molecules (specific lipids, antiamyloidogenic drugs, polyphenols, heteroaromatic compounds, unnatural peptides and peptidomimetics, antibodies) interacting with A in all aggregation forms, ii) PET or MRI contrast agents detecting such interaction, iii) molecules stimulating BBB crossing via the transcytotic route. Several artificial and cellular models will be used to fine-tune such features and to improve NPs biocompatibility, non-immunogenicity, non-toxicity and physical stability. Eventually, absorption, distribution, metabolism and excretion will be studied using animal models of AD. Different routes (i.v., oral, nasal) and protocols (two-step, NPs cocktails, aerosols) of administration will be utilized to boost NPs brain delivery. The prediction is that NPs will detect, disaggregate and remove A brain deposits. In any case, NPs will interact with blood A, withdrawing the excess of brain peptide by a sink effect.


Grant
Agency: European Commission | Branch: H2020 | Program: CSA | Phase: GERI-4-2015 | Award Amount: 1.86M | Year: 2016

EQUAL-IST aims at introducing structural changes to enhance gender equality within Information Systems and Technology Research institutions, which have been demonstrated to be among the research sectors most affected by gender inequalities at all levels. The project aims at supporting seven RPOs from Northern, Southern and Central European countries plus a CSI country, in developing and implementing Gender Equality Action Plans. All the 7 RPOs of the EQUAL-IST consortium are at a starting stage in the setting up of GEPs and they have also ensured the support of the highest management levels both from their faculties and university as whole. The project will combine gender mainstreaming and positive actions on 3 main levels: HR practices and management processes, research design and delivery, student services and institutional communication. For addressing and solving issues of horizontal and vertical segregation in research and administrative careers, work life balance, gender neutral-blind approaches to IST research, gender gaps in students enrollment, EQUAL-IST will try to operate at the same time on organizational structures, discourses and behaviors. In addition, EQUAL-IST will promote a participatory approach towards Gender Equality Policies based on co-design and at the same time ensuring the active dialogue with and involvement of top decision makers at the partner RPOs. By setting up a dedicated crowdsourcing- online collaborative platform the project will support both the initial internal assessment of the RPOs and the GEPs design process. EQUAL-IST toolkits and guidelines, lessons learned and used methodologies will be disseminated broadly in Europe and other CSI countries with a communication strategy focused on IST Research Institutions and RFOs and through collaboration with the EURAXESS network, in order to support ERA objectives in relation to gender equality in research.


Grant
Agency: European Commission | Branch: H2020 | Program: CSA | Phase: INFRASUPP-01-2016 | Award Amount: 2.00M | Year: 2017

RISCAPE will provide systematic, focused, high quality, comprehensive, consistent and peer-reviewed international landscape analysis report on the position and complementarities of the major European research infrastructures in the international research infrastructure landscape. To achieve this, RISCAPE will establish a close links with a stakeholder panel representing the main user groups of the report, including representatives from ESFRI, the OECD and Member state funding agencies to ensure usability and the focus of the Report. It will also benefit from close co-operation with other projects and initiatives in the European research infrastructures development to ensure consistency with the existing landscape work. Particularly, RISCAPE builds on the European Research Infrastructures (RIs) in the ESFRI landscape report (2016) and on the landscape analysis done or currently underway in the H2020 cluster projects. RISCAPE leverages the experts on the European RIs with extensive knowledge on the disciplines involved and RI development in Europe and the project benefits from the contacts and tools developed in the cluster- and international RI collaboration projects to maximize the discipline-specific usability of the results. A key factor in the RISCAPE analysis is that the complementarities will be analyzed in a way which is natural and suitable for the discipline and RI in question. The resulting Report and the used methods will be independently peer reviewed to maximize the usability and objectivity of the information provided for the EU strategic RI development and policy. The project answers directly to the European Commission strategy on EU international cooperation in research and innovation, particularly on the need to obtain objective information in order to help implement the (EC) strategic approach.


News Article | December 16, 2016
Site: www.eurekalert.org

Researchers at the University of Turku, Finland, have identified a new way of blocking the spread of cancer. Calcium channel blockers, which are used to lower blood pressure, block breast and pancreatic cancer invasion by inhibiting cellular structures By screening already approved drugs, the team led by Postdoctoral Researcher Guillaume Jacquemet and Academy Professor Johanna Ivaska has discovered that calcium channel blockers can efficiently stop cancer cell invasion in vitro. Calcium channel blockers are currently used to treat hypertension, also known as high blood pressure, but their potential use in blocking cancer cell metastases has not been previously reported. Cancer kills because of its ability to spread throughout the body and form metastases. Therefore, developing drugs that block the ability of cancer cells to disseminate is a major anti-cancer therapeutic avenue. Developing new drugs, however, is a very lengthy and expensive process and many promising drugs fail clinical trials because of unanticipated toxicity and side effects. Thus, finding new targets for drugs already in use to treat other diseases, in other words drug repurposing, is an emerging area in developing anti-cancer therapies. - Identification of anti-hypertension drugs as potential therapeutics against breast and pancreatic cancer metastasis was a big surprise. The targets of these drugs were not know to be present in cancer cells and therefore no one had considered the possibility that these drugs might be effective against aggressive cancer types, says Professor Ivaska. For several years, the research team from the Turku Centre for Biotechnology lead by Professor Johanna Ivaska has focused their efforts on understanding how cancer cells move and invade surrounding tissue. The team has identified that aggressively spreading cancer cells express a protein called Myosin-10 which drives cancer cell motility. - Myosin-10 expressing cancers have a large number of structures called filopodia. They are sticky finger-like structures the cancer cells extend to sense their environment and to navigate - imagine a walking blind spider, explains Dr Jacquemet. The team found that calcium channel blockers target specifically these sticky fingers rendering them inactive, thus efficiently blocking cancer cell movement. This suggest that they might be effective drugs against cancer metastasis. However, at this stage much more work is required to assess if these drugs would be efficient against cancer progression. The team and their collaborators are currently assessing the efficiency of calcium channel blockers to stop the spreading of breast and pancreatic cancer using pre-clinical models and analysing patient data. The findings were published in Nature Communications journal on 2 December 2016. Original publication: L-type calcium channels regulate filopodia stability and cancer cell invasion downstream of integrin signalling. Jacquemet G, Baghirov H, Georgiadou M, Sihto H, Peuhu E, Cettour-Janet P, He T, Perälä M, Kronqvist P, Joensuu H, Ivaska J. Nat Commun. 2016 Dec 2;7:13297. doi: 10.1038/ncomms13297.


News Article | November 2, 2015
Site: phys.org

The bulk of the protein on our plates originates in Brazil, because the protein fodder consumed by food-producing animals consists mostly of soy grown there. If the vision proposed by the ScenoProt project, coordinated by the Natural Resources Institute Finland (Luke), becomes reality, by 2030 our food production will no longer be dependent on a handful of large Brazilian companies. "This project seeks to increase Finland's self-sufficiency in protein production from the current less-than-twenty to sixty per cent. A similar change must take place in the whole of Europe, as soy cultivation destroys rain forest in Brazil, accelerating the climate change," says Principal Research Scientist Anne Pihlanto of Luke. New foodstuffs pave the way to a healthier diet Efforts are taken to increase self-sufficiency in protein protection by developing foodstuffs in which protein originates in new sources, such as insects and mushrooms, and by processing vegetable raw materials to form more usable products. By 2030, we will be in better health because we will consume less meat and more vegetables. "Foodstuffs developed in the course of the project will be turned into products, making them well-known brands that are attractive to consumers," Pihlanto says. Consumers are engaged in the planning of foodstuffs The ScenoProt project will span six years, with the protein production problem being investigated from a number of perspectives. The research conducted at Luke is related to plant production, animal nutrition, processing technology and food healthiness, as well as to the bearing capacity of nature. Futurologists at the University of Turku are investigating various ways of achieving the objectives set for the year 2030. The University of Jyväskylä is testing the practical options with a number of companies. Dutch TNO is the best expert concerning the economic aspects associated with the breeding of insects, while the University of Helsinki is involved in the research focused on the various health impacts. In addition, a company called Makery will bring their expertise in product planning and consumer surveys to the project. Consumers will be engaged in the planning of prototypes for new types of foodstuffs within the scope of the project. The marketing potential of new foodstuffs both on the domestic and export markets will be surveyed. Explore further: Products of biotechnological origin using vegetable and fruit by-products generated by the industry


News Article | November 17, 2016
Site: www.sciencedaily.com

Knowing the likely course of cancer can influence treatment decisions. Now a new prediction model published in Lancet Oncology offers a more accurate prognosis for a patient's metastatic castration-resistant prostate cancer. The approach was as novel as the result -- while researchers commonly work in small groups, intentionally isolating their data, the current study embraces the call in Joe Biden's "Cancer Moonshot" to open their question and their data, collecting previously published clinical trial data and calling for worldwide collaboration to evaluate its predictive power. That is, researchers crowdsourced the question of prostate cancer prognosis, eventually involving over 550 international researchers and resulting in 50 computational models from 50 different teams. The approach was intentionally controversial. "Scientists like me who mine open data have been called 'research parasites'. While not the most flattering name, the idea of leveraging existing data to gain new insights is a very important part of modern biomedical research. This project shows the power of the parasites," says James Costello, PhD, senior author of the paper, investigator at the University of Colorado Cancer Center, assistant professor in the Department of Pharmacology at the CU School of Medicine, and director of Computational and Systems Biology Challenges within the Sage Bionetworks/DREAM organization. The project was overseen as a collaborative effort between 16 institutions, led by academic research institutions including CU Cancer Center, open-data initiatives including Project Data Sphere, Sage Bionetworks, and the National Cancer Institute's DREAM Challenges, and industry and research partners including Sanofi, AstraZeneca, and the Prostate Cancer Foundation. Challenge organizers made available the results from five completed clinical trials. Teams were challenged to connect a deep set of clinical measurements to overall patient survival, organizing their insights into novel computational models to better predict patient survival based on clinical data. "The idea is that if a patient comes into the clinic and has these measurements and test results, can we put this data in a model to say if this patient will progress slowly or quickly. If we know the features of patients at the greatest risk, we can know who should receive standard treatment and who might benefit more from a clinical trial," Costello says. The most successful of the 50 models was submitted by a team led by Tero Aittokallio, PhD, from the Institute for Molecular Medicine Finland, FIMM, at University of Helsinki, and professor in the Department of Mathematics and Statistics at University of Turku, Finland. "My group has a long-term expertise in developing multivariate machine learning models for various biomedical applications, but this Challenge provided the unique opportunity to work on clinical trial data, with the eventual aim to help patients with metastatic castration-resistant prostate cancer," Aittokallio says. Basically, the model depended on not only groups of single patient measurements to predict outcomes, but on exploring which interactions between measurements were most predictive -- for example, data describing a patient's blood system composition and immune function were only weakly predictive of survival on their own, but when combined became an important part of the winning model. The model used a computational learning strategy technically referred to as an ensemble of penalized Cox regression models, hence the model's name ePCR. This model then competed with 49 other entries, submitted by other teams working independently around the world. "Having 50 independent models allowed us to do two very important things. First when a single clinical feature known to be predictive of patient survival is picked out by 40 of the 50 teams, this greatly strengthens our overall confidence. Second, we were able to discover important clinical features we hadn't fully appreciated before," Costello says. In this case, many models found that in addition to factors like prostate-specific antigen (PSA) and lactate dehydrogenase (LDH) that have long been known to predict prostate cancer performance, blood levels of an enzyme called asparate aminotransferease (AST) is an important predictor of patient survival. This AST is an indirect measure of liver function and the fact that disturbed levels of AST are associated with poor patient performance implies that studies could evaluate the role of AST in prostate cancer. "The benefits of a DREAM Challenge are the ability to attract talented individuals and teams from around the world, and a rigorous framework for the assessment of methods. These two ingredients came together for our Challenge, leading to a new benchmark in metastatic prostate cancer," says paper first author, Justin Guinney, PhD, director of Computational Oncology for Sage Bionetworks located at Fred Hutchinson Cancer Research Center. "A goal of the Project Data Sphere initiative is to spark innovation -- to unlock the potential of valuable data by generating new insights and opening up a new world of research possibilities. Prostate Cancer DREAM Challenge did just that. To witness cancer clinical trial data from Project Data Sphere be used in research collaboration and ultimately help improve patient care in the future is extremely rewarding!" says Liz Zhou, MD, MS, director of Global Health Outcome Research at Sanofi. The goal now is to make the ePCR model publicly accessible through an online tool with an eye towards clinical application. In fact, the National Cancer Institute (NCI) has contracted the winning team to do exactly this. Soon, when patients face difficult decisions about the best treatment for metastatic castration-resistant prostate cancer, ePCR tool could be an important piece of the decision-making process.


Jaaskelainen S.K.,University of Turku
Clinical Neurophysiology | Year: 2012

Primary burning mouth syndrome (BMS) is severe, disabling and chronic intraoral pain condition for which no local or systemic cause can be found and clinical examination is normal. It mostly affects elderly citizens, especially postmenopausal women with prevalence up to 12-18%. In addition to spontaneous burning pain, patients may complain of taste alterations. Recent neurophysiologic, psychophysical, neuropathological, and functional imaging studies have elucidated that several neuropathic mechanisms, mostly subclinical, act at different levels of the neuraxis and contribute to the pathophysiology of primary BMS. Demonstration of loss of small diameter nerve fibres in the tongue epithelium explains thermal hypoesthesia and increase in taste detection thresholds found in quantitative sensory testing. As in neuropathic pain, decreased brain activation to heat stimuli has been demonstrated with fMRI in BMS patients. However, it seems that the clinical diagnosis of primary BMS encompasses at least three distinct, subclinical neuropathic pain states that may overlap in individual patients. The first subgroup (50-65%) is characterized by peripheral small diameter fibre neuropathy of intraoral mucosa. The second subgroup (20-25%) consists of patients with subclinical lingual, mandibular, or trigeminal system pathology that can be dissected with careful neurophysiologic examination but is clinically indistinguishable from the other two subgroups. The third subgroup (20-40%) fits the concept of central pain that may be related to hypofunction of dopaminergic neurons in the basal ganglia. The neurogenic factors acting in these subgroups differ, and will require different treatment strategies. In the future, with proper use of diagnostic tests, BMS patients may benefit from interventions specifically targeted at the underlying pathophysiological mechanisms. © 2011 International Federation of Clinical Neurophysiology.


Nevalainen T.J.,University of Turku | Cardoso J.C.R.,University of Algarve
Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics | Year: 2012

Vertebrate group XII phospholipases A2 (GXII PLA2, conserved domain pfam06951) are proteins with unique structural and functional features within the secreted PLA2 family. In humans, two genes (GXIIA PLA2 and GXIIB PLA2) have been characterised. GXIIA PLA2 is enzymatically active whereas GXIIB PLA2 is devoid of catalytic activity. Recently, putative homologues of the vertebrate GXII PLA2s were described in non-vertebrates. In the current study a total of 170 GXII PLA2 sequences were identified in vertebrates, invertebrates, non-metazoan eukaryotes, fungi and bacteria. GXIIB PLA 2 was found only in vertebrates and the searches failed to identify putative GXII PLA2 homologues in Archaea. Comparisons of the predicted functional domains of GXII PLA2s revealed considerable structural identity within the Ca2 +-binding and the catalytic sites among the various organisms suggesting that functional conservation may have been retained across evolution. The preservation of GXII PLA2 family members from bacteria to human indicates that they have emerged early in evolution and evolved via gene/genome duplication events prior to Eubacteria. Gene duplicates were identified in some invertebrate taxa suggesting that species-specific duplications occurred. The analysis of the GXII PLA2 homologue genome environment revealed that gene synteny and gene order are preserved in vertebrates. Conservation of GXII PLA2s indicates that important functional roles involved in species survival and were maintained across evolution and may be dependent on or independent of the enzyme's phospholipolytic activity. © 2012 Elsevier Inc.


Yegutkin G.G.,University of Turku | Wieringa B.,University of Turku | Robson S.C.,Radboud University Nijmegen | Jalkanen S.,University of Turku | Jalkanen S.,Beth Israel Deaconess Medical Center
FASEB Journal | Year: 2012

Extracellular ATP and ADP trigger inflammatory, vasodilatatory, and prothrombotic signaling events in the vasculature, and their turnover is governed by networks of membrane-associated enzymes. The contribution of soluble activities to intravascular nucleotide homeostasis remains controversial. By using thin-layer chromatographic assays, we revealed transphosphorylation of [γ-32P]ATP and AMP by human and murine sera, which was progressively inhibited by specific adenylate kinase (AK) inhibitor Ap5A. This phosphotransfer reaction was diminished markedly in serum from knockout mice lacking the major AK isoform, AK1, and in human serum immunodepleted of AK1. We also showed that ∼75% ADP in cell-free serum is metabolized via reversible AK1 reaction 2ADP • ATP + AMP. The generated ATP and AMP are then metabolized through the coupled nucleotide pyrophosphatase/phosphodiesterase and 5′-nucleotidase/CD73 reactions, respectively. Constitutive presence of another nucleotide-converting enzyme, nucleoside triphosphate diphosphohydrolase-1 (NTPDase1, known as CD39), was ascertained by the relative deficiency of serum from CD39-null mice to dephosphorylate [3H]ADP and [γ-32P]ATP, and also by diminished [3H]ADP hydrolysis by human serum pretreated with NTPDase1 inhibitors, POM-1 and ARL-67156. In summary, we have identified hitherto unrecognized soluble forms of AK1 and NTPDase1/CD39 that contribute in the active cycling between the principal platelet-recruiting agent ADP and other circulating nucleotides. © FASEB.


Tertti K.,University of Turku | Ekblad U.,University of Turku | Koskinen P.,University of Turku | Vahlberg T.,University of Turku | Ronnemaa T.,University of Turku
Diabetes, Obesity and Metabolism | Year: 2013

Aims: We compared metformin with insulin as treatment of gestational diabetes mellitus (GDM). Furthermore, we aimed to characterize metformin-treated patients needing additional insulin to achieve prespecified glucose targets. Methods: We conducted a single centre randomized controlled study with non-inferiority design comparing metformin and insulin in the treatment of 217 GDM patients having birth weight as primary outcome variable. Results: There were no significant differences in mean birth weight expressed in grams [+15 (90% confidence interval (CI): -121 to 89)] or SD units [+0.04 (90% CI: -0.27 to 0.18)] between the metformin and insulin groups. There were no significant differences in neonatal or maternal data between the groups. Only 23 (20.9%) of the 110 patients in the metformin group needed additional insulin. Compared with the patients on metformin only, those needing additional insulin were older (p=0.04), their oral glucose tolerance test had been performed earlier and diabetes therapy started earlier in gestation (p=0.01 and p=0.004, respectively). The risk for additional insulin was 4.6-fold in women with baseline serum fructosamine concentration above median compared with those below median. Conclusions: Metformin is an effective alternative to insulin in the treatment of GDM patients. Serum fructosamine may help in predicting the adequacy of metformin treatment alone. © 2012 Blackwell Publishing Ltd.


Nocentini A.,University of Florence | Menesini E.,University of Florence | Salmivalli C.,University of Turku
Journal of Adolescence | Year: 2013

The development of bullying behavior was examined across three years in a sample of 515 adolescents (46% females) from 41 classrooms. At time 1, the students were in grades 9 and 10 (mean age. =. 14.5 years; SD. =. .54). Results of a multilevel growth model showed that both baseline level and change of bullying varied significantly across individuals as well as across classrooms. At the individual level, gender, aggression and competition for social dominance were related with baseline level of bullying. Competition for social dominance and class change were additionally associated with increases in bullying over time. At the classroom level, pro-bullying behaviors were associated with higher baseline level of bullying, whereas anti-bullying behaviors with decreases in bullying over time. Finally, a cross-level interaction underlined that the link between aggression and bullying was moderated by the pro-bullying behaviors within each class. Results are discussed according to the child by environment perspective. © 2013 The Foundation for Professionals in Services for Adolescents.


Huhtaniemi I.,Imperial College London | Huhtaniemi I.,University of Turku
Asian Journal of Andrology | Year: 2014

Although suppressed serum testosterone (T) is common in ageing men, only a small proportion of them develop the genuine syndrome of low T associated with diffuse sexual (e.g., erectile dysfunction), physical (e.g. loss of vigor and frailty) and psychological (e.g., depression) symptoms. This syndrome carries many names, including male menopause or climacterium, andropause and partial androgen deficiency of the ageing male (PADAM). Late-onset hypogonadism (LOH) describes it best and is therefore generally preferred. The decrease of T in LOH is often marginal, and hypogonadism can be either due to primary testicular failure (low T, high luteinizing hormone (LH)) or secondary to a hypothalamic-pituitary failure (low T, low or inappropriately normal LH). The latter form is more common and it is usually associated with overweight/obesity or chronic diseases (e.g., type 2 diabetes mellitus, the metabolic syndrome, cardiovascular and chronic obstructive pulmonary disease, and frailty). A problem with the diagnosis of LOH is that often the symptoms (in 20%-40% of unselected men) and low circulating T (in 20% of men >70 years of age) do not coincide in the same individual. The European Male Ageing Study (EMAS) has recently defined the strict diagnostic criteria for LOH to include the simultaneous presence of reproducibly low serum T (total T <11 nmol l -1 and free T <220 pmol l-1 ) and three sexual symptoms (erectile dysfunction, and reduced frequency of sexual thoughts and morning erections). By these criteria, only 2% of 40- to 80-year-old men have LOH. In particular obesity, but also impaired general health, are more common causes of low T than chronological age per se. Evidence-based information whether, and how, LOH should be treated is sparse. The most logical approach is lifestyle modification, weight reduction and good treatment of comorbid diseases. T replacement is widely used for the treatment, but evidence-based information about its real benefits and short- and long-term risks, is not yet available. In this review, we will summarize the current concepts and controversies in the pathogenesis, diagnosis and treatment of LOH. © 2014 AJA, SIMM & SJTU. All rights reserved.


Ketola T.,University of Turku
Corporate Social Responsibility and Environmental Management | Year: 2014

This paper builds and tests a RaMoNe pyramid with three dimensions: rationale, morals and needs. The pyramid maps out where companies currently stand in corporate responsibility (CR) and why; and why they should change and how. The conscious economic rationale of companies has led to choices between five levels of CR, demonstrated by an earlier paper in this journal. These alternatives exemplify preconscious levels of moral development, but the highest level, virtue ethical behaviour, has not so far had its counterpart in CR. There are subconscious needs behind the rationale and morals, but the highest level, self-transcendence needs, has not yet had its match in CR. The conceptual part of this research develops the sixth level of CR to match the virtue ethical behaviour and self-transcendence needs. The RaMoNe pyramid is tested in four food sector companies, thereby building a model on a case study previously published in this journal. © 2013 John Wiley & Sons, Ltd and ERP Environment.


Karlsson H.K.,University of Turku
Molecular Psychiatry | Year: 2015

Positron emission tomography (PET) studies suggest opioidergic system dysfunction in morbid obesity, while evidence for the role of the dopaminergic system is less consistent. Whether opioid dysfunction represents a state or trait in obesity remains unresolved, but could be assessed in obese subjects undergoing weight loss. Here we measured brain μ-opioid receptor (MOR) and dopamine D2 receptor (D2R) availability in 16 morbidly obese women twice—before and 6 months after bariatric surgery—using PET with [11C]carfentanil and [11C]raclopride. Data were compared with those from 14 lean control subjects. Receptor-binding potentials (BPND) were compared between the groups and between the pre- and postoperative scans among the obese subjects. Brain MOR availability was initially lower among obese subjects, but weight loss (mean=26.1 kg, s.d.=7.6 kg) reversed this and resulted in ~23% higher MOR availability in the postoperative versus preoperative scan. Changes were observed in areas implicated in reward processing, including ventral striatum, insula, amygdala and thalamus (P's<0.005). Weight loss did not influence D2R availability in any brain region. Taken together, the endogenous opioid system plays an important role in the pathophysiology of human obesity. Because bariatric surgery and concomitant weight loss recover downregulated MOR availability, lowered MOR availability is associated with an obese phenotype and may mediate excessive energy uptake. Our results highlight that understanding the opioidergic contribution to overeating is critical for developing new treatments for obesity.Molecular Psychiatry advance online publication, 13 October 2015; doi:10.1038/mp.2015.153. © 2015 Macmillan Publishers Limited


Seppala J.K.,University of Turku
Journal of applied clinical medical physics / American College of Medical Physics | Year: 2011

The use of solid carbon fiber table materials in radiotherapy has become more common with the implementation of image-guided radiotherapy (IGRT), since the solid materials give less imaging artifacts than the so-called tennis racket couchtops. The downside of the solid carbon fiber couch inserts is that they increase the beam attenuation, resulting in increased surface doses and inaccuracies in determine the dose in the patient. The purpose of this study was to evaluate the interaction of 6 and 15 MV photons with eight different couch inserts. The presented results enable direct comparison of the attenuation properties of the studied couchtops. With a direct posterior beam the maximum attenuations reach 3.6% and 2.4% with 6 and 15 MV, respectively. The measured maximum attenuation by a couchtop with an oblique gantry angle was 10.8% and 7.4% at 6 and 15 MV energies, respectively. The skin-sparing effect was decreased substantially with every couchtop. The highest increases in surface doses were recorded to be four- and threefold, as compared to the direct posterior open field surface doses of 6 and 15 MV, respectively. In conclusion, the carbon fiber tabletops decrease the skin-sparing effect of megavoltage photon energies. The increased beam attenuation and skin doses should be taken into account in the process of treatment planning.


Jartti T.,University of Turku | Jartti L.,Turku City Hospital | Ruuskanen O.,University of Turku | Soderlund-Venermo M.,University of Helsinki
Current Opinion in Pulmonary Medicine | Year: 2012

PURPOSE OF REVIEW: The first era in the discoveries of respiratory viruses occured between 1933 and 1965 when influenza virus, enteroviruses, adenovirus, respiratory syncytial virus, rhinovirus, parainfluenza virus and coronavirus (CoV) were found by virus culture. In the 1990s, the development of high throughput viral detection and diagnostics instruments increased diagnostic sensitivity and enabled the search for new viruses. This article briefly reviews the clinical significance of newly discovered respiratory viruses. RECENT FINDINGS: In 2001, the second era in the discoveries of respiratory viruses began, and several new respiratory viruses and their subgroups have been found: human metapneumovirus, CoVs NL63 and HKU1, human bocavirus and human rhinovirus C and D groups. SUMMARY: Currently, a viral cause of pediatric respiratory illness is identifiable in up to 95% of cases, but the detection rates decrease steadily by age, to 30-40% in the elderly. The new viruses cause respiratory illnesses such as common cold, bronchitis, bronchiolitis, exacerbations of asthma and chronic obstructive pulmonary disease and pneumonia. Rarely, acute respiratory failure may occur. The clinical role of other new viruses, KI and WU polyomaviruses and the torque teno virus, as respiratory pathogens is not clear. © 2012 Lippincott Williams & Wilkins, Inc.


Chonmaitree T.,University of Texas Medical Branch | Ruohola A.,University of Turku | Hendley J.O.,University of Virginia
Pediatric Infectious Disease Journal | Year: 2012

Viruses play an important role in acute otitis media (AOM) pathogenesis, and live viruses may cause AOM in the absence of pathogenic bacteria. Detection of AOM pathogens generally relies on bacterial culture of middle ear fluid. When viral culture is used and live viruses are detected in the middle ear fluid of children with AOM, the viruses are generally accepted as AOM pathogens. Because viral culture is not sensitive and does not detect the comprehensive spectrum of respiratory viruses, polymerase chain reaction assays are commonly used to detect viral nucleic acids in the middle ear fluid. Although polymerase chain reaction assays have greatly increased the viral detection rate, new questions arise on the significance of viral nucleic acids detected in the middle ear because nucleic acids of multiple viruses are detected simultaneously, and nucleic acids of specific viruses are detected repeatedly and in a high proportion of asymptomatic children. This article first reviews the role of live viruses in AOM and presents the point-counterpoint arguments on whether viral nucleic acids in the middle ear represent an AOM pathogen or a bystander status. Although there is evidence to support both directions, helpful information for interpretation of the data and future research direction is outlined. © 2012 by Lippincott Williams & Wilkins.


Paakkonen M.,University of Helsinki | Paakkonen M.,University of Turku | Peltola H.,University of Helsinki
Archives of Disease in Childhood | Year: 2012

Acute septic arthritis of childhood is a potentially devastating disease that causes permanent disability and can result in death. Traditional treatment consists of a prolonged course of intravenous antibiotics combined with aggressive surgery. However, this approach is challenged by trials showing satisfactory outcomes with shorter treatment and less invasive surgery. Diagnostic arthrocentesis alone and an antibiotic for a fortnight, including initial intravenous administration for 2-4 days, suffice in most non-neonatal cases. A good penetrating agent, such as clindamycin or a first-generation cephalosporin, exceptionally high doses, and administration four times a day are probably key factors. If the symptoms and signs subside within a few days, and the serum C-reactive protein level drops below 20 mg/l, the antibiotic can usually be safely discontinued. Methicillin-resistant Staphylococcus aureus is a concern, but fortunately, most strains have retained susceptibility to clindamycin. The above guidance is not applicable to neonates and immunocompromised patients who may require a different approach.


Rantala M.J.,University of Turku
Proceedings. Biological sciences / The Royal Society | Year: 2013

According to the 'good genes' hypothesis, females choose males based on traits that indicate the male's genetic quality in terms of disease resistance. The 'immunocompetence handicap hypothesis' proposed that secondary sexual traits serve as indicators of male genetic quality, because they indicate that males can contend with the immunosuppressive effects of testosterone. Masculinity is commonly assumed to serve as such a secondary sexual trait. Yet, women do not consistently prefer masculine looking men, nor is masculinity consistently related to health across studies. Here, we show that adiposity, but not masculinity, significantly mediates the relationship between a direct measure of immune response (hepatitis B antibody response) and attractiveness for both body and facial measurements. In addition, we show that circulating testosterone is more closely associated with adiposity than masculinity. These findings indicate that adiposity, compared with masculinity, serves as a more important cue to immunocompetence in female mate choice.


Hilakivi-Clarke L.,Georgetown University | De Assis S.,Georgetown University | Warri A.,Georgetown University | Warri A.,University of Turku
Journal of Mammary Gland Biology and Neoplasia | Year: 2013

Women are using estrogens for many purposes, such as to prevent pregnancy or miscarriage, or to treat menopausal symptoms. Estrogens also have been used to treat breast cancer which seems puzzling, since there is convincing evidence to support a link between high lifetime estrogen exposure and increased breast cancer risk. In this review, we discuss the findings that maternal exposure to the synthetic estrogen diethylstilbestrol during pregnancy increases breast cancer risk in both exposed mothers and their daughters. In addition, we review data regarding the use of estrogens in oral contraceptives and as postmenopausal hormone therapy and discuss the opposing effects on breast cancer risk based upon timing of exposure. We place particular emphasis on studies investigating how maternal estrogenic exposures during pregnancy increase breast cancer risk among daughters. New data suggest that these exposures induce epigenetic modifications in the mammary gland and germ cells, thereby causing an inheritable increase in breast cancer risk for multiple generations. © 2013 Springer Science+Business Media New York.


Condamine F.L.,Montpellier SupAgro | Sperling F.A.H.,University of Alberta | Wahlberg N.,University of Turku | Rasplus J.-Y.,Montpellier SupAgro | Kergoat G.J.,Montpellier SupAgro
Ecology Letters | Year: 2012

The latitudinal diversity gradient (LDG) is one of the most striking ecological patterns on our planet. Determining the evolutionary causes of this pattern remains a challenging task. To address this issue, previous LDG studies have usually relied on correlations between environmental variables and species richness, only considering evolutionary processes indirectly. Instead, we use a phylogenetically integrated approach to investigate the ecological and evolutionary processes responsible for the global LDG observed in swallowtail butterflies (Papilionidae). We find evidence for the 'diversification rate hypothesis' with different diversification rates between two similarly aged tropical and temperate clades. We conclude that the LDG is caused by (1) climatically driven changes in both clades based on evidence of responses to cooling and warming events, and (2) distinct biogeographical histories constrained by tropical niche conservatism and niche evolution. This multidisciplinary approach provides new findings that allow better understanding of the factors that shape LDGs. © 2012 Blackwell Publishing Ltd/CNRS.


Hietanen A.,University of Turku | Kanerva L.T.,University of Turku
European Journal of Organic Chemistry | Year: 2012

A three-step, one-pot synthesis and diastereoresolution sequence is described in anhydrous toluene starting from methyl α-D-2,3,4-tri-O- acetylgalacto- (1a), -manno- (1b) and -glucopyranosides (1c). The reaction sequence, including consecutive transformations through the aldehyde [PhI(OAc) 2, 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)] and cyanohydrin [basic resin or (R)-oxynitrilase] into the (6R)-cyanohydrin ester (lipase) is shown to proceed in a one-pot cascade, except that the basic resin (when used) should be removed before the addition of the enzymatic acylation reagents. We have shown that the effective transformation of 1a (75 % reaction yield) through labile intermediates gives the stable (6R)-cyanohydrin butanoate (85 % de). Further diastereomeric purification by chromatography is possible, although the product is already of high diastereopurity. (6R)-Cyanohydrin esters are obtained through acylation with Burkholderia cepacia lipase. The (6S)-ester (de 99 %) is produced by Candida rugosa lipase when the sequence is started from 1c whereas the other sugar derivatives are less suited to the reaction with lipase. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Ruminski A.M.,University of California at San Diego | King B.H.,University of California at San Diego | Salonen J.,University of Turku | Snyder J.L.,U.S. National Institute for Occupational Safety and Health | Sailor M.J.,University of California at San Diego
Advanced Functional Materials | Year: 2010

Sensing of the volatile organic compounds (VOCs) isopropyl alcohol (IPA) and heptane in air using sub-millimeter porous silicon-based sensor elements is demonstrated in the concentration range 50-800 ppm. The sensor elements are prepared as one-dimensional photonic crystals (rugate filters) by programmed electrochemical etch of p++ silicon, and analyte sensing is achieved by measurement of the wavelength shift of the photonic resonance. The sensors are studied as a function of surface chemistry: ozone oxidation, thermal oxidation, hydrosilylation (1-dodecene), electrochemical methylation, reaction with dicholorodimethylsilane and thermal carbonization with acetylene. The thermally oxidized and the dichlorodimethylsilane-modified materials show the greatest stability under atmospheric conditions. Optical microsensors are prepared by attachment of the porous Si layer to the distal end of optical fibers. The acetylated porous Si microsensor displays a greater response to heptane than to IPA, whereas the other chemical modifications display a greater response to IPA than to heptane. The thermal oxide sensor displays a strong response to water vapor, while the acetylated material shows a relatively weak response. The results suggest that a combination of optical fiber sensors with different surface chemistries can be used to classify VOC analytes. Application of the miniature sensors to the detection of VOC breakthrough in a full-scale activated carbon respirator cartridge simulator is demonstrated. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Soitamo A.J.,University of Turku | Jada B.,University of Turku | Lehto K.,University of Turku
BMC Plant Biology | Year: 2011

Background: RNA silencing is used in plants as a major defence mechanism against invasive nucleic acids, such as viruses. Accordingly, plant viruses have evolved to produce counter defensive RNA-silencing suppressors (RSSs). These factors interfere in various ways with the RNA silencing machinery in cells, and thereby disturb the microRNA (miRNA) mediated endogene regulation and induce developmental and morphological changes in plants. In this study we have explored these effects using previously characterized transgenic tobacco plants which constitutively express (under CaMV 35S promoter) the helper component-proteinase (HC-Pro) derived from a potyviral genome. The transcript levels of leaves and flowers of these plants were analysed using microarray techniques (Tobacco 4 × 44 k, Agilent).Results: Over expression of HC-Pro RSS induced clear phenotypic changes both in growth rate and in leaf and flower morphology of the tobacco plants. The expression of 748 and 332 genes was significantly changed in the leaves and flowers, respectively, in the HC-Pro expressing transgenic plants. Interestingly, these transcriptome alterations in the HC-Pro expressing tobacco plants were similar as those previously detected in plants infected with ssRNA-viruses. Particularly, many defense-related and hormone-responsive genes (e.g. ethylene responsive transcription factor 1, ERF1) were differentially regulated in these plants. Also the expression of several stress-related genes, and genes related to cell wall modifications, protein processing, transcriptional regulation and photosynthesis were strongly altered. Moreover, genes regulating circadian cycle and flowering time were significantly altered, which may have induced a late flowering phenotype in HC-Pro expressing plants. The results also suggest that photosynthetic oxygen evolution, sugar metabolism and energy levels were significantly changed in these transgenic plants. Transcript levels of S-adenosyl-L-methionine (SAM) were also decreased in these plants, apparently leading to decreased transmethylation capacity. The proteome analysis using 2D-PAGE indicated significantly altered proteome profile, which may have been both due to altered transcript levels, decreased translation, and increased proteosomal/protease activity.Conclusion: Expression of the HC-Pro RSS mimics transcriptional changes previously shown to occur in plants infected with intact viruses (e.g. Tobacco etch virus, TEV). The results indicate that the HC-Pro RSS contributes a significant part of virus-plant interactions by changing the levels of multiple cellular RNAs and proteins. © 2011 Soitamo et al; licensee BioMed Central Ltd.


Maksimainen M.,University of Eastern Finland | Paavilainen S.,University of Turku | Hakulinen N.,University of Eastern Finland | Rouvinen J.,University of Eastern Finland
FEBS Journal | Year: 2012

Crystal structures of native and α-d-galactose-bound Bacillus circulans sp. alkalophilusβ-galactosidase (Bca-β-gal) were determined at 2.40 and 2.25 Å resolutions, respectively. Bca-β-gal is a member of family 42 of glycoside hydrolases, and forms a 460 kDa hexameric structure in crystal. The protein consists of three domains, of which the catalytic domain has an (α/β) 8 barrel structure with a cluster of sulfur-rich residues inside the β-barrel. The shape of the active site is clearly more open compared to the only homologous structure available in the Protein Data Bank. This is due to the number of large differences in the loops that connect the C-terminal ends of the β-strands to the N-terminal ends of the α-helices within the (α/β) 8 barrel. The complex structure shows that galactose binds to the active site as an α-anomer and induces clear conformational changes in the active site. The implications of α-d-galactose binding with respect to the catalytic mechanism are discussed. In addition, we suggest that β-galactosidases mainly utilize a reverse hydrolysis mechanism for synthesis of galacto-oligosaccharides. Database -The coordinates for free and α-d-galactose-bound Bca-β-gal structures have been deposited in the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank under accession codes and, respectively. Crystal structures of native and α-d-galactose-bound Bacillus circulans sp. alkalophilusβ-galactosidase were determined. The shape of the active site is more open compared to the homological structure. The complex structure shows that α-galactose has bound to the active site and induced clear conformational changes in the active site. The implications of structures to catalytic mechanism and transglycosylation are discussed. © 2012 The Authors Journal compilation © 2012 FEBS.


Sainio J.,University of Turku
Computer Physics Communications | Year: 2010

This paper presents, to the author's knowledge, the first graphics processing unit (GPU) accelerated program that solves the evolution of interacting scalar fields in an expanding universe. We present the implementation in NVIDIA's Compute Unified Device Architecture (CUDA) and compare the performance to other similar programs in chaotic inflation models. We report speedups between one and two orders of magnitude depending on the used hardware and software while achieving small errors in single precision. Simulations that used to last roughly one day to compute can now be done in hours and this difference is expected to increase in the future. The program has been written in the spirit of LATTICEEASY and users of the aforementioned program should find it relatively easy to start using CUDAEASY in lattice simulations. The program is available at http://www.physics.utu.fi/theory/particlecosmology/cudaeasy/ under the GNU General Public License. © 2010 Elsevier B.V. All rights reserved.


Lainema T.,University of Turku
Simulation and Gaming | Year: 2010

A key element in organizational decision making is the progress of time and the ability to live with it. This article discusses the factor of time in decision making and how time can be taken into account in computerized simulation gaming. The discussion is based on recent definitions and classifications of time. The author reflects on these classifications and argues that embedding a richer time conception could increase the application domain of simulation gaming in the organizational context. Finally, the author theorizes on the implications of continuous processing in simulation gaming. The results indicate that continuous gaming provides an intense and meaningful learning environment. © The Author(s) 2010.


Saljo R.,Gothenburg University | Saljo R.,University of Turku
Journal of Computer Assisted Learning | Year: 2010

The purpose of this article is to offer some reflections on the relationships between digital technologies and learning. It is argued that activities of learning, as they have been practised within institutionalized schooling, are coming under increasing pressure from the developments of digital technologies and the capacities to store, access and manipulate information that such resources offer. Thus, the technologies do not merely support learning; they transform how we learn and how we come to interpret learning. The metaphors of learning currently emerging as relevant in the new media ecology emphasize the transformational and performative nature of such activities, and of knowing in general. These developments make the hybrid nature of human knowing and learning obvious; what we know and master is, to an increasing extent, a function of the mediating tools we are familiar with. At a theoretical and practical level, this implies that the interdependences between human agency, minds, bodies and technologies have to serve as foundations when attempting to understand and improve learning. Attempts to account for what people know without integrating their mastery of increasingly sophisticated technologies into the picture will lack ecological validity. © 2010 Blackwell Publishing Ltd.


Toppari J.,University of Turku
Birth defects research. Part A, Clinical and molecular teratology | Year: 2010

Cryptorchidism and hypospadias are common genital birth defects that affect 2-9% and 0.2-1% of male newborns, respectively. The incidence of both defects shows large geographic variation, and in several countries increasing trends have been reported. The conditions share many risk factors, and they are also interlinked to the risk of testis cancer and poor semen quality. Testicular Dysgenesis Syndrome (TDS) may underlie many cases of all these male reproductive health problems. Genetic defects in androgen production or action can cause both cryptorchidism and hypospadias, but these are not common. A monogenic reason for cryptorchidism or hypospadias has been identified only in a small proportion of all cases. Environmental effects appear to play a major role in TDS. Exposure to several persistent chemicals has been found to be associated with the risk of cryptorchidism, and exposure to anti-androgenic phthalates has been shown to be associated with hormonal changes predisposing to male reproductive problems. Despite progress in identification of endocrine-disrupting substances, we are still far from knowing all the risk factors for these birth defects, and advice for prevention must be based on precautionary principles. © 2010 Wiley-Liss, Inc.


Hamidi H.,University of Turku
British Journal of Cancer | Year: 2016

Cancer is a complex disease and progresses within a dynamically evolving extracellular matrix that controls virtually every aspect of the tumour and tumour-associated cells. Interactions with the extracellular microenvironment are predominately mediated by a family of cell-surface transmembrane receptors called integrins. Integrin–matrix engagement leads to the formation of adhesion plaques, consisting of signalling and adaptor proteins, at the plasma membrane that link the extracellular matrix to the regulation of the cell cytoskeleton. In this review, we will highlight exciting data that identify new roles for integrins and integrin-dependent signalling in cancer away from the plasma membrane, discuss the implications of integrin-dependent regulation of Met and ErbB2 growth factor receptors and highlight the role of specific integrins in different stages of cancer development including maintenance of cancer stem cells.British Journal of Cancer advance online publication 29 September 2016; doi:10.1038/bjc.2016.312 www.bjcancer.com. © 2016 The Author(s)


Peltier G.,Aix - Marseille University | Aro E.-M.,University of Turku | Shikanai T.,Kyoto University
Annual Review of Plant Biology | Year: 2016

Oxygenic photosynthesis converts solar energy into chemical energy in the chloroplasts of plants and microalgae as well as in prokaryotic cyanobacteria using a complex machinery composed of two photosystems and both membrane-bound and soluble electron carriers. In addition to the major photosynthetic complexes photosystem II (PSII), cytochrome b6f, and photosystem I (PSI), chloroplasts also contain minor components, including a well-conserved type I NADH dehydrogenase (NDH-1) complex that functions in close relationship with photosynthesis and likewise originated from the endosymbiotic cyanobacterial ancestor. Some plants and many microalgal species have lost plastidial ndh genes and a functional NDH-1 complex during evolution, and studies have suggested that a plastidial type II NADH dehydrogenase (NDH-2) complex substitutes for the electron transport activity of NDH-1. However, although NDH-1 was initially thought to use NAD(P)H as an electron donor, recent research has demonstrated that both chloroplast and cyanobacterial NDH-1s oxidize reduced ferredoxin. We discuss more recent findings related to the biochemical composition and activity of NDH-1 and NDH-2 in relation to the physiology and regulation of photosynthesis, particularly focusing on their roles in cyclic electron flow around PSI, chlororespiration, and acclimation to changing environments. Copyright © 2016 by Annual Reviews. All rights reserved.


Syrjanen K.,University of Turku | Syrjanen K.,Barretos Cancer Hospital | Syrjanen S.,University of Turku
Human Pathology | Year: 2013

Since first suggested (in 1983), the etiological role for human papillomavirus (HPV) in sinonasal carcinomas has been subject to constantly increasing interest. To perform systematic review and formal meta-analysis of the literature reporting on HPV detection in sinonasal squamous cell carcinomas (SCC), literature was searched through May 2012. The effect size was calculated as event rates (95% CI), with homogeneity testing using Cochran Q and I 2 statistics. Meta-regression was used to test the impact of study-level covariates (HPV detection method, geographic origin, papilloma type) on effect size, and potential publication bias was estimated using funnel plot symmetry. Thirty-five studies were eligible, covering 492 sinonasal SCCs from different geographic regions. Altogether, 133 (27.0%) cases tested HPV-positive; effect size 0.305 (95% CI, 0.260-0.355; fixed effects model), and 0.330 (95% CI, 0.249-0.423; random effects model. In meta-analysis stratified by (i) HPV detection technique and (ii) geographic study origin, the between-study heterogeneity was significant only for the latter; P =.526, and P =.0001, respectively. In maximum likelihood meta-regression, HPV detection method (P =.511) and geographic origin of the study (P =.812) were not significant study-level covariates. Some evidence for publication bias was found only among polymerase chain reaction-based studies and among studies from Europe and North America but with negligible effect on summary effect size estimates. In sensitivity analysis, all meta-analytic results were robust to all one-by-one study removals. In formal meta-regression, the variability in HPV detection rates reported in sinonasal SCCs was not explained by the HPV detection method or geographic origin of the study. © 2013 Elsevier Inc.


Rantanen I.,University of Turku | Tuominen R.,University of Turku
International Archives of Occupational and Environmental Health | Year: 2011

Objective: To examine the extent and relative value of presenteeism and absenteeism and work-related factors affecting them among health care professionals. Methods: Physicians and nurses estimated their hours of absenteeism and presenteeism during the last 4 weeks due to health reasons, and how much their work capacity had been reduced during their presenteeism hours. Socio-economic background, factors related to work and work conditions and possible chronic and acute diseases were solicited. Results: Presenteeism was more common but indicated lower monetary value than absenteeism. Job satisfaction explained the probability and magnitude of presenteeism, but not absenteeism. Experience of acute disease(s) during the study period of 4 weeks significantly predicted the probability of both presenteeism and absenteeism. Conclusions: Experience of presenteeism seemed to be common among health care workers, and it had significant economic value, although not as significant as absenteeism had. © 2010 Springer-Verlag.


Toikka L.A.,University of Turku | Suominen K.-A.,University of Turku
Journal of Physics B: Atomic, Molecular and Optical Physics | Year: 2014

We show how boundary effects can cause a Bose-Einstein condensate to periodically oscillate between a (circular) array of quantized vortex-antivortex pairs and a (ring) dark soliton. If the boundary is restrictive enough, the ring dark soliton becomes long-lived. © 2014 IOP Publishing Ltd.


Henttunen K.,University of Turku | Vilja I.,University of Turku
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2014

It is stated that a class of f(R) gravity models seem to obtain ΛCDM behavior for high redshifts and general relativistic behavior locally at high curvatures. In the present Letter, we numerically study polytropic configurations that resemble stars like young sun with Hu and Sawicki's f(R) gravity field equations and compare the spacetime at the boundary to the general relativistic counterpart. These polytropes are stationary spherically symmetric configurations and have regular metrics at the origin. Since Birkhoff's theorem does not apply for modified gravity, the solution outside may deviate from Schwarzschild-de Sitter spacetime. At the boundary, Post-Newtonian parametrization was used to determine how much the studied model deviates from the general relativistic ΛCDM model. © 2014 The Authors.


Suominen K.-A.,University of Turku
Journal of Modern Optics | Year: 2014

APLIP is a method for using a STIRAP-like three-state configuration with two laser pulses for continuous extension of a molecular bond, introduced in 1998. It is based on time-dependent light-induced potential surfaces (LIP). In VibLIP one extends the idea into a method for tailoring the vibrational state while changing the electronic state, introduced in 2000. Here I discuss the extension of both methods to situations that involve more than three electronic states, and note the possibility of using the method on adiabatic transport of atoms between microtraps or equivalent structures. © 2014 Taylor and Francis.


Pellonpaa J.-P.,University of Turku
Foundations of Physics | Year: 2014

We define a complete measurement of a quantum observable (POVM) as a measurement of the maximally refined (rank-1) version of the POVM. Complete measurements give information on the multiplicities of the measurement outcomes and can be viewed as state preparation procedures. We show that any POVM can be measured completely by using sequential measurements or maximally refinable instruments. Moreover, the ancillary space of a complete measurement can be chosen to be minimal. © 2013 Springer Science+Business Media New York.


Lehtinen J.,University of Turku | Kuusela T.,University of Turku
Applied Physics B: Lasers and Optics | Year: 2014

An external cavity quantum cascade laser (EC-QCL) is applied in the photoacoustic detection of solid samples. The EC-QCL used has a broad tuning range of 676 cm-1 (970-1,646 cm-1) in the mid-infrared region, which enables accurate broadband spectroscopy of large molecules. The high spectral power density of the EC-QCL is combined with an extremely sensitive optical cantilever microphone of the photoacoustic detector to achieve an ultimate sensitivity. The carbon black, polyethylene, and hair fiber samples were measured with the EC-QCL photoacoustic detection using electrical amplitude modulation to demonstrate the possibilities of the setup. The same measurements were repeated with a Fourier transform infrared (FTIR) spectrometer combined with a photoacoustic detector for a comparison. The EC-QCL photoacoustic setup yielded roughly a decade better signal-to-noise ratios than the FTIR setup with the same measurement time. © 2013 Springer-Verlag Berlin Heidelberg.


Laitinen T.,University of Central Lancashire | Huttunen-Heikinmaa K.,University of Turku | Valtonen E.,University of Turku | Dalla S.,University of Central Lancashire
Astrophysical Journal | Year: 2015

To understand the origin of Solar Energetic Particles (SEPs), we must study their injection time relative to other solar eruption manifestations. Traditionally the injection time is determined using the Velocity Dispersion Analysis (VDA) where a linear fit of the observed event onset times at 1 AU to the inverse velocities of SEPs is used to derive the injection time and path length of the first-arriving particles. VDA does not, however, take into account that the particles that produce a statistically observable onset at 1 AU have scattered in the interplanetary space. We use Monte Carlo test particle simulations of energetic protons to study the effect of particle scattering on the observable SEP event onset above pre-event background, and consequently on VDA results. We find that the VDA results are sensitive to the properties of the pre-event and event particle spectra as well as SEP injection and scattering parameters. In particular, a VDA-obtained path length that is close to the nominal Parker spiral length does not imply that the VDA injection time is correct. We study the delay to the observed onset caused by scattering of the particles and derive a simple estimate for the delay time by using the rate of intensity increase at the SEP onset as a parameter. We apply the correction to a magnetically well-connected SEP event of 2000 June 10, and show it to improve both the path length and injection time estimates, while also increasing the error limits to better reflect the inherent uncertainties of VDA. © 2015. The American Astronomical Society. All rights reserved.


Seyednasrollah F.,University of Turku | Laiho A.,University of Turku | Elo L.L.,University of Turku
Briefings in Bioinformatics | Year: 2013

RNA-sequencing (RNA-seq) has rapidly become a popular tool to characterize transcriptomes. A fundamental research problem in many RNA-seq studies is the identification of reliable molecular markers that show differential expression between distinct sample groups. Together with the growing popularity of RNA-seq, a number of data analysis methods and pipelines have already been developed for this task.Currently, however, there is no clear consensus about the best practices yet, which makes the choice of an appropriate method a daunting task especially for a basic user without a strong statistical or computational background. To assist the choice, we perform here a systematic comparison of eight widely used software packages and pipelines for detecting differential expression between sample groups in a practical research setting and provide general guidelines for choosing a robust pipeline. In general, our results demonstrate how the data analysis tool utilized can markedly affect the outcome of the data analysis, highlighting the importance of this choice. © The Author 2013. Published by Oxford University Press.


Sierla M.,University of Helsinki | Rahikainen M.,University of Turku | Salojarvi J.,University of Helsinki | Kangasjarvi J.,University of Helsinki | Kangasjarvi S.,University of Turku
Antioxidants and Redox Signaling | Year: 2013

Significance: Interplay among apoplastic and chloroplastic redox signaling networks is emerging as a key mechanism in plant stress responses. Recent Advances: Recent research has revealed components involved in apoplastic and chloroplastic redox signaling. Also, the sequence of events from stress perception, activation of apoplastic reactive oxygen species (ROS) burst through NADPH oxidases, cytoplasmic and chloroplastic Ca2+-transients, and organellar redox signals to physiological responses is starting to emerge. Moreover, a functional overlap between light acclimation and plant immunity in photosynthetically active tissues has been demonstrated. Critical Issues: Any deviations from the basal cellular redox balance may induce acclimation responses that continuously readjust cellular functions. However, diversion of resources to stress responses may lead to attenuation of growth, and exaggeration of defensive reactions may thus be detrimental to the plant. The ultimate outcome of acclimation responses must therefore be tightly controlled by the redox signaling networks between organellar and apoplastic signaling systems. Future Directions: Two major questions still remain to be solved: the sensory mechanism for ROS and the components involved in relaying the signals from the apoplast to the chloroplast. A comprehensive view of regulatory networks will facilitate the understanding on how environmental factors affect the production of phytonutrients and biomass in plants. Translation of such information from model plants to crop species will be at the cutting edge of research in the near future. These challenges give a frame for future studies on ROS and redox regulation of stress acclimation in photosynthetic organisms. © Copyright 2013, Mary Ann Liebert, Inc.


Jarvelainen J.,University of Turku
International Journal of Information Management | Year: 2013

Information technology (IT) incidents that make data inaccessible may cause businesses to lose customers, reputation and market position. Previous studies on information management have identified data availability as a key priority, and the literature on disaster recovery and business continuity describes ways of preparing for and avoiding IT incidents. However, no frameworks for information system continuity management (ISCM) have yet been validated. This research draws on a framework for business continuity management, and extends it to the context of information systems. The framework is validated in a survey of IT managers and chief information officers in large private and public organisations operating in Finland. The results suggest that the embeddedness of continuity practices in an organisation has perceived business impacts whereas, in contradiction of previous theory, there is no such direct relation in the case of organisational alertness and preparedness. The theoretical contribution is to validate the ISCM framework statistically. On the practical level, social factors such as committed managers and employees are influential in decreasing negative business impacts. Further research on the embeddedness of continuity practices is called for. © 2013 Elsevier Ltd. All rights reserved.


Mantymaki M.,University of Turku | Salo J.,University of Oulu | Salo J.,Aalto University
International Journal of Information Management | Year: 2013

Spending real money on virtual goods and services has become a popular form of online consumer behavior, particularly among teenagers. This study builds on the Unified Theory of Acceptance and Use of Technology (UTAUT) to examine the role of motivation, social influence, measured with perceived network size as well as user interface and facilitating conditions in predicting the intention to engage in purchasing in social virtual worlds. The research model is tested with data from 1045 users of Habbo Hotel, world's most popular virtual world for teenagers. The results underscore the role of perceived network size and motivational factors in explaining in-world purchase decisions. The study shows that virtual purchasing behavior is substantially influenced by the factors driving usage behavior. Hence, virtual purchasing can be understood as a means to enhance the user experience. For virtual world operators, reinforcing the sense of presence of user's social network offers a means to promote virtual purchasing. © 2013.


Jarvit S.,University of Turku | Gollanf P.J.,University of Turku | Aro E.-M.,University of Turku
Frontiers in Plant Science | Year: 2013

It has been known fora long time that the thylakoid lumen provides the environment for oxygen evolution, plastocyanin-mediated electron transfer, and photoprotection. More recently lumenal proteins have been revealed to play roles in numerous processes, most often linked with regulating thylakoid biogenesis and the activity and turnover of photosynthetic protein complexes, especially the photosystem II and NAD(P)H dehydrogenase-like complexes. Still, the functions of the majority of lumenal proteins in Arabidopsis thaliana are unknown. Interestingly, while the thylakoid lumen proteome of at least 80 proteins contains several large protein families, individual members of many protein families have highly divergent roles. This is indicative of evolutionary pressure leading to neofunctionalization of lumenal proteins, emphasizing the important role of the thylakoid lumen for photosynthetic electron transfer and ultimately for plant fitness. Furthermore, the involvement of anterograde and retrograde signaling networks that regulate the expression and activity of lumen proteins is increasingly pertinent. Recent studies have also highlighted the importance of thiol/disulfide modulation in controlling the functions of many lumenal proteins and photosynthetic regulation pathways. © 2013 Järvi, Gollan and Aro.


Kankaanpaa P.,University of Turku | Paavolainen L.,University of Jyväskylä | Tiitta S.,University of Turku | Karjalainen M.,University of Jyväskylä | And 6 more authors.
Nature Methods | Year: 2012

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors. © 2012 Nature America, Inc. All rights reserved.


Kuismanen H.,University of Turku | Vilja I.,University of Turku
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The framework for soft leptogenesis minimally extended with a dark matter (DM) sector is studied. A heavy singlet neutrino superfield acts as the source for (s)lepton asymmetry and by coupling to the singlet DM superfield it produces a DM particle density through decays. The nature of DM generated is twofold depending on whether the Yukawa and DM couplings are either small or large. With sufficiently small Yukawa and DM couplings DM annihilations into minimal supersymmetric standard model particles are slow and as a consequence all DM particles form the DM component. The solutions to Boltzmann equations are given and the dependence between the DM masses and coupling are presented in this weak coupling regime. Also, the behavior of the efficiency of producing asymmetric DM is determined with weak couplings. We note that a different outcome arises if the couplings are larger because then the asymmetric DM component is dominant due to the effectiveness of DM decays into the minimal supersymmetric standard model sector. © 2013 American Physical Society.


Nordberg A.,Karolinska University Hospital | Rinne J.O.,University of Turku | Kadir A.,Karolinska University Hospital | Lngstrom B.,Uppsala University
Nature Reviews Neurology | Year: 2010

In Alzheimer disease (AD), which is the most common cause of dementia, the underlying disease pathology most probably precedes the onset of cognitive symptoms by many years. Thus, efforts are underway to find early diagnostic markers as well as disease-modifying treatments for this disorder. PET enables various brain systems to be monitored in living individuals. In patients with AD, PET can be used to investigate changes in cerebral glucose metabolism, various neurotransmitter systems, neuroinflammation, and the protein aggregates that are characteristic of the disease, notably the amyloid deposits. These investigations are helping to further our understanding of the complex pathophysiological mechanisms that underlie AD, as well as aiding the early and differential diagnosis of the disease in the clinic. In the future, PET studies will also be useful for identifying new therapeutic targets and monitoring treatment outcomes. Amyloid imaging could be useful as early diagnostic marker of AD and for selecting patients for anti-amyloid-Β therapy, while cerebral glucose metabolism could be a suitable PET marker for monitoring disease progression. For the near future, multitracer PET studies are unlikely to be used routinely in the clinic for AD, being both burdensome and expensive; however, such studies are very informative in a research context. © 2010 Macmillan Publishers Limited. All rights reserved.


Berdyugin A.,University of Turku | Piirola V.,University of Turku | Teerikorpi P.,University of Turku
Astronomy and Astrophysics | Year: 2014

Aims. Interstellar polarization of starlight at high galactic latitudes gives information on the direction of the local Galactic magnetic field and the distribution of cosmic dust in wide "windows" perpendicular to the Galactic plane. Polarization data allow us to construct for the first time high-latitude polarization maps with resolution and sky coverage high enough to examine in detail the distribution of the interstellar polarization and the direction of the Galactic magnetic field around Galactic poles. Methods. We measured the polarization for more than 2400 new stars at distances of up to 600 pc and within 60° and 30° from the north and south Galactic poles. Here we describe the measurements and properties of the resulting total sample of about 3600 stars (completeness, radial distribution), and present polarization maps of the regions around the north (b > 30°) and south (b > 60°) poles. Results. The new interstellar polarization maps give wider and higher resolution views around the Galactic poles than previous maps. The major patterns in the maps are significant asymmetries in the polarization, one in the northern sky directly across the local spiral and the second between the northern and southern Galactic hemispheres. We confirm that there is significantly more interstellar polarization at high southern latitudes than at high northern latitudes within the local spiral. A comparison of our optical polarization map with the proposed models using local dust- and gas shells, (i.e., Weaver's Loop I superbubble, Wolleben's two-bubble model, the interaction between the Local Bubble and the Loop I superbubble) reveals interesting features. 1) The optical and radio polarizations are lower in the eastern than in the western branch of Loop I, which may be caused by a weaker effective magnetic field in the eastern part where the diffuse IRAS emission is bright; this illustrates that low optical polarization does not always imply little dust. 2) We can see a clear signature of the western side of Wolleben's S2 shell (at 35 < l < 55), while there is no alignment of the polarization directions along the suggested wall of S2 in the eastern part, though the alignment along S1 is visible. 3) In the upper parts of the suggested interaction zone between the Local Bubble and the Loop I superbubble our data show polarizations aligned along the zone contour. The week and rather randomly directed polarizations measured previously in the eastern part of this region may reflect the shorter distances (<250 pc) in the investigated sample of stars. © ESO, 2013.


Kiviniemi A.,University of Turku | Virta P.,University of Turku
Bioconjugate Chemistry | Year: 2011

The potential of aminoglycosides to induce RNA-invasion has been demonstrated. For this purpose, aminoglycoside-3′-conjugates of 2′-O-methyl oligoribonucleotides have been synthesized entirely on a solid phase. The synthesis includes an automated oligonucleotide chain elongation to solid-supported neomycin, ribostamycin, and methyl neobiosamine, and a two-step deprotection/release of the solid-supported conjugate, which allows exploitation of a simple protecting group scheme. Conjugates have been targeted to a 19F labeled HIV-1 TAR RNA model (Trans Activation Response element of HIV), which allows monitoring of the invasion by 19F NMR spectroscopy. A remarkably enhanced invasion, compared to that resulting from the corresponding unmodified 2′-O-methyl oligoribonucleotide (5′-CAGGCUCA-3′), has been obtained by the neomycin conjugate. The increased affinity results from a cooperative binding of the neomycin moiety and hybridization, though the invasion may also follow a mechanism, in which the first molar equivalent of the conjugate induces hybridization of the second. © 2011 American Chemical Society.


Saarinen J.,University of Turku | Teerikorpi P.,University of Turku
Astronomy and Astrophysics | Year: 2014

Aims. We study the influence of relevant quantities, including the density of dark energy (DE), to the predicted Hubble outflow around a system of galaxies. In particular, we are interested in the difference between two models: 1) the standard ΛCDM model, with the everywhere constant DE density, and 2) the "Swiss cheese model", where the Universe is as old as the standard model and the DE density is zero on short scales, including the environment of the system. Methods. We calculated the current predicted outflow patterns of dwarf galaxies around the Local Group-like system, using different values for the mass of the group, the local DE density, and the time of ejection of the dwarf galaxies, which are treated as test particles. These results are compared with the observed Hubble flow around the Local Group. Results. The predicted distance-velocity relations around galaxy groups are not very sensitive indicators of the DE density, owing to the observational scatter and the uncertainties caused by the mass used for the group and a range in the ejection times. In general, the Local Group outflow data agree with the local DE density being equal to the global one, if the Local Group mass is about 4 × 1012 M; a lower mass 2 × 1012 M could suggest a zero local DE density. The dependence of the inferred DE density on the mass is a handicap in this and other common dynamical methods. This emphasizes the need to use different approaches together, for constraining the local DE density. © ESO, 2014.


Photosynthetic electron flow operates in two modes, linear and cyclic. In cyclic electron flow (CEF), electrons are recycled around photosystem I. As a result, a transthylakoid proton gradient (ApH) is generated, leading to the production of ATP without concomitant production of NADPH, thus increasing the ATP/NADPH ratio within the chloroplast. At least two routes for CEF exist: a PROTON GRADIENT REGULATION5-PGRL1-and a chloroplast NDH-like complex mediated pathway. This review focuses on recent findings concerning the characteristics of both CEF routes in higher plants, with special emphasis paid on the crucial role of CEF in under challenging environmental conditions and developmental stages. © 2015 Suorsa.


Julkunen I.,University of Turku | Partinen M.,VitalMed Research Center
Nature Reviews Neurology | Year: 2014

A pandemic influenza vaccine with a specific type of vaccine antigen has been linked to an increased incidence of narcolepsy in children from 2009-2010. However, the recent retraction of an article that reported a putative autoantigen means that the search for the mechanisms behind the vaccine-narcolepsy connection continues. © 2014 Macmillan Publishers Limited. All rights reserved.


Cayuela L.,University of Granada | De la Cruz M.,Polytechnic University of Mozambique | Ruokolainen K.,University of Turku
Ecography | Year: 2011

Researchers in ecology commonly use multivariate analyses (e.g. redundancy analysis, canonical correspondence analysis, Mantel correlation, multivariate analysis of variance) to interpret patterns in biological data and relate these patterns to environmental predictors. There has been, however, little recognition of the errors associated with biological data and the influence that these may have on predictions derived from ecological hypotheses. We present a permutational method that assesses the effects of taxonomic uncertainty on the multivariate analyses typically used in the analysis of ecological data. The procedure is based on iterative randomizations that randomly re-assign non identified species in each site to any of the other species found in the remaining sites. After each re-assignment of species identities, the multivariate method at stake is run and a parameter of interest is calculated. Consequently, one can estimate a range of plausible values for the parameter of interest under different scenarios of re-assigned species identities. We demonstrate the use of our approach in the calculation of two parameters with an example involving tropical tree species from western Amazonia: 1) the Mantel correlation between compositional similarity and environmental distances between pairs of sites, and; 2) the variance explained by environmental predictors in redundancy analysis (RDA). We also investigated the effects of increasing taxonomic uncertainty (i.e. number of unidentified species), and the taxonomic resolution at which morphospecies are determined (genus-resolution, family-resolution, or fully undetermined species) on the uncertainty range of these parameters. To achieve this, we performed simulations on a tree dataset from southern Mexico by randomly selecting a portion of the species contained in the dataset and classifying them as unidentified at each level of decreasing taxonomic resolution. An analysis of covariance showed that both taxonomic uncertainty and resolution significantly influence the uncertainty range of the resulting parameters. Increasing taxonomic uncertainty expands our uncertainty of the parameters estimated both in the Mantel test and RDA. The effects of increasing taxonomic resolution, however, are not as evident. The method presented in this study improves the traditional approaches to study compositional change in ecological communities by accounting for some of the uncertainty inherent to biological data. We hope that this approach can be routinely used to estimate any parameter of interest obtained from compositional data tables when faced with taxonomic uncertainty. © 2011 The Authors.


Viitanen T.P.,University of Turku | Maki M.T.,University of Turku | Seppanen M.P.,University of Turku | Suominen E.A.,University of Turku | Saaristo A.M.,University of Turku
Plastic and Reconstructive Surgery | Year: 2012

Background: Lymphedema remains a challenging clinical problem that often lacks curative treatment options. Recent reports have shown that microvascular lymph node transfer from the groin area into axillas of lymphedematous patients may improve lymphatic drainage, but the effect on donor-site lymphatic flow has not been studied. These patients may be more prone to develop lymphedema at donor sites as well; therefore, the authors aim was to evaluate postoperative donor-site lymphatic function. Methods: The authors performed lymphatic groin flap transfer to the axilla in 13 lymphedema patients. In 10 patients, the lymph node transfer was performed simultaneously with lower abdominal breast reconstruction. Postoperative lymphatic vessel function of the donor site was evaluated by lymphoscintigraphy and limb circumference measurements. For semiquantitative evaluation of lymphatic drainage, a numerical transport index was used. Results: In six of 10 patients, postoperative lymphoscintigraphy revealed minor changes in lymphatic flow of the donor-site limbs. The transport index was considered slightly abnormal in two of 10 patients. None of the 13 patients had changes in lower limb circumferences during the 8-to 56-month follow-up. Conclusions: Lymph node transfer can be easily combined with lower abdominal breast reconstruction, and the popularity of this technique is increasing rapidly. Even though none of our patients had developed symptoms of postoperative lymphedema, the results of the first lymphoscintigrams show that it is important to reduce the surgical trauma to the lymphatic flap donor site. Clinical Question/Level of Evidence: Therapeutic, IV. © 2012 by the American Society of Plastic Surgeons.


Islam A.K.M.N.,University of Turku
Computers and Education | Year: 2013

This paper investigates the outcomes of e-learning systems adoption and use by conceptualizing three e-learning systems adoption outcome constructs namely perceived learning assistance, perceived community building assistance and perceived academic performance. Utilizing these constructs, the paper proposes a research model for assessing the possible outcomes of e-learning systems adoption and use. The study collected longitudinal survey data from 249 university students participating in hybrid courses using a popular learning management system, Moodle. Partial least squares (PLS) approach was then used to test the research model. The findings suggest that beliefs about perceived usefulness and perceived ease of use, and how an e-learning system is used influence students' perceived learning assistance and perceived community building assistance. In turn, perceived learning assistance and perceived community building assistance influence the students' perceived academic performance. © 2013 Elsevier Ltd. All rights reserved.


Syrjanen K.,University of Turku | Syrjanen K.,Barretos Cancer Hospital
Anticancer Research | Year: 2012

Background: Since the first reports (in 1979) suggesting an etiological role for human papillomavirus (HPV) in bronchial squamous cell carcinoma, literature reporting HPV detection in lung cancer has expanded rapidly, but a comprehensive meta-analysis has yet to be published. We performed a systematic review and formal meta-analysis of the literature reporting on HPV detection in lung cancer. Materials and Methods: MEDLINE and Current Contents were searched through April 2012. The effect size was calculated as event rates and their 95% Confidence intervals (CI), with homogeneity testing using Cochran's Q and I2 statistics. Meta-regression was used to test the impact of study-level co-variates (HPV detection method, geographical origin of study, cancer histology) on effect size, and potential publication bias was estimated using funnel plot symmetry (Begg and Mazumdar rank correlation, Egger's regression, and Duval and Tweedie's trim and fill method). Results: One hundred studies were eligible, covering 7,381 lung cancer cases from different geographical regions. Altogether, 1,653 (22.4%) samples tested HPV-positive; effect size was 0.348 (95% CI=0.333-0.363; fixed-effects model), and 0.220 (95% CI=0.18-0.259; random effects model). There was significant heterogeneity between the studies stratified by HPV detection technique, but the random effects in between-strata comparison was not significant (p=0.193). When stratified by i) different geographical regions, and ii) different histological types, the between-strata comparison was significant (p=0.0001). However, in meta-regression, HPV detection method (p=0.473), geographical origin (p=0.298) and histological type (p=0.589) were not significant study-level co-variates. No evidence for significant publication bias was found in funnel plot symmetry testing. In sensitivity analysis, all meta-analytic results seemed robust to all one-by-one study removals. Conclusion: These meta-analytic results imply that the reported variability in HPV detection rates in lung cancer is better explained by geographical study origin and histological types of cancer than by the HPV detection method itself. In formal meta-regression, however, none of these three factors were significant study-level co-variates accounting for the heterogeneity of the summary effect size estimates, i.e. HPV prevalence in lung cancer.


In Northern Namibia, the climate is highly polarised between dry and wet seasons, and local communities have lived with these varying weather extremes for centuries. However, the recent changes in socio-environmental dynamics—associated with urbanisation, inappropriate spatial planning, and population growth—have disturbed the river system in the area. These changes, together with torrential seasonal rains, have aggravated the social impacts of the flood events. By using various qualitative and quantitative data sources, and comparative analyses between the flood dynamics in urban and rural environments, this research studies local residents’ coping strategies to endure the irregular flood events from the perspective of socio-ecological resilience. Particular interest is placed on the learning processes that enhance the residents’ capability to cope and the role of indigenous knowledge. Indigenous knowledge (IK) has been emphasised as a source of resilience in both theory and practice, as it is built upon learning from past experiences of natural hazards. The findings reveal that the floods are a result of complex and relational development without the necessary linear relationship between the causes and effects. The abrupt socio-ecological changes, together with the multiple stressors related to poverty, have made residents more vulnerable to the flood events and attenuated the communities’ coping strategies based on IK. Instead of focusing on the communities’ capacity to self-organise, the focus of resilience building needs to be directed to emphasising the broader socio-political processes, which are making the communities vulnerable in the first place. © 2015, Springer-Verlag Berlin Heidelberg.


The development of the DNA theory of inheritance culminated in the publication of the molecular structure of DNA 60 years ago. This paper describes this development, beginning with the discovery of DNA as a chemical substance by Friedrich Miescher in 1869, followed by its basic chemical analysis and demonstration of its participation in the structure of chromosomes. Subsequently it was discovered by Oswald Avery in 1944 that DNA was the genetic material, and then Erwin Chargaff showed that the proportions of the bases included in the structure of DNA followed a certain law. These findings, in association with the biophysical studies of Maurice Wilkins and Rosalind Franklin with Raymond Gosling, led James Watson and Francis Crick to the discovery of the double-helical structure of DNA in 1953. The paper ends with a short description of the development of the DNA theory of inheritance after the discovery of the double helix. © 2014 Indian Academy of Sciences.


Isolauri E.,University of Turku | Rautava S.,University of Turku | Salminen S.,University of Turku
Gastroenterology Clinics of North America | Year: 2012

Gut microbiota composition can discriminate between allergic and healthy children, and the distinction may precede clinical manifestations of disease. The mother provides the first inoculum of bacteria, which influences the risk of becoming allergic later in life. Bifidobacterium species are major determinants of disease risk. Specific probiotics may modulate early microbial colonization, which represents the first intervention target in allergic disease, together with their ability to reverse the increased intestinal permeability characteristic of children with atopic eczema and food allergy. Probiotics also enhance gut-specific IgA responses, which are frequently defective in children with food allergy. In addition, probiotics have the potential to alleviate allergic inflammation locally and systemically. © 2012.


Saraste A.,University of Turku | Kajander S.,University of Turku | Han C.,University of Turku | Nesterov S.V.,University of Turku | Knuuti J.,University of Turku
Journal of Nuclear Cardiology | Year: 2012

Positron emission tomography (PET) enables quantitative measurements of myocardial blood flow (MBF) and myocardial flow reserve (MFR). Recent developments and improved availability of PET technology have resulted in growing interest in translation of quantitative flow analysis from mainly a research tool to routine clinical practice. Quantitative PET measurements of absolute MBF and MFR have potential to improve accuracy of myocardial perfusion imaging in diagnosis of multivessel coronary artery disease as well as definition of the extent and functional importance of stenoses. This article reviews recent advances and experience in the quantitative myocardial perfusion imaging together with issues that need to be resolved for quantitative analysis to become clinical reality. © 2012 American Society of Nuclear Cardiology.


Parvinen K.,University of Turku | Parvinen K.,International Institute For Applied Systems Analysis
Theoretical Population Biology | Year: 2013

We investigate the joint evolution of public goods cooperation and dispersal in a metapopulation model with small local populations. Altruistic cooperation can evolve due to assortment and kin selection, and dispersal can evolve because of demographic stochasticity, catastrophes and kin selection. Metapopulation structures resulting in assortment have been shown to make selection for cooperation possible. But how does dispersal affect cooperation and vice versa, when both are allowed to evolve as continuous traits? We found four qualitatively different evolutionary outcomes. (1) Monomorphic evolution to full defection with positive dispersal. (2) Monomorphic evolution to an evolutionarily stable state with positive cooperation and dispersal. In this case, parameter changes selecting for increased cooperation typically also select for increased dispersal. (3) Evolutionary branching can result in the evolutionarily stable coexistence of defectors and cooperators. Although defectors could be expected to disperse more than cooperators, here we show that the opposite case is also possible: Defectors tend to disperse less than cooperators when the total amount of cooperation in the dimorphic population is low enough. (4) Selection for too low cooperation can cause the extinction of the evolving population. For moderate catastrophe rates dispersal needs to be initially very frequent for evolutionary suicide to occur. Although selection for less dispersal in principle could prevent such evolutionary suicide, in most cases this rescuing effect is not sufficient, because selection in the cooperation trait is typically much stronger. If the catastrophe rate is large enough, a part of the boundary of viability can be evolutionarily attracting with respect to both strategy components, in which case evolutionary suicide is expected from all initial conditions. © 2013 Elsevier Inc.


Wahlberg N.,University of Turku | Wheat C.W.,University of Stockholm | Pena C.,University of Turku
PLoS ONE | Year: 2013

The macroevolutionary history of the megadiverse insect order Lepidoptera remains little-known, yet coevolutionary dynamics with their angiospermous host plants are thought to have influenced their diversification significantly. We estimate the divergence times of all higher-level lineages of Lepidoptera, including most extant families. We find that the diversification of major lineages in Lepidoptera are approximately equal in age to the crown group of angiosperms and that there appear to have been three significant increases in diversification rates among Lepidoptera over evolutionary time: 1) at the origin of the crown group of Ditrysia about 150 million years ago (mya), 2) at the origin of the stem group of Apoditrysia about 120 mya and finally 3) a spectacular increase at the origin of the stem group of the quadrifid noctuoids about 70 mya. In addition, there appears to be a significant increase in diversification rate in multiple lineages around 90 mya, which is concordant with the radiation of angiosperms. Almost all extant families appear to have begun diversifying soon after the Cretaceous/Paleogene event 65.51 mya. © 2013 Wahlberg et al.


Ivaska J.,VTT Technical Research Center of Finland | Ivaska J.,University of Turku | Heino J.,University of Turku
Cell and Tissue Research | Year: 2010

The emergence of multicellular animals could only take place once evolution had produced molecular mechanisms for cell adhesion and communication. Today, all metazoans express integrin-type adhesion receptors and receptors for growth factors. Integrins recognize extracellular matrix proteins and respective receptors on other cells and, following ligand binding, can activate the same cellular signaling pathways that are regulated by growth factor receptors. Recent reports have indicated that the two receptor systems also collaborate in many other ways. Here, we review the present information concerning the role of integrins as assisting growth factor receptors and the interplay between the receptors in cell signaling and in the orchestration of receptor recycling.


Uusi-Oukari M.,University of Turku | Korpi E.R.,University of Helsinki
Pharmacological Reviews | Year: 2010

The γ-aminobutyric acid (GABA) type A receptor system, the main fast-acting inhibitory neurotransmitter system in the brain, is the pharmacological target for many drugs used clinically to treat, for example, anxiety disorders and epilepsy, and to induce and maintain sedation, sleep, and anesthesia. These drugs facilitate the function of pentameric GABAA receptors that exhibit widespread expression in all brain regions and large structural and pharmacological heterogeneity as a result of composition from a repertoire of 19 subunit variants. One of the main problems in clinical use of GABAA receptor agonists is the development of tolerance. Most drugs, in long-term use and during withdrawal, have been associated with important modulations of the receptor subunit expression in brain-region-specific manner, participating in the mechanisms of tolerance and dependence. In most cases, the molecular mechanisms of regulation of subunit expression are poorly known, partly as a result of neurobiological adaptation to altered neuronal function. More knowledge has been obtained on the mechanisms of GABAA receptor trafficking and cell surface expression and the processes that may contribute to tolerance, although their possible pharmacological regulation is not known. Drug development for neuropsychiatric disorders, including epilepsy, alcoholism, schizophrenia, and anxiety, has been ongoing for several years. One key step to extend drug development related to GABAA receptors is likely to require deeper understanding of the adaptational mechanisms of neurons, receptors themselves with interacting proteins, and finally receptor subunits during drug action and in neuropsychiatric disease processes. Copyright © 2010 by The American Society for Pharmacology and Experimental Therapeutics.


Valtonen T.M.,University of Turku | Kangassalo K.,University of Turku | Polkki M.,University of Turku | Rantala M.J.,University of Turku
PLoS ONE | Year: 2012

Environmental conditions experienced by parents are increasingly recognized to affect offspring performance. We set out to investigate the effect of parental larval diet on offspring development time, adult body size and adult resistance to the bacterium Serratia marcescens in Drosophila melanogaster. Flies for the parental generation were raised on either poor or standard diet and then mated in the four possible sex-by-parental diet crosses. Females that were raised on poor food produced larger offspring than females that were raised on standard food. Furthermore, male progeny sired by fathers that were raised on poor food were larger than male progeny sired by males raised on standard food. Development times were shortest for offspring whose one parent (mother or the father) was raised on standard and the other parent on poor food and longest for offspring whose parents both were raised on poor food. No evidence for transgenerational effects of parental diet on offspring disease resistance was found. Although paternal effects have been previously demonstrated in D. melanogaster, no earlier studies have investigated male-mediated transgenerational effects of diet in this species. The results highlight the importance of not only considering the relative contribution each parental sex has on progeny performance but also the combined effects that the two sexes may have on offspring performance. © 2012 Valtonen et al.


Paturi P.,University of Turku
Superconductor Science and Technology | Year: 2010

The vortex path model is applied to Jc() data of YBa 2Cu3O6+x (YBCO) thin films with different densities and types of columnar defects. The films were prepared by laser deposition from micro-and nanograined undoped and BaZrO3-doped nanograined targets. It is found that in the ab-axis direction the model gives parameters which can be interpreted in terms of vortices trapped in the Cu-O spacer layers. In the c direction the model gives estimates of average vortex path shapes and explains the shoulders close to the ab peak frequently observed in the Jc() data without the need for assuming changes in the electronic mass anisotropy. © 2010 IOP Publishing Ltd.


Markus V.,University of Turku | Janne L.,University of Turku | Urpo L.,University of Turku
TrAC - Trends in Analytical Chemistry | Year: 2011

The use of antibodies in immunodiagnostics has achieved new insights with recombinant technologies. This review summarizes the methods used to produce recombinant antibodies and those to tailor their properties. Finally, we address the advantages and the possibilities of recombinant antibodies in immunoanalytical applications through examples with the main focus on applications related to food quality and safety analysis. © 2011 Elsevier Ltd.


Johnson M.T.J.,University of Toronto | Ives A.R.,University of Wisconsin - Madison | Ahern J.,University of Turku | Salminen J.-P.,University of Turku
New Phytologist | Year: 2014

Summary: Plant species vary greatly in defenses against herbivores, but existing theory has struggled to explain this variation. Here, we test how phylogenetic relatedness, tradeoffs, trait syndromes, and sexual reproduction affect the macroevolution of defense. To examine the macroevolution of defenses, we studied 26 Oenothera (Onagraceae) species, combining chemistry, comparative phylogenetics and experimental assays of resistance against generalist and specialist herbivores. We detected dozens of phenolic metabolites within leaves, including ellagitannins (ETs), flavonoids, and caffeic acid derivatives (CAs). The concentration and composition of phenolics exhibited low to moderate phylogenetic signal. There were clear negative correlations between multiple traits, supporting the prediction of allocation tradeoffs. There were also positively covarying suites of traits, but these suites did not strongly predict resistance to herbivores and thus did not act as defensive syndromes. By contrast, specific metabolites did correlate with the performance of generalist and specialist herbivores. Finally, that repeated losses of sex in Oenothera was associated with the evolution of increased flavonoid diversity and altered phenolic composition. These results show that secondary chemistry has evolved rapidly during the diversification of Oenothera. This evolution has been marked by allocation tradeoffs between traits, some of which are related to herbivore performance. The repeated loss of sex appears also to have constrained the evolution of plant secondary chemistry, which may help to explain variation in defense among plants. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.


Maund J.R.,Queen's University of Belfast | Maund J.R.,Copenhagen University | Reilly E.,Queen's University of Belfast | Mattila S.,University of Turku
Monthly Notices of the Royal Astronomical Society | Year: 2014

The acquisition of late-time imaging is an important step in the analysis of pre-explosion observations of the progenitors of supernovae. We present late-time Hubble Space Telescope Advanced Camera for Surveys Wide-Field Channel observations of the sites of five Type IIP SNe: 1999ev, 2003gd, 2004A, 2005cs and 2006my. Observations were conducted using the F435W, F555W and F814W filters.We confirm the progenitor identifications for SNe 2003gd, 2004A and 2005cs, through their disappearance. We find that a source previously excluded as being the progenitor of SN 2006my has now disappeared. The late-time observations of the site of SN 1999ev cast significant doubt over the nature of the source previously identified as the progenitor in pre-explosion Wide Field Planetary Camera 2 images. The use of image subtraction techniques yields improved precision over photometry conducted on just the pre-explosion images alone. In particular, we note the increased depth of detection limits derived on pre-explosion frames in conjunction with late-time images. We use spectral energy distribution fitting techniques to explore the effect of different reddening components towards the progenitors. For SNe 2003gd and 2005cs, the pre-explosion observations are sufficiently constraining that only limited amounts of dust (either interstellar or circumstellar) are permitted. Assuming only a Galactic reddening law, we determine the initial masses for the progenitors of SNe 2003gd, 2004A, 2005cs and 2006my of 8.4 ± 2.0, 12.0 ± 2.1, 9.5+3.4 -2.2 and 9.8 ± 1.7M⊙, respectively. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Maund J.R.,Queen's University of Belfast | Mattila S.,University of Turku | Ramirez-Ruiz E.,University of California at Santa Cruz | Eldridge J.J.,University of Auckland
Monthly Notices of the Royal Astronomical Society | Year: 2014

The progenitor of the Type IIP supernova (SN) 2008bk was discovered in pre-explosion g'r'i'IYJHKs images, acquired with European Southern Observatory Very Large Telescope FOcal Reducer and low dispersion Spectrograph, High Acuity Wide field K-band Imager and Infrared Spectrometer and Array Camera instruments and the Gemini Multi-Object Spectrograph-South instrument. The wealth of pre-explosion observations makes the progenitor of this SN one of the best studied, since the detection of the progenitor of SN 1987A. Previous analyses of the properties of the progenitor were hampered by the limited quality of the photometric calibration of the pre-explosion images and the crowded nature of the field containing the SN. We present new late-time observations of the site of SN 2008bk acquired with identical instrument and filter configurations as the pre-explosion observations, and confirm that the previously identified red supergiant (RSG) star was the progenitor of this SN and has now disappeared. Image subtraction techniques were used to conduct precise photometry of the now missing progenitor, independently of blending from any nearby stars. The nature of the surrounding stellar population and their contribution to the flux attributed to the progenitor in the pre-explosion images are probed using Hubble Space Telescope Wide Field Camera 3 Ultraviolet-Visible/Infrared observations. In comparison with MARCS synthetic spectra, we find the progenitor was a highly reddened RSG with luminosity log(L/L⊙) = 4.84+0.10 -0.12, corresponding to an initial mass of Minit = 12.9+1.6 -1.8 M⊙. The temperature of the progenitor was hotter than previously expected for RSGs (T ~ 4330 K), but consistent with new temperatures derived for RSGs using spectral energy distribution fitting techniques. We show that there is evidence for significant extinction of the progenitor, possibly arising in the circumstellar medium, but that this dust yields a similar reddening law to dust found in the interstellar medium (E(B - V) = 0.77 with RV = 3.1). Our improved analysis, which carefully accounts for the systematics, results in a more precise and robust mass estimate, making the progenitor of SN 2008bk the most well understood progenitor of a Type IIP SN from pre-explosion observations. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Ekblad M.,University of Turku | Gissler M.,Finnish National Institute for Health and Welfare | Gissler M.,Nordic School of Public Health | Lehtonen L.,University of Turku | And 2 more authors.
Archives of General Psychiatry | Year: 2010

Context: Prenatal smoking exposure modulates brain development, which may deviate mental development of the offspring. Objective: To study the effects of prenatal smoking exposure on psychiatric morbidity and mortality among Finnish young adults by means of population-based longitudinal register data. Design: Information on maternal smoking as reported by the mothers (0, <10, or >10 cigarettes a day) and other background factors (maternal age and parity and child's sex, gestational age, birth weight, and 5-minute Apgar score) was derived from the Finnish Medical Birth Register. Information on children's psychiatric diagnoses related to outpatient visits (1998-2007), children's inpatient care (1987-2007), and mothers' psychiatric inpatient care (1969-1989) was derived from the Finnish Hospital Discharge Register. Information on deaths and their causes for the children (1987-2007) was received from the Cause-of-Death Register. Setting: Population-based study of all singletons born in Finland from 1987 to 1989 with information on prenatal smoking exposure. Patients: The source population included all singleton births in Finland from January 1, 1987, through December 31, 1989 (n=175 869), excluding children with major congenital anomalies (3.1%) and children who died during the first week of life (0.3%). Main Outcome Measures: Psychiatric morbidity and mortality. Results: The prevalence of maternal smoking was 15.3%. The risk of psychiatric morbidity was significantly higher in the exposed children than in the unexposed children. Among the offspring of mothers who smoked fewer than 10 cigarettes a day, 21.0% had any psychiatric diagnoses (adjusted odds ratio [OR], 1.53 [95% confidence interval (CI), 1.47-1.60]) compared with 24.7% among those of mothers who smoked more than 10 cigarettes a day (1.85 [1.74-1.96]) and 13.7% in the unexposed children (the reference group). The risk was significantly increased for most of the psychiatric diagnoses. The strongest effects were in psychiatric disorders due to psychoactive substance use and in behavioral and emotional disorders. The risk of mortality was significantly higher in children exposed to more than 10 cigarettes a day (OR, 1.69 [95% CI, 1.31-2.19]) compared with unexposed children. Conclusion: Prenatal smoking exposure is associated with an increased risk of psychiatric morbidity, whereas prenatal exposure to more than 10 cigarettes a day increases the risk of mortality in childhood, adolescence, and young adulthood. ©2010 American Medical Association. All rights reserved.


Sillanpaa M.,University of Turku | Shinnar S.,Yeshiva University
New England Journal of Medicine | Year: 2010

Background: There are few studies on long-term mortality in prospectively followed, well-characterized cohorts of children with epilepsy. We report on long-term mortality in a Finnish cohort of subjects with a diagnosis of epilepsy in childhood. Methods: We assessed seizure outcomes and mortality in a population-based cohort of 245 children with a diagnosis of epilepsy in 1964; this cohort was prospectively followed for 40 years. Rates of sudden, unexplained death were estimated. The very high autopsy rate in the cohort allowed for a specific diagnosis in almost all subjects. Results: Sixty subjects died (24%); this rate is three times as high as the expected age-and sex-adjusted mortality in the general population. The subjects who died included 51 of 107 subjects (48%) who were not in 5-year terminal remission (i.e., ≥5 years seizure-free at the time of death or last follow-up). A remote symptomatic cause of epilepsy (i.e., a major neurologic impairment or insult) was also associated with an increased risk of death as compared with an idiopathic or cryptogenic cause (37% vs. 12%, P<0.001). Of the 60 deaths, 33 (55%) were related to epilepsy, including sudden, unexplained death in 18 subjects (30%), definite or probable seizure in 9 (15%), and accidental drowning in 6 (10%). The deaths that were not related to epilepsy occurred primarily in subjects with remote symptomatic epilepsy. The cumulative risk of sudden, unexplained death was 7% at 40 years overall and 12% in an analysis that was limited to subjects who were not in long-term remission and not receiving medication. Among subjects with idiopathic or cryptogenic epilepsy, there were no sudden, unexplained deaths in subjects younger than 14 years of age. Conclusions: Childhood-onset epilepsy was associated with a substantial risk of epilepsy-related death, including sudden, unexplained death. The risk was especially high among children who were not in remission. (Funded by the Finnish Epilepsy Research Foundation.) Copyright © 2010 Massachusetts Medical Society.


Larjava H.,University of British Columbia | Koivisto L.,University of British Columbia | Heino J.,University of Turku | Hakkinen L.,University of British Columbia
Experimental Cell Research | Year: 2014

Cell surface integrin receptors mediate cell adhesion, migration and cellular signaling in all nucleated cells. They are activated by binding to extracellular ligands or by intracellular proteins, such as kindlins that engage with their cytoplasmic tails. Cells in the periodontal tissues express several integrins with overlapping ligand-binding capabilities. A distinct phenotype in the periodontium has only been described for knockouts or mutations of three integrin subunits, α11, β6 and β2. Integrin α11β1 appears to have some regulatory function in the periodontal ligament of continuously erupting incisors in mice. Integrin αvβ6 is expressed in the junctional epithelium (JE) of the gingiva. Animals deficient in this receptor develop classical signs of periodontal disease, including inflammation, apical migration of the JE and bone loss, suggesting that it plays a role in the regulation of periodontal inflmmation, likely through activation of transforming growth factor-β1. Lack of integrin activation in the JE is also associated with periodontitis. Patients with kindlin-1 mutations have severe early-onset periodontal disease. Finally, patients with mutations in the leukocyte-specific β2 integrin subunit have severe periodontal problems due to lack of transiting neutrophils in the periodontal tissues. © 2014 Elsevier Inc.


Varelius J.,University of Turku
Journal of Medical Ethics | Year: 2014

In this article, I assess the position that voluntary euthanasia (VE) and physician-assisted suicide (PAS) ought not to be accepted in the cases of persons who suffer existentially but who have no medical condition, because existential questions do not fall within the domain of physicians' professional expertise. I maintain that VE and PAS based on suffering arising from medical conditions involves existential issues relevantly similar to those confronted in connection with existential suffering. On that basis I conclude that if VE and PAS based on suffering arising from medical conditions is taken to fall within the domain of medical expertise, it is not consistent to use the view that physicians' professional expertise does not extend to existential questions as a reason for denying requests for VE and PAS from persons who suffer existentially but have no medical condition.


Koivisto M.,University of Turku
Vision Research | Year: 2012

Reentrant processing has been proposed as a critical mechanism in visual perception of an object's features. In order to test whether reentry is critical for visual awareness of object presence, the success of reentry was manipulated with object substitution masking (OSM) while participants performed a forced-choice target present-absent task and rated their subjective confidence in each trial. Signal detection analyses were performed on the data from the forced-choice task and on the subjective confidence ratings. The results showed that OSM reduced sensitivity to the presence of the target, indicating that reentry is critical for awareness of object presence. Consistent with the idea that OSM leaves feedforward processing intact, confidence ratings in reported target-absent trials were lower for misses (target present, no response) than for correct rejections (target absent, no response), implying that a target-related sensory signal was available for subjective ratings in spite of reported absence of the target. The results suggest that reentry is critical for encoding the target representation into a stable, consciously reportable form. © 2012 Elsevier Ltd.


A bias in reproduction towards sons, which are energetically more costly than daughters, has been suggested to shorten parental lifespan, but previous results have been mixed. Reproductive costs should be most evident in low rather than high resource settings, and are not expected to be severe in men, because women pay higher direct costs of reproduction. We, therefore, used demographic data from pre-industrial Finland to investigate whether the number of sons and daughters born affected their parents' post-reproductive survival and whether this was related to parent's resource availability. Irrespective of access to resources, mothers, but not fathers, with many sons suffered from reduced post-reproductive survival, and this association decreased as mothers aged. Our results provide evidence that Finnish mothers traded long post-reproductive lifespan for giving birth to many sons.


PURPOSE OF REVIEW: Several studies show that the number of FcγRI (CD64) on the surface of neutrophils increases in infections. However, in spite of increased research interest in recent years, there is no clear general view on the usability of neutrophil FcγRI in clinical infection diagnostics. This review tries to bring the clarity to this matter. RECENT FINDINGS: It is shown here that although the high number of FcγRI on neutrophils is a sensitive marker of bacterial infection, it is highly expressed also in DNA virus infections. As a consequence, neutrophil FcγRI cannot be used in distinguishing between bacterial and viral infections. It is also clear that FcγRI on neutrophils cannot be used in distinguishing between Gram-positive and Gram-negative bacterial infections or between microbiologically confirmed and clinically diagnosed bacterial infections. In addition, neutrophil FcγRI cannot be used to reliably detect RNA virus infections, inflammatory diseases, or cancer. SUMMARY: The best clinical benefit from the quantitative analysis of FcγRI on neutrophils will be obtained when it is used simultaneously with a reliable bacterial infection marker. DNA virus score point is an efficient novel method in differentiating between DNA and RNA virus infections. © 2010 Wolters Kluwer Health | Lippincott Williams & Wilkins.


Matos-Maravi P.F.,University of Turku | Pena C.,University of Turku | Willmott K.R.,University of Florida | Freitas A.V.L.,University of Campinas | Wahlberg N.,University of Turku
Molecular Phylogenetics and Evolution | Year: 2013

The so-called "Taygetis clade" is a group of exclusively Neotropical butterflies classified within Euptychiina, one of the largest subtribes in the subfamily Satyrinae. Since the distribution of the ten genera belonging to this group ranges throughout the entire Neotropics, from lowlands to lower montane habitats, it offers a remarkable opportunity to study the region's biogeographic history as well as different scenarios for speciation in upland areas. We inferred a robust and well-sampled phylogeny using DNA sequences from four genes (4035. bp in total) using maximum parsimony and Bayesian inference. We estimated divergence times using the Bayesian relaxed clock method calibrated with node ages from previous studies. Ancestral ranges of distribution were estimated using the dispersal-extinction-cladogenesis (DEC) model as implemented in the program Lagrange. We propose several taxonomic changes and recognize nine well-supported natural genera within the "Taygetis clade": Forsterinaria (subsuming Guaianaza syn. nov.), Parataygetis, Posttaygetis, Harjesia (excluding Harjesia griseola and Harjesia oreba), Pseudodebis (including Taygetomorpha syn. nov.,), Taygetina (subsuming Coeruleotaygetis syn. nov., Harjesia oreba comb. nov., Taygetis weymeri comb. nov. and Taygetis kerea comb. nov.), Taygetis (excluding Taygetis ypthima, Taygetis rectifascia, Taygetis kerea and Taygetis weymeri), and two new genera, one containing Harjesia griseola, and the other Taygetis ypthima and Taygetis rectifascia. The group diversified mainly during late Miocene to Pliocene, coinciding with the period of drastic changes in landscape configuration in the Neotropics. Major dispersals inferred from the Amazon basin towards northwestern South America, the Atlantic forests and the eastern slope of the Andes have mostly shaped the evolution and diversification of the group. Furthermore, expansion of larval dietary repertoire might have aided net diversification in the two largest genera in the clade, Forsterinaria and Taygetis. © 2012 Elsevier Inc.


Main K.M.,Copenhagen University | Skakkebaek N.E.,Copenhagen University | Virtanen H.E.,University of Turku | Toppari J.,University of Turku
Best Practice and Research: Clinical Endocrinology and Metabolism | Year: 2010

The prevalence of male reproductive disorders, such as testicular cancer and impaired semen quality, is increasing in many, albeit not all, countries. These disorders are aetiologically linked with congenital cryptorchidism and hypospadias by common factors leading to perinatal disruption of normal testis differentation, the testicular dysgenesis syndrome (TDS). There is recent evidence that also the prevalence of genital malformations is increasing and the rapid pace of increase suggests that lifestyle factors and exposure to environmental chemicals with endocrine disrupting properties may play a role. Recent prospective studies have established links between perinatal exposure to persistent halogenated compounds and cryptorchidism, as well as between phthalates and anti-androgenic effects in newborns. Maternal alcohol consumption, mild gestational diabetes and nicotine substitutes were also identified as potential risk factors for cryptorchidism. It may be the cocktail effect of many simultaneous exposures that result in adverse effects, especially during foetal life and infancy. © 2009 Elsevier Ltd. All rights reserved.


Sipila J.O.T.,University of Turku | Soilu-Hanninen M.,University of Turku
European Journal of Neurology | Year: 2015

Background and purpose: A Swiss study recently reported surgery as a potential risk factor for developing Guillain-Barré syndrome (GBS). It was sought to establish this in the Finnish adult population. Methods: Persons over 16 years of age who received a diagnosis of GBS in 2004-2013 were identified from the patient register of Turku University Hospital and their patient records were analyzed to identify possible triggers. Results: A cohort of 69 adult patients with GBS (63.8% men) was identified giving an annual incidence of 1.82/100 000. Of these, four (5.8%) had experienced a surgical procedure during the preceding 6 weeks with a relative risk of 6.28 (95% confidence interval 4.15-9.47, P < 0.001) compared with the general study population or a risk of 1.25/100 000 operations. No difference between genders was found. Only two (2.9%) patients had received a vaccination [one against seasonal influenza (P = 0.888) and one against pandemic influenza (Pandemrix®, GlaxoSmithKline Biologicals, Rixensart, Belgium, relative risk 2.85, 95% confidence interval 1.27-6.38, P = 0.011)] during the preceding 6 weeks. The most common GBS triggers identified were respiratory tract infections in 30 cases (43.5%) and gastroenteritis in 16 cases (23.2%) whilst two patients (2.9%) had had both. Conclusions: The overall incidence of GBS in the adult population of southwestern Finland was similar to previous studies worldwide and the most common triggers were respiratory tract infections and gastroenteritis. Surgery was a rare risk factor and of vaccinations only the one against pandemic influenza raised the risk of GBS. © 2014 EAN.


Liippo J.,University of Turku | Kousa P.,Helsinki Asthma and Allergy Association in Finland | Lammintausta K.,University of Turku
Contact Dermatitis | Year: 2011

Background. Chlorhexidine is used for disinfection of skin and mucosae in medicine and dentistry. Prolonged exposure may lead to contact sensitization and allergic contact dermatitis or stomatitis. Objectives. The purpose of this study was to analyse the sources of chlorhexidine exposure and sensitization, and to obtain data on the prevalence of sensitization and chlorhexidine-related contact allergy. Patients andmethods. From 1999, patch testing was performed with chlorhexidine digluconate (0.5% aq.) on 7610 general dermatology patients with suspected contact allergy at the Turku University Hospital Dermatology Department. The medical records were reviewed concerning the patients' exposure to chlorhexidine. Results. A positive patch reaction to chlorhexidine was seen in 36 patients (0.47%). Current dermatitis or stomatitis caused by chlorhexidine-containing topicalmedicaments was seen in 5 patients. Chlorhexidine sensitization contributed to the current dermatitis in 11 patients. A history of earlier exposure to chlorhexidine-containing products was recalled by only 16 sensitized patients, whereas no exposure was revealed in 4 cases. Conclusions. Chlorhexidine-containing corticosteroid creams, skin disinfectants and oral hygiene products are principal sources of chlorhexidine contact sensitization. Exposure tochlorhexidine in cosmeticsmayleadto delayed improvement of eczema in sensitized patients, emphasizing the importance of identifying the potential cosmetic sources. © 2011 John Wiley & Sons A/S.


Helajarvi H.,University of Turku
Duodecim; lääketieteellinen aikakauskirja | Year: 2013

The health-promoting effects of physical exercise are scientifically proven, but the health risks of sitting still remain rather poorly known. Technological development of the society will by no means cut down sitting. Should too much sitting be considered as one of the independent factors increasing the risk of metabolic diseases and its reduction as a health-promoting measure? Innovative solutions made possible by the new technology to cut down on sitting and to increase physical activity may prove to be important future tools for promoting health.


Tikkanen M.,University of Turku | Aro E.-M.,University of Turku
Trends in Plant Science | Year: 2014

Highly flexible regulation of photosynthetic light reactions in plant chloroplasts is a prerequisite to provide sufficient energy flow to downstream metabolism and plant growth, to protect light reactions against photodamage, and to ensure controlled cellular signaling from the chloroplast to the nucleus. Such comprehensive regulation occurs via the control of excitation energy transfer to and between the two photosystems (PSII and PSI), of the electrochemical gradient across the thylakoid membrane (δpH), and of electron transfer from PSII to PSI electron acceptors. In this opinion article, we propose that these regulatory mechanisms, functioning at different levels of photosynthetic energy conversion, might be interconnected and describe how the concomitant and integrated function of these mechanisms might enable plants to acclimate to a full array of environmental changes. © 2013 Elsevier Ltd.


Lehtonen T.K.,University of Turku | Lehtonen T.K.,Åbo Akademi University
Oecologia | Year: 2014

Discrete colour morphs have provided important insights into the evolution of phenotypic diversity. One of the mechanisms that can help to explain coexistence of ecologically similar colour morphs and incipient species is (colour) biased aggression, which has the potential to promote continued existence of the morphs in a frequency-dependent manner. I addressed colour biases in territorial aggression in a field-based study on a Neotropical cichlid fish species, Amphilophus sagittae, which has two ecologically indistinguishable colour morphs that mate assortatively. I found that A. sagittae, in particular females, were more aggressive towards models of their own colour than those mimicking colours of the other morph. Such a behavioural pattern should result in a selection regime that benefits the rarer morph, and hence could help explain how novel, rare phenotypes may avoid competitive exclusion. © 2014 Springer-Verlag Berlin Heidelberg.


Lehti L.,University of Turku
Journal of Pragmatics | Year: 2011

The article examines innovative ways of genre-mixing in an emergent genre, the politician's blog. Based on prototype theory, the study presents a division of French politicians' blogs into sub-genres. The criteria used to distinguish these sub-genres are medium, communicative purpose, participant roles and rhetorical structure. The material used in the study consists of 80 French politicians' blogs and the writings posted on these blogs during the month of September 2007, which was a period outside actual election campaign. The analysis revealed five different sub-genres: diary, scrapbook, notice-board, essay and polemic. Each sub-genre is discussed in detail on the basis of a prototypical blog of the type in question. © 2010 Elsevier B.V.


Jokilehto T.,Åbo Akademi University | Jokilehto T.,University of Turku | Jaakkola P.M.,Åbo Akademi University | Jaakkola P.M.,University of Turku
Journal of Cellular and Molecular Medicine | Year: 2010

Tumour hypoxia is a well-known microenvironmental factor that causes cancer progression and resistance to cancer treatment. This involves multiple mechanisms of which the best-understood ones are mediated through transcriptional gene activation by the hypoxia-inducible factors (HIFs). HIFs in turn are regulated in response to oxygen availability by a family of iron- and 2-oxoglutarate-dependent dioxygenases, the HIF prolyl hydroxylases (PHDs). PHDs inactivate HIFs in normoxia by activating degradation of the HIF-α subunit but release HIF activation in poorly oxygenated conditions. The function of HIF in tumours is fairly well characterized but our understanding on the outcome of PHDs in tumours is much more limited. Here we review the function of PHDs on the HIF system, the expression of PHDs in human tumours as well as their putative function in cancer. The PHDs may have either tumour promoting or suppressing activity. Their outcome in cancer depends on the cell and cancer type-specific expression and on the availability of diverse natural PHD inhibitors in tumours. Moreover, besides the action of PHDs on HIF, recent data suggest PHD function in non-HIF signalling. Together the data illustrate a complex operation of the oxygen sensors in cancer. © 2010 The Authors Journal compilation © 2010 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.


Rautava S.,University of Turku
Journal of Developmental Origins of Health and Disease | Year: 2015

The significance of contact with microbes in early life for subsequent health has been the subject of intense research during the last 2 decades. Disturbances in the establishment of the indigenous intestinal microbiome caused by cesarean section delivery or antibiotic exposure in early life have been linked to the risk of immune-mediated and inflammatory conditions such as atopic disorders, inflammatory bowel disease and obesity later in life. Distinct microbial populations have recently been discovered at maternal sites including the amniotic cavity and breast milk, as well as meconium, which have previously been thought to be sterile. Our understanding of the impact of fetal microbial contact on health outcomes is still rudimentary. Breast milk is known to modulate immune and metabolic programming. The breast milk microbiome is hypothesized to guide infant gut colonization and is affected by maternal health status and mode of delivery. Immunomodulatory factors in breast milk interact with the maternal and infant gut microbiome and may mediate some of the health benefits associated with breastfeeding. The intimate connection between the mother and the fetus or the infant is a potential target for microbial therapeutic interventions aiming to support healthy microbial contact and protect against disease. © Cambridge University Press and the International Society for Developmental Origins of Health and Disease 2015


Into T.,University of Turku | Portinari L.,University of Turku
Monthly Notices of the Royal Astronomical Society | Year: 2013

Colour-M*/L (mass-to-light) relations are a popular recipe to derive stellar mass in external galaxies. Stellar mass estimates often rely on near-infrared (NIR) photometry, considered an optimal tracer since it is little affected by dust and by the 'frosting' effect of recent star formation episodes. However, recent literature has highlighted that theoretical estimates of the NIR M*/L ratio strongly depend on the modelling of the asymptotic giant branch (AGB) phase. We use the latest Padova isochrones, with detailed modelling of the thermally pulsing AGB phase, to update theoretical colour-M*/L relations in the optical and NIR and discuss the consequences for the estimated stellar masses in external galaxies. We also discuss the effect of attenuation by interstellar dust on colour-M*/L relations in the statistical case of large galaxy samples. © 2013 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society.


Russell J.C.,University of California at Berkeley | Russell J.C.,University of Auckland | Ruffino L.,French National Center for Scientific Research | Ruffino L.,University of Turku
Proceedings of the Royal Society B: Biological Sciences | Year: 2012

Local spatio-temporal resource variations can strongly influence the population dynamics of small mammals. This is particularly true on islands which are bottom-up driven systems, lacking higher order predators and with high variability in resource subsidies. The influence of resource fluctuations on animal survival may be mediated by individual movement among habitat patches, but simultaneously analysing survival, resource availability and habitat selection requires sophisticated analytical methods. We use a Bayesian multi-state capture-recapture model to estimate survival and movement probabilities of non-native black rats (Rattus rattus) across three habitats seasonally varying in resource availability. We find that survival varies most strongly with temporal rainfall patterns, overwhelming minor spatial variation among habitats. Surprisingly for a generalist forager, movement between habitats was rare, suggesting individuals do not opportunistically respond to spatial resource subsidy variations. Climate is probably the main driver of rodent population dynamics on islands, and even substantial habitat and seasonal spatial subsidies are overwhelmed in magnitude by predictable annual patterns in resource pulses. Marked variation in survival and capture has important implications for the timing of rat control.


Heikkila M.,University of Helsinki | Kaila L.,University of Helsinki | Mutanen M.,University of Oulu | Pena C.,University of Turku | Wahlberg N.,University of Turku
Proceedings of the Royal Society B: Biological Sciences | Year: 2012

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous-Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis, a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae. © 2011 The Royal Society.


Zvereva E.L.,University of Turku | Kozlov M.V.,University of Turku
Water, Air, and Soil Pollution | Year: 2011

Identifying the factors responsible for the diversity of responses of biota to industrial pollution is crucial for predicting the fates of polluted ecosystems. A meta-analysis based on 49 field studies conducted around 47 point polluters demonstrated that the individual (growth and reproduction) and community (abundance and species richness) characteristics of bryophytes in polluted habitats are reduced to about a half of the values observed in unpolluted sites. Non-ferrous smelters cause a stronger reduction in species richness and larger changes in species composition than other types of polluters. The magnitudes of the effects of pollution on the abundances of individual bryophyte species are not linked with their taxonomic position, life form or Ellenberg indicator values for light, moisture and nitrogen. The variation in species' responses to pollution is mostly explained by differences in their reproductive characteristics; bryophyte species that possess special forms of vegetative reproduction and those that produce abundant sporophytes are more successful in polluted habitats. Ranking of bryophyte species according to their sensitivity to pollution is independent of the type of the polluter. Changes in bryophyte cover follow changes in tree cover, but not changes in the cover of the vascular field layer in the same pollution gradients. Pollution impacts cause stronger adverse effects on bryophytes in warmer climates. © Springer Science+Business Media B.V. 2010.


Okhotin A.,University of Turku
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2016

A famous theorem by Greibach ("The hardest context-free language", SIAM J. Comp., 1973) states that there exists such a contextfree language L0 that every context-free language over any alphabet is reducible to L0 by a homomorphic reduction-in other words, is representable as an inverse homomorphic image h-1(L0), for a suitable homomorphism h. This paper establishes similar characterizations for conjunctive grammars, that is, for grammars extended with a conjunction operator. © Springer International Publishing Switzerland 2016.


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

This paper deals with the concept of manipulation, understood as preference misrepresentation, in the light of the main theoretical results focusing on their practical significance. It also reviews some indices measuring the degree of manipulability of choice functions. Moreover, the results on complexity of manipulation as well as on safe manipulability are briefly touched upon. © Springer-Verlag Berlin Heidelberg 2016.


The taxonomic revision of Australian species of the genus Nemophora Hoffmannsegg is based on investigation of type materials of all described taxa. Lectotypes are designated for Nemotois opalina Meyrick, 1912; N. panaeola Turner, 1913; N. sparsella Walker, 1863; N. topazias Meyrick, [1893]; N. orichalcias Meyrick, [1893]; and N. selasphora Turner, 1913. N. topazias Meyrick, syn. nov. and N. selasphora Turn er, syn. n. are synonymized with Nemophora laurella (Newman, 1856). Two new species, Nemophora doddi sp. nov. and N. turneri sp. nov., are described from Queensland. The fauna of Australia currently includes seven valid species of Nemophora, which form a monophyletic laurella species-group. Keys to species based on external characters and on male genitalia are provided; adults and male genitalia are described and illustrated. © Copyright 2016 Magnolia Press.


Klemola N.,University of Turku | Andersson T.,University of Turku | Ruohomaki K.,University of Turku | Klemola T.,University of Turku
Ecology | Year: 2010

Population cycles of herbivores are thought to be driven by trophic interaction mechanisms, either between food plant and herbivore or between the herbivorous prey and its natural enemies. Observational data have indicated that hymenopteran parasitoids cause delayed density-dependent mortality in cyclic autumnal moth (Epirrita autumnata) populations. We experimentally tested the parasitism hypothesis of moth population cycles by establishing a four-year parasitoid-exclusion experiment, with parasitoid-proof exclosures, parasitoid-permeable exclosures, and control plots. The exclusion of parasitoids led to high autumnal moth abundances, while the declining abundance in both the parasitoid-permeable exclosures and the control plots paralleled the naturally declining density in the study area and could be explained by high rates of parasitism. Our results provide firm experimental support for the hypothesis that hymenopteran parasitoids have a causal relationship with the delayed density-dependent component required in the generation of autumnal moth population cycles. ©2010 by the society of America.


Laine S.K.,University of Turku | Hentunen T.,University of Turku | Laitala-Leinonen T.,University of Turku
Gene | Year: 2012

The adult bone marrow, situated within the bone cavity, comprises three distinct stem cell populations: hematopoietic stem cells (HSCs), mesenchymal stromal/stem cells (MSCs) and endothelial progenitor/stem cells (EPCs). HSCs are a well-characterized population of self-renewing cells that give rise to all blood cells. The definition of MSCs is more complex due to the limited understanding of MSC properties. In general, MSCs are considered multipotent stromal cells that are able to differentiate into various cell types, including osteoblasts, chondrocytes and adipocytes. Compared to HSCs and MSCs, EPCs are a newly discovered population of stem/progenitor cells with the capacity to differentiate into endothelial cells, the cells forming the inner lining of a blood vessel. Although functionally different, HSCs, MSCs and EPCs, like stem cells in general, share the ability to self-renew and differentiate into one or more cell types. The homeostasis inside the bone marrow and within the entire body is sustained by an intricate network of growth factors and transcription factors that orchestrate the proliferation and differentiation of these multipotent stem/progenitor cells. Increasing evidence indicates that microRNAs (miRNAs), small non-coding RNAs, are among the key players of this concert. This review summarizes the current insights into miRNA-mediated regulation of bone marrow stem/progenitor cell maintenance and differentiation. Furthermore, the potential contribution of miRNAs in bone marrow stem cell niches is discussed. © 2012 Elsevier B.V.


Morosinotto C.,University of Turku | Thomson R.L.,University of Turku | Korpimaki E.,University of Turku
Journal of Animal Ecology | Year: 2010

1. Breeding territory choice constitutes a crucial antipredator behaviour for animals that determines reproductive success and survival during the breeding season. On arrival to breeding grounds migrant prey face a multitude of 'waiting' predators already settled within the landscape. 2. We studied territory selection and reproductive investment of migrant pied flycatcher (Ficedula hypoleuca) relative to breeding pygmy owls (POs) (Glaucidium passerinum) and Tengmalm's owls (TOs) (Aegolius funereus). Diurnal POs present a greater predation threat to adult flycatchers (up to 80% songbirds in diet) compared with nocturnal TOs (up to 36%). 3. During territory selection, pied flycatchers strongly avoided POs (occupation: 42% in presence vs. 92% in absence of owl nest) but not TOs (80%vs. 75%). This suggests that flycatchers are able to distinguish between two potential predators, avoiding dangerous POs but not obviously responding to the less risky TOs. 4. Flycatchers responded to presence of PO nests with c. 4-day delay in the start of egg-laying. A significantly prolonged nest building period contributed to this potentially costly breeding delay. Flycatchers further significantly reduced initial reproductive investment in presence of POs by laying 8·2% smaller clutch sizes, even if laying date was controlled. No breeding delay and clutch size reduction was found relative to TO presence. 5. Our results highlight flexibility in breeding territory selection and reproductive strategies as antipredator responses to perceived risk in a multi-predator environment. This supports the idea that for prey, not all predators are equal. ©2009 The Authors. Journal compilation ©2009 British Ecological Society.


Tikkanen M.,University of Turku | Tikkanen M.,University of Geneva | Aro E.-M.,University of Turku
Biochimica et Biophysica Acta - Bioenergetics | Year: 2012

In higher plants, the photosystem (PS) II core and its several light harvesting antenna (LHCII) proteins undergo reversible phosphorylation cycles according to the light intensity. High light intensity induces strong phosphorylation of the PSII core proteins and suppresses the phosphorylation level of the LHCII proteins. Decrease in light intensity, in turn, suppresses the phosphorylation of PSII core, but strongly induces the phosphorylation of LHCII. Reversible and differential phosphorylation of the PSII-LHCII proteins is dependent on the interplay between the STN7 and STN8 kinases, and the respective phosphatases. The STN7 kinase phosphorylates the LHCII proteins and to a lesser extent also the PSII core proteins D1, D2 and CP43. The STN8 kinase, on the contrary, is rather specific for the PSII core proteins. Mechanistically, the PSII-LHCII protein phosphorylation is required for optimal mobility of the PSII-LHCII protein complexes along the thylakoid membrane. Physiologically, the phosphorylation of LHCII is a prerequisite for sufficient excitation of PSI, enabling the excitation and redox balance between PSII and PSI under low irradiance, when excitation energy transfer from the LHCII antenna to the two photosystems is efficient and thermal dissipation of excitation energy (NPQ) is minimised. The importance of PSII core protein phosphorylation is manifested under highlight when the photodamage of PSII is rapid and phosphorylation is required to facilitate the migration of damaged PSII from grana stacks to stroma lamellae for repair. The importance of thylakoid protein phosphorylation is highlighted under fluctuating intensity of light where the STN7 kinase dependent balancing of electron transfer is a prerequisite for optimal growth and development of the plant. This article is part of a Special Issue entitled: Photosystem II. © 2011 Elsevier B.V. All rights reserved.


Mulo P.,University of Turku | Sakurai I.,University of Turku | Aro E.-M.,University of Turku
Biochimica et Biophysica Acta - Bioenergetics | Year: 2012

The Photosystem (PS) II of cyanobacteria, green algae and higher plants is prone to light-induced inactivation, the D1 protein being the primary target of such damage. As a consequence, the D1 protein, encoded by the psbA gene, is degraded and re-synthesized in a multistep process called PSII repair cycle. In cyanobacteria, a small gene family codes for the various, functionally distinct D1 isoforms. In these organisms, the regulation of the psbA gene expression occurs mainly at the level of transcription, but the expression is fine-tuned by regulation of translation elongation. In plants and green algae, the D1 protein is encoded by a single psbA gene located in the chloroplast genome. In chloroplasts of Chlamydomonas reinhardtii the psbA gene expression is strongly regulated by mRNA processing, and particularly at the level of translation initiation. In chloroplasts of higher plants, translation elongation is the prevalent mechanism for regulation of the psbA gene expression. The pre-existing pool of psbA transcripts forms translation initiation complexes in plant chloroplasts even in darkness, while the D1 synthesis can be completed only in the light. Replacement of damaged D1 protein requires also the assistance by a number of auxiliary proteins, which are encoded by the nuclear genome in green algae and higher plants. Nevertheless, many of these chaperones are conserved between prokaryotes and eukaryotes. Here, we describe the specific features and fundamental differences of the psbA gene expression and the regeneration of the PSII reaction center protein D1 in cyanobacteria, green algae and higher plants. This article is part of a Special Issue entitled Photosystem II. © 2011 Elsevier B.V. All rights reserved.


Hayward A.D.,University of Sheffield | Holopainen J.,University of Helsinki | Pettay J.E.,University of Turku | Lummaa V.,University of Sheffield
Proceedings of the Royal Society B: Biological Sciences | Year: 2012

Severe food shortage is associated with increased mortality and reduced reproductive success in contemporary and historical human populations. Studies of wild animal populations have shown that subtle variation in environmental conditions can influence patterns of mortality, fecundity and natural selection, but the fitness implications of such subtle variation on human populations are unclear. Here, we use longitudinal data on local grain production, births, marriages and mortality so as to assess the impact of crop yield variation on individual age-specific mortality and fecundity in two pre-industrial Finnish populations. Although crop yields and fitness traits showed profound year-to-year variation across the 70-year study period, associations between crop yields and mortality or fecundity were generally weak. However, post-reproductive individuals of both sexes, and individuals of lower socio-economic status experienced higher mortality when crop yields were low. This is the first longitudinal, individual based study of the associations between environmental variation and fitness traits in pre-industrial humans, which emphasizes the importance of a portfolio of mechanisms for coping with low food availability in such populations. The results are consistent with evolutionary ecological predictions that natural selection for resilience to food shortage is likely to weaken with age and be most severe on those with the fewest resources. © 2012 The Royal Society.


Medvedev A.S.,University of Oulu | Medvedev A.S.,University of Turku | Poutanen J.,University of Oulu
Monthly Notices of the Royal Astronomical Society | Year: 2013

The aim of this paper is to investigate a possible contribution of the rotation-powered pulsars and pulsar wind nebulae to the population of ultraluminous X-ray sources (ULXs). We first develop an analytical model for the evolution of the distribution function of pulsars over the spin period and find both the steady-state and the time-dependent solutions. Using the recent results on the X-ray efficiency dependence on pulsar characteristic age, we then compute the X-ray luminosity function (XLF) of rotation-powered pulsars. In a general case, it has a broken power-law shape with a high-luminosity cutoff, which depends on the distributions of the birth spin period and the magnetic field. Using the observed XLF of sources in the nearby galaxies and the condition that the pulsar XLF does not exceed that, we find the allowed region for the parameters describing the birth period distribution.We find that the mean pulsar period should be greater than 10-40 ms. These results are consistent with the constraints obtained from the X-ray luminosity of core-collapse supernovae. We estimate that the contribution of the rotation-powered pulsars to the ULX population is at a level exceeding 3 per cent. For a wide birth period distribution, this fraction grows with luminosity and above 1040 erg s-1 pulsars can dominate the ULX population. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Salminen J.-P.,University of Turku | Karonen M.,University of Turku
Functional Ecology | Year: 2011

1. Tannins are one of the most studied groups of plant secondary metabolites in research related to chemical ecology. They are traditionally thought to form an important factor of plant defence against herbivorous insects. 2.For a long time, tannins' anti-herbivore activity was thought to derive from their protein precipitation capacity that rendered plant tissues non-nutritious and unpalatable for herbivores. Recent evidence suggests that tannin activity cannot be explained quite this simply, as tannin oxidation should also be taken into account as a defence mechanism for plants. 3.Tannins show very high variability in their structures with several hundred unique molecules detected in plants. These molecules are unevenly distributed in the plant kingdom and only very seldom-if ever-do two plant species share the same tannin pool. In many cases tannin composition varies even within organs of the same plant species and individual. Still, the overall tannin composition of many plant species is as of yet unknown. 4.Chemical ecology of tannins is challenging due to its multi-disciplinary nature. To facilitate research on tannins, we must provide ecologists and chemists with methodological and collaborative alternatives that enable the true and holistic investigation of all important questions that may arise from the field. So far this has not been possible with the tannin oxidation hypothesis, since simple and widely usable methods have not been available. 5.The aim of this review is to give a clear but detailed view of the chemical ecology of tannins and the methodology used to study them. In addition, we introduce a new method to estimate the oxidative activity of all types of tannins and other phenolics that might cause oxidative stress to herbivores. Hopefully our arguments and method will lead to clear changes in the approaches we take to tannins and their exciting biological activities, and we will witness a new era of flourishing and productive research in the chemical ecology of tannins. © 2011 The Authors. Functional Ecology © 2011 British Ecological Society.


Haavisto F.,University of Turku | Valikangas T.,University of Turku | Jormalainen V.,University of Turku
Oecologia | Year: 2010

In the marine littoral, strong grazing pressure selects for macroalgal defenses such as the constitutive and inductive production of defense metabolites. Induced defenses are expected under spatiotemporally varying grazing pressure and should be triggered by a reliable cue from herbivory, thereby reducing grazing pressure via decreased herbivore preference and/or performance. Although induced resistance has frequently been demonstrated in brown macroalgae, it is yet to be investigated whether induced macroalgal resistance shows genetic variation, a prerequisite for evolutionary responses to selection. In addition, consequences of induced resistance on herbivore performance have rarely been tested while the role of brown algal phlorotannins as inducible defense metabolites remains ambiguous. Using preference bioassays, we tested various cues, e.g., natural grazing, waterborne cues or simulated grazing to induce resistance in the brown alga Fucus vesiculosus. Further, we investigated whether there are induced responses in phlorotannin content, genetic variation in induced resistance or incurred performance costs to the mesoherbivore isopod, Idotea baltica. We found that both direct grazing and waterborne grazing cues decreased the palatability of F. vesiculosus, while increasing the total phlorotannin content. Since the sole presence of the herbivore also increased the total soluble phlorotannins, yet failed to stimulate deterrence, we concluded that phlorotannins alone do not explain increased resistance. Induced resistance varied between algal genotypes and thus showed potential for evolutionary responses to variation in grazing pressure. Induced resistance also incurred performance costs for female I. baltica via reduced egg production. Our results show that the induced resistance of F. vesiculosus decreases grazing pressure by deterring herbivores as well as impairing their performance. Resistance may be induced in advance by waterborne cues and spread effectively throughout the F. vesiculosus belt. Through lowering herbivore performance, induced resistance may also reduce future grazing pressure by decreasing the population growth rate of I. baltica. © Springer-Verlag 2009.


Brommer J.E.,University of Turku
Current Biology | Year: 2014

The evolution of a senescent decline in the performance of organisms as they grow old is thought to be an unavoidable aspect of life. A genotype-age interaction in performance is the 'fingerprint' of evolved senescence, which has now for the first time been detected in a plant. © 2014 Elsevier Ltd.


Jylkka J.,University of Turku
Minds and Machines | Year: 2011

It has been argued that prototypes cannot compose, and that for this reason concepts cannot be prototypes (Osherson and Smith in Cognition 9:35-58, 1981; Fodor and Lepore in Cognition 58:253-270, 1996; Connolly et al. in Cognition 103:1-22, 2007). In this paper I examine the intensional and extensional approaches to prototype compositionality, arguing that neither succeeds in their present formulations. I then propose a hybrid extensional theory of prototype compositionality, according to which the extension of a complex concept is determined as a function of what triggers its constituent prototypes. I argue that the theory escapes the problems traditionally raised against extensional theories of compositionality. © 2010 Springer Science+Business Media B.V.


Rautava S.,University of Turku | Kainonen E.,University of Turku | Salminen S.,University of Turku | Isolauri E.,University of Turku
Journal of Allergy and Clinical Immunology | Year: 2012

Background: Probiotics have shown promising potential in reducing the risk of eczema in infants. Optimal probiotic intervention regimen remains to be determined. Objective: We investigated whether maternal probiotic supplementation during pregnancy and breast-feeding reduces the risk of developing eczema in high-risk infants. Methods: This was a parallel, double-blind placebo-controlled trial of 241 mother-infant pairs. Mothers with allergic disease and atopic sensitization were randomly assigned to receive (1) Lactobacillus rhamnosus LPR and Bifidobacterium longum BL999 (LPR+BL999), (2) L paracasei ST11 and B longum BL999 (ST11+BL999), or (3) placebo, beginning 2 months before delivery and during the first 2 months of breast-feeding. The infants were followed until the age of 24 months. Skin prick tests were performed at the ages of 6, 12, and 24 months. Results: Altogether 205 infants completed the follow-up and were included in the analyses. The risk of developing eczema during the first 24 months of life was significantly reduced in infants of mothers receiving LPR+BL999 (odds ratio [OR], 0.17; 95% CI, 0.08-0.35; P < .001) and ST11+BL999 (OR, 0.16; 95% CI, 0.08-0.35; P < .001). The respective ORs for chronically persistent eczema were 0.30 (95% CI, 0.12-0.80; P = .016) and 0.17 (95% CI, 0.05-0.56; P = .003). Probiotics had no effect on the risk of atopic sensitization in the infants. No adverse effects were related to the use of probiotics. Conclusion: Prevention regimen with specific probiotics administered to the pregnant and breast-feeding mother, that is, prenatally and postnatally, is safe and effective in reducing the risk of eczema in infants with allergic mothers positive for skin prick test. © 2012 American Academy of Allergy, Asthma & Immunology.


Mikkola S.,University of Turku | Tanikawa K.,Japan National Astronomical Observatory
Monthly Notices of the Royal Astronomical Society | Year: 2013

The logarithmic Hamiltonian leapfrog algorithm solves the two-body problem with only a phase error. This is true independent of orbital eccentricity and thus it provides an algorithmic regularization. The algorithm gives regular results even for collision orbits when the potential is of 1/r type and it can be used for substeps in connection with extrapolation methods to obtain high accuracy. This applies also in problems in which there are many 1/r-type singularities, such as the few-body problem. A new surprising result is that a simple modification of the logarithmic leapfrog produces exact trajectories also for the quasi-Keplerian problem with a 1/r2 term in the potential © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Peroxiredoxins (Prx) are enzymes that catalyze the reduction of hydrogen peroxide and alkyl hydroperoxides. Prxs are ubiquitous enzymes with representatives found in Bacteria, Archaea and Eukarya. Many 1-cysteine peroxiredoxins (1-CysPrx) are dual-function enzyme with both peroxidase and acidic Ca2+-independent phospholipase A2 (aiPLA2) activities. The functions proposed for 1-CysPrx/aiPLA2 include the protection of cell membrane phospholipids against oxidative damage (peroxidation) and the metabolism (hydrolysis) of phospholipids, such as those of lung surfactant. The peroxidase active site motif PVCTTE of 1-CysPrx contains the conserved catalytic cysteine residue, and the esterase (lipase) motif GXSXG of the enzyme contains the conserved catalytic serine residue. In addition to the classic lipase motif GXSXG, various 1-CysPrx/aiPLA2s have closely related variant putative lipase motifs containing the catalytic serine residue. The PLA2 moieties are prevalent and highly homologous in vertebrate and bacterial 1-CysPrx/aiPLA2s that is consistent with a high degree evolutional conservation of the enzyme. © 2010.


Salo H.,University of Turku | Makinen J.,University of Turku
Atmospheric Environment | Year: 2014

We provide the first detailed case study using Sphagnum papillosum moss bags for active magnetic monitoring of airborne industrial pollution in order to evaluate the actual role of various emission sources and the competence of current environmental protection actions relative to the air quality. The origin and spatial spreading of particulate matter (PM) based on magnetic, chemical, and SEM-EDX analyses was studied around the Industrial Park in Harjavalta, SW Finland. The data was collected during two 6-month sampling periods along 8km transects in 2010-2011. The results support our hypothesis that the main emission source of PM is not the Cu-Ni smelter's pipe as presumed in previous chemical monitorings. We argue that the hot spot area within the severe impact pollution zone is related to slag processing and/or other unidentified industrial activity. At short distances various dust-providing sources outweigh the fly-ash load from the Cu-Ni smelter's pipe. Active magnetic monitoring by moss bags will help in planning environmental actions as well as in improvement of health conditions for industrial staff and town residents living next to the Industrial Park. © 2014 Elsevier Ltd.


Radevici I.,University of Turku | Radevici I.,Moldova State University
Journal of Rare Earths | Year: 2014

The luminescent properties of ZnSe, ZnSe:Cr (0.05 at.% Cr), ZnSe:Yb (0.03 at.% Yb) and ZnSe:Cr:Yb (0.05 at.% Cr, 0.05 at.% Yb) crystals, doped during the growth process by the chemical vapor transport method, were studied within the temperature interval of 6-300 K. At the 6 K temperature in the visible spectral range 2 bands were observed: a band in the excitonic spectral region and a band of self-activated luminescence. It was shown that co-doping of zinc selenide crystals with the chromium and ytterbium led to the combination of the impurities influence on the photoluminescent properties. At the liquid helium temperature in the middle infrared range of the spectra of the ytterbium and chromium co-doped crystal a band with the maximum localized at 1.7 μm was observed, which was overlapped with a complex band in the middle-IR spectral range, characteristic for the chromium doped ZnSe crystals. On the basis of obtained data an interaction mechanism of the chromium and ytterbium co-doping impurities was proposed. Guided by the existent model of the ytterbium ion incorporation in the selenide sublattice of the ZnSe crystals, an assumption about stabilization of single charged chromium ions in the zinc sublattice crystal nodes, by means of formation of the local charge compensating clusters, was made. It was assumed that the resonant energy transfer from one chromium ion to another, which led to the concentration quenching of the IR emission in the ZnSe:Cr PL spectra, would lead to the broadening of the IR emission in the spectra of ytterbium and chromium co-doped zinc selenide crystals.


Forssell H.,University of Turku
Journal of orofacial pain | Year: 2012

To characterize pain related to primary burning mouth syndrome (BMS) in terms of intensity, interference, and distress caused by the pain, as well as factors influencing the pain across a period of 2 weeks, and to study the use of coping and management strategies on a daily basis. Fifty-two female patients with primary BMS completed a 2-week pain diary. Pain intensity, interference, distress, and mood on a 0 to 10 numeric rating scale (NRS), as well as pain amplifying and alleviating factors, were recorded three times a day. The use of treatments (medication or other means) and coping strategies were recorded at the end of each day. Coefficient of variation, repeated measures analysis of variance, and correlative methods were used to assess the between- and within-subject variation, pain patterns, and associations between various pain scores. The overall mean pain intensity score of the 14 diary days was 3.1 (SD: 1.7); there was considerable variation in pain intensity between patients. Most patients experienced intermittent pain. On average, pain intensity increased from the morning to the evening. Intercorrelations between pain intensity, interference, distress, and mood were high, varying between rs = .75 and rs = .93 (P < .001). Pungent or hot food or beverages, stress, and tiredness were the most frequently mentioned pain-amplifying factors. The corresponding pain-alleviating factors were eating, sucking pastilles, drinking cold beverages, and relaxation. Thirty (58%) patients used pain medication and 35% reported using other means to alleviate their BMS pain. There was large variation in the use of coping strategies -between subjects. There were considerable differences in pain, in factors influencing the pain, and in pain behavior across BMS patients. This indicates that patient information and education as well as treatment of BMS pain should be individualized.


Lonnberg T.A.,University of Turku
ChemBioChem | Year: 2012

A 2′-O-methyl-RNA oligonucleotide containing a single free 2′-OH group flanking a branching phosphotriester linkage was prepared as a model for phosphate-branched RNA by using an orthogonally protected dimeric phosphoramidite building block in solid-phase synthesis. The strategy allows the synthesis of phosphate-branched oligonucleotides, the three branches of which may be of any desired sequence. Hydrolytic reactions of the phosphotriester linkages in such oligonucleotides were studied at physiological pH in the presence (and absence) of various complementary oligonucleotides. The fully hybridized oligonucleotide model is an order of magnitude more stable than its single-stranded counterpart, which, in turn, is an order of magnitude more stable than its trinucleoside phosphotriester core lacking any oligonucleotide arms. Furthermore, kinked structures obtained by hybridizing the phosphate-branched oligonucleotide with partially complementary oligonucleotides are three to five times more stable than fully double-stranded ones and only approximately three times less stable than the so-called RNA X structure, which has been postulated to incorporate an RNA phosphotriester linkage. The results indicate that when the intrinsically unstable RNA phosphotriester linkage is embedded in an oligonucleotide of appropriate tertiary structure, its half-life can be at least several hours. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Osterholm A.,Åbo Akademi University | Lindfors T.,Åbo Akademi University | Kauppila J.,University of Turku | Damlin P.,University of Turku | Kvarnstrom C.,University of Turku
Electrochimica Acta | Year: 2012

In this paper we report a simple, one-step method for direct electrochemical incorporation of graphene oxide (GO) into conducting polymer films without the use of any additional dopants. Polypyrrole (PPy) and poly(3,4-ethylenedioxythiophene) (PEDOT) were successfully electropolymerized in as-prepared aqueous GO dispersions using potentiostatic polymerization. When dispersed in water, the GO flakes carry a negative surface charge which allows them to serve as counter ions and hence be incorporated into the polymer films during electropolymerization. The incorporation of GO was verified using XPS whereas vibrational spectroscopy was used to confirm the successful formation of the two conducting polymers. The surface morphologies of the polymer-GO films were investigated with SEM. The incorporation of GO into PPy resulted in a distinctly different and more porous surface morphology than that observed in PPy films synthesized in the presence of conventional counter ions. The PEDOT-GO film, on the other hand, had a very smooth surface morphology similar to that of PEDOT films polymerized in the presence of other polyanions. As these composite films are aimed for electrochemical device applications, their redox behavior and electrochemical capacitance properties were also investigated using cyclic voltammetry and electrochemical impedance spectroscopy (EIS). The polymer-GO films exhibited good electrochemical reversibility during cycling in 0.1 M KCl. The PPy films exhibited high redox capacitance regardless of the counter ion used in electropolymerization whereas PEDOT-GO had lower redox capacitance than PEDOT-PSS. © 2012 Elsevier Ltd. All rights reserved.


Kari J.,University of Turku
Fundamenta Informaticae | Year: 2016

The tiling problem is the decision problem to determine if the infinite plane can be tiled by copies of finitely many given Wang tiles. The problem is known since the 1960's to be undecidable. The undecidability is closely related to the existence of aperiodic Wang tile sets. There is a known method to construct small aperiodic tile sets that simulate iterations of one-dimensional piecewise linear functions using encodings of real numbers as Sturmian sequences. In this paper we provide details of a similar simulation of two-dimensional piecewise affine functions by Wang tiles. Mortality of such functions is undecidable, which directly yields another proof of the undecidability of the tiling problem. We apply the same technique on the hyperbolic plane to provide a strongly aperiodic hyperbolic Wang tile set and to prove that the hyperbolic tiling problem is undecidable. These results are known in the literature but using different methods.


Saarela A.,University of Turku
Fundamenta Informaticae | Year: 2016

We study the question of what can be said about a word based on the numbers of occurrences of certain factors in it. We do this by defining a family of equivalence relations that generalize the so called k-Abelian equivalence. The characterizations and answers we obtain are linear algebraic. We also use these equivalence relations to help us in solving some problems related to repetitions and palindromes, and to point out that some previous results about Sturmian words and k-Abelian equivalence hold in a more general form.


Mazzola L.,University of Turku | Piilo J.,University of Turku | Maniscalco S.,University of Turku
Physical Review Letters | Year: 2010

We study the dynamics of quantum and classical correlations in the presence of nondissipative decoherence. We discover a class of initial states for which the quantum correlations, quantified by the quantum discord, are not destroyed by decoherence for times tt̄, on the other hand, classical correlations do not change in time and only quantum correlations are lost due to the interaction with the environment. Therefore, at the transition time t̄ the open system dynamics exhibits a sudden transition from classical to quantum decoherence regime. © 2010 The American Physical Society.


Haavisto L.E.,University of Turku | Sipila J.I.,University of Turku
Clinical Otolaryngology | Year: 2013

Objectives: The aim of the study was to compare rhinomanometry, acoustic rhinometry and subjective estimation of the nasal obstruction before and after septoplasty and to evaluate the long-term results of septal surgery. Design: Prospective long-term follow-up, before and after septoplasty. Setting: University tertiary-care hospital, referral centre. Participants: The study included 30 adult patients who were operated on because of septal deviation. Main outcome measures: Pre-operatively, acoustic rhinometry and active anterior rhinomanometry were performed on each subject after decongestion of the nose. A visual analogue scale for unilateral nasal obstruction was filled in by the patients. The measurements were repeated both 6 months and 10 years post-operatively. Results: A significant change in acoustic values was found during the long-term follow-up of 10 years. The mean minimal cross-sectional area on the more obstructive side was 0.35 cm2 pre-operatively. Six months after operation, it was 0.52 cm2, and 10 years after operation, it was 0.68 cm2. The mean resistance fell from pre-operative 1.16 Pa/mL/s to 0.41 Pa/mL/s during the first 6 months, but rose again to 1.21 Pa/mL/s after 10 years. Despite a tendency of improvement, no statistically significant change was found between pre-operative and postoperative values in VAS. Six months after operation 69% of the patients were satisfied with the result, and after ten years the amount of satisfied patients was 83%. Conclusions: We found an increase in acoustic values, but an increase in nasal resistance in the long-term follow-up. Other factors than nasal area may have an impact on nasal resistance and the feeling of nasal obstruction. The small size on the sample interfered with the results. © 2013 Blackwell Publishing Ltd.


Skilton M.R.,University of Sydney | Raitakari O.T.,University of Turku | Celermajer D.S.,University of Sydney
Hypertension | Year: 2013

Reduced fetal growth is associated with increased systolic blood pressure. Recently, we found an inverse association between serum ω-3 fatty acids and systolic blood pressure in young adults born with impaired fetal growth. We investigated the associations of dietary intake in childhood of the long-chain ω-3 fatty acids eicosapentaenoic acid and docosahexaenoic acid with blood pressure parameters in children born with reduced birth weight. We analyzed data from 3457 children aged 8 to 15 years participating in the continuous National Health and Nutrition Examination Survey 2003-2004, 2005-2006, and 2007-2008. Dietary intake was assessed by two 24-hour dietary recalls, birth weight by questionnaire, and blood pressure was measured. Systolic blood pressure was 1.1 mm Hg higher in those with reduced (<10th centile) compared with normal birth weight (≥10th centile), consistent with previous findings, although not statistically significant (P=0.40); however, pulse pressure was significantly higher in these children (3.4 mm Hg). In the 354 participants with reduced birth weight, when compared with children with the lowest tertile of intake, those who had the highest tertile of dietary eicosapentaenoic acid and docosahexaenoic acid intake had significantly lower systolic blood pressure (-4.9 mm Hg [95% confidence interval,-9.7 to-0.1]) and pulse pressure (-7.7 mm Hg [95% confidence interval,-15.0 to-0.4]). High-dietary intakes of eicosapentaenoic acid and docosahexaenoic acid are associated with lower systolic blood pressure and pulse pressure in children born with reduced birth weight. These data are consistent with the hypothesis that long-chain ω-3 fatty acids reduce blood pressure in those with impaired fetal growth. © 2013 American Heart Association, Inc.


Kotaja N.,University of Turku
Fertility and Sterility | Year: 2014

In mammals, male gametes are produced inside the testis by spermatogenesis, which has three phases: mitotic proliferation of spermatogonia, meiosis of spermatocytes, and haploid differentiation of spermatids. The genome of male germ cells is actively transcribed to produce phase-specific gene expression patterns. Male germ cells have a complex transcriptome. In addition to protein-coding messenger RNAs, many noncoding RNAs, including microRNAs (miRNAs), are produced. The miRNAs are important regulators of gene expression. They function mainly post-transcriptionally to control the stability or translation of their target messenger RNAs. The miRNAs are expressed in a cell-specific manner during spermatogenesis to participate in the control of each step of male germ cell differentiation. Genetically modified mouse models have demonstrated the importance of miRNA pathways for normal spermatogenesis, and functional studies have been designed to dissect the roles of specific miRNAs in distinct cell types. Clinical studies have exploited the well-defined expression profiles of miRNAs, and human spermatozoal or seminal plasma miRNAs have been explored as potential biomarkers for male factor infertility. This review article discusses the current findings that support the central role of miRNAs in the regulation of spermatogenesis and male fertility. Copyright © 2014 American Society for Reproductive Medicine, Published by Elsevier Inc.


Aro H.T.,University of Turku | Alm J.J.,University of Turku | Moritz N.,University of Turku | Makinen T.J.,University of Turku | Lankinen P.,University of Turku
Acta Orthopaedica | Year: 2012

Background and purpose Immediate implant stability is a key factor for success in cementless total hip arthroplasty (THA). Low bone mineral density (BMD) and age-related geometric changes of the proximal femur may jeopardize initial stability and osseointegration. We compared migration of hydroxyapatite-coated femoral stems in women with or without low systemic BMD. Patients and methods 61 female patients with hip osteoarthritis were treated with cementless THA with anatomically designed hydroxyapatite-coated femoral stems and ceramic-ceramic bearing surfaces (ABG-II). Of the 39 eligible patients between the ages of 41 and 78 years, 12 had normal systemic BMD and 27 had osteopenia or osteoporosis. According to the Dorr classification, 21 had type A bone and 18 had type B. Translational and rotational migration of the stems was evaluated with radiostereometric analysis (RSA) up to 2 years after surgery. Results Patients with low systemic BMD showed higher subsidence of the femoral stem during the first 3 months after surgery than did those with normal BMD (difference = 0.6, 95% CI: 0.11.1; p = 0.03). Low systemic BMD (odds ratio (OR) = 0.1, CI: 0.006-1.0; p = 0.02), low local hip BMD (OR = 0.3, CI: 0.10.7; p = 0.005) and ageing (OR = 1.1, CI: 1.0-1.2; p = 0.02) were risk factors for delayed translational stability. Ageing and low canal flare index were risk factors for delayed rotational stabilization (OR = 3, CI: 1.1-9; p = 0.04 and OR = 1.1, CI: 1.0-1.2; p = 0.02, respectively). Harris hip score and WOMAC score were similar in patients with normal systemic BMD and low systemic BMD. Interpretation Low BMD, changes in intraosseous dimensions of the proximal femur, and ageing adversely affected initial stability and delayed osseointegration of cementless stems in women. Copyright © 2011 Nordic Orthopaedic Federation.


Saaristo A.M.,University of Turku | Niemi T.S.,University of Turku | Viitanen T.P.,University of Turku | Tervala T.V.,University of Turku | And 2 more authors.
Annals of Surgery | Year: 2012

OBJECTIVE: Postoperative lymphedema after breast cancer surgery is a challenging problem. Recently, a novel microvascular lymph node transfer technique provided a fresh hope for patients with lymphedema. We aimed to combine this new method with the standard breast reconstruction. METHODS: During 2008-2010, we performed free lower abdominal flap breast reconstruction in 87 patients. For all patients with lymphedema symptoms (n = 9), we used a modified lower abdominal reconstruction flap containing lymph nodes and lymphatic vessels surrounding the superficial circumflex vessel pedicle. Operation time, donor site morbidity, and postoperative recovery between the 2 groups (lymphedema breast reconstruction and breast reconstruction) were compared. The effect on the postoperative lymphatic vessel function was examined. RESULTS: The average operation time was 426 minutes in the lymphedema breast reconstruction group and 391 minutes in the breast reconstruction group. The postoperative abdominal seroma formation was increased in patients with lymphedema. Postoperative lymphoscintigraphy demonstrated at least some improvement in lymphatic vessel function in 5 of 6 patients with lymphedema. The upper limb perimeter decreased in 7 of 9 patients. Physiotherapy and compression was no longer needed in 3 of 9 patients. Importantly, we found that human lymph nodes express high levels of endogenous lymphatic vessel growth factors. Transfer of the lymph nodes and the resulting endogenous growth factor expression may thereby induce the regrowth of