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Warsaw, Poland

The Polish Academy of science, headquartered in Warsaw, is the top Polish institution having the character of an academy of science. Being a society of distinguished scholars as well as a network of research institutes, it is responsible for spearheading the development of science in Poland. It was established in 1951, during the period of Poland People's Republic. Wikipedia.


Sato J.J.,Fukuyama University | Wolsan M.,Polish Academy of Sciences
Naturwissenschaften | Year: 2012

Umami is one of basic tastes that humans and other vertebrates can perceive. This taste is elicited by Lamino acids and thus has a special role of detecting nutritious, protein-rich food. The T1R1 + T1R3 heterodimer acts as the principal umami receptor. The T1R1 protein is encoded by the Tas1r1 gene. We report multiple inactivating (pseudogenizing) mutations in exon 3 of this gene from four phocid and two otariid species (Pinnipedia). Jiang et al. (Proc Natl Acad Sci U S A 109:4956-4961, 2012) reported two inactivating mutations in exons 2 and 6 of this gene from another otariid species. These findings suggest lost or greatly reduced umami sensory capabilities in these species. The widespread occurrence of a nonfunctional Tas1r1 pseudogene in this clade of strictly carnivorous mammals is surprising. We hypothesize that factors underlying the pseudogenization of Tas1r1 in pinnipeds may be driven by the marine environment to which these carnivorans (Carnivora) have adapted and may include: the evolutionary change in diet from tetrapod prey to fish and cephalopods (because cephalopods and living fish contain little or no synergistic inosine 5′-monophosphate that greatly enhances umami taste), the feeding behavior of swallowing food whole without mastication (because the T1R1 + T1R3 receptor is distributed on the tongue and palate), and the saltiness of sea water (because a high concentration of sodium chloride masks umami taste). © Springer-Verlag 2012. Source


Nikiforuk A.,Polish Academy of Sciences
Behavioural Pharmacology | Year: 2012

Chronic stress exerts detrimental effects on higher order executive functions that are governed by the prefrontal cortex. Experimental data suggest that dopamine D1 receptor-mediated hypodopaminergic dysfunction may underlie stress-induced cognitive deficits. However, although the involvement of D1 receptors in working memory is well established, less is known about their role in the modulation of set-shifting ability. Therefore, the aim of the present study was to examine the impact of the selective D1 receptor agonist, SKF 81297, on the attentional set-shifting task performance of rats subjected to repeated restraint stress and of unrestrained controls. The acute administration of SKF 81297 to control rats facilitated extradimensional set-shifting. However, only intermediate doses (0.1 and 0.3 mg/kg) were effective, whereas no effect was observed after the administration of either lower (0.01 mg/kg) or higher (1 mg/kg) doses. This dose-response curve was shifted to the left in stressed animals as the effectiveness of SKF 81297 (as compared with either vehicle-treated controls or stressed animals) was found only after the administration of lower drug doses (0.01 and 0.1 mg/kg). The beneficial effects of SKF 81297 on the attentional set-shifting task performance of stressed rats may have therapeutic implications for the treatment of frontal-like disturbances, particularly cognitive inflexibility, in stress-related psychiatric disorders. © 2012 Wolters Kluwer Health | Lippincott Williams & Wilkins. Source


Sobolewski A.L.,Polish Academy of Sciences
Physical Chemistry Chemical Physics | Year: 2015

Structural and electronic properties of ferroelectric columnar clusters constructed from benzene-1,3,5-tricarboxylic acid, (B3CA)N, were investigated at the Hartree-Fock level. It is shown that B3CA stacks form helix-shaped molecular tubes which are stabilized by intermolecular hydrogen bonds. It is furthermore shown that the strong electric field generated by the uniaxial alignment of the carboxyl groups can split an optically prepared exciton into an electron-hole pair and can drive the charge carriers to the opposite ends of the tube. Some consequences of the phenomenon for photovoltaic applications are discussed. © the Owner Societies 2015. Source


Siwiak M.,Polish Academy of Sciences
PLoS computational biology | Year: 2010

Translation is still poorly characterised at the level of individual proteins and its role in regulation of gene expression has been constantly underestimated. To better understand the process of protein synthesis we developed a comprehensive and quantitative model of translation, characterising protein synthesis separately for individual genes. The main advantage of the model is that basing it on only a few datasets and general assumptions allows the calculation of many important translational parameters, which are extremely difficult to measure experimentally. In the model, each gene is attributed with a set of translational parameters, namely the absolute number of transcripts, ribosome density, mean codon translation time, total transcript translation time, total time required for translation initiation and elongation, translation initiation rate, mean mRNA lifetime, and absolute number of proteins produced by gene transcripts. Most parameters were calculated based on only one experimental dataset of genome-wide ribosome profiling. The model was implemented in Saccharomyces cerevisiae, and its results were compared with available data, yielding reasonably good correlations. The calculated coefficients were used to perform a global analysis of translation in yeast, revealing some interesting aspects of the process. We have shown that two commonly used measures of translation efficiency - ribosome density and number of protein molecules produced - are affected by two distinct factors. High values of both measures are caused, i.a., by very short times of translation initiation, however, the origins of initiation time reduction are completely different in both cases. The model is universal and can be applied to any organism, if the necessary input data are available. The model allows us to better integrate transcriptomic and proteomic data. A few other possibilities of the model utilisation are discussed concerning the example of the yeast system. Source


Kaminski J.,Polish Academy of Sciences
Energy | Year: 2011

The paper presents an analysis of market power in the Polish power sector. The study is carried out for the structure that was established by the last consolidation undertaken by the government in 2007, using a game theoretic model of the power generation market (the PolMark model). The model is run under five scenarios and eight cases. The scenarios distinguish between assumptions on strategic behaviour, whereas the cases distinguish assumptions on coal prices. The following measures are discussed in this study: electricity prices, production volumes, consumer and producer surpluses, dead weight welfare loss, CO2, SO2, NOx emissions and fuel supplies to power producers. The results confirm that the potential to exert market power in the Polish power generation sector may influence significantly electricity prices and production volumes. The analysis indicates that under the competitive scenario the average wholesale electricity price would be approximately 14.7% lower and the production would be 6.7% higher when compared to the reference scenario. Furthermore, apart from surplus transfer between producers and consumers, the dead weight loss was estimated at the level of 123.6 M€. This value reflects the net social loss resulting from uncompetitive market equilibrium. © 2011 Elsevier Ltd. Source


Stroinski A.,Polish Academy of Sciences
Annales Zoologici | Year: 2013

A new extraordinary monotypic genus of Ricaniidae is described from Mahé Island (The Seychelles archipelago) with a new species Mahecania trinigromaculata gen. et sp. nov. Photographs, drawings and SEM images are presented. Discussion is provided on unique and rare characters presented for this genus. © Fundacja Natura optima dux. Source


The taxonomic and distributional data concerning the representatives of the Quadrideres interioris species-group were revised. Lectotypes for Q. interioris (Gebien, 1911), Q. lesnei Koch, 1956 and Q. volcanicus Koch, 1956 were designated. Q. kaszabi sp. nov. and Q. rex sp. nov. were described. An identification key is provided to all known species of the Q. interioris species-group. This paper brings the total species number within the genus Quadrideres to 18. © Fundacja Natura optima dux. Source


Platyhypnum Loeske of 1911 is a legitimate generic name which cannot be considered as a homonym of Platy-hypnum Hampe of 1877. Platyhypnum is lectotypified with P. dilatatum (Wilson ex Schimp.) Loeske and this makes is the oldest candidate for a name of the segregate encompassing the broad-leaved species of the traditionally conceived genus Hygrohypnum Lindb. Platyhypnum consists of nine species and seven following new combinations are necessary: P. alpestre (Hedw.) Ochyra, comb. nov., P. bestii (Renauld & Bryhn) Ochyra, comb. nov., P. cochlearifolium (De Not.) Ochyra, comb. nov., P. duriusculum (De Not.) Ochyra, comb. nov., P. montanum (Lindb.) Ochyra, comb. nov., P. norvegicum (Schimp.) Ochyra, comb. nov., P. smithii (Sw.) Ochyra, comb. nov., and P. tsuruzigamicum (Cardot) Ochyra, comb. nov. Platyhypnidium M.Fleisch. of 1923 is an illegitimate name including the lectotype of an earlier generic name (Platyhypnum) and the new generic name Torrentaria Ochyra is proposed to replace it with T. riparioides (Hedw.) Ochyra, comb. nov., as its generitype. The following new combinations are proposed under this generic name: Torrentaria afrorusciformis (Broth.) Ochyra, comb. nov., T. aquatica (A.Jaeger) Ochyra, comb. nov., T. brotheri (Paris) Ochyra, comb. nov., T. fuegiana (Cardot) Ochyra, comb. nov., T. grolleana (Ochyra & Bednarek-Ochyra) Ochyra, comb. nov., T. hedbergii (P.de la Varde) Ochyra, comb. nov., T. intermedia (Herzog) Ochyra, comb. nov., T. lusitanica (Schimp.) Ochyra, comb. nov., T. macowaniana (Paris) Ochyra, comb. nov., T. mutata (Ochyra & Vanderpoorten) Ochyra, comb. nov., T. obscura (Besch.) Ochyra, comb. nov., T. peruviensis (R.S.Williams) Ochyra, comb. nov., T. subrusciformis (Müll. Hal.) Ochyra, comb. nov., and T. torrenticola (Ochyra, Schmidt & Bültman) Ochyra, comb. nov. © 2012 J. Cramer in Gebr. Borntraeger Verlagsbuchhandlung, Stuttgart, Germany. Source


Malinowski J.,Polish Academy of Sciences
IEEE Transactions on Reliability | Year: 2013

A general model of a complex technical system is considered. The system is built of multiple two-state components which can be either operable or failed. The functioning of a component is influenced in a specific way by the other components' states, thus the components are not mutually s-independent. Failures occur randomly, and are handled by several repair teams. If a repair team is available when a failure occurs, then the repair (or replacement) is started immediately; otherwise the component waits in the repair queue. It is assumed that each component's time to failure is exponentially distributed, and the failure intensity depends on the other components' states. No assumption is made about the components' repair time distributions. The model's complexity makes it impossible to analytically compute the parameters of the system's failure-repair process. For this reason, the sought parameters are evaluated using a combination of Monte Carlo simulation and statistical estimation. Finding the confidence interval is a non-trivial task. The first part of the paper is theoretical; the conditions under which the failure-repair process is recurrent are given, and the confidence intervals for the sought parameters are defined. The second part has an applicable character; a commodity transport network is considered as an exemplary system with inter-component dependencies, and the algorithm estimating its reliability parameters is presented with some illustrative examples. © 1963-2012 IEEE. Source


Kusnierczyk P.,Polish Academy of Sciences
Archivum Immunologiae et Therapiae Experimentalis | Year: 2013

Killer cell immunoglobulin-like receptors (KIRs) are expressed on natural killer cells and minor subpopulations of thymus-derived (T) lymphocytes. KIRs may have a long cytoplasmic tail and inhibit cell activation upon ligand (HLA class I) binding, or they may have a short cytoplasmic tail and activate a cell after ligand binding. They are encoded by up to 14 genes present in different individuals in different combinations, whence their associations with several human diseases. KIR involvement in the fate of kidney allograft has not been extensively studied; nevertheless some associations had already been noticed. Their results are not concordant: some authors found no effect of KIR genotype, whereas others detected protective effect of KIR2DL2/KIR2DS2 or KIR-KIR ligand mismatch. We found an association of KIR2DS4 gene with acute rejection and a protective effect of KIR2DS5 gene. Interestingly, in patients, whose end-stage renal disease was caused by glomerulonephritis, the effect of KIR2DS4 was stronger than HLA mismatch, whereas opposite was true for recipients with other causes of renal failure. © 2013 L. Hirszfeld Institute of Immunology and Experimental Therapy, Wroclaw, Poland. Source


Bialynicki-Birula I.,Polish Academy of Sciences
Classical and Quantum Gravity | Year: 2015

The fluctuations of spacetime geometries at finite temperature are evaluated within the linearized theory of gravity. These fluctuations are described by the probability distribution of various configurations of the gravitational field. The field configurations are described by the linearized Riemann-Weyl tensor without any reference to the metric. The probability distribution of various configurations is described by the Wigner functional of the gravitational field. It has a foam-like structure; dominant configurations are those with large changes of geometry at nearby points. In the high-temperature limit one obtains the Bolzmann distribution that enables one to identify the expression for the total energy of the gravitational field. The appearance of the same expression for the total energy when the gravitational field is treated as a collection of gravitons and as the high-temperature limit of the Wigner functional proves the consistency of the whole procedure. Striking differences are found between the fluctuations of the electromagnetic field and the gravitational field; among them is the divergence in the gravitational case of the probability distribution at zero temperature. This divergence is of the 'infrared type' because it occurs in integrals over the wave vector at small k. © 2015 IOP Publishing Ltd. Source


Schmitt C.,French Atomic Energy Commission | Mazurek K.,Polish Academy of Sciences | Nadtochy P.N.,Omsk State University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2014

Various approaches are currently used to interpret experimental data on fission. We critically examine a wide set of observables measured for fission of Po206,210 nuclei at medium excitation energy, and illustrate the ambiguity in current analysis. Dynamical calculations based on the four-dimensional Langevin equation using a macroscopic potential energy landscape are performed, and found to consistently describe available measurements. This observation calls into question the robustness of recent analysis based on statistical-model calculations and concluding, on the contrary, to substantial shell effects at the fission saddle point in Po206,210. The inconsistency in interpretation reached by the two approaches shows that, depending on the system, the conclusion can be strongly model-dependent. Although this may not be surprising, it emphasizes the today still limited reliability of firmly extracting fundamental nuclear properties from customary analysis. © 2014 The Authors. Source


Bednarski H.,Polish Academy of Sciences
Journal of Magnetism and Magnetic Materials | Year: 2014

We present a detailed analysis of the role of various interaction mechanisms contributing to the bound magnetic polaron (BMP) molecule Hamiltonian with the purpose of gaining an insight into the origin of the ferromagnetic interaction between BMPs. Explicitly, it appears that the BMP molecule Hamiltonian without interatomic direct exchange interaction does not lead to appearance of the parallel alignment of polaronic clouds in the lowest energy state even for large magnitudes of the polaronic exchange fields (up to ~65 meV in Cd0.95Mn0.05Se). Also, it appears that for the range of moderate values of polaronic exchange fields (16-25 meV in Cd 0.95Mn0.05Se), the regular Hubbard BMP pair Hamiltonian must be supplemented with the direct interatomic (Heisenberg) exchange interaction to form a minimal model Hamiltonian of BMP molecule with the parallel alignment of the polaronic clouds in the lowest energy state. © 2013 Elsevier B.V. Source


Blasiak P.,Polish Academy of Sciences
New Journal of Physics | Year: 2015

We consider a typical realization of a qubit as a single particle in two-path interferometric circuits built from phase shifters, beam splitters and detectors. This framework is often taken as a standard example illustrating various paradoxes and quantum effects, including non-locality. In this paper we show that it is possible to simulate the behaviour of such circuits in a classical manner using stochastic gates and two kinds of particles, real ones and ghosts, which interact only locally. The model has built-in limited information gain and state disturbance in measurements which are blind to ghosts. We demonstrate that predictions of the model are operationally indistinguishable from the quantum case of a qubit, and allegedly 'non-local' effects arise only on the epistemic level of description by the agent whose knowledge is incomplete due to the restricted means of investigating the system. © 2015 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft. Source


Blasiak P.,Polish Academy of Sciences
Annals of Physics | Year: 2015

Contextuality lays at the heart of quantum mechanics. In the prevailing opinion it is considered as a signature of "quantumness" that classical theories lack. However, this assertion is only partially justified. Although contextuality is certainly true of quantum mechanics, it cannot be taken by itself as discriminating against classical theories. Here we consider a representative example of contextual behaviour, the so-called Mermin-Peres square, and present a discrete toy model of a bipartite system which reproduces the pattern of quantum predictions that leads to contradiction with the assumption of non-contextuality. This illustrates that quantum-like contextual effects have their analogues within classical models with epistemic constraints such as limited information gain and measurement disturbance. © 2014 Elsevier Inc.. Source


Sowinski T.,Polish Academy of Sciences
Few-Body Systems | Year: 2015

The ground-state properties of the two-flavored mixture of a few attractive fermions confined in a one-dimensional harmonic trap is studied. It is shown that for slightly imbalanced system the pairing between fermions of opposite spins has completely different features that in the balanced case. The fraction of correlated pairs is suppressed by the presence of additional particle and another uncorrelated two-body orbital dominates in the ground-state of the system. © 2015, Springer-Verlag Wien. Source


Pedrycz W.,University of Alberta | Pedrycz W.,Polish Academy of Sciences
Expert Systems with Applications | Year: 2010

Cognitive maps and fuzzy cognitive maps offer interesting and transparent modeling capabilities by functioning at a level of conceptual entities (nodes) and their relationships expressed either at the qualitative level of excitatory/inhibitory relationships or being further numerically quantified as encountered in fuzzy cognitive maps. While there has been a vast array of conceptual enhancements, a relatively less attention has been paid to the design of the maps especially when dealing with an algorithmic way of forming the map. The objective of this study is to offer a design strategy in which starting with experimental evidence in the form of numeric data, those data are transformed into a finite and small number of concepts (nodes) of the map and afterwards the connections of the map are estimated. We show that techniques of Granular Computing, especially fuzzy clustering are effectively used to form concepts (nodes) of well-articulated semantics. In the sequel, we show the use of global optimization in the form of Particle Swarm Optimization (PSO) to carry out calibration of the connections of the interrelationships between the nodes of the map. Numeric examples are concerned with the representation of time series and their visualization in the form of fuzzy cognitive maps. Further interpretation of the maps is also discussed. © 2010 Elsevier Ltd. All rights reserved. Source


Zuber K.,Polish Academy of Sciences | Singh B.,McMaster University
Nuclear Data Sheets | Year: 2015

The evaluated spectroscopic data are presented for known nuclides of mass 61 (Sc,Ti,V,Cr,Mn,Fe,Co,Ni, Cu,Zn,Ga,Ge). Excited-state data are nonexistent for 61Sc, 61Ti, 61V, and 61Ge. Significant amounts of new data have been added since the previous NDS evaluation of A=61 nuclides (1999Bh04). 61Sc nuclide is now experimentally known, but without any knowledge of its half-life. The ground state half-lives of 61Ti and 61V are now determined. Excited-state data have become available for 61Cr, 61Mn and 61Ga, while for 61Ge, five excited states were erroneously assigned in the previous evaluation, these have been omitted here. Improved and extensive high-spin excitations are available for 61Fe, 61Cu and 61Zn, including several new superdeformed structures in 61Cu and 61Zn. Thermal neutron capture γ-ray data are available in detail from 2004Ra23. The radioactive decay schemes of 61Sc and 61Ti are not known, while those for 61V, 61Fe and 61Ge are poorly known. This work benefited from the earlier full evaluations of A=61 published by 1999Bh04, 1983Ek01 and 1975Au05 and the one published in an 'update' mode by 1992Zh31. The data and conclusions presented in the current work supersede those in all the previous evaluations. © 2015 Elsevier Inc. Source


Moscicki T.,Polish Academy of Sciences
Physica Scripta | Year: 2014

Laser ablation of boron and tungsten is studied theoretically. The effect of disparate masses of boron and tungsten on parameters of the laser-ablated plasma plume is studied. A theoretical model is applied, which describes both the target heating and formation of the plasma and its expansion. Calculations are made for the third harmonic of a nanosecond Nd:YAG laser. The calculated distributions of plasma temperature, velocity and electron density in the early phase of expansion show that the plasma temperature is higher in the case of heavier tungsten, but the velocity is higher in the case of lighter boron, which is in agreement with experimental findings. In addition, the absorption coefficient of 355 nm radiation, the emission coefficient, the mass density and heat capacity of boron and tungsten plasma are compared. © 2014 The Royal Swedish Academy of Sciences. Source


Fischer F.D.,University of Leoben | Svoboda J.,Academy of Sciences of the Czech Republic | Petryk H.,Polish Academy of Sciences
Acta Materialia | Year: 2014

Mathematical and physical aspects of the applicability of the Onsager, Prigogine as well as the Glansdorff and Ziegler thermodynamic extremal principles (TEPs) to non-equilibrium thermodynamics are examined for systems at fixed temperature with respect to their ability to provide kinetic equations approved in materials science. TEPs represent an alternative to the classical phenomenological equations approach. As TEPs are, more or less, a pure mathematical tool, they cannot significantly contribute to a deeper physical understanding. However, if a system can be described by discrete characteristic (thermodynamic) parameters, it is demonstrated that application of Onsager's TEP or Ziegler's TEP represents a systematic way to derive a set of explicit evolution equations for these parameters. This approach can significantly simplify the treatment of the problem and, thus, can also be applied to rather complex systems, for which the classical approach, involving application of phenomenological equations, fails. The application of TEPs is demonstrated on plasticity with respect to constitutive equations as well as on grain growth and coarsening with respect to evolution equations of discrete parameters. No exploitation of Prigogine's TEP has been reported for applications in materials science. Contrarily, Prigogine's TEP can be invalidated if the coefficients of the dissipation function depend on the evolution of state variables with time. This is demonstrated by a further practical example worked out for the solute drag phenomenon. Glansdorff's and Prigogine's evolution criterion, however, is always fulfilled near the equilibrium state of convex Gibbs energy. Extensions of TEPs to non-linear non-equilibrium thermodynamics are demonstrated for homogeneous and quasi-homogeneous dissipation functions. © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. Source


Bozek P.,AGH University of Science and Technology | Broniowski W.,Polish Academy of Sciences | Broniowski W.,Jan Kochanowski University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

Collective flow and femtoscopy in ultrarelativistic 3He-Au collisions are investigated within the 3+1-dimensional (3+1D) viscous event-by-event hydrodynamics. We evaluate elliptic and triangular flow coefficients as functions of the transverse momentum. We find the typical long-range ridge structures in the two-particle correlations in the relative azimuth and pseudorapidity, in the pseudorapidity directions of both Au and 3He. We also make predictions for the pionic interferometric radii, which decrease with the transverse momentum of the pion pair. All features found hint on collectivity of the dynamics of the system formed in 3He-Au collisions, with hydrodynamics leading to quantitative agreement with the up-to-now released data. © 2015 The Authors. Source


Bialik R.J.,Polish Academy of Sciences
Journal of Hydrology and Hydromechanics | Year: 2013

The focus of this paper is on the analysis of the influence of near-bed turbulence structures with the inclusion of existing coherent structures on the entrainment of saltating particles in a water stream from the Lagrangian perspective. The interactions between turbulence structures and initiation of particles movement is the key for better understanding of the physics of sediment transport and particles behaviour. These aims are addressed by use of a 3D relevant model of spherical saltating particles, in which a special procedure has been designed to produce coherent structures. In this method, the spectra of turbulent kinetic energy, consisting of four ranges, are used to generate the time series of turbulent velocities in the streamwise, vertical and transversal directions. Numerical results suggest that the initiation of sediment movement is strongly correlated to positive streamwise velocity fluctuations and as such, supports earlier laboratory experimental and field observations, showing that the sweeps and outward interactions play a crucial role in the initiation of saltating particles' movement. Source


Diagnoses of the 68 described genera of Cochylini are provided along with redescriptions and comments where necessary. Platphalonidia is synonymized with Phalonidia, and Platphalonia Razowski, gen. n. is described. Source


Pawlowski J.,University of Geneva | Holzmann M.,University of Geneva | Tyszka J.,Polish Academy of Sciences
Marine Micropaleontology | Year: 2013

The limitations of a traditional morphology-based classification of Foraminifera have been demonstrated by molecular phylogenetic studies for several years now. Despite the accumulation of molecular data, no alternative higher-level taxonomic system incorporating these data has been proposed yet. Here, we present a new supraordinal classification of Foraminifera based on an updated SSU rDNA phylogeny completed with the description of major morphological trends in the evolution of this group. According to the new system, multi-chambered orders are grouped in two new classes: Tubothalamea and Globothalamea. Naked and single-chambered Foraminifera possessing agglutinated or organic-walled tests are arranged into a paraphyletic assemblage of "monothalamids". The new system maintains some multi-chambered calcareous orders, such as Rotaliida, Miliolida, Robertinida and Spirillinida, although their definitions have been modified in some cases to include agglutinated taxa. The representatives of the planktonic order Globigerinida are tentatively included in the order Rotaliida. The agglutinated Textulariida are probably paraphyletic. The position of the order Lagenida is uncertain because reliable molecular data are only available for one species. The new classification system separates orders or families, which differ in basic chamber shapes, prevailing mode of coiling and distance between successive apertures. It appears that these features correspond better to the main evolutionary trends in Foraminifera than wall composition and structure, both used in traditional classification. © 2013 Elsevier B.V. Source


The arctic-alpine Ranunculus glacialis s. l. is distributed in high-mountain ranges of temperate Europe and in the North, where it displays an extreme disjunction between the North Atlantic Arctic and Beringia. Based on comprehensive sampling and employing plastid and nuclear marker systems, we (i) test whether the European/Beringian disjunction correlates with the main evolutionary diversification, (ii) reconstruct the phylogeographic history in the Arctic and in temperate mountains and (iii) assess the susceptibility of arctic and mountain populations to climate change. Both data sets revealed several well-defined lineages, mostly with a coherent geographic distribution. The deepest evolutionary split did not coincide with the European/Beringian disjunction but occurred within the Alps. The Beringian lineage and North Atlantic Arctic populations, which reached their current distribution via rapid postglacial colonization, show connections to two divergent pools of Central European populations. Thus, immigration into the Arctic probably occurred at least twice. The presence of a rare cpDNA lineage related to Beringia in the Carpathians supports the role of these mountains as a stepping stone between temperate Europe and the non-European Arctic, and as an important area of high-mountain biodiversity. The temperate and arctic ranges presented contrasting phylogeographic histories: a largely static distribution in the former and rapid latitudinal spread in the latter. The persistence of ancient lineages with a strictly regional distribution suggests that the ability of R. glacialis to survive repeated climatic changes within southern mountain ranges is greater than what recently was predicted for alpine plants from climatic envelope modelling. © 2012 Blackwell Publishing Ltd. Source


Zwierzycki M.,Polish Academy of Sciences
Journal of Physics Condensed Matter | Year: 2014

The exceptionally high mobility of carriers in graphene is one of its defining characteristics, especially in view of potential applications. Therefore it is of both practical and fundamental importance to understand the mechanisms responsible for limiting the values of the mobility. The aim of the paper is to study theoretically one such mechanism, i.e. scattering on ripples. The transport properties of rippled graphene are studied using the single-band tight-binding model. Both the bond-length variation, corresponding to the vector potential in the effective mass picture, and the fluctuating scalar potential are included in the formalism. The samples are modeled as self-similar surfaces characterized by the roughness exponent, with values ranging from those typical for graphene on SiO2 to those seen for suspended samples. The range of calculated resistivities and mobilities overlaps with those from experiments. The results presented in this paper support the notion of rippling as one of the important factors limiting the mobility of carriers in graphene. © 2014 IOP Publishing Ltd. Source


Sztwiertnia K.,Polish Academy of Sciences
Materials Letters | Year: 2014

The inspiration for the writing of this letter was the paper of Hutchinson, 2012 [1]. He demonstrated and analyzed the mechanisms proposed to explain the development of the Cube={0 0 1}〈1 0 0 component during recrystallization and grain growth. The evolution of this component during the annealing of rolled fcc metals with medium to high stacking fault energy (SFE) was, for decades, the main test for the competing theories of oriented growth (OG) and oriented nucleation (ON). Some of the conclusions of Hutchinson, especially those concerning OG simulation, require further comment. In this paper, it is shown that the more realistic model (such as that cited by Hutchinson) strongly prefers the Cube and R-Brass={2 3 6}〈3 8 5 textures as developing for the materials with copper and brass type rolling textures, respectively. In contrast to his opinion about the OG simulation, the presented model does not predict components that are not found in actual textures. © 2014 Elsevier B.V. Source


Jablonski A.,Polish Academy of Sciences
Journal of Physics D: Applied Physics | Year: 2014

The development of analytical techniques based on measurements of electron elastic-backscattering probabilities stimulated an interest in the theoretical description of such phenomena. The most accurate and reliable theoretical models involve Monte Carlo (MC) simulations of electron trajectories in solids; however, this approach generally requires considerable computer effort. It has been shown that the performance of a modified analytical theory originally proposed by Oswald et al (1993 J. Electron Spectrosc. Relat. Phenom. 61 251), designated with the acronym OKGM, compares reasonably well with MC calculations. The MC data are usually underestimated by the OKGM model, and the mean percentage deviation, averaged over nine elements and five energies up to 5 keV, is equal to 8.8% for typical experimental configurations. However, the agreement between ratios of backscattering probabilities from MC simulations and the OKGM model agree much better due to the fact that underestimation of backscattering probability by the OMGM theory is partially cancelled. The percentage deviation between ratios from these theoretical models decreases to 3.14%. The OKGM model should then be useful for determining inelastic mean free paths (IMFPs) from measured elastic-peak intensities. The accuracy of the obtained IMFPs is comparable with IMFPs from MC simulations. © 2014 IOP Publishing Ltd. Source


Linker for activation of T cells (LAT) is a raft-associated, transmembrane adapter protein critical for T-cell development and function. LAT expression is transiently upregulated upon T-cell receptor (TCR) engagement, but molecular mechanisms conveying TCR signaling to enhanced LAT transcription are not fully understood. Here we found that a Jurkat subline J.CaM2, initially characterized as LAT deficient, conditionally re-expressed LAT upon the treatment with a protein kinase C activator, phorbol 12-myristate 13-acetate (PMA). We took advantage of the above observation for studying cis-elements and trans-acting factors contributing to the activation-induced expression of LAT. We identified a LAT gene region spanning nucleotide position −14 to +357 relative to the ATG start codon as containing novel cis-regulatory elements that were able to promote PMA-induced reporter transcription in the absence of the core LAT promoter. Interestingly, a point mutation in LAT intron 1, identified in J.CaM2 cells, downmodulated LAT promoter activity by 50%. Mithramycin A, a selective Sp1 DNA-binding inhibitor, abolished LAT expression upon PMA treatment as did calcium ionophore ionomycin (Iono) and valproic acid (VPA), widely used as an anti-epileptic drug. Our data introduce J.CaM2 cells as a model for dissecting drivers and blockers of activation induced expression of LAT.Genes and Immunity advance online publication, 9 June 2016; doi:10.1038/gene.2016.25. © 2016 Macmillan Publishers Limited Source


Jaskolski M.,Polish Academy of Sciences
Acta Crystallographica Section D: Biological Crystallography | Year: 2014

This letter identifies recent examples of misrepresentation of biological helical structures and expresses concern about the continuing indulgent attitude towards distortion of scientific facts. It also teaches a simple trick to distinguish right- from left-handedness. © 2014 International Union of Crystallography. Source


Jakobisiak M.,Medical University of Warsaw | Golab J.,Medical University of Warsaw | Golab J.,Polish Academy of Sciences | Lasek W.,Medical University of Warsaw
Cytokine and Growth Factor Reviews | Year: 2011

Interleukin 15 participates in the development of important immune antitumor mechanisms. It activates CD8+ T cells, natural killer (NK) cells, NK T cells, and can promote the formation of antitumor antibodies. IL-15 can also protect T effector cells from the action of T regulatory cells and reverse tolerance to tumor-associated antigens. In pre-clinical studies IL-15 has been found to demonstrate potentiated antitumor effects following pre-association with IL-15Rα, or when used in combination with chemotherapy, adoptive therapy, monoclonal antibodies, and tumor vaccines. Although a clinical trial based on application of IL-15 in tumor patients has already begun, it is important to be aware of its potential side effects, including induction of autoimmunity and promotion of proliferation, survival, and dissemination of some tumor cells. © 2011 Elsevier Ltd. Source


Gusakov M.E.,Saint Petersburg State Polytechnic University | Haensel P.,Polish Academy of Sciences | Kantor E.M.,RAS Ioffe Physical - Technical Institute
Monthly Notices of the Royal Astronomical Society | Year: 2014

Observations of massive (M ≈2.0 M⊙) neutron stars (NSs), PSRs J1614-2230 and J0348+0432, rule out most of the models of nucleon-hyperon matter employed in NS simulations. Here, we construct three possible models of nucleon-hyperon matter consistent with the existence of 2 M⊙ pulsars as well as with semi-empirical nuclear matter parameters at saturation, and semi-empirical hypernuclear data. Our aim is to calculate for these models all the parameters necessary for modelling dynamics of hyperon stars (such as equation of state, adiabatic indices, thermodynamic derivatives, relativistic entrainment matrix, etc.), making them available for a potential user. To this aim a general non-linear hadronic Lagrangian involving σωρφσ* meson fields, as well as quartic terms in vector-meson fields, is considered. A universal scheme for calculation of thel = 0, 1 Landau Fermi-liquid parameters and relativistic entrainment matrix is formulated in the mean-field approximation. Use of this scheme allow us to obtain numerical tables with the equation of state, Landau quasi-particle effective masses, adiabatic indices, the l = 0, 1 Landau Fermi-liquid parameters, and the relativistic entrainment matrix for the selected models of nucleon-hyperon matter. These data are available online and suitable for numerical implementation in computer codes modelling various dynamical processes in NSs, in particular, oscillations of superfluid NSs and their cooling. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society. Source


Ochrymiuk T.,Polish Academy of Sciences
Applied Thermal Engineering | Year: 2016

Aiming to increase engine efficiency, the trend of turbine entrance temperature is still towards higher levels. Since heat transfer experiments under realistic operating conditions are both costly and time consuming. To reduce the design cost and time a combined complementary numerical and experimental approach is more frequently used nowadays. To improve this procedure at the test facility for Rotating Cascades (RGG) at DLR wind tunnel measurements were carried out assisted by 3D numerical simulations applying TRACE a CFD code developed at DLR. After a successful validation of the numerical code this combination provides quantities which are very difficult or impossible to measure. With courtesy of MTU Aero Engines during the German research program E3E a high pressure turbine stage test rig was developed. At DLR this test rig was slightly modified to enable heat transfer measurements at the over-tip casing. A matrix of operating points was selected and filled up with numerical simulation results focusing on the over-tip casing region of the rotor. Aerodynamic characteristics as well as heat transfer parameters such as wall heat transfer coefficients were investigated. © 2016 Elsevier Ltd. All rights reserved. Source


Bentivegna E.,Max Planck Institute For Gravitationsphysik | Korzynski M.,Polish Academy of Sciences
Classical and Quantum Gravity | Year: 2013

We present the numerical evolution of a family of conformally-flat, infinite, expanding cubic black-hole lattices. We solve for the initial data using an initial-data prescription presented recently, along with a new multigrid solver developed for this purpose. We then apply the standard tools of numerical relativity to calculate the time development of this initial dataset and derive quantities of cosmological relevance, such as the scaling of proper lengths. Similarly to the case of S3 lattices, we find that the length scaling remains close to the analytical solution for Friedmann- Lemaître-Robertson-Walker cosmologies throughout our simulations, which span a window of about one order of magnitude in the growth of the scale factor. We highlight, however, a number of important departures from the Friedmann-Lemaître-Robertson-Walker class. © 2013 IOP Publishing Ltd. Source


Barnes E.,University of Maryland University College | Cywinski L.,Polish Academy of Sciences | Das Sarma S.,University of Maryland University College
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

The generalized master equation of Nakajima-Zwanzig (NZ) type has been used extensively to investigate the coherence dynamics of the central spin model with a nuclear bath in a narrowed state characterized by a well-defined value of the Overhauser field. We reconsider the perturbative NZ approach and apply it to the exactly solvable case of a system with uniform hyperfine couplings. This is motivated by the fact that the effective-Hamiltonian-based theory suggests that the dynamics of the realistic system at low magnetic fields and short times can be mapped onto the uniform coupling model. We show that the standard NZ approach fails to reproduce the exact solution of this model beyond very short times, while the effective-Hamiltonian calculation agrees very well with the exact result on time scales during which most of the coherence is lost. Our key finding is that, in order to extend the time scale of applicability of the NZ approach in this case, instead of using a single projection operator one has to use a set of correlated projection operators which properly reflect the symmetries of the problem and greatly improve the convergence of the theory. This suggests that the correlated projection operators are crucial for a proper description of narrowed-state free-induction decay at short times and low magnetic fields. Our results thus provide important insights toward the development of a more complete theory of central spin decoherence applicable in a broader regime of time scales and magnetic fields. © 2011 American Physical Society. Source


Paszko B.,Polish Academy of Sciences
Phytotaxa | Year: 2013

This paper presents a re-evaluation of the taxonomic and morphological relationships of Calamagrostis emodensis var. breviseta. Examination of morphological characters has shown that Calamagrostis emodensis var. breviseta was incorrectly linked with C. emodensis at the time of description, and indicates that it is conspecific with C. macrolepis. It is here reduced to a synonym of the latter species. © 2013 Magnolia Press. Source


Morawiec A.,Polish Academy of Sciences
Scripta Materialia | Year: 2011

A partial explanation of the phenomenon of abnormal growth of Goss-oriented grains in silicon steel is proposed. It follows from an observation that texture evolves toward Goss orientation if grains of low surface energy have a high probability of growth. A corresponding simulation starts with primary recrystallization texture and results in a strong Goss texture. To explain the development of early secondaries in subsurface layers, an option is considered that in addition to capillary forces, the growth is caused by surface-induced lattice instabilities. © 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. Source


Herman A.,Academy of Cosmetics and Health | Herman A.P.,Polish Academy of Sciences
Skin Pharmacology and Physiology | Year: 2013

Caffeine is being increasingly used in cosmetics due to its high biological activity and ability to penetrate the skin barrier. This alkaloid is frequently used as a hydrophilic model substance in human and animal skin penetration as well as different synthetic membrane using Franz diffusion cell experiments. The commercially available topical formulations of caffeine normally contain 3% caffeine. As for a cosmetic purpose, caffeine is used as an active compound in anti-cellulite products because it prevents excessive accumulation of fat in cells. This alkaloid stimulates the degradation of fats during lipolysis through inhibition of the phosphodiesterase activity. Caffeine has potent antioxidant properties. It helps protect cells against the UV radiation and slows down the process of photoaging of the skin. Moreover, caffeine contained in cosmetics increases the microcirculation of blood in the skin and also stimulates the growth of hair through inhibition of the 5-α-reductase activity. Copyright © 2012 S. Karger AG, Basel. Source


Zarzycki P.,Polish Academy of Sciences | Kerisit S.,Pacific Northwest National Laboratory | Rosso K.M.,Pacific Northwest National Laboratory
Journal of Physical Chemistry C | Year: 2015

We present classical molecular simulations of the adsorption free energy profiles for the aqueous Fe(II) ion approaching key low index crystal faces of goethite at neutral surface charge conditions. Calculated profiles show minima corresponding to stable outer- and inner-sphere adsorbed structures. We analyzed the energetics and kinetics of most possible interfacial electron transfer reactions, as well as analyzing the same for subsurface migration pathways of injected electrons through calculating the Marcus free energy surfaces. We conclude that inner-sphere Fe(II)-complex formation is required for the interfacial electron transfer to occur, but the energetic cost of moving from the outer-sphere to inner-sphere geometry may prevent electron injection at some faces. We also show that some surfaces, especially (101), (100) and (001), are more energetically prone toward reduction than others. We demonstrate that subsurface charge migration in directions parallel to the surface, which run along the iron chains, is more energetically plausible than conduction through the resistive crystal bulk phase. Collectively this leads to the conclusion that Fe(II)-catalyzed recrystallization of goethite most likely proceeds by short path length electron migration through specific goethite surfaces along specific directions, until capture at Fe sites structurally susceptible to reduction and release. © 2015 American Chemical Society. Source


Stecko S.,Polish Academy of Sciences
Journal of Organic Chemistry | Year: 2014

Total synthesis of anticonvulsant amino acid, lacosamide, is reported. The key step is stereospecific allyl cyanate-to-isocyanate rearrangement, which proceeds with chirality transfer. The enantiopure starting material for the rearrangement step was accessed from ethyl l-lactate. © 2014 American Chemical Society. Source


Zmihorski M.,Polish Academy of Sciences
Biodiversity and Conservation | Year: 2010

This study aimed to evaluate the impact of windthrow and two types of its management on the bird community of a managed, pine-dominated forest (NE Poland), where a windstorm event occurred in 2002. In 2007, the bird species composition was assessed using the point count method in three types of habitat: windthrow left undisturbed for natural regeneration, managed windthrow (all fallen trees removed), and intact forest (undisturbed by the windstorm, used as the control). In total, 2,365 individual birds of 70 species were recorded in the three analyzed habitats. The mean number of individuals per point and species per point was significantly higher in the natural windthrow than in the two other habitats. The diversity of the bird community was higher in the natural and managed windthrow, as compared to the control. The bird community of the control was significantly more similar to that of the natural windthrow than to the one in the managed windthrow. These results lead to a conclusion that the bird community was affected more by the clearing and artificial replanting following the windthrow than by the windthrow itself. © 2010 Springer Science+Business Media B.V. Source


Ligeza P.,Polish Academy of Sciences
IEEE Transactions on Instrumentation and Measurement | Year: 2014

The main drawback of standard hot-wire anemometric methods consists of the difficulty in their employment and a considerable measurement uncertainty in the case of flows in which high-amplitude fluctuations of temperature or other physical quantities occur. It is caused by the interaction between these fluctuations and measurement signal. In this paper, we propose a method for the determination of 2-or 3-D velocity vector of fluids flow or gases based on the employment of several detectors of fluctuations of temperature, velocity, or other physical quantity propagating with the velocity equal to the velocity of flow of the medium or higher by a known value. By analyzing the signals obtained by the detectors, the times of flight required for flat isophase surface of fluctuation to travel between the detectors in the direction of velocity vector are determined. On their basis, the flow velocity vector is calculated using the system of equations of motion of flat isophase surface of fluctuation. In this paper, we present an idea of this measurement method, developed sensor and measurement system, algorithm for signal processing, examples of measurement signals, and we also show the potential area of applicability. Considering the fact that the proposed measurement method is based on measurement of the path and time of flight of a fluctuation, the system implements an absolute measurement of velocity vector and does not require any calibration to be carried out in the flow of known parameters. In addition, the measurement is insensitive to the change in the parameters of the flowing medium. © 2013 IEEE. Source


Capsule The number of territories of birds nesting in abandoned crop fields was most strongly positively affected by field size and the presence of a railway embankment. Aims To assess the influence of different habitat features on the number of birds nesting in abandoned crop fields. Methods A breeding bird survey was conducted in spring 2002 using the mapping method on 67 abandoned fields located in southwest Poland. The associations between eight habitat features of the abandoned fields and the numbers of particular species and groups of birds, as well as the whole bird community, were tested with a GLM. Results The models for eight individual species revealed the following ranking, in terms of number of species affected by each predictor: area of fields (5), railway embankments and adjacent crop fields (4), roads and power lines (2), and number of trees (1). The number of the most numerous group of birds (species nesting on the ground, 79% of all breeding pairs) was affected by four predictors: field area, railway embankments, power lines and roads. The number of all birds was affected by six predictors: field area, railway embankments, power lines, roads, ditches and trees. Conclusion Limited effects of trees, hedgerows and ditches on the number of territories suggest that abandoned fields without woody vegetation are attractive breeding habitats for many farmland birds. One of the effective ways of protecting farmland bird species in central Europe may be the preservation of abandoned fields in their present form, especially those <5 ha in area. © 2010 British Trust for Ornithology. Source


Nowakowski B.,Polish Academy of Sciences
Nonlinear Analysis: Real World Applications | Year: 2013

In this paper we investigate the existence of the H1-uniform attractor and long-time behavior of solutions to non-autonomous micropolar fluid equations in three dimensional cylindrical domains. In our considerations we take into account that the existence of global and strong solutions is proved under the assumption on smallness of change of the initial and the external data along the axis of the cylinder. Therefore, we refine the concept of the uniform attractor by adopting the idea which was proposed by J.W. Cholewa and T. Dłotko (1998) in [9]. © 2013 Elsevier Ltd. All rights reserved. Source


Gozdz W.T.,Polish Academy of Sciences
Langmuir | Year: 2015

The nanoparticles built of bicontinuos lyotropic phases of cubic symmetry are studied within the framework of the Landau-Brazovskii functional that correctly predicts the structure of soft monocrystals and thin films of bicontinuos lyotropic phases. A detailed description of the geometry and topology of cubosomes is presented. This level of description of the internal structure of cubosomes is not easily accessible by experimental techniques. I show that the internal structure of the cubosomes may be extremely rich. © 2015 American Chemical Society. Source


Nowakowski B.,Polish Academy of Sciences
Nonlinear Analysis: Real World Applications | Year: 2013

We examine the so-called micropolar equations in three dimensional cylindrical domains under Navier boundary conditions. These equations form a generalization of the ordinary incompressible Navier-Stokes model, taking the structure of the fluid into account. We prove that under certain smallness assumption on the rate of change of the initial data and the external data there exists a unique and strong solution for any finite time T. © 2012 Published by Elsevier Ltd. Source


Karbowski J.,Polish Academy of Sciences
PLoS ONE | Year: 2012

During mammalian development the cerebral metabolic rate correlates qualitatively with synaptogenesis, and both often exhibit bimodal temporal profiles. Despite these non-monotonic dependencies, it is found based on empirical data for different mammals that regional metabolic rate per synapse is approximately conserved from birth to adulthood for a given species (with a slight deviation from this constancy for human visual and temporal cortices during adolescence). A typical synapse uses about (7±2).10 3glucose molecules per second in primate cerebral cortex, and about five times of that amount in cat and rat visual cortices. A theoretical model for brain metabolic expenditure is used to estimate synaptic signaling and neural spiking activity during development. It is found that synaptic efficacy is generally inversely correlated with average firing rate, and, additionally, synapses consume a bulk of metabolic energy, roughly 50-90% during most of the developmental process (except human temporal cortex <50%. Overall, these results suggest a tight regulation of brain electrical and chemical activities during the formation and consolidation of neural connections. This presumably reflects strong energetic constraints on brain development. © 2012 Jan Karbowski. Source


Demiaszkiewicz A.W.,Polish Academy of Sciences
Annals of parasitology | Year: 2012

The present study was conducted on 31 males and females of the European bison, eliminated during the winter seasons 2007-2011 in the Białowieza Primeval Forest, Poland. The caeca of 14 free-ranging bison, aged from 3 months up to 16 years, the most favorable infection site for the large intestine nematodes, were investigated during the winter of 2007/2008. The parasitological autopsies of the large intestines of 9 free-ranging bison aged from 5 months up to 10 years as well as 9 bison kept in the close reserves aged from one up to 20 years were done during the winter seasons of 2008-2011 to determine localization of nematodes in large intestine and the total intensity of parasite infection. Five species of nematodes (i.e., Trichuris ovis, Oesophagostomum venulosum, O. radiatum, Ashworthius sidemi, Nematodirus helvetianus) were found in dissected caecum of bison culled during the winter of 2007/2008. During the seasons of 2008-2010, 6 species of nematodes were found in the large intestine of bison (i.e., T. ovis, O. venulosum, O. radiatum, A. sidemi, N. roscidus and Bunostomum trigonocephalum). We did not find any nematodes in the lumen of the large intestine of captive bison culled during the seasons of 2010/2011. The results of the present study indicate that the intensity of infection by the large intestine nematodes of the European bison in the Białowieza Primeval Forest has stayed at the comparable level throughout the last 20 years; however the number of nematode species has increased. The observed level of parasitic infection is typical of subclinical parasitoses. Source


Rosspeintner A.,University of Geneva | Angulo G.,Polish Academy of Sciences | Vauthey E.,University of Geneva
Journal of the American Chemical Society | Year: 2014

To access the intrinsic, diffusion free, rate constant of bimolecular photoinduced electron transfer reactions, fluorescence quenching experiments have been performed with 14 donor/acceptor pairs, covering a driving-force range going from 0.6 to 2.4 eV, using steady-state and femtosecond time-resolved emission, and applying a diffusion-reaction model that accounts for the static and transient stages of the quenching for the analysis. The intrinsic electron transfer rate constants are up to 2 orders of magnitude larger than the diffusion rate constant in acetonitrile. Above ∼1.5 eV, a slight decrease of the rate constant is observed, pointing to a much weaker Marcus inverted region than those reported for other types of electron transfer reactions, such as charge recombination. Despite this, the driving force dependence can be rationalized in terms of Marcus theory. © 2014 American Chemical Society. Source


Dmowski W.,Polish Academy of Sciences
Journal of Fluorine Chemistry | Year: 2012

This review provides an overview of several synthetic applications of 1,2-dibromotetrafluoroethane leading to convenient preparation of numerous fluorine compounds containing -CF 2CF 2- moiety via ionic and free radical reactions. © 2012 Elsevier B.V. Source


Bardyszewski W.,University of Warsaw | Lepkowski S.P.,Polish Academy of Sciences
Physical Review B - Condensed Matter and Materials Physics | Year: 2014

We present a theoretical description of excitonic spectra in GaN-based quantum wells in a wide range of magnetic fields taking into account built-in strain and electric fields, and valence band mixing due to the quantum well confinement. Our calculations performed for the GaN/AlGaN quantum wells reveal a nonlinear behavior of the excitonic Zeeman splitting on magnetic field. We have determined that the low magnetic field g-factor dependence on the quantum well width shows a steplike variation due to the reordering of the light- and heavy-hole valence subbands. Sharp change of the g factor is also predicted for InGaN/GaN quantum wells grown on a virtual metamorphic InGaN substrate. © 2014 American Physical Society. Source


Rosspeintner A.,University of Geneva | Koch M.,University of Geneva | Angulo G.,Polish Academy of Sciences | Vauthey E.,University of Geneva
Journal of the American Chemical Society | Year: 2012

The effect of viscosity on the bimolecular electron transfer quenching of a series of coumarins by N,N-dimethylaniline was investigated using steady-state and time-resolved fluorescence spectroscopy. The data reveal that the static and transient stages of the quenching become dominant as viscosity increases. When extracting the quenching rate constants using a simple Stern-Volmer analysis, a decrease of the rate constant with increasing driving force is observed above ∼2 cP. However, this apparent Marcus inverted region, already reported several times with the same system in micelles and room temperature ionic liquids, totally vanishes when analyzing the data with a model accounting for the static and transient stages of the quenching. It appears that the apparent Marcus inverted region arises from the neglect of these quenching regimes together with the use of fluorophores with different excited-state lifetimes. © 2012 American Chemical Society. Source


Bieniasz L.K.,Polish Academy of Sciences
Journal of Electroanalytical Chemistry | Year: 2013

Digital simulation of transient experiments at channel and tubular electrodes can be performed approximately but relatively cheaply, by means of the integral equation based approach introduced by Singh and Dutt [J. Electroanal. Chem. 182 (1985) 259]. Unfortunately, the use of the series expansion for the relevant integral transformation kernel, suggested by Singh and Dutt, makes such calculations overly slow. A new series expansion is proposed in the present study, which, when combined with the former expansion, yields inexpensive approximations to the kernel and its moment integrals. The relative error of these approximations is at the level of 10-16. The approximations are incorporated into the adaptive Huber method, developed by the present author. The method is shown to provide automatic solutions to the representative integral equations describing chronoamperometry for irreversible charge transfer and cyclic voltammetry for irreversible and reversible charge transfer. Desired accuracy of the solutions is selected simply by specifying a value of the error tolerance parameter. Errors corresponding to the range from about 10-2 of the maximum solution value, down to about 10 -7 or even smaller, can be easily obtained at a modest computational cost. © 2013 Elsevier B.V. All rights reserved. Source


Bieniasz L.K.,Polish Academy of Sciences
Journal of Electroanalytical Chemistry | Year: 2013

Diffusion of reactants inside spherical spatial domains, in the absence of homogeneous reactions, is characteristic of some electrochemical systems, such as amalgam mercury drop electrodes. Simulation of transient experiments in such systems can be performed by the classical integral equation method [see, for example, R.S. Nicholson, I. Shain, Anal. Chem. 36 (1964) 706]. This requires an accurate computation of a specific integral transformation kernel function and its moment integrals. Based on formerly known series expansions, highly accurate (16 digits) and cost-optimised procedures serving for this purpose have been designed in this work. The procedures have been combined with the adaptive Huber method developed by the present author. The resulting simulation technique has been tested on simple examples of relevant integral equations, including models of potential step chronoamperometry and cyclic voltammetry. The method is shown to provide automatic solutions, with a user-selected target accuracy. Errors corresponding to the range from about 10-2 of the maximum solution value, down to about 10-7 or even smaller, can be easily obtained at a modest computational cost. © 2013 Elsevier B.V. All rights reserved. Source


Zoladz J.A.,University School of Physical Education in Cracow | Pilc A.,Polish Academy of Sciences
Journal of Physiology and Pharmacology | Year: 2010

It is well documented that physical activity can induce a number of various stimuli which are able to enhance the strength and endurance performance of muscles. Moreover, regular physical activity can preserve or delay the appearance of several metabolic disorders in the human body. Physical exercise is also known to enhance the mood and cognitive functions of active people, although the physiological backgrounds of these effects remain unclear. In recent years, since the pioneering study in the past showed that physical activity increases the expression of the brain derived neurothophic factor (BDNF) in the rat brain, a number of studies were undertaken in order to establish the link between that neurothrophin and post-exercise enhancement of mood and cognitive functions in humans. It was recently demonstrated that physical exercise can increase plasma and/or serum BDNF concentration in humans. It was also reported that physical exercise or electrical stimulation can increase the BDNF expression in the skeletal muscles. In the present review, we report the current state of research concerning the effect of a single bout of exercise and training on the BDNF expression in the brain, in both the working muscles as well as on its concentrations in the blood. We have concluded that there may be potential benefits of the exercise-induced enhancement of the BDNF expression and release in the brain as well as in the peripheral tissues, resulting in the improvement of the functioning of the body, although this effect, especially in humans, requires more research. Source


We demonstrate a technique for controlling the content of multiple microdroplets in time. We use this system to rapidly and quantiatively determine the solubility diagrams of two model proteins (lysozyme and ribonuclease A). Source


Biosynthesis of antimicrobial secondary metabolites in response to microbial infection is one of the features of the plant immune system. Particular classes of plant secondary metabolites involved in plant defence are often produced only by species belonging to certain phylogenetic clades. Brassicaceae plants have evolved the ability to synthesise a wide range of sulfur-containing secondary metabolites, including glucosinolates and indole-type phytoalexins. A subset of these compounds is produced by the model plant Arabidopsis thaliana. Genetic tools available for this species enabled verification of immune functions of glucosinolates and camalexin (A. thaliana phytoalexin), as well as characterisation of their respective biosynthetic pathways. Current knowledge of the biosynthesis of Brassicaceae sulfur-containing metabolites suggests that the key event in the evolution of these compounds is the acquisition of biochemical mechanisms originating from detoxification pathways into secondary metabolite biosynthesis. Moreover, it is likely that glucosinolates and Brassicaceae phytoalexins, traditionally considered as separate groups of compounds, have a common evolutionary origin and are interconnected on the biosynthetic level. This suggests that the diversity of Brassicaceae sulfur-containing phytochemicals reflect phylogenetic clade-specific branches of an ancient biosynthetic pathway. Plant protection: Glucosinolates and indole-type phytoalexins constitute a highly diversified group of sulfur-containing secondary metabolites from Brassicaceae with multiple functions in plant-environment interactions. Recent studies delivered evidence for the function of these compounds in plant immunity and shed light on the evolution of their biosynthesis. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source


Prokop P.,Polish Academy of Sciences | Poreba G.J.,Silesian University of Technology
Land Degradation and Development | Year: 2012

Rapid increase in population and growing demand for agricultural products has generated changes in land use and upland farming systems and resulted in erosion and land degradation over large tracts of northeast India. The spatial variation of soil erosion rates was studied, in a small catchment under a modified form of shifting cultivation on the hilly Meghalaya Plateau, using the 137Cs technique. Soil erosion and deposition patterns are much influenced by land use. The estimated annual soil loss from cultivated fields ranged from 32 to 79Mgha-1y-1 and reached only 0·5Mgha-1y-1 from degraded grassland. Calculated soil erosion rates from cultivated fields exceed that which can be produced by weathering of new soil from parent materials. Observed intensification of agricultural production will lead to progressive conversion of cultivated fields into degraded grasslands and other changes to land use in the upper part of the Meghalaya Plateau. © 2012 John Wiley & Sons, Ltd. Source


Karpinski S.,Warsaw University of Life Sciences | Szechynska-Hebda M.,Warsaw University of Life Sciences | Szechynska-Hebda M.,Polish Academy of Sciences | Wituszynska W.,Warsaw University of Life Sciences | Burdiak P.,Warsaw University of Life Sciences
Plant, Cell and Environment | Year: 2013

This review confronts the classical view of plant immune defence and light acclimation with recently published data. Earlier findings have linked plant immune defences to nucleotide-binding site leucine-rich repeat (NBS-LRR)-dependent recognition of pathogen effectors and to the role of plasma membrane-localized NADPH-dependent oxidoreductase (AtRbohD), reactive oxygen species (ROS) and salicylic acid (SA). However, recent results suggest that plant immune defence also depends on the absorption of excessive light energy and photorespiration. Rapid changes in light intensity and quality often cause the absorption of energy, which is in excess of that required for photosynthesis. Such excessive light energy is considered to be a factor triggering photoinhibition and disturbance in ROS/hormonal homeostasis, which leads to cell death in foliar tissues. We highlight here the tight crosstalk between ROS- and SA-dependent pathways leading to light acclimation, and defence responses leading to pathogen resistance. We also show that LESION SIMULATING DISEASE 1 (LSD1) regulates and integrates these processes. Moreover, we discuss the role of plastid-nucleus signal transduction, photorespiration, photoelectrochemical signalling and 'light memory' in the regulation of acclimation and immune defence responses. All of these results suggest that plants have evolved a genetic system that simultaneously regulates systemic acquired resistance (SAR), cell death and systemic acquired acclimation (SAA). © 2012 Blackwell Publishing Ltd. Source


Medvedev N.,German Electron Synchrotron | Jeschke H.O.,Goethe University Frankfurt | Ziaja B.,German Electron Synchrotron | Ziaja B.,Polish Academy of Sciences
New Journal of Physics | Year: 2013

In this paper, we present a novel theoretical approach, which allows the study of nonequilibrium dynamics of both electrons and atoms/ions within free-electron laser excited semiconductors at femtosecond time scales. The approach consists of the Monte-Carlo method treating photoabsorption, high-energy-electron and core-hole kinetics and relaxation processes. Low-energy electrons localized within the valence and conduction bands of the target are treated with a temperature equation, including source terms, defined by the exchange of energy and particles with high-energy electrons and atoms. We follow the atomic motion with the molecular dynamics method on the changing potential energy surface. The changes of the potential energy surface and of the electron band structure are calculated at each time step with the help of the tight-binding method. Such a combination of methods enables investigation of nonequilibrium structural changes within materials under extreme ultraviolet (XUV) femtosecond irradiation. Our analysis performed for diamond irradiated with an XUV femtosecond laser pulse predicts for the first time in this wavelength regime the nonthermal phase transition from diamond to graphite. Similar to the case of visible light irradiation, this transition takes place within a few tens of femtoseconds and is caused by changes of the interatomic potential induced by ultrafast electronic excitations. It thus occurs well before the heating stimulated by electron-phonon coupling starts to play a role. This allows us to conclude that this transition is nonthermal and represents a general mechanism of the response of solids to ultrafast electron excitations. © IOP Publishing and Deutsche Physikalische Gesellschaft. Source


Szewczyk B.,Polish Academy of Sciences
Frontiers in Aging Neuroscience | Year: 2013

Zinc is an essential trace element, whose importance to the function of the central nervous system (CNS) is increasingly being appreciated. Alterations in zinc dyshomeostasis has been suggested as a key factor in the development of several neuropsychiatric disorders. In the CNS, zinc occurs in two forms: the first being tightly bound to proteins and, secondly, the free, cytoplasmic, or extracellular form found in presynaptic vesicles. Under normal conditions, zinc released from the synaptic vesicles modulates both ionotropic and metabotropic post-synaptic receptors. While under clinical conditions such as traumatic brain injury, stroke or epilepsy, the excess influx of zinc into neurons has been found to result in neurotoxicity and damage to postsynaptic neurons. On the other hand, a growing body of evidence suggests that a deficiency, rather than an excess, of zinc leads to an increased risk for the development of neurological disorders. Indeed, zinc deficiency has been shown to affect neurogenesis and increase neuronal apoptosis, which can lead to learning and memory deficits. Altered zinc homeostasis is also suggested as a risk factor for depression, Alzheimer's disease (AD), aging, and other neurodegenerative disorders. Under normal CNS physiology, homeostatic controls are put in place to avoid the accumulation of excess zinc or its deficiency. This cellular zinc homeostasis results from the actions of a coordinated regulation effected by different proteins involved in the uptake, excretion and intracellular storage/trafficking of zinc. These proteins include membranous transporters (ZnT and Zip) and metallothioneins (MT) which control intracellular zinc levels. Interestingly, alterations in ZnT and MT have been recently reported in both aging and AD. This paper provides an overview of both clinical and experimental evidence that implicates a dysfunction in zinc homeostasis in the pathophysiology of depression, AD, and aging. © 2013 Szewczyk. Source


Meissner M.,Polish Academy of Sciences
Acta Physica Polonica A | Year: 2010

In the present study, the acoustic characteristics of coupled rooms were investigated using the computer modelling application based on the modal expansion method. A numerical procedure enables the computation of shape and frequency of eigenmodes, and allows one to predict sound decay times at any point of a room space. Results of numerical simulation have shown that along with a change in a coupling area the effect of a mode degeneration appeared and there are two main reasons for this. First, a mode degeneration is associated with a convergence of frequencies of neighbouring modes with a decrease of coupling area. Another reason for the mode degeneration are variations in a sequence of modes with a change in the coupling area. It was demonstrated that in the coupled rooms several modes exhibit a considerable localization. A degree of mode localization was described theoretically by the "existence surface" of mode and it was found that the localization phenomenon has a great effect on the reverberation process because for some absorbing material distributions it caused the double-slope decay characterized by steep initial and slow late sound decays. Source


Milkowski M.,Polish Academy of Sciences
Software - Practice and Experience | Year: 2010

In this paper, we show how an open-source, language-independent proofreading tool has been built. Many languages lack contextual proofreading tools; for many others, only partial solutions are available. Using existing, largely language-independent tools and collaborative processes it is possible to develop a practical style and grammar checker and to fight the digital divide in countries where commercial linguistic application software is unavailable or too expensive for average users. The described solution depends on relatively easily available language resources and does not require a fully formalized grammar nor a deep parser, yet it can detect many frequent context-dependent spelling mistakes, as well as grammatical, punctuation, usage, and stylistic errors. Copyright © 2010 John Wiley & Sons, Ltd. Source


Simple statistical formulas for estimating various biogeochemical properties of suspended particulate matter in the southern Baltic Sea are presented in this paper. These include formulas for estimating mass concentrations of suspended particulate matter (SPM), particulate organic matter (POM), particulate organic carbon (POC) and total chlorophyll a (Chl a). Two different approaches have been adopted. The first approach was to use the available empirical material (the results of field measurements and laboratory analyses of discrete water samples) and find statistical formulas for estimating the biogeochemical properties of suspended particulate matter from those of inherent optical properties (IOPs), which are potentially retrievable from remote sensing measurements. The second approach was to find formulas that would enable biogeochemical properties of suspended particulate matter to be estimated directly from spectral values of the remotesensing reflectance Rrs. The latter was based on statistical analyses of a synthetic data set of Rrs obtained from numerical simulations of radiative transfer for which the available empirical material on seawater IOPs and biogeochemistry served as input data. Among the empirical formulas based on seawater IOPs that could be used as a step in two-stage remote sensing algorithms (the other step is estimating certain IOPs from reflectance), the best error statistics are found for estimates of SPM and POM from the particulate backscattering coefficient bbp in the blue region of light wavelengths (443 nm), and for estimates of POC and Chl a from the coefficient of light absorption by the sum of all non-water (i.e. suspended and dissolved) constituents of seawater an, in the blue (443 nm) and green (555 nm) parts of the spectrum respectively. For the semi-empirical formulas under consideration, which could serve as starting points in the development of local onestage (direct) remote sensing algorithms, the best error statistics are found when SPM, POM and POC are estimated from the same blue-to-red band reflectance ratio (R rs(490)/Rrs(645)(with estimated SPM reaching a better precision than estimated POM and POC), and when Chl a is estimated from the green-to-red band ratio (Rrs(555)/Rrs(645)). © Polish Academy of Sciences, Institute of Oceanology, 2014. Source


Senatorski P.,Polish Academy of Sciences
Geophysical Research Letters | Year: 2014

Radiated seismic energy is expressed in terms of slip velocities by using an overdamped dynamics approximation. This formulation is used to estimate the radiated energy from earthquake finite-fault models. A correction term is found to show that the approximation underestimates the radiated energy as defined by the full dynamics. The accuracy of the overdamped dynamics solution depends on the rupture history. Two dislocational earthquake models illustrate the dependence of the correction term on the rupture speed and slipping area size. The radiated seismic energies estimated from the finite-fault models and from seismic waves are compared for real-world earthquakes. The results are consistent in most cases. Discrepancies between two estimates suggest that both the finite-fault models and energy estimations from teleseismic data should be revised. © 2014. American Geophysical Union. All Rights Reserved. Source


Piskorz T.K.,University of Warsaw | Ochab-Marcinek A.,Polish Academy of Sciences
Journal of Physical Chemistry B | Year: 2014

Fluorescence correlation spectroscopy (FCS) is frequently used to study the processes of restricted diffusion. The most important quantity to determine is the size of the structures that hinder the Brownian motion of the molecules. We study three qualitatively different models of restricted diffusion, widely applied in biophysics and material science: Diffusion constrained by elastic force (i), walking confined diffusion (ii), and hop diffusion (iii). They cover the diversity of statistical behaviors, from purely Gaussian (i) to sharply non-Gaussian on intermediate time scales (ii) and, additionally, discrete (iii). We test whether one can use the Gaussian approximation of the FCS autocorrelation function to interpret the non-Gaussian data. We show that (i-iii) have approximately the same mean square displacements. Using simulations, we show that the FCS data suspected of restricted diffusion can be reliably interpreted using one archetypal model (i). Even if the underlying mechanism of the restriction is different or unknown, the accuracy of fitting the confinement size is excellent, and diffusion coefficients are also estimated with a good accuracy. This study gives a physical insight into the statistical behavior of different types of restricted diffusion and into the ability of fluorescence correlation spectroscopy to distinguish between them. © 2014 American Chemical Society. Source


Taleb A.,Chimie Paristech | Stafiej J.,Polish Academy of Sciences
Corrosion Science | Year: 2011

This work reports on the numerical simulation results of the grain size effect on the corrosion processes using a cellular automata model. The material considered consists of domains and their edges. The domains represent the monocrystalline cores while their edges represent the intergranular defects. Either a periodic pattern or randomly generated domains of Voronoï tessellation are used. The model parameters, taking into account the polycrystalline aspect of corrosion, are the domain density and the corrosion probabilities of metal grain core and grain boundary sites. The corrosion probability for grain edge is taken as higher than for the grain core. A complicated surface structure appears with a high geometrical roughness if the density of defects is not too high. A strong correlation between the roughness evolution, the metal crystalline properties and the corrosion mechanism of the metal dissolution was established. © 2011 Elsevier Ltd. Source


Mege D.,CNRS Nantes Laboratory of Planetology and Geodynamics | Mege D.,Polish Academy of Sciences | Bourgeois O.,CNRS Nantes Laboratory of Planetology and Geodynamics
Earth and Planetary Science Letters | Year: 2011

Martian global climate models that account for evidence of past glaciations reported in tropical to mid-latitude regions of Mars predict accumulation of water ice in Valles Marineris during past periods of high obliquity. Observational evidence for such glaciations is given here. Topographic basement ridges of tectonic origin are common in Valles Marineris, and display sackung features, an assemblage of tectonic patterns that are diagnostic of deep-seated gravitational slope deformation. This deformation is most easily explained by paraglacial ridge failure subsequent to ridge wall debuttressing and decohesion following the retreat of glaciers. This interpretation is supported by extensive bibliographic analysis of sackung triggers on Earth, by morphological evidence of subglacial erosion of the lower parts of Valles Marineris wallslopes, of periglacial erosion of their upper parts and by the presence of various types of glacial landforms on the floors of Valles Marineris troughs. The age of these equatorial glaciations is found to be older than 1.4. Gy and younger than 3.5. Gy. © 2011 Elsevier B.V. Source


Piotrowski A.P.,Polish Academy of Sciences
Information Sciences | Year: 2015

Novel Evolutionary Algorithms are usually tested on sets of artificially-constructed benchmark problems. Such problems are often created to make the search of one global extremum (usually minimum) tricky. In this paper it is shown that benchmarking heuristics on either minimization or maximization of the same set of artificially-created functions (with equal bounds and number of allowed function calls) may lead to very different ranking of tested algorithms. As Evolutionary Algorithms and other heuristic optimizers are developed in order to be applicable to real-world problems, such result may raise doubts on the practical meaning of benchmarking them on artificial functions, as there is little reason that searching for the minimum of such functions should be more important than searching for their maximum. Thirty optimization heuristics, including a number of variants of Differential Evolution, as well as other kinds of Evolutionary Algorithms, Particle Swarm Optimization, Direct Search methods and-following the idea borrowed from No Free Lunch-pure random search are tested in the paper. Some discussion regarding the choice of the mean or the median performance for comparison is addressed and a short debate on the overall performance of particular methods is given. © 2014 Elsevier Inc. All rights reserved. Source


Danicki E.J.,Polish Academy of Sciences
Wave Motion | Year: 2010

An elastic body with periodic teeth of finite height (a comb), insonified by incident ultrasonic wave and applied, with sliding contact, to the surface of another elastic body (a substrate), constitutes a typical arrangement of ultrasonic nondestructive testing system exploiting comb transducers. The arising scattering problem of incident wave on periodic voids between the teeth and the sliding teeth-substrate contact is considered in the full-wave formulation. In physical interpretation, the vibrating teeth generate surface Rayleigh wave in the substrate by the incident wave pressure exerted on the substrate. In fact, the interface waves are generated which differ from the Rayleigh wave in both the propagation velocity and the wave-mode shape. These interface waves, their velocity and modal shape are the main subject of this paper; an approximated formula is presented for the relation between the most important Bloch components of interface modes in the considered periodic system. © 2010 Elsevier B.V. Source


Broniowski W.,Polish Academy of Sciences | Rybczynski M.,Jan Kochanowski University
Physical Review C - Nuclear Physics | Year: 2010

We investigate the influence of the central two-body nucleon-nucleon correlations on several quantities observed in relativistic heavy-ion collisions. It is demonstrated with explicit Monte Carlo simulations that the basic correlation measures observed in relativistic heavy-ion collisions, such as the fluctuations of participant eccentricity, initial size fluctuations, or the fluctuations of the number of sources producing particles, are all sensitive to the inclusion of the two-body correlations. The effect is at the level of about 10-20%. Moreover, the realistic (Gaussian) correlation function gives indistinguishable results from the hard-core repulsion, with the expulsion distance set to 0.9fm. Thus, we verify that for investigations of the considered correlation measures, it is sufficient to use the Monte Carlo generators accounting for the hard-core repulsion. © 2010 The American Physical Society. Source


The article concentrates on the changes of ownership ongoing in Polish agriculture in the period 1989-2004. Since Polish agriculture was above all private in nature throughout the period of communism, the changes in question were actually more limited than in other Central and East European Countries (CEEC). Those that have taken place have first and foremost involved the privatisation of the old State Farms, whose assets were taken over by individually-owned farms or commercial-law companies, with the intermediation of the Treasury Agricultural Property Agency established for the purpose. A major element of the assets undergoing privatisation was agricultural land. The size of the ownership change has varied from region to region. In the West and North, where more than half of all farmland was in the State Farm hands to 1989, there was a marked increase in the share of land under private ownership. On the other hand, in Central and Eastern Poland, the changes were very limited, concerning only the transfer of land between private farms. Important reasons accounting for the limited activity on the market for land in this part of Poland include the agrarian overpopulation and the widespread treatment of land as a form of the "insurance policy" against job losses. The ownership changes have further encouraged polarisation where farm size structure is concerned. Farms increased in size in the regions where the large average area has long been a typical feature. In turn, the areas characterised by the excessive agrarian fragmentation have not seen any more major changes in the size structure over the recent period. A detailed analysis of the changes in ownership over the market economy period is preceded by a discussion of the history of land ownership in Polish agriculture, with a particular emphasis being placed on the Communist era. The legal and social bases conditioning ownership change are also discussed. Source


Liepe J.,Imperial College London | Filippi S.,Imperial College London | Komorowski M.,Polish Academy of Sciences | Stumpf M.P.H.,Imperial College London
PLoS Computational Biology | Year: 2013

Our understanding of most biological systems is in its infancy. Learning their structure and intricacies is fraught with challenges, and often side-stepped in favour of studying the function of different gene products in isolation from their physiological context. Constructing and inferring global mathematical models from experimental data is, however, central to systems biology. Different experimental setups provide different insights into such systems. Here we show how we can combine concepts from Bayesian inference and information theory in order to identify experiments that maximize the information content of the resulting data. This approach allows us to incorporate preliminary information; it is global and not constrained to some local neighbourhood in parameter space and it readily yields information on parameter robustness and confidence. Here we develop the theoretical framework and apply it to a range of exemplary problems that highlight how we can improve experimental investigations into the structure and dynamics of biological systems and their behavior. © 2013 Liepe et al. Source


Wolanski M.,Polish Academy of Sciences
Open biology | Year: 2012

AdpA, one of the most pleiotropic transcription regulators in bacteria, controls expression of several dozen genes during Streptomyces differentiation. Here, we report a novel function for the AdpA protein: inhibitor of chromosome replication at the initiation stage. AdpA specifically recognizes the 5' region of the Streptomyces coelicolor replication origin (oriC). Our in vitro results show that binding of AdpA protein decreased access of initiator protein (DnaA) to the oriC region. We also found that mutation of AdpA-binding sequences increased the accessibility of oriC to DnaA, which led to more frequent replication and acceleration of Streptomyces differentiation (at the stage of aerial hyphae formation). Moreover, we also provide evidence that AdpA and DnaA proteins compete for oriC binding in an ATP-dependent manner, with low ATP levels causing preferential binding of AdpA, and high ATP levels causing dissociation of AdpA and association of DnaA. This would be consistent with a role for ATP levels in determining when aerial hyphae emerge. Source


Rogula-Kozlowska W.,Polish Academy of Sciences
Bulletin of Environmental Contamination and Toxicology | Year: 2014

The road traffic impact on the concentrations of 13 fractions of particulate matter (PM) and their components was assessed. PM was sampled at two points in Katowice (southern Poland), a background point beyond the effects of road traffic, and a near-highway traffic point. The samples were analyzed for organic and elemental carbon, 8 water-soluble ions, 24 elements, and 16 polycyclic aromatic hydrocarbons (PAHs). The traffic emissions (mainly particles from car exhaust) enriched the ultrafine, submicron, and fine PM particles with elemental carbon. The traffic-caused re-suspension of the road and soil dust affecting the concentrations and chemical composition of the coarse PM fraction. However, for each PM fraction, the carcinogenic equivalent ratios, assumed as a measure of the hazard from 16 PAHs in this paper, were similar at the two sampling points. The traffic emissions from the highway appeared to have a weaker influence on the concentrations and chemical composition of PM in a typical urban area of southern Poland than elsewhere in Europe. © 2014 The Author(s). Source


Worch R.,Polish Academy of Sciences
Acta Biochimica Polonica | Year: 2014

The release of influenza RNA inside the host cell occurs through the fusion of two membranes, the viral envelope and that of the cellular endosome. The fusion is mediated by the influenza hemagglutinin protein (HA), in particular by the fusion peptide (HAfp) located in the N-terminal fragment of HA2 subunit. This protein fragment anchors in the internal endosomal membrane, whereas the C-terminal HA2 part comprises a transmembrane domain (TMD) embedded in the viral envelope. A drop of pH in the endosome acts as the main trigger for HA2 large conformational change that leads to anchoring of the fusion peptide, close contact of the membranes and the subsequent fusion. Throughout the years the major research effort was focused on a 20-aminoacid fragment (HAfp1-20), shown by NMR to adopt a 'boomerang'- like structure. However, recent studies showed that extending HAfp1-20 by three highly conserved residues W21-Y22-G23 leads to formation of a unique, tight helical hairpin structure. This review summarizes recently discovered structural aspects of influenza fusion peptides and their relations with the membrane fusion mechanism. Source


Graczykowski C.,Polish Academy of Sciences
Computers and Structures | Year: 2015

The paper describes various approaches for the mathematical modelling of Adaptive Inflatable Structures (AIS) along with the corresponding numerical methods. The introductory part presents a general idea of adaptive impact absorption (AIA) and the concept of inflatable structures equipped with controllable valves serving for internal pressure control. Application of AIS for adaptive absorption of the impact loading is briefly explained. The paper focuses on diverse methods of modelling of inflatable structures, which are based on interaction between solid walls and fluid enclosed inside. Modelling of the solid walls is based on rigid body dynamics or initial-boundary value problem of solid mechanics. In turn, modelling of the fluid utilizes either classical equilibrium thermodynamics or Navier-Stokes equations. Consequently, four possible combinations of the above approaches are distinguished, precisely analyzed and applied for the modelling of different types of inflatable structures. Each model takes into account controllable valves, which requires introducing additional coupling between parameters defining the valves and selected results of the analysis. Corresponding numerical methods include classical methods of solving ordinary differential equations, finite volume method (FVM) applied for problems with mobile boundaries, finite element method (FEM) applied for problems involving additional ODEs and, finally, FEM coupled with FVM. Proposed numerical methods and software tools are utilized for the simulation of adaptive pneumatic cylinders, adaptive pneumatic fenders and membrane valves. © 2015 Elsevier Ltd. Source


Bzdak A.,Polish Academy of Sciences
Acta Physica Polonica B | Year: 2010

It is argued that a standard measurement of multiplicities in proton-proton collisions is sufficient to construct a single nucleon fragmentation function. A proposed method is based on measurement of mean values of produced particles and pairs of particles in symmetric and asymmetric rapidity bins. Source


Kaliszewicz A.,Polish Academy of Sciences
Ecological Research | Year: 2011

The green hydra, Hydra viridissima, has three sexes: hermaphrodite, male, and female. I investigated the reproductive strategies of the green hydra and the relationship between asexual budding and sexual reproduction. The proportion of mature individuals in the asexually reproducing population increased with increasing temperature. Sexual reproduction did not interrupt asexual budding in hermaphrodites or males; sexual reproduction did interrupt asexual budding in females. Sexual reproduction also resulted in exponential population growth during the reproductive season. The number of asexual buds on each parental individual was positively correlated with the parental individual size in asexual individuals and in males. The same positive correlation was found between the number of testicles and the size of males. These correlations reflect a common tendency in asexual and sexual reproduction: larger parental individuals have a greater number of propagules or gametes. No correlation was found between size and buds or size and gonads in hermaphrodites; hermaphrodites had at most one asexual bud and were significantly larger than males, females, and asexual individuals. The larger size of hermaphrodites supports the hypothesis that producing both female and male gonads is more energetically costly than producing only one type of gamete (gonochorism). © 2010 The Ecological Society of Japan. Source


The aim of this paper was to examine spatial distribution of badger setts (N = 20) and fox dens (N = 42) in relation to habitat availability (estimated on the basis of 100 random points) and human impact on their environment (settlements, sylviculture practice). Badgers displayed a tendency to locate their setts close to habitats of moderate fertility, but avoided poor and young Scotch pine monocultures created by humans (<50 years old). Generally, foxes did not show any preference as to location of their dens, but they settled significantly closer (within 31-1486 m, median 497 m) to human settlements than badgers did (403-1841 m, median 675 m). Also, distances to open areas were different for both species, but not significantly. In comparison to foxes (2%), badgers more frequently (30%) settled in Strictly Protected Areas where human activity in sylviculture had not been as intensive as in surrounding areas for many years. It allows confirming that disturbances in forest ecosystems caused by human sylviculture (especially cultivation of young coniferous monoculture) influence the spatial distribution of badger setts to some degree. It can also be concluded that foxes are less anthropophobic than badgers in the Kampinos Forest. Source


Powell C.J.,U.S. National Institute of Standards and Technology | Jablonski A.,Polish Academy of Sciences
Journal of Electron Spectroscopy and Related Phenomena | Year: 2010

We give a survey of information needed for quantitative surface analyses by X-ray photoelectron spectroscopy (XPS). We describe four terms (the inelastic mean free path, the effective attenuation length, the mean escape depth, and the information depth) that are commonly used as descriptors of the surface sensitivity of an XPS experiment. Due to the complicating effects of elastic scattering, numerical values for each measure are generally different. Analytical formulae are given for each quantity. We describe procedures for determination of surface composition (with an emphasis on three types of relative sensitivity factors), measurements of overlayer-film thickness, and determination of composition-versus-depth information from angle-resolved XPS. Information is given on measurements of photoelectron intensities and the effects of sample morphology and sample roughness. Sources of data are given for all parameters needed for quantitative XPS. We discuss some major remaining uncertainties in quantitative XPS analyses and describe expected future areas of growth in XPS applications. © 2009 Elsevier B.V. Source


The high-temperature ratio (HTR) method which exploits changes in the LiF:Mg,Ti glow-curve due to high-LET radiation, has been used for several years to estimate LET in an unknown radiation field. As TL efficiency is known to decrease after doses of densely ionizing radiation, a LET estimate is used to correct the TLD-measured values of dose. The HTR method is purely empirical and its general correctness is questionable. The validity of the HTR method was investigated by theoretical simulation of various mixed radiation fields. The LETeff values estimated with the HTR method for mixed radiation fields were found in general to be incorrect, in some cases underestimating the true values of dose-averaged LET by an order of magnitude. The method produced correct estimates of average LET only in cases of almost mono-energetic fields (i.e. in non-mixed radiation conditions). The value of LETeff found by the HTR method may therefore be treated as a qualitative indicator of increased LET, but not as a quantitative estimator of average LET. However, HTR-based correction of the TLD-measured dose value (HTR-B method) was found to be quite reliable. In all cases studied, application of this technique improved the result. Most of the measured doses fell within 10% of the true values. A further empirical improvement to the method is proposed. One may therefore recommend the HTR-B method to correct for decreased TL efficiency in mixed high-LET fields. © 2009 Elsevier Ltd. All rights reserved. Source


Korona T.,University of Warsaw | Dodziuk H.,Polish Academy of Sciences
Journal of Chemical Theory and Computation | Year: 2011

The recent syntheses of complexes involving some small molecules in opened fullerenes and those of hydrogen molecule(s) in C60 and C 70 are accompanied in the literature by numerous computations for endohedral fullerene complexes which cope with the problem of the stability of these complexes. In this contribution, stabilization energies of endohedral complexes of C60 and C70 with H2, N 2, CO, HCN, H2O, H2S, NH3, CH 4, CO2, C2H2, H2CO, and CH3OH guests have been estimated using symmetry-adapted perturbation theory, which, contrary to the standard DFT and some other approaches, correctly describes the dispersion contribution of the host-guest interactions. On the basis of these calculations, the endohedral complexes with all these guests were found stable in the larger fullerene, while the C60 cage was found too small to host the latter four molecules. Except for H2 and H 2CO, a stabilization effect for most guests in the C60 cage is about 30 kJ/mol. For H2 and H2O guests, a typical supramolecular effect is observed; namely, the stabilization in the smaller cage is equal to or larger than that in the larger C70 host. Except for the water molecule where the induction interaction plays a non-negligible role, in all complexes the main stabilization effect comes from the dispersion interaction. The information on the stability of hypothetical endohedral fullerene complexes and physical factors contributing to it can be of importance in designing future experiments contributing to their applications. © 2011 American Chemical Society. Source


Radon M.,Jagiellonian University | Broclawik E.,Polish Academy of Sciences | Pierloot K.,Catholic University of Leuven
Journal of Chemical Theory and Computation | Year: 2011

The energetics of various electromeric states for two heme complexes with an iron-oxo (FeO3+) group, FeO(P)+ and FeO(P)Cl (P = porphin), have been investigated, employing DFT and correlated ab initio methods (CASPT2, RASPT2). Our interest focused in particular on tri- and pentaradicaloid iron(IV)-oxo porphyrin radical states as well as iron(V)-oxo states. Surprisingly, the iron(V)-oxo ground state is predicted for both models in vacuo. However, the presence of a polarizable medium, such as a solvent or a protein environment, favors the iron(IV)-oxo porphyrin radical cation, which is predicted to be the actual ground state of FeO(P)Cl under such conditions. Nonetheless, the iron(V)-oxo electromer is still expected to lie only a few kcal/mol above the ground state-a conclusion coming from both CASPT2 and RASPT2 calculations with a very large active space and further supported by a calibration with respect to coupled cluster CCSD(T) calculations for a simplified small model. The DFT results turn out to be strongly functional-dependent and thereby inconclusive. The widely used B3LYP functional-although correctly predicting the iron(IV)-oxo porphyrin radical ground state for FeO(P)Cl-seems to place the iron(V)-oxo states much too high in energy, as compared to the present CASPT2, RASPT2, and CCSD(T) results. © 2011 American Chemical Society. Source


Krolikowska M.,Polish Academy of Sciences | Dybczynski P.A.,Adam Mickiewicz University
Monthly Notices of the Royal Astronomical Society | Year: 2013

Dynamics of a complete sample of small perihelion distance near-parabolic comets discovered in the years 2006-2010 are studied (i.e. of 22 comets of qosc < 3.1 au). First, osculating orbits are obtained after a very careful positional data inspection and processing, including where appropriate, the method of data partitioning for determination of pre- and post-perihelion orbit for tracking then its dynamical evolution. The non-gravitational acceleration in the motion is detected for 50 per cent of investigated comets, in a few cases for the first time. Different sets of non-gravitational parameters are determined from preand post-perihelion data for some of them. The influence of the positional data structure on the possibility of the detection of non-gravitational effects and the overall precision of orbit determination is widely discussed. Secondly, both original and future orbits were derived by means of numerical integration of swarms of virtual comets obtained using aMonte Carlo cloning method. This method allows us to followthe uncertainties of orbital elements at each step of dynamical evolution. The complete statistics of original and future orbits that includes significantly different uncertainties of 1/avalues is presented, also in the light of our results obtained earlier. Basing on 108 comets examined by us so far, we conclude that only one of them, C/2007 W1 Boattini, seems to be a serious candidate for an interstellar comet. We also found that 53 per cent of 108 nearparabolic comets escaping in the future from the Solar system, and the number of comets leaving the Solar system as so called Oort spike comets (i.e. comets suffering very small planetary perturbations) is 14 per cent. Anewmethod for cometary orbit quality assessment is also proposed by means of modifying the original method, introduced by Marsden, Sekanina & Everhart. This new method leads to a better diversification of orbit quality classes for contemporary comets. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society. Source


The effect of realimentation of fattening pigs on gain composition and intramuscular fat content in the longissimus dorsi muscle and their relationship to meat tenderness was investigated in 60 gilts. From day 90 to 168 of age, Group C (control) was fed according to the requirements, while from day 90 to 118 of age, Group R was fed restrictively (protein and energy) and Group P was fed restrictively with protein alone. This period was followed by adequate feeding. Comparative slaughter techniques were used; animals were slaughtered at the beginning of the study (day 90), at the end of the restriction period (day 118), and after two periods of realimentation (day 146 and day 168). Interactions between experimental treatments indicated that muscle protein gain (p < 0.05), muscle fat gain (p < 0.01), and shear force (p < 0.01) differed depending on period of realimentation. Muscle protein deposition differed only during the second period of realimentation, where Group R deposited more protein compared with Groups C and P (6.0, 4.5 and 5.0 g/d, respectively). Muscle fat deposition during the first period of realimentation was lower in Groups R and P than in Group C (0.73, 0.74 and 1.20 g/d, respectively) while in the second period Group R deposited considerably more fat than Groups C and P (2.39, 1.20 and 1.23 g/d, respectively). At the end of the first period, the shear force of Groups R and P was lower when compared with Group C (2.44, 2.79 and 3.22 kg, respectively); however, at final age it did not differ between treatments. © 2010 Taylor & Francis. Source


Piechota M.,Polish Academy of Sciences
Genome biology | Year: 2010

BACKGROUND: Various drugs of abuse activate intracellular pathways in the brain reward system. These pathways regulate the expression of genes that are essential to the development of addiction. To reveal genes common and distinct for different classes of drugs of abuse, we compared the effects of nicotine, ethanol, cocaine, morphine, heroin and methamphetamine on gene expression profiles in the mouse striatum. RESULTS: We applied whole-genome microarray profiling to evaluate detailed time-courses (1, 2, 4 and 8 hours) of transcriptome alterations following acute drug administration in mice. We identified 42 drug-responsive genes that were segregated into two main transcriptional modules. The first module consisted of activity-dependent transcripts (including Fos and Npas4), which are induced by psychostimulants and opioids. The second group of genes (including Fkbp5 and S3-12), which are controlled, in part, by the release of steroid hormones, was strongly activated by ethanol and opioids. Using pharmacological tools, we were able to inhibit the induction of particular modules of drug-related genomic profiles. We selected a subset of genes for validation by in situ hybridization and quantitative PCR. We also showed that knockdown of the drug-responsive genes Sgk1 and Tsc22d3 resulted in alterations to dendritic spines in mice, possibly reflecting an altered potential for plastic changes. CONCLUSIONS: Our study identified modules of drug-induced genes that share functional relationships. These genes may play a critical role in the early stages of addiction. Source


Kosmaczewska A.,Polish Academy of Sciences
International Journal of Molecular Sciences | Year: 2014

For many years, the role of interleukin-2 (IL-2) in autoimmune responses was established as a cytokine possessing strong pro-inflammatory activity. Studies of the past few years have changed our knowledge on IL-2 in autoimmune chronic inflammation, suggesting its protective role, when administered at low-doses. The disrupted balance between regulatory and effector T cells (Tregs and Teffs, respectively) is a characteristic of autoimmune diseases, and is dependent on homeostatic cytokines, including IL-2. Actually, inherent defects in the IL-2 signaling pathway and/or levels leading to Treg compromised function and numbers as well as Th17 expansion have been attributed to autoimmune disorders. In this review, we discuss the role of IL-2 in the pathogenesis of autoimmune diseases. In particular, we highlight the impact of the dysregulated IL-2 pathway on disruption of the Treg/Th17 balance, reversal of which appears to be a possible mechanism of the low-dose IL-2 treatment. The negative effects of IL-2 on the differentiation of follicular helper T cells (Tfh) and pathogenic Th17 cells, both of which contribute to autoimmunity, is emphasized in the paper as well. We also compare the current IL-2-based therapies of animal and human subjects with immune-mediated diseases aimed at boosting the Treg population, which is the most IL-2-dependent cell subset desirable for sufficient control of autoimmunity. New perspectives of therapeutic approaches focused on selective delivery of IL-2 to inflamed tissues, thus allowing local activity of IL-2 to be combined with its reduced systemic and pleiotropic toxicity, are also proposed in this paper. © 2014 by the authors; licensee MDPI, Basel, Switzerland. Source


Blomberg M.R.A.,University of Stockholm | Borowski T.,Polish Academy of Sciences | Himo F.,University of Stockholm | Liao R.-Z.,University of Stockholm | Siegbahn P.E.M.,University of Stockholm
Chemical Reviews | Year: 2014

The study focused on the mechanisms of redox-active metalloenzymes, while computational results on structural and spectroscopic issues which were directly related to the mechanisms were rarely treated. There were also some results for metalloenzymes that were not redox-active, such as the section on zinc-containing enzymes, since the modeling aspects were similar. The most difficult situations to describe with the cluster model were the cases where the model changes its charge, such as in the calculations of redox potentials and pKa values. It was observed that the group of Noodleman had the largest experience during the early years of DFT-cluster modeling for the calculation of redox potentials of metalloenzyme systems. Source


Kazrani A.A.,International Institute of Molecular and Cell Biology | Kowalska M.,International Institute of Molecular and Cell Biology | Czapinska H.,International Institute of Molecular and Cell Biology | Bochtler M.,International Institute of Molecular and Cell Biology | Bochtler M.,Polish Academy of Sciences
Nucleic Acids Research | Year: 2014

PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not 5-methylcytosine (5mC) or cytosine. Here, we report a crystal structure of the enzyme at 2.35 Å resolution. Although the protein has been crystallized in the absence of DNA, the structure is very informative. It shows that PvuRts1I consists of an N-terminal, atypical PD-(D/E)XK catalytic domain and a C-terminal SRA domain that might accommodate a flipped 5hmC or 5ghmC base. Changes to predicted catalytic residues of the PD-(D/E)XK domain or to the putative pocket for a flipped base abolish catalytic activity. Surprisingly, fluorescence changes indicative of base flipping are not observed when PvuRts1I is added to DNA substrates containing pyrrolocytosine in place of 5hmC (5ghmC). Despite this caveat, the structure suggests a model for PvuRts1I activity and presents opportunities for protein engineering to alter the enzyme properties for biotechnological applications. © 2014 The Author(s) 2014. Source


Van Hameren A.,Polish Academy of Sciences
Computer Physics Communications | Year: 2011

OneLOop is a program to evaluate the one-loop scalar 1-point, 2-point, 3-point and 4-point functions, for all kinematical configurations relevant for collider-physics, and for any non-positive imaginary parts of the internal squared masses. It deals with all UV and IR divergences within dimensional regularization. Furthermore, it provides routines to evaluate these functions using straightforward numerical integration. Program summary: Program title: OneLOop Catalogue identifier: AEJO-v1-0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJO-v1-0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 12 061 No. of bytes in distributed program, including test data, etc.: 74 163 Distribution format: tar.gz Programming language: Fortran Computer: Workstations Operating system: Linux, Unix RAM: Negligible Classification: 4.4, 11.1 Nature of problem: In order to reach next-to-leading order precision in the calculation of cross sections of hard scattering processes, one-loop amplitudes have to be evaluated. This is done by expressing them as linear combination of one-loop scalar functions. In a concrete calculation, these functions eventually have to be evaluated. If the scattering process involves unstable particles, consistency requires the evaluation of these functions with complex internal masses. Solution method: Expressions for the one-loop scalar functions in terms of single-variable analytic functions existing in literature have been implemented. Restrictions: The applicability is restricted to the kinematics occurring in collider-physics. Running time: The evaluation of the most general 4-point function with 4 complex masses takes about 180 μs, and the evaluation of the 4-point function with 4 real masses takes about 18 μs on a 2.80 GHz Intel Xeon processor. © 2011 Elsevier B.V. All rights reserved. Source


Recently developed techniques of DNA barcoding and next-generation sequencing (NGS) overcome previous limitations of evaluation of animal diet composition and together are promising method in molecular ecology. The objective was to compare standard ABI Sanger sequencing with new high throughput sequencing (Illumina MiSeq) technique and the two selected plant barcodes (rbcL gene and trnL intron) in terms of the identification of host plant composition for the selected beetle species - the Centricnemus leucogrammus weevil. A comparison of two sequencing techniques showed that NGS (in this case Illumina) gave more exhaustive results than the Sanger method. Moreover, it was proven that a two-locus barcoding systems (rbcL and trnL) is sufficient for host plant identification from DNA isolated from insect bodies, at least at the genus level. A comparison of host plant composition among distant populations revealed that the studied species did not feed uniformly across its range. This probably reveals an ecological adaptation of geographically and genetically isolated populations. These findings, beside broadening basic knowledge on the use of barcoding and sequencing techniques for host plant identifications in insect populations, can have implications for conservation studies and strategies for rare and endangered species. © Institute of Systematics and Evolution of Animals, PAS, Krako´w, 2014. Source


Stronen A.V.,Polish Academy of Sciences | Paquet P.C.,Raincoast Conservation Foundation | Paquet P.C.,University of Victoria
Biological Conservation | Year: 2013

Hybridization processes are widespread throughout the taxonomic range and require conservation recognition. Science can help us understand hybridization processes but not whether and when we ought to conserve hybrids. Important questions include the role of humans in hybridization and the value we place on natural and human-induced hybrids concerning their ecological function. Certain hybrids resulting from human actions have replaced the ecological role of extirpated or extinct parent taxa and this ecological role should be preserved. Conservation policies must increasingly recognize populations of wild organisms that hybridize naturally within the context of their historical ecological role. Natural selection acts on individual organisms and the range of characteristics displayed by individual hybrids constitute raw material for evolution. Guidelines must consider the conservation value of individuals and the ethical aspects of removing hybrids for the purpose of conserving population genetic integrity. Conservation policies should focus on protecting the ecological role of taxa affected by hybridization. An informative example is North American canids (Canis), where body size, prey availability, and human landscape modifications may interact and impose local selective pressures. Gray wolves (Canis lupus) and eastern wolves (Canis lycaon or Canis lupus lycaon) or Great Lakes wolves appear to hybridize naturally within the context of their historical ecological role. In contrast, eastern coyotes (C. latrans) exhibit wolf ancestry and have partly replaced the ecological role of an extirpated parent taxa in parts of northeastern North America. The need for advancing conservation policies that reflect our current understanding of ecology and evolution is urgent. © 2013 Elsevier Ltd. Source


Malinowski J.,Polish Academy of Sciences
IEEE Transactions on Reliability | Year: 2010

This paper presents a new, efficient method of enumerating all minimal tie-sets connecting selected nodes in a mesh-structured network. More precisely, it gives a solution of the following problem: given a network modeled by an undirected graph G=(V, E), V, and E being the sets of G's vertices, and edges, find each minimal tie-set connecting all nodes of W = {v1, ⋯, vk} , a subset of V. (Note that for W = V the sought tie-sets are the spanning trees of G.) This task is fulfilled in two steps. In the first step, the sets P2, ⋯ , Pk are found, where Pi is the set of all loop-free paths connecting v1 to vi. This can be done by performing a breadth-first search on G. In the second step, a recursive procedure gradually merges the paths belonging to different sets Pi, and accomplishes the main task in k-2 iterations. Thus, the new method can be named Acyclic Paths Mergence (APM). This method is compared to the well known Backtracking algorithm; all spanning trees of a small graph are found using both approaches, and the APM method proves more efficient. This difference in efficiency is likely to grow with the size of G. Moreover, the similar complexity of the Backtracking, and the Edge Replacement (another classic algorithm finding all spanning trees in a graph) methods, and wider applicability of the APM method, are additional arguments in favor of the latter. © 2010 IEEE. Source


Bochtler M.,International Institute of Molecular and Cell Biology | Bochtler M.,Polish Academy of Sciences
Biological Chemistry | Year: 2012

Phytopathogen transcription activator-like effectors (TALEs) bind DNA in a sequence specific manner in order to manipulate host transcription. TALE specificity correlates with repeat variable diresidues in otherwise highly stereotypical 34-35mer repeats. Recently, the crystal structures of two TALE DNA-binding domains have illustrated the molecular basis of the TALE cipher. The structures show that the TALE repeats form a right-handed superhelix that is wound around largely undistorted B-DNA to match its helical parameters. Surprisingly, repeat variable residue 1 is not in contact with the bases. Instead, it is involved in hydrogen bonding interactions that stabilize the overall structure of the protein. Repeat variable residue 2 contacts the top strand base and forms sequence-specific hydrogen bonds and/or van der Waals contacts. Very unexpectedly, bottom strand bases are exposed to solvent and do not make any direct contacts with the protein. This review contains a summary of TALE biology and applications and a detailed description of the recent breakthroughs that have provided insights into the molecular basis of the TALE code. Copyright © 2011-2012 by Walter de Gruyter. Source


Massel S.R.,Polish Academy of Sciences
Coastal Engineering | Year: 2012

The impact of a meteorite into the ocean surface is a rare phenomenon. However, it can be catastrophic, especially for the coastal area. The aim of the paper is to describe the evolution of the tsunami impulse due to meteorite impact in shallow water, including energy dissipation due to bottom friction and wave breaking. As the exact nonlinear solutions for tsunami transformation with energy loss due to wave breaking are not known, the linearised equations of motion are used and energy loss is parameterised accordingly. To describe the evolution of tsunami impulse in shallow water, the Hilbert Transform technique was introduced. It facilitates considerably the evaluation of the tsunami impulse transformation, its run-up and coast inundation range. Examples are included to illustrate the applicability of the theoretical derivations. © 2012 Elsevier B.V. Source


The precise regulation of microRNA (miRNA) biogenesis seems to be critically important for the proper functioning of all eukaryotic organisms. Even small changes in the levels of specific miRNAs can initiate pathological processes, including carcinogenesis. Accordingly, there is a great need to develop effective methods for the regulation of miRNA biogenesis and activity. In this study, we focused on the final step of miRNA biogenesis; i.e., miRNA processing by Dicer. To test our hypothesis that RNA molecules can function not only as Dicer substrates but also as Dicer regulators, we previously identified by SELEX a pool of RNA oligomers that bind to human Dicer. We found that certain of these RNA oligomers could selectively inhibit the formation of specific miRNAs. Here, we show that these specific inhibitors can simultaneously bind both Dicer and pre-miRNAs. These bifunctional riboregulators interfere with miRNA maturation by affecting pre-miRNA structure and sequestering Dicer. Based on these observations, we designed a set of short oligomers (12 nucleotides long) that were capable of influencing pre-miRNA processing in vitro, both in reactions involving recombinant human Dicer and in cytosolic extracts. We propose that the same strategy may be used to develop effective and selective regulators to control the production of any miRNA. Overall, our findings indicate that the interactions between pre-miRNAs and other RNAs may form very complex regulatory networks that modulate miRNA biogenesis and consequently gene expression. Source


Sosnowski S.,Polish Academy of Sciences
Polimery/Polymers | Year: 2011

Anew, exact Monte Carlo algorithm for the simulation of living/controlled polymerization processes is proposed. In the algorithm macromolecules are represented by doubly linked lists, which are natural models of macromolecules. It allows modelling of elementary reactions by forming/breaking of links in the doubly linked list. As a result the algorithm has a very simple structure and high efficiency. All details of the modeled system: kinetics, molecular weight distributions, microstructure of macromolecules, etc., are accessible at any moment of simulation. Practical aspects of implementation of the new algorithm were emphasized: data structures, flowcharts, and source codes (Pascal). Source


Accumulation of sediments in the lake basins of the Starogard Lakeland, Northern Poland, an area which was entirely ice-covered during the last glaciation, started at different times, beginning during the Late Glacial. Sedimentation continued till the beginning of the Holocene (Preboreal). The principal factor causing the asynchronous start of the lake development was the variation in melting processes of buried dead-ice blocks. The preservation of dead-ice masses in some depressions until the Preboreal leads to the conclusion that the ultimate disappearance of permafrost in the study area occurred only at the beginning of the Holocene. Source


Kosciuczuk E.M.,Polish Academy of Sciences
Molecular biology reports | Year: 2012

Cathelicidins are small, cationic, antimicrobial peptides found in humans and other species, including farm animals (cattle, horses, pigs, sheep, goats, chickens, rabbits and in some species of fish). These proteolytically activated peptides are part of the innate immune system of many vertebrates. These peptides show a broad spectrum of antimicrobial activity against bacteria, enveloped viruses and fungi. Apart from exerting direct antimicrobial effects, cathelicidins can also trigger specific defense responses in the host. Their roles in various pathophysiological conditions have been studied in mice and humans, but there are limited information about their expression sites and activities in livestock. The aim of the present review is to summarize current information about these antimicrobial peptides in farm animals, highlighting peptide expression sites, activities, and future applications for human and veterinary medicine. Source


Schlichtholz P.,Polish Academy of Sciences | Houssais M.-N.,University of Paris Descartes
Journal of Geophysical Research: Oceans | Year: 2011

Hydrographic data and atmospheric reanalysis from 1982 to 2005 are used to show a strong link of the Atlantic water temperature (AWT) anomalies observed in the transition zone between the Norwegian Atlantic current and the West Spitsbergen current in summer to the surface heat flux (SHF) anomalies observed over the Barents Sea open water in the preceding late winter. A mechanism proposed for this link is formation of ocean temperature anomalies in a deep mixed layer and their subsequent westward export by a branch of Atlantic water recirculating in the western Barents Sea. The SHF anomalies over the Barents Sea are due to advection of temperature and humidity by anomalous winds across the Arctic ice edge and do not strongly depend on the North Atlantic oscillation (NAO). Correlations of up to about 0.9 between the AWT anomalies and indices of atmospheric variability over the Barents Sea open prospects for seasonal AWT predictability. It is also shown that the wind-forcing responsible for positive AWT anomalies is involved in a cyclonic perturbation of the atmospheric circulation over the Nordic Seas. This perturbation generates, through influence on the sea ice distribution, a lobe of SHF anomalies in the marginal ice zone (MIZ) on the eastern (Barents Sea) and western (Greenland Sea) sides of the Nordic Seas which has the opposite sign to the open water lobe. In contrast to the Barents Sea MIZ, the diabatic heating of the atmosphere by upward SHF anomalies in the Greenland Sea MIZ competes with cold advection. Copyright 2011 by the American Geophysical Union. Source


Kowalczyk P.,Polish Academy of Sciences
Finite Elements in Analysis and Design | Year: 2012

A computational model that allows to explicitly determine transversely isotropic elastic constants of uni-directional fiber-matrix composite tow as functions of microstructure parameters has been developed in this study. These relationships are not given in the form of analytical formulae (as it is in the case of approximate analytical models) but in the form of an extensive database of numerically evaluated results for different microstructure instances and a numerical scheme that interpolates the results. To build the database, a standard finite-element-based homogenization technique of a periodic RVE is employed. The technique is enhanced by introduction of averaging procedure over different shapes of the 2D fiber layout pattern in the tow cross-section. As a result, a numerical algorithm is provided that may be easily employed in FE codes as a part of a regular constitutive subroutine. Sensitivity of the composite elastic constants with respect to the microstructure parameters is also directly available from the model. © 2011 Elsevier B.V. All rights reserved. Source


Heggie D.C.,University of Edinburgh | Giersz M.,Polish Academy of Sciences
Monthly Notices of the Royal Astronomical Society | Year: 2014

Using a Monte Carlo code, we construct a dynamic evolutionary model of the Galactic globular clusterM22 (NGC 6656). The initial conditions are chosen so that, after about 12 Gyr of stellar and dynamical evolution, the model is an approximate fit to the surface brightness and velocity dispersion profiles of the cluster, to its mass function and to the current binary fraction. Depending on the distribution of black hole natal kicks, we predict that the presentday population of stellar-mass black holes ranges from about 40 (no kicks) down to essentially zero (kicks distributed like those of neutron stars). Provided that natal kicks do not eject all new black holes, it is suggested that clusters with a present-day half-mass relaxation time above about 1 Gyr are the ones that may still retain an appreciable population of black holes. © 2014 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society. Source


Schlichtholz P.,Polish Academy of Sciences
Geophysical Research Letters | Year: 2011

A strong control of sea ice area (SIA) in the Nordic Seas in the period 1982-2006 by oceanic heat variability is reported. In particular, variability of summer Atlantic water temperature in the Barents Sea Opening explains about 75% of the variance of the following winter SIA anomalies which opens prospects for seasonal predictability of regional sea ice cover. A strong link of winter SIA anomalies to variability in the previous spring sea surface temperature on the western (Greenland Sea) and eastern (Barents Sea) sides of the Nordic Seas indicates that the oceanic control of sea ice cover in these areas mainly results from postsummer surface reemergence of oceanic heat anomalies generated by earlier atmospheric forcing. In particular, late winter North Atlantic Oscillation and anomalous winds across the Barents Sea ice edge significantly influence next winter sea ice cover on the western and eastern sides of the Nordic Seas, respectively. Copyright 2011 by the American Geophysical Union. Source


Teisseyre R.,Polish Academy of Sciences
Bulletin of the Seismological Society of America | Year: 2011

We present a confrontation between the classic elasticity and asymmetric continuum theories in order to point out the abilities of the two approaches and their deficiencies. The role of independent strain and rotation waves is discussed and some related particular examples are given. Source


Starkel L.,Polish Academy of Sciences
Quaternary International | Year: 2011

Reconstruction of Holocene climatic changes should be based on correlation of proxy data representing various sediment facies and ecosystem characteristics. In addition to long-term fluctuations in such data, various extreme events, such as downpours, floods, and slope failures, whose type and frequency fluctuate in time, have also been recorded. Events may reflect global, regional or local changes. Examples from Poland are used to illustrate general principles. The observation of present-day processes and their erosional or deposition effects linked with proxy indicators from the past should help in interpretation of environmental changes in the Holocene and to inferences about the causative mechanisms. © 2010 Elsevier Ltd and INQUA. Source


Gulyaeva T.L.,Polish Academy of Sciences | Veselovsky I.S.,Moscow State University
Journal of Geophysical Research: Space Physics | Year: 2012

[1] The global electron content (GEC) derivation is initiated by summing up the total electron content of each cell of Global Positioning System GPS-TEC global map multiplied by the cell area. Algorithm of GEC calculation is improved in the present paper using the electron density varying with height through the total volume of a spherical layer in near-Earth space up to 20,200 km (GPS orbit) reconstructed from TEC with the International Reference Ionosphere model extended to the Plasmasphere (IRI-Plas). An analytical model is first derived for two-phase typical GEC storm profile by a common epoch analysis of 10 storms during 2001-2011 with the starting time put at the origin of the negative phase of GEC departure from the quiet reference (5 day median). It is found that GEC depletion occurs synchronously with decrease of the solar wind velocity and the outset of recovery of the magnetospheric ring current (the equatorial Dst index) and the auroral electrojet (AE index). Thus, the GEC is an indicator of the plasma injection in the ionosphere and plasmasphere with the solar wind energy inducing the positive phase of GEC storm during 24 h with electron number increased by 10-20% followed by a negative phase with GEC decrease by 10-20% during 40 h of a plasma release (ejection) into the magnetosphere tail beyond the three Earth radii (GPS orbit). © 2012. American Geophysical Union. All Rights Reserved. Source


Wojnar R.,Polish Academy of Sciences
Bulletin of the Polish Academy of Sciences: Technical Sciences | Year: 2014

The thermal effects of a stationary Stokesian flow through an elastic micro-porous medium are compared with the entropy produced by Darcy's flow. A micro-cellular elastic medium is considered as an approximation of the elastic porous medium. It is shown that after asymptotic two-scale analysis these two approaches, one analytical, starting from Stoke's equation and the second phenomenological, starting from Darcy's law give the same result. The incompressible and linearly compressible fluids are considered, and it is shown that in micro-porous systems the seepage of both types of fluids is described by the same equations. Copyright © BPASTS-2014. Source


Zawadzki W.,Polish Academy of Sciences | Rusin T.M.,Orange Customer Service Sp. Z o. O.
Journal of Physics Condensed Matter | Year: 2011

We review recent research on Zitterbewegung (ZB, trembling motion) of electrons in semiconductors. A brief history of the subject is presented, the trembling motion in semi-relativistic and spin systems is considered and its main features are emphasized. ZB of charge carriers in monolayer and bilayer graphene as well as in carbon nanotubes is elaborated in some detail. We describe the effects of an external magnetic field on ZB using monolayer graphene as an example. The nature of electron ZB in crystalline solids is explained. We also review various simulations of the trembling motion in a vacuum and in semiconductors, and mention ZB-like wave phenomena in sonic and photonic periodic structures. An attempt is made to quote all the relevant literature on the subject. © 2011 IOP Publishing Ltd. Source


Rudnicki L.,Polish Academy of Sciences
Journal of Russian Laser Research | Year: 2011

I start with a brief report of the topic of entropic uncertainty relations for the position and momentum variables. Then I investigate the discrete Shannon entropies related to the case of a finite number of detectors set to measure the probability distributions in the position and momentum spaces. I derive the uncertainty relation for the sum of the Shannon entropies which generalizes the previous approach by I. Bialynicki-Birula based on an infinite number of detectors (bins). © 2011 Springer Science+Business Media, Inc. Source


Senatorski P.,Polish Academy of Sciences
Physics of the Earth and Planetary Interiors | Year: 2012

Two alternative formulations of the apparent stress, representing homogeneous crack and triangle pulse rupture models, are tested. They are termed seismic state equations and express the apparent stress, τ a, as a function of, respectively, two or three other earthquake parameters: seismic moment, M 0, rupture area, A, and, in the latter case, mean slip acceleration, g. The number of parameters is the key difference between the two models. A variety of possible τ a-M 0 scalings is obtained by substitution of different moment-area relations, M 0-A, into the seismic state equations, τ a(M 0,A,g). Both seismic state equations enable us to explain the observed τ a-M 0 global trend. However, the triangle pulse solution fits the empirical trend with much higher correlation coefficient. Also the trends obtained for regional data sets are more consistent with the pulse model than with the crack one. © 2012 Elsevier B.V. Source


Sobolewski A.L.,Polish Academy of Sciences | Domcke W.,TU Munich
Physical Chemistry Chemical Physics | Year: 2012

The photochemistry of the hydrogen-bonded oxotitanium porphyrin-water complex (TiOP-H2O) has been explored with electronic-structure calculations. It is shown that intramolecular charge-transfer processes, which are initiated by the excitation of the Soret band of TiOP, accumulate electronic charge on the oxygen atom of TiOP, which in turn abstracts a hydrogen atom from water by an exoenergetic and essentially barrierless hydrogen-transfer reaction, resulting in the TiPOH-OH biradical. About 75% of the absorbed photon energy is thus stored as chemical energy in two ground-state radicals. Absorption of a second photon by TiPOH can result in the detachment of the H radical and recovery of the photocatalyzer TiOP. Again, about 75% of the photon energy is stored in the dissociation energy of TiPOH. Overall, a water molecule is decomposed into H and OH radicals by the absorption of two visible photons. Exoenergetic radical recombination reactions can yield molecular hydrogen, molecular oxygen or hydrogen peroxide as closed-shell products. © 2012 the Owner Societies. Source


The present work analyzes the influence of seepage and desorption processes on the initial conditions of coal and gas mini-outbursts. A series of laboratory experiments incorporating coal briquettes and three different gases, namely carbon dioxide, methane or nitrogen were carried out. Experiments relied on mini-outburst inducing. Space and time pressure distributions along the briquettes were recorded. A comparative analysis of the results revealed that the observed differences in mini-outbursts initial conditions cannot be explained by means of a simple coal or gas property such as sorption capacity, desorption rate, seepage rate, or viscosity of gas. On the contrary, the efficiency of accumulated gas releasing processes - desorption and diffusion inside of the coal grains and seepage through the briquette coupled processes - seems to explain the observed variations. © 2013 Elsevier Ltd. All rights reserved. Source


Marcelli A.,National Institute of Nuclear Physics, Italy | Cricenti A.,CNR Institute of Structure of Matter | Kwiatek W.M.,Polish Academy of Sciences | Petibois C.,University of Bordeaux Segalen
Biotechnology Advances | Year: 2012

Extremely brilliant infrared (IR) beams provided by synchrotron radiation sources are now routinely used in many facilities with available commercial spectrometers coupled to IR microscopes. Using these intense non-thermal sources, a brilliance two or three order of magnitude higher than a conventional source is achievable through small pinholes (< 10 μm) with a high signal to-noise ratio. IR spectroscopy is a powerful technique to investigate biological systems and offers many new imaging opportunities. The field of infrared biological imaging covers a wide range of fundamental issues and applied researches such as cell imaging or tissue imaging. Molecular maps with a spatial resolution down to the diffraction limit may be now obtained with a synchrotron radiation IR source also on thick samples. Moreover, changes of the protein structure are detectable in an IR spectrum and cellular molecular markers can be identified and used to recognize a pathological status of a tissue. Molecular structure and functions are strongly correlated and this aspect is particularly relevant for imaging. We will show that the brilliance of synchrotron radiation IR sources may enhance the sensitivity of a molecular signal obtained from small biosamples, e.g., a single cell, containing extremely small amounts of organic matter. We will also show that SR IR sources allow to study chemical composition and to identify the distribution of organic molecules in cells at submicron resolution is possible with a high signal-to-noise ratio. Moreover, the recent availability of two-dimensional IR detectors promises to push forward imaging capabilities in the time domain. Indeed, with a high current synchrotron radiation facility and a Focal Plane Array the chemical imaging of individual cells can be obtained in a few minutes. Within this framework important results are expected in the next years using synchrotron radiation and Free Electron Laser (FEL) sources for spectro-microscopy and spectral-imaging, alone or in combination with Scanning Near-field Optical Microscopy methods to study the molecular composition and dynamic changes in samples of biomedical interest at micrometric and submicrometric scales, respectively. © 2012 Elsevier Inc. Source


Michalski R.,Polish Academy of Sciences
Mini-Reviews in Medicinal Chemistry | Year: 2014

Ion chromatography is a well-established regulatory method for analyzing anions and cations in environmental, food and many other samples. It offers an enormous range of possibilities for selecting stationary and mobile phases. Additionally, it usually helps to solve various separation problems, particularly when it is combined with different detection techniques. Ion chromatography can also be used to determine many ions and substances in clinical and pharmaceutical samples. It provides: availability of high capacity stationary phases and sensitive detectors; simple sample preparation; avoidance of hazardous chemicals; decreased sample volumes; flexible reaction options on a changing sample matrix to be analyzed; or the option to operate a fully-automated system. This paper provides a short review of the ion chromatography applications for determining different inorganic and organic substances in clinical and pharmaceutical samples. Source


Jamroz P.,Polish Academy of Sciences
IEEE Sensors Journal | Year: 2011

A two-sensor correction method employs a relationship between the dynamic coefficients of the probes. This algebraic relationship is reduced to a proportion or a hyperbola and it depends on the sensors diameter ratio. It results from the application of fundamental equations governing the Nusselt number. This paper presents the analytical results of investigations on that relationship with particular use of the well-known experimental formulas governing the heat transfer between the gases and the pair of sensors. © 2010 IEEE. Source


Isoprene, an aliphatic unsaturated hydrocarbon (C5H8), is a key volatile released to the atmosphere by broad-leaf forest vegetation. Data obtained from field and laboratory experiments clearly prove that isoprene is a precursor of secondary organic aerosol (SOA). In this work evidence is provided that in-cloud transformations of isoprene coupled with S(IV)-autoxidation is a potentially important route for aqueous SOA through the formation of polar organosulfates and organosulfites with MWs of 182, 180 and 166, 164, respectively. Recently, MW 182 organosulfates have been observed in substantial abundance in ambient fine aerosol. Results from comprehensive LC/(-)ESI-QTRAP-MS/MS analysis revealed oxygenated polar species with a C5 skeleton bearing - OSO3H (MW 182, 180) and -OSO2H (MW 166, 164) moieties. The structures of these products were elucidated by detailed interpretation of negative-ion electrospray-ionization mass spectra, and additionally, in case of the MW 182 organosulfates, by comparison of chromatographic and mass spectrometric profiles with synthesized standards. The formation of C5 organosulfur products is explained through sulfate/sulfite radical-induced oxidation in the aqueous particle phase. © 2015 Elsevier Ltd. Source


Braunstein S.L.,University of York | Pirandola S.,University of York | Zyczkowski K.,Jagiellonian University | Zyczkowski K.,Polish Academy of Sciences
Physical Review Letters | Year: 2013

We show that, in order to preserve the equivalence principle until late times in unitarily evaporating black holes, the thermodynamic entropy of a black hole must be primarily entropy of entanglement across the event horizon. For such black holes, we show that the information entering a black hole becomes encoded in correlations within a tripartite quantum state, the quantum analogue of a one-time pad, and is only decoded into the outgoing radiation very late in the evaporation. This behavior generically describes the unitary evaporation of highly entangled black holes and requires no specially designed evolution. Our work suggests the existence of a matter-field sum rule for any fundamental theory. Published by the American Physical Society under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI. Source


Liu S.,Fuzhou University | Tang Z.-R.,Fuzhou University | Sun Y.,Argonne National Laboratory | Colmenares J.C.,Polish Academy of Sciences | Xu Y.-J.,Fuzhou University
Chemical Society Reviews | Year: 2015

The severe consequences of fossil fuel consumption have resulted in a need for alternative sustainable sources of energy. Conversion and storage of solar energy via a renewable method, such as photocatalysis, holds great promise as such an alternative. One-dimensional (1D) nanostructures have gained attention in solar energy conversion because they have a long axis to absorb incident sunlight yet a short radial distance for separation of photogenerated charge carriers. In particular, well-ordered spatially high dimensional architectures based on 1D nanostructures with well-defined facets or anisotropic shapes offer an exciting opportunity for bridging the gap between 1D nanostructures and the micro and macro world, providing a platform for integration of nanostructures on a larger and more manageable scale into high-performance solar energy conversion applications. In this review, we focus on the progress of photocatalytic solar energy conversion over controlled one-dimension-based spatially ordered architecture hybrids. Assembly and classification of these novel architectures are summarized, and we discuss the opportunity and future direction of integration of 1D materials into high-dimensional, spatially organized architectures, with a perspective toward improved collective performance in various artificial photoredox applications. This journal is © The Royal Society of Chemistry. Source


Morawiec A.,Polish Academy of Sciences
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2016

In their recent paper, Sutton et al. (2015 Proc. R. Soc. A 471, 20150442. (doi:10.1098/rspa.2015.0442)) criticized previousmetrics in the space ofmacroscopic boundary parameters and proposed a new function instead. However, some aspects of their analysis need to be clarified. In particular, reasons for introducing one of the criticized metrics are explained, and deficiencies of the new function are indicated. © 2016 The Author(s). Source


Barnes E.,University of Maryland University College | Cywinski L.,Polish Academy of Sciences | Das Sarma S.,University of Maryland University College
Physical Review Letters | Year: 2012

We solve the long-standing central spin problem for a general set of inhomogeneous bath couplings and a large class of initial bath states. We compute the time evolution of the coherence of a central spin coupled to a spin bath by resumming all orders of the time-convolutionless master equation, thus avoiding the need to assume weak coupling to the bath. The fully quantum, non-Markovian solution is obtained in the large-bath limit and is valid up to a time scale set by the largest coupling constant. Our result captures the full decoherence of an electron spin qubit coupled to a nuclear spin bath in a GaAs quantum dot for experimentally relevant parameters. In addition, our solution is quite compact and can readily be used to make quantitative predictions for the decoherence process and to guide the design of nuclear state preparation protocols. © 2012 American Physical Society. Source


Miszczak J.A.,Polish Academy of Sciences
Computer Physics Communications | Year: 2013

The presented package for the Mathematica computing system allows the harnessing of quantum random number generators (QRNG) for investigating the statistical properties of quantum states. The described package implements a number of functions for generating random states. The new version of the package adds the ability to use the on-line quantum random number generator service and implements new functions for retrieving lists of random numbers. Thanks to the introduced improvements, the new version provides faster access to high-quality sources of random numbers and can be used in simulations requiring large amount of random data. © 2012 Elsevier B.V. All rights reserved. Source


The role of human impact on the natural environment was studied in the Jaszcze and Jamne catchments in the Gorce Mountains (Western Polish Carpathians). Analysis of land use and land cover changes using GIS techniques and cartographic materials between 1954 and 2004 indicates an increase in forest area by 11.5% and 18.5%, respectively, at the expense of arable land and grassland areas. Agricultural abandonment often occurred on steep slopes (above 10°) with skeletal (shallow) soils at higher elevations (above 800m a.s.l.). In addition, the density of dirt roads decreased from 6.97km/km2 in 1981 to 4.3km/km2 in 2008. In former agricultural areas, long expanses of terraces have either disappeared or experienced shallow mass movements. The statistical reports and questionnaire survey indicate reduced income from farm activities in this region. As a result of LULC changes and stream transformation, the Jaszcze and Jamne stream channels were shortened, straightened, and narrowed, with tendency to incision estimated at 1cm per year over the past 40 years. The changes observed in the environment under human impact, accelerated following 1989, are representative of the Western Polish Carpathians. © 2014 Elsevier Ltd. Source


Jablonski A.,Polish Academy of Sciences
Computer Physics Communications | Year: 2013

Theoretical models of electron transport in condensed matter require an effective source of the Chandrasekhar H(x,omega) function. A code providing the H(x,omega) function has to be both accurate and very fast. The current revision of the code published earlier [A. Jablonski, Comput. Phys. Commun. 183 (2012) 1773] decreased the running time, averaged over different pairs of arguments x and omega, by a factor of more than 20. The decrease of the running time in the range of small values of the argument x, less than 0.05, is even more pronounced, reaching a factor of 30. The accuracy of the current code is not affected, and is typically better than 12 decimal places. © 2012 Elsevier B.V. All rights reserved. Source


Papp M.,Polish Academy of Sciences
Current Protocols in Pharmacology | Year: 2012

Described in this unit is a chronic mild stress (CMS) procedure used for predicting an antidepressant response. Following exposure to a variety of mild stressors for a period of several weeks, rat behavior is modified in a number of ways. Among these is a substantial reduction in consumption of a 1% sucrose solution. Chronic administration of antidepressant drugs reverses diminished enthusiasm for sucrose in these subjects. While most antidepressants must be administered for at least 3 to 5 weeks to normalize behavior, there are treatments that display a more rapid onset of action. More recently, it has been shown that the CMS-induced deficit in sucrose consumption can also be reversed by second-generation antipsychotics. Based on these findings, the CMS model can be employed in discovery programs aimed at identifying antianhedonic drugs (e.g., antidepressants and antipsychotics) that act more quickly than existing agents. © 2012 by John Wiley & Sons, Inc. Source


Misiorny M.,Julich Research Center | Misiorny M.,Adam Mickiewicz University | Barnaa J.,Adam Mickiewicz University | Barnaa J.,Polish Academy of Sciences
Physical Review Letters | Year: 2013

Spin-polarized transport through bistable magnetic adatoms or single-molecule magnets (SMMs), which exhibit both uniaxial and transverse magnetic anisotropy, is considered theoretically. The main focus is on the impact of transverse anisotropy on transport characteristics and the adatom's or SMM's spin. In particular, we analyze the role of quantum tunneling of magnetization (QTM) in the mechanism of the current-induced spin switching, and show that the QTM phenomenon becomes revealed as resonant peaks in the average values of the molecule's spin and in the charge current. These features appear at some resonant fields and are observable when at least one of the electrodes is ferromagnetic. © 2013 American Physical Society. Source


Sowinski T.,Polish Academy of Sciences
Physical Review Letters | Year: 2012

It is shown that the extended Hubbard Hamiltonian describing atoms confined in an optical lattice always contains commonly neglected terms which can significantly change the dynamical properties of the system. Particularly for bosonic systems, they can be exploited for creating orbital states on demand via the parametric resonance phenomenon. This indicates an additional application for optical lattices, namely, the study and emulation of interactions between particles and lattice vibrations. © 2012 American Physical Society. Source


Medford J.,Harvard University | Cywinski A.,Polish Academy of Sciences | Barthel C.,Harvard University | Marcus C.M.,Harvard University | And 2 more authors.
Physical Review Letters | Year: 2012

We investigate the scaling of coherence time T 2 with the number of π pulses n π in a singlet-triplet spin qubit using Carr-Purcell-Meiboom-Gill (CPMG) and concatenated dynamical decoupling (CDD) pulse sequences. For an even numbers of CPMG pulses, we find a power law T 2(n π)γ e, with γ e=0. 72±0.01, essentially independent of the envelope function used to extract T 2. From this surprisingly robust value, a power-law model of the noise spectrum of the environment, S(ω)∼ω -β, yields β=γ e/(1-γ e)=2.6±0.1. Model values for T 2n π using β=2.6 for CPMG with both even and odd n π up to 32 and CDD orders 3 through 6 compare very well with the experiment. © 2012 American Physical Society. Source


Fedriani J.M.,CSIC - Donana Biological Station | Zywiec M.,Polish Academy of Sciences | Delibes M.,CSIC - Donana Biological Station
Ecology | Year: 2012

The persistence of mutualisms despite the strong incidence of exploiters could be explained if exploiters deny one or more services (i.e., cheat) while eventually supplying some subtler but critical services. Pulp feeders usually ingest fruit reward without dispersing seeds and thus are considered to be mainly cheaters or thieves of seed-disperser mutualisms. By consuming the fruit pulp, however, they could release seeds from pulp inhibitory effect, enhancing germination and, potentially, subsequent seedling emergence, growth, survival, and thus local recruitment. We evaluated such a largely neglected hypothesis by considering the interaction between Pyrus bourgaeana and its pulp feeders. We experimentally showed that pericarp removal had a consistent strong positive effect on seed performance (e.g., lower rotting and higher germination percentages) and seedling fate (greater emergence, growth, and survival to two years old). Interestingly, these relatively large positive effects of depulpation on plant fitness persisted for a surprisingly long time. Though seedlings experienced higher mortality under fruiting conspecifics, the benefits of depulpation were not overridden by high propagule mortality beneath fruiting trees or in adverse microhabitats after two years of monitoring. Specifically, the cumulative probability of establishment for depulped seeds was 4-25 times higher than for seeds in whole ripe fruits. Thus, under some circumstances, pulp feeders can provide essential services to endozoochorous plants. Our study contributes to clarifying the apparent paradox of plant-frugivore mutualisms that persist in the face of exploitation by pulp feeders. Because "thieves" and "mutualists" refer to the extremes of a complex continuum, and because organisms displaying concurrent cheating and honest behaviors during different host stages are likely prevalent, the persistent language of mutualists vs. thieves, cheaters, or exploiters might be misleading. © 2012 by the Ecological Society of America. Source


Sorbjan Z.,Marquette University | Sorbjan Z.,Polish Academy of Sciences
Quarterly Journal of the Royal Meteorological Society | Year: 2010

Three gradient-based scaling systems for the stably stratified boundary layer are introduced and examinedbyusing data collected during the SHEBAfieldprogramme in theArctic. The resulting similarity functions forfluxes andvariances are expressed in an analytical form, which is expected to be essentially unaffected by self-correlation in a very stable regime. The flux Richardson number Rf is found to be proportional to the Richardson number Ri, with the proportionality coefficient varying slightly with stability, from 1.11 to 1.47. The Prandtl number decreases from 0.9 in nearly neutral conditions to 0.7 for larger values of Ri. The negative correlation coefficient between the vertical velocity and temperature, -rwθ, has a local maximum at Ri of about 0.08, and monotonically decreases with larger values of the Richardson number. The turbulent kinetic energy budget indicates that for Ri > 0.7, turbulence must be non-stationary, i.e. decaying or sporadic. Turbulence within the stably stratified boundary layer can be classified by four regimes: 'nearly neutral' (0 < Ri < 0.02), 'weakly stable' (0.02 < Ri < 0.12), 'very stable' (0.12 < Ri < 0.7), and 'extremely stable' (Ri > 0.7). © 2010 Royal Meteorological Society. Source


Domanska A.,Polish Academy of Sciences
RNA Biology | Year: 2015

Rsp5 ubiquitin ligase is required for ubiquitination of a wide variety of proteins involved in essential processes. Rsp5 was shown to be involved in regulation of lipid biosynthesis, intracellular trafficking of proteins, response to various stresses, and many other processes. In this article, we provide a comprehensive review of the nuclear and cytoplasmic functions of Rsp5 with a focus on biogenesis of different RNAs. We also briefly describe the participation of Rsp5 in the regulation of the RNA polymerase II complex, and its potential role in the regulation of other RNA polymerases. Moreover, we emphasize the function of Rsp5 in the coordination of the different steps of rRNA, mRNA and tRNA metabolism in the context of protein biosynthesis. Finally, we highlight the involvement of Rsp5 in controlling diverse cellular mechanisms at multiple levels and in adaptation of the cell to changing growth conditions. © 2015 Taylor & Francis Group, LLC. Source


Pniewski T.,Polish Academy of Sciences
Current Pharmaceutical Biotechnology | Year: 2012

Prevention of hepatitis B, one of the most prevalent human diseases, still requires cheap and commonly available vaccines. Oral vaccines, including plant-based formulations, have been considered as alternatives or supplements for standard injection vaccines, due to the assumed low-cost production and simplified vaccination. Although plant production of HBV antigens is sufficiently efficient, despite almost 20 years of research still no anti-HBV plant-based vaccine has been developed. The basic difficulty has been to elaborate an effective immunisation procedure. Immunisation by parenteral priming and oral boosting with raw plant tissue adjuvanted with the cholera toxin, although effective, seemed to be unfeasible and controversial. Exclusively oral immunisation using lyophilised tissue, despite its appropriate form, appeared also impractical because of too low efficiency. Oral tolerance turned out to be the main barrier for anti-HBV plantbased vaccines. Based on previous results and knowledge on the mucosal immune system, a possible vaccine may consist of two components, parenteral for priming and oral for boosting. Probably the oral constituent could independently serve for further booster vaccinations. Both vaccine components can be produced in plants and used after some processing - purification for the injection constituent and lyophilisation for the oral one. Lyophilised tissue can be converted into tablets, capsules, etc. Previous and recent data show that the injection-oral immunisation regime may be efficient. A combination of parenteral and oral vaccination offers good prospects for a truly efficacious plant-derived anti-HBs vaccine and even a partial substitution of parenteral vaccines by an oral formula may prove to be economically reasonable. © 2012 Bentham Science Publishers. Source


Kaluzna E.M.,Polish Academy of Sciences
Reviews in Medical Virology | Year: 2014

MicroRNAs (miRNAs) are a class of small, evolutionarily conserved, noncoding RNA that regulate several important cellular processes. The versatility of these molecules allowed the accurate predictions that they would also affect the replication and life cycle of HCV. In this review, emphasis has been given to two selected miRNAs: miR-155 and miR-196b. Recent data indicate that miR-155 is overexpressed in HCV-infected patients, inducing an inflammatory state, and promoting virus replication and persistence even after the completion of antiviral treatment. It is also associated with the increased proliferation and inhibited apoptosis of hepatocytes, which promotes the growth of liver tumors. In contrast, miR-196b is reported as a factor inhibiting HCV replication with cytoprotective, anti-inflammatory, and antioxidant properties. Growing evidence suggests that these molecules could be used as potential prognostic and predictive factors and their antagonists or mimics as a promising therapeutic approach in HCV-infected patients. © 2014 John Wiley & Sons, Ltd. Source


Shirokov M.E.,Russian Academy of Sciences | Shulman T.,Polish Academy of Sciences
Communications in Mathematical Physics | Year: 2015

We propose examples of low dimensional quantum channels demonstrating different forms of superactivation of one-shot zero-error capacities, in particular, the extreme superactivation (this complements the recent result of Cubitt and Smith). We also describe classes of quantum channels whose zero-error classical and quantum capacities cannot be superactivated. We consider implications of the superactivation of one-shot zero-error capacities to analysis of reversibility of a tensor-product channel with respect to families of pure states. Our approach based on the notions of complementary channel and of transitive subspace of operators makes it possible to study the superactivation effects for infinite-dimensional channels as well. © 2015, Springer-Verlag Berlin Heidelberg. Source


Kotko P.,Polish Academy of Sciences
Journal of High Energy Physics | Year: 2014

Abstract: We study matrix elements of Fourier-transformed straight infinite Wilson lines as a way to calculate gauge invariant tree-level amplitudes with off-shell gluons. The off-shell gluons are assigned “polarization vectors” which (in the Feynman gauge) are transverse to their off-shell momenta and define the direction of the corresponding Wilson line operators. The infinite Wilson lines are first regularized to prove the correctness of the method. We have implemented the method in a computer FORM program that can calculate gluonic matrix elements of Wilson line operators automatically. In addition we formulate the Feynman rules that are convenient in certain applications, e.g. proving the Ward identities. Using both the program and the Feynman rules we calculate a few examples, in particular the matrix elements corresponding to gauge invariant g*g*g*g and g*g*g*g*g processes. An immediate application of the approach is in the high energy scattering, as in a special kinematic setup our results reduce to the form directly related to Lipatov’s vertices. Thus the results we present can be directly transformed into Lipatov’s vertices, in particular into RRRP and RRRRP vertices with arbitrary “orientation” of reggeized gluons. Since the formulation itself is not restricted to high-energy scattering, we also apply the method to a decomposition of an ordinary on-shell amplitude into a set of gauge invariant objects. © 2014, The Author(s). Source


Van Hameren A.,Polish Academy of Sciences
Journal of High Energy Physics | Year: 2014

It is shown how tree-level multi-gluon helicity amplitudes with an arbitrary number of off-shell external gluons can be calculated via BCFW recursion. Compact expressions for helicity amplitudes for scattering processes of three and four gluons, with up to three of them off-shell, are presented. Also, maximum-helicity-violating configurations are identified for up to two off-shell gluons, and the expressions for their helicity amplitudes for an arbitrary number of on-shell gluons are derived. © 2014 The Author(s). Source


Paszko B.,Polish Academy of Sciences | Ma H.,Yunnan University
Journal of Systematics and Evolution | Year: 2011

Principal component analysis of specimen measurements revealed morphological variation within Chinese Calamagrostis epigeios correlated with differences in geographical distribution. We conducted a morphological examination of specimens from the range of the species, with the goal of developing a treatment for its Chinese members reflecting the global diversity complex. The confusing taxonomy of this complex is clarified with the recognition of three species in China, namely C. epigeios, C. extremiorientalis, and C. macrolepis. Calamagrostis epigeios is an exclusively temperate grass occurring in the northwestern, northern, and northeastern parts of China. It has spikelets 4-7 mm long, glumes equal or subequal, awn arising near the middle of the lemma back, upper leaf surface smooth and with shallow ribs and furrows. Calamagrostis extremiorientalis is a tropical and subtropical grass that occurs in the southwest provinces of China (except Xizang) throughout south central provinces and east to the northeastern parts of China. It is morphologically similar to C. epigeios. However, C. extremiorientalis has the awn arising from the upper one-third of the lemma back, upper leaf surface scabrid because of the presence of short stiff hairs, and with tall ribs and deep furrows. Calamagrostis macrolepis occurs in the northwestern, northern, and northeastern parts of China. It has a robust habit, spikelets 6.5-11mmlong, and glumes unequal, the upper 1-1.5mm shorter than the lower. New synonyms, descriptions, and citations of representative specimens are provided for each species, along with an identification key. © 2011 Institute of Botany, Chinese Academy of Sciences. Source


Jablonski A.,Polish Academy of Sciences
Journal of Electron Spectroscopy and Related Phenomena | Year: 2013

XPS spectrometers are typically equipped with the Mg Kα radiation and/or Al Kα radiation sources. However, for some analyses, it is convenient to use the laboratory sources emitting high energy X-rays, e.g. to avoid coincidence of peaks due to photoelectrons and Auger electrons, or to increase the information depth. On the other hand, the mathematical formalism of quantitative XPS analysis is based on the theoretical photoemission cross section that is valid for photoelectrons emitted with a relatively low kinetic energy (the so-called dipole approximation - DA). For high kinetic energy photoelectrons, the photoemission cross section needs to be modified with nondipolar parameters. An important issue for an analyst is the correction of the formalism of quantitative analysis for the photoelectron elastic scattering effects. The Monte Carlo program has been developed for simulation of transport of photoelectrons emitted from polycrystalline or amorphous solids by four X-ray radiation sources: Mg Kα, Al Kα, Zr Lα and Ti Kα. Calculations were performed for photoelectrons emitted in elemental solids with a wide range of atomic numbers: Al, Cu, Ag and Au. The photoelectron emission event was described within the DA and the model modified with the multipole correction (non-dipole approximation - NDA). It has been found that, in a typical XPS configuration, the dipole approximation is of sufficient accuracy for the Mg Kα and Al Kα radiation sources. The difference between photoelectron signal intensities calculated within the DA and NDA did not exceed 8% when elastic photoelectron elastic scattering is neglected. For high-energy radiation sources, Zr Lα and Ti Kα, the difference may reach 25% in this geometry, and thus the NDA model is recommended for calculations. The photoelectron elastic collisions are found to decrease the difference between the DA and NDA models. An important result of the present analysis is the observation that the NDA formalism can be corrected for elastic scattering effects in the same way as the DA formalism, i.e. with two parameters, Q x and βx. Furthermore, the expressions for calculating these parameters derived for the DA model and for the Mg Kα and Al Kα sources are found to be also applicable to photoelectron emitted by the Zr Lα and Ti Kα sources. However, new expressions valid for all four radiation sources have been tentatively derived in the present work. © 2013 Elsevier B.V. All rights reserved. Source


Wender M.,Polish Academy of Sciences
Journal of Neuroimmunology | Year: 2011

ADEM is a disease that is characterized by an inflammatory reaction and demyelination in the central nervous system, with a distinct tendency to a peripheral localization of pathological changes. ADEM happens to occur with a temporal, and probably also with a causative relationship to viral, exanthematous diseases, as well as to preventive vaccinations. However, there are still many unresolved problems with respect to the relationship of ADEM to multiple sclerosis (MS), especially in instances with a multiphasic course of the disease. Many question marks can also be raised in cases, in which the examinations were unable to determine the exact preceding or causative factor. A lot of studies on cytokines and chemokines in blood plasma and CSR from patients with ADEM have enabled investigators to get a better insight into some stages of immunopathological processes, leading to an evolvement of the disease, without a more important impact on the clinical diagnosis. © 2010 Elsevier B.V. Source


Bratek L.,Polish Academy of Sciences
Journal of Physics A: Mathematical and Theoretical | Year: 2010

According to the Staruszkiewicz definition, a relativistic dynamical system is said to be fundamental if its Casimir invariants are parameters, not constants of motion. This property is the classical counterpart of quantum irreducibility idea, which makes fundamental dynamical systems particularly interesting. An example of a fundamental dynamical system is provided by the fundamental relativistic rotator known also as the (m, s) particle. Recently, however, it turns out that the rotator is defective as a dynamical system. Therefore, as a first step toward finding a well behaving fundamental dynamical system, a class of breathing rotators, being a natural extension of the smallest class containing the fundamental relativistic rotator, is considered. A breathing rotator is a relativistic dynamical system consisting of its worldline and a single null vector. Surprisingly, fundamental dynamical systems from this extended class also turn out to be defective. © 2010 IOP Publishing Ltd. Source


Bolejko K.,Polish Academy of Sciences
Astronomy and Astrophysics | Year: 2010

Context. Dark energy is now one of the most important and topical problems in cosmology. The first step to reveal its nature is to detect the evolution of dark energy or to prove beyond doubt that the cosmological constant is indeed constant. However, in the standard approach to cosmology, the Universe is described by the homogeneous and isotropic Friedmann models. Aims. We aim to show that in the perturbed universe (even if perturbations vanish if averaged over sufficiently large scales) the distance-redshift relation is not the same as in the unperturbed universe. This has a serious consequence when studying the nature of dark energy and, as shown here, can impair the analysis and studies of dark energy. Methods. The analysis is based on two methods: the linear lensing approximation and the non-linear Szekeres Swiss-Cheese model. The inhomogeneity scale is ∼50 Mpc, and both models have the same density fluctuations along the line of sight. Results. The comparison between linear and non-linear methods shows that non-linear corrections are not negligible. When inhomogeneities are present the distance changes by several percent. To show how this change influences the measurements of dark energy, ten future observations with 2% uncertainties are generated. It is shown the using the standard methods (i.e. under the assumption of homogeneity) the systematics due to inhomogeneities can distort our analysis, and may lead to a conclusion that dark energy evolves when in fact it is constant (or vice versa). Conclusions. Therefore, if future observations are analysed only within the homogeneous framework then the impact of inhomogeneities (such as voids and superclusters) can be mistaken for evolving dark energy. Since the robust distinction between the evolution and non-evolution of dark energy is the first step to understanding the nature of dark energy a proper handling of inhomogeneities is essential. © ESO 2010. Source


Aenczykowski P.,Polish Academy of Sciences
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The sets of charged-lepton (L) and quark (D,U) masses may be parametrized in a Z3-symmetric language appropriate for the discussion of Koide's formula. Experiment suggests that at the low-energy scale the relevant phase parameters δf take on possibly exact values of δL=3δD/2=3δU=2/9. For k f (the other parameter relevant for the pattern of masses), a similarly simple expression (kL=1) is known for charged leptons only. Using the Fritzsch-Xing decomposition of quark-mixing matrices, we show that the suggested pattern of low-energy quark masses is consistent with an earlier conjecture that kD,U≈1 in the weak basis. © 2013 American Physical Society. Source


Mlynarski J.,Jagiellonian University | Mlynarski J.,Polish Academy of Sciences | Gut B.,Jagiellonian University
Chemical Society Reviews | Year: 2012

The key role of carbohydrates in biological processes and their visible existence in our everyday life have stimulated the interest of leading research groups on the smart and simple synthesis of common and rare sugar molecules. Now, more than 120 years after Fischer's first synthesis of (d)-glucose (1890), we are witnessing important development in this field of total synthesis. Using modern methods of direct activation of carbonyl compounds chemists can prepare sugars in an elegant and efficient way similar to that of Nature. This tutorial review presents recent impressive progress in the area of de novo synthesis of carbohydrates by using organocatalytic direct aldol reaction as a key step. © 2012 The Royal Society of Chemistry. Source


Maassen A.,Polish Academy of Sciences
Acta biochimica Polonica | Year: 2011

Besides the previously described nitric oxide-detoxification activity we identified new features of class-1 non-symbiotic hemoglobin from Medicago sativa (Mhb1). Under in vitro conditions, using peroxidase in-gel activity assay, the Mhb1 protein was shown to possess also peroxidase-like activity. Due to this activity, in the presence of nitrite and hydrogen peroxide, the protein can mediate autonitration and nitration of other proteins at tyrosine residues, as revealed by tandem mass spectrometry and immune assay approaches. Mhb1 through its multifunctional activities can affect different components of signal transduction cascades operating during plant response to infections. This influence is manifested by Mhb1-mediated selective up-regulation of expression of certain pathogen inducible genes in Pseudomonas syringae infected Arabidopsis thaliana plants which overproduce Mhb1, as revealed by reverse transcription-quantitative real-time PCR analysis. Changes in expression level of these genes can influence such processes as synthesis of secondary metabolites, protein degradation and biosynthesis of ethylene. They can also result in alteration of pathogen-induced defense response of Mhb1 transgenic plants. Source


Krolikowska M.,Polish Academy of Sciences | Dybczynski P.A.,Adam Mickiewicz University
Monthly Notices of the Royal Astronomical Society | Year: 2010

Since 1950, when Oort published his hypothesis, several important new facts have been established in this field. At present, there are still questions surrounding the apparent source region (or regions) of long-period comets, the definition of dynamically new comets and the characteristics of the hypothetical Oort Cloud. Our aim in this investigation is to look for the apparent source of selected long-period comets and to refine the definition of dynamically new comets.Based on pure gravitational original orbits, all comets studied in this paper are widely called dynamically new. However, we show that the incorporation of non-gravitational forces into the orbit determination process significantly changes the situation.We have determined the precise non-gravitational orbits of all investigated comets. Then, we have followed numerically their past and future motions during one orbital period. Applying the ingenious method of Sitarski of creating swarms of virtual comets compatible with observations, we have been able to derive the uncertainties of original and future orbital elements, as well as the uncertainties of previous and next perihelion distances.We conclude that the past and future evolutions of cometary orbits under Galactic tide perturbations is the only way to find which comets are really dynamically new. In our sample, fewer than 30 per cent of comets are, in fact, dynamically new. Most of these have small previous perihelion distances. However, 60 per cent of these will be lost on hyperbolic orbits in the future. This evidence suggests that the investigation into the apparent source of long-period comets is challenging.We have also shown that a significant percentage of long-period comets can visit the zone of visibility during at least two or three consecutive perihelion passages. © 2010 The Authors. Journal compilation © 2010 RAS. Source


Gorecki M.,Polish Academy of Sciences
Organic and Biomolecular Chemistry | Year: 2015

To better understand structure-activity relationship (SAR) results, closely related to the structural features of (-)-Oseltamivir, four chiroptical methods, i.e. electronic circular dichroism (ECD), optical rotatory dispersion (ORD), vibrational circular dichroism (VCD), and Raman optical activity (ROA), utilizing different solvents, were employed in an effort to discover a set of the most probable conformations. Such multi-chiroptical approaches supported by quantum chemical calculations pointed out that different conformers are stable in chloroform, acetonitrile and water solutions of (-)-Oseltamivir. In this way, the most probable structures responsible for reported SAR results were established for the first time. It turned out that one of the predominant conformers in a solution is in excellent agreement with the X-ray analysis derived solid-state structure determined for (-)-Oseltamivir phosphate. © 2015 The Royal Society of Chemistry. Source


Zawilska J.B.,Medical University of Lodz | Zawilska J.B.,Polish Academy of Sciences
Current Drug Abuse Reviews | Year: 2011

Recently, a new class of "designer drugs" has emerged on the drug use market, known as "legal highs" or "herbal highs". They include a wide range of products, from natural plant-originated substances to synthetic compounds, that can be purchased both online and from high street retailers. "Legal highs" mimic psychoactive effects of illicit drugs of abuse. However, they are claimed to consist of compounds that are legal to sell, possess and use. Based on the spectrum of their actions on the cognitive processes, mood, and behavior "legal highs" can be classified into three basic categories: amphetamine- and ecstasy-like psychostimulants, hallucinogens, and synthetic cannabinoids ("spice"). This review surveys the current state of knowledge regarding the pharmacological properties of "legal highs". It also addresses the negative consequences of using these products. © 2011 Bentham Science Publishers Ltd. Source


Kaminski R.,Polish Academy of Sciences
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The model is presented to describe the f2(1270) meson photoproduction as a result of pion-pion interactions in the final state. Treating tensor mesons as objects dynamically created due to final state interactions is a convenient and straightforward way to employ data from ππ scattering like phase shifts and inelasticities for description of (photo)production reactions while retaining proper analytical structure of amplitudes, two-particle unitarity, and crossing symmetry. The model presented here can provide experimentally testable quantities like differential cross sections and ππ mass distributions as well as the strengths of partial waves corresponding to various f2(1270) helicities which are essential for partial wave analyses. It can also be used to compute moments of angular distribution and spin density matrix elements where partial wave interference effects are important. © 2013 American Physical Society. Source


Kuczynski W.,Polish Academy of Sciences
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2010

In spite of numerous papers dedicated to the subject, the behavior of the helical pitch in the smectic C- phase near the smectic A phase is still controversial. In particular, it is not clear to what extent the measured pitch values are influenced by surface effects. In order to shed light on this problem, careful pitch measurements have been performed using different methods and sample preparations. We have found that the diffraction of light on planar-oriented samples may give incorrect pitch results because of strong influence of the surfaces and possibly of the sample texture on the helical structure. We have demonstrated that using appropriate preparation of samples the bulk properties of the helix can be determined. It has been found that a maximum of pitch can indeed occur but then only when very close to the transition point smectic C- →smectic A (about 0.1 K). The results of helical pitch measurements have been compared with predictions of theories. © 2010 The American Physical Society. Source


A double asymmetric induction in the synthesis of α-aminophosphonic acids is described. It involves the nucleophilic addition of anions of enantiomeric dimenthyl phosphites to both (+)-(S)- and (-)-(R)-enantiomers of N-(p-tolylsulfinyl)benzaldimine and subsequent acidic hydrolysis of the adducts formed. The match and mismatch effects were observed. © 2013 Wiley Periodicals, Inc. Source


A new type of nucleoside-metallacarborane conjugate is presented. 3,3,3-Tricarbonyl-closo- 3,1,2-ReC2B9H10 is used as a modifying unit. The method is based on the de novo formation of a metallacarborane complex via the reaction of [NEt4] 2[ReBr3(CO)3] with the uridine-bearing carborane as a boron cluster ligand. The uridine-tricarbonyl rhenacarborane represents an example of a novel type of nucleoside-metallacarborane conjugate bearing a therapeutically important rhenium component. © ARKAT-USA, Inc. Source


Kielbasinski P.,Polish Academy of Sciences
Phosphorus, Sulfur and Silicon and the Related Elements | Year: 2011

Enzymes, which are very efficient catalysts developed by nature to control chemical transformations in vivo, are also capable of adopting non-natural substrates, among them heteroorganic derivatives, and are also capable of working in non-aqueous media. Being intrinsically chiral, enzymes recognize any type of chirality of the substrates. This feature has been utilized for the stereoselective transformations of a variety of organosulfur compounds, resulting in the preparation of chiral non-racemic sulfur products. Copyright © Taylor and Francis Group, LLC. Source


A logarithmic transformation of flow is applied to the estimation of baseflow. Such a transformation has been applied in several hydrological studies since the discovery that flow is well described by a log-normal distribution. However, the main purpose of previous applications was normalisation of the error between simulated and observed flows. The new approach proposed here consists of an application of log-transform that leads to a formulation of the rainfall-flow process as a rate of change, instead of a typical mass balance problem. It applies a stochastic transfer function approach to log-transformed flow, enabling the problem to be stated in a statistically rigorous form. The difficulty in obtaining good hydrological predictions in extreme conditions lies both in the nonlinear character of processes governed by extreme hydrological signals and in the scarcity and inaccuracy of extreme flow measurements, particularly in early records. It has previously been shown that a log-transformed lowflow (LTLF) model allows for the decomposition of the simulated flow into slow and fast components that can be interpreted as baseflow and runoff. This paper compares the baseflow estimates obtained from the LTLF model with those obtained from other flow separation techniques, i.e. theWittenberg nonlinear storage model and the Chapman linear filter. Also, the conditions for the applicability of the LTLF formulation are stated and the discussion is illustrated using some "monstrous", i.e. difficult to model, catchments from the UK and Poland. A rainfall-flow model based on the logarithm of flow gives a good representation of baseflow for catchments with a well-defined baseflow component. © 2010 IAHS Press. Source


Bednarek P.,Polish Academy of Sciences
Current Opinion in Plant Biology | Year: 2012

In plants, a host's responses to an attempted infection include activation of various secondary metabolite pathways, some of which are specific for particular plant phylogenetic clades. Phytochemicals that represent respective end products in plant immunity have been stereotypically linked to antimicrobial properties. However, in many cases, owing to the lack of unequivocal evidence for direct antibiotic action in planta, alternative functions of secondary metabolites should be considered. Correspondingly, recent findings have identified novel, and rather unexpected, functions of phytochemicals in plant immunity that mediate regulatory pathways for conserved defence responses. It also seems likely that these conserved responses can be regulated by clade-specific phytochemicals. © 2012 Elsevier Ltd. Source


Kielbowicz-Matuk A.,Polish Academy of Sciences
Plant Science | Year: 2012

Abiotic and biotic stresses frequently impose constraints on plant distribution and affect agricultural productivity. Various aspects of the multiplicity and the complexity of stress responsive gene networks have been previously studied. Many of individual transcription factors in plants and their family classes that regulate the expression of several genes in responses to environmental stresses have been identified. One such class of transcription regulators is the C2H2 class of zinc finger proteins. Numerous members of the C2H2-type zinc finger family have been shown to play diverse roles in the plant stress response and the hormone signal transduction. Transcription profiling analyses have demonstrated that the transcript level of many C2H2-type zinc finger proteins is elevated under different abiotic stress conditions such as low temperature, salt, drought, osmotic stress and oxidative stress. Some C2H2-type proteins are additionally involved in the biotic stress signaling pathway. Moreover, it has been reported that overexpression of some C2H2-type zinc finger protein genes resulted in both the activation of some stress-related genes and enhanced tolerance to various stresses. Current genetic studies have focused on possible interactions between different zinc finger transcription factors during stresses to regulate transcription. This review highlights the role of the C2H2 class of the zinc finger proteins in regulating abiotic and biotic stress tolerance in the plants. © 2011 Elsevier Ireland Ltd. Source


Pieczyska E.,Polish Academy of Sciences
Journal of Modern Optics | Year: 2010

Infrared imaging and thermomechanical behavior of stress-induced martensite transformation occurring in shape memory alloys is presented. TiNi shape memory alloy specimens have been subjected to a modified program of a stress-controlled tension test, i.e. at various stages of the martensite transformation the loading was kept constant for 3 min. After that the specimen was reloaded to the martensite transformation limit, followed by unloading, when the reverse transformation occurred. During the loading and unloading processes the specimen mechanical parameters and the infrared radiation from the specimen surface were continuously recorded. By comparison of the obtained stress-strain curves and the elaborated temperature characteristics, the current state and the progress of the martensite transformation developing in the shape memory alloy under these conditions has been studied. © 2010 Taylor & Francis. Source


Pugaczowa-Michalska M.,Polish Academy of Sciences
Intermetallics | Year: 2012

The electronic band structure and magnetic properties of Mn 2FeB, Mn 2CoB and Mn 2NiB Heusler alloys are examined using the full-potential non-orthogonal local-orbital basis method (FPLO). Results of the calculations predict that the Hg 2CuTi crystal structure is more stable than the L2 1 structure and the ground state of these alloys is ferrimagnetic. Both, the theoretical lattice parameter and the magnetic moment on Mn in site A increase with the replacement of Fe by Co atom and then by Ni atom. Band structure of Mn 2FeB and Mn 2CoB shows half-metallic features in some high-symmetry directions in the Brillouin zone. The highest spin-polarization at Fermi energy (88%) is expected for Mn 2FeB. © 2012 Elsevier Ltd. All rights reserved. Source


Schimrosczyk D.,Polish Academy of Sciences
Annales Zoologici | Year: 2010

Anchophthalmus muelleri sp. nov. from Tanzania is described and illustrated. The distribution map is provided. © Fundacja Natura optima dux. Source


A lagged regression analysis between an index of observed summertime Atlantic water temperature (AWT) variability at the entrance to the Barents Sea in the period 1982–2005 and year-round atmospheric (NCEP/NCAR) reanalysis data is used to show that subsurface oceanic heat anomalies in high latitudes are significant precursors of wintertime atmospheric variability in middle latitudes. In particular, positive AWT anomalies precede predominantly westerly wind anomalies in high latitudes and easterly wind anomalies in middle latitudes. The mid-latitude wind anomalies, while being generally equivalent barotropic in the upper troposphere, have a strong low-level baroclinic contribution over Eurasia. The near-surface easterly wind anomalies in this area are locally deflected southward, maintaining cold spots near orography. The summertime oceanic anomalies explain about 40 % of the variance in the surface air temperature averaged over Eurasia from 35° to 45°N and about 50 % of the variance in surface winds over the Far East Asia in the following winter. We suggest that the remote connections arise from reorganization of the mid-latitude storm tracks. The AWT anomalies explain about 60 % of the variance in the upper-tropospheric storm track activity averaged over the Pacific and Eurasia from 35° to 55°N and in the lower-tropospheric poleward synoptic eddy heat flux over western Eurasia. Finally, we show that the AWT-associated wintertime atmospheric anomalies appear in quadrature with the concurrent anomalies associated with the North Atlantic Oscillation. These findings suggest that oceanic heat anomalies in high latitudes may be a useful predictor of atmospheric variability. © 2015 The Author(s) Source


Pawela L.,Polish Academy of Sciences | Sladkowski J.,University of Silesia
Physica A: Statistical Mechanics and its Applications | Year: 2013

We study the possible advantages of adopting quantum strategies in multi-player evolutionary games. We base our study on the three-player Prisoner's Dilemma (PD) game. In order to model the simultaneous interaction between three agents we use hypergraphs and hypergraph networks. In particular, we study two types of networks: a random network and a SF-like network. The obtained results show that in the case of a three-player game on a hypergraph network, quantum strategies are not necessarily stochastically stable strategies. In some cases, the defection strategy can be as good as a quantum one. © 2012 Elsevier B.V. All rights reserved. Source


Cywinski L.,Polish Academy of Sciences
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

I present a theory of environmental noise spectroscopy via dynamical decoupling of a qubit at an optimal working point. Considering a sequence of n pulses and pure dephasing due to quadratic coupling to Gaussian distributed noise ξ(t), I use the linked-cluster (cumulant) expansion to calculate the coherence decay. Solutions allowing for reconstruction of spectral density of noise are given. For noise with correlation time shorter than the time scale on which coherence decays, the noise filtered by the dynamical decoupling procedure can be treated as effectively Gaussian at large n, and well-established methods of noise spectroscopy can be used to reconstruct the spectrum of ξ2(t) noise. On the other hand, for noise of dominant low-frequency character (1/fβ noise with β>1), an infinite-order resummation of the cumulant expansion is necessary, and it leads to an analytical formula for coherence decay having a power-law tail at long times. In this case, the coherence at time t depends both on spectral density of ξ(t) noise at ω=nπ/t, and on the effective low-frequency cutoff of the noise spectrum, which is typically given by the inverse of the data acquisition time. Simulations of decoherence due to purely transverse noise show that the analytical formulas derived in this paper apply in this often encountered case of an optimal working point, provided that the number of pulses is not very large, and that the longitudinal qubit splitting is much larger than the transverse noise amplitude. © 2014 American Physical Society. Source


Krupa-Kozak U.,Polish Academy of Sciences
Nutrition | Year: 2014

Low bone mineral density (BMD), osteopenia, and osteoporosis are frequent complications of celiac disease (CD). The etiology of pathologic bone alterations in CD is multifactorial; however, two main mechanisms are involved: intestinal malabsorption and chronic inflammation. A strict gluten-free diet (GFD) is thought to be the only effective treatment for CD; but treating bone complications related to CD remains complex.The objective of this review is to elucidate the bones problems related to CD and to increase awareness of osteoporosis development, considered as a sign of atypical CD presentation. Currently, a question of whether GFD alone is an effective treatment to correct the bone alterations in patients with CD is under debate. This review presents factors contributing to pathologic bone derangement, recent research on the epidemiology of low BMD, osteoporosis, and fractures, and the treatment of bone problems in patients with CD. The roles of calcium and transport mechanisms are additionally presented. © 2014 The Authors. Source


Paszkowicz W.,Polish Academy of Sciences
Materials and Manufacturing Processes | Year: 2013

Genetic algorithms (GAs) are a helpful tool in optimization, simulation, modelling, design, and prediction purposes in various domains of science including materials science, medicine, technology, economy, industry, environment protection, etc. Reported uses of GAs led to solving of numerous complex computational tasks. In materials science and related fields of science and technology, GAs are routinely used for materials modeling and design, for optimization of material properties, the method is also useful in organizing the material or device production at the industrial scale. Here, the most recent (years 2008-2012) applications of GAs in materials science and in related fields (solid state physics and chemistry, crystallography, production, and engineering) are reviewed. The representative examples selected from recent literature show how broad is the usefulness of this computational method. © 2013 Taylor and Francis Group, LLC. Source


Kozak L.P.,Polish Academy of Sciences
Frontiers in Endocrinology | Year: 2011

Evidence that adult humans have functional brown adipose tissue has stirred interest in the possibility that the impressive effectiveness of induction of brown adipocytes to reduce obesity in mice may be translated to the human condition. A major focus recently on the identification of signaling and transcription factor that stimulate the induction of brown adipocytes has come from transgenic and gene KO models. However, these models have created a very complex picture of the regulatory mechanisms for brown fat induction. In this review insights into the critical regulatory pathways involved in brown adipocyte induction in the retroperitoneal fat depot of mice are described from quantitative trait locus (QTL) analy- sis of allelic variability determining Ucp1 levels and brown adipocyte induction in A/J vs. B6 mice.The key observation is that recombinant genotypes, found in recombinant inbred stains and backcross and intercross progeny, show transgressive variation for Ucp1 mRNA levels. These genetic crosses also show that the levels of Ucp1 mRNA are determined by interactions that control the levels of PPARα, PGC-1α, and type 2 deiodinase (DIO2) and that each factor is controlled by a subset of QTLs that also control Ucp1 expression.These results indicate that induction of Ucp1 in the retroperitoneal fat depot involves synergy between signaling and transcription factors that vary depending upon the environmental conditions. Inherent in this model is the idea that there is a high level of redundancy that can involve any factor with the potential to influence expression of the core factors, PPARα, PGC-1a, and DIO2. © 2011 Kozak. Source


Piotrowski A.P.,Polish Academy of Sciences
Information Sciences | Year: 2013

Differential Evolution (DE) is one of the most popular optimization methods for real-valued problems and a large number of its variants have been proposed so far. However, bringing together different ideas that already led to successful DE versions is rare in the literature. In the present paper a novel DE algorithm is proposed, in which three among the most efficient concepts already applied separately within DE framework are gathered together, namely: (1) the adaptation of algorithm control parameters and probabilities of using different mutation strategies; (2) the use of Nelder-Mead algorithm as a local search method hybridized with DE; and (3) the splitting mutation into Global and Local models, when Local mutation model is based on the concept of neighborhood of individuals organized on a ring topology. The performance of the novel algorithm, called Adaptive Memetic DE with Global and Local neighborhood-based mutation operators is compared with 13 different DE variants on a set of 25 popular problems which include rotated, shifted and hybrid composition functions. It is found that, although none DE algorithm outperforms all the others for the majority of problems, on average the proposed approach perform better than all 13 DE algorithms selected for comparison. The proposed algorithm is another heuristic approach developed to solve optimization problems. The question may arise, whether proposing novel methods is useful as No Free Lunch theorems for optimization state that the expected performance of all possible heuristics on all possible problems is equal. In the last section of the paper the limitations and implications of No Free Lunch theorems are discussed based on rich, but unfortunately frequently neglected literature. A very simple continuous and differentiable minimization problem is proposed, for which it is empirically verified that each among considered 14 DE algorithms perform poorer than random sampling. It is also empirically shown that when all considered DE algorithms search for the maximum of the proposed problem, they found lower minimum than DE algorithms searching for the minimum. Such result is not unexpected according to No Free Lunch theorems and should be considered as a precaution from generalization of good performance of heuristic optimization methods. © 2013 Elsevier Inc. All rights reserved. Source


BACKGROUND:: Recent studies indicated the involvement of some chemokines in the development of diabetic neuropathy; however, participation of the chemokine-C-motif ligand (XCL) subfamily remains unknown. The goal of this study was to examine how microglial inhibition by minocycline hydrochloride (MC) influences chemokine-C-motif ligand 1 (XCL1)–chemokine-C-motif receptor 1 (XCR1)/G protein–coupled receptor 5 expression and the development of allodynia/hyperalgesia in streptozotocin-induced diabetic neuropathy. METHODS:: The studies were performed on streptozotocin (200 mg/kg, intraperitoneally)-induced mouse diabetic neuropathic pain model and primary glial cell cultures. The MC (30 mg/kg, intraperitoneally) was injected two times daily until day 21. XCL1 and its neutralizing antibody were injected intrathecally, and behavior was evaluated with von Frey and cold plate tests. Quantitative analysis of protein expression of glial markers, XCL1, and/or XCR1 was performed by Western blot and visualized by immunofluorescence. RESULTS:: MC treatment diminished allodynia (0.9 ± 0.1 g; n = 7 vs. 3.8 ± 0.7 g; n = 7) and hyperalgesia (6.5 ± 0.6 s; n = 7 vs. 16.5 ± 1 s; n = 7) in the streptozotocin-induced diabetes. Repeated MC administration prevented microglial activation and inhibited the up-regulation of the XCL1/XCR1 levels. XCL1 administration (10 to 500 ng/5 μl; n = 9) in naive mice enhanced nociceptive transmission, and injections of neutralizing XCL1 (4 to 8 μg/5 μl; n = 10) antibody into the mice with diabetic neuropathic pain diminished allodynia/hyperalgesia. Microglia activation evoked in primary microglial cell cultures resulted in enhanced XCL1 release and XCR1 expression. Additionally, double immunofluorescence indicated the widespread coexpression of XCR1-expressing cells with spinal neurons. CONCLUSIONS:: In diabetic neuropathy, declining levels of XCL1 evoked by microglia inhibition result in the cause of analgesia. The putative mechanism corroborating this finding can be related to lower spinal expression of XCR1 together with the lack of stimulation of these XCR1 receptors, which are localized on neurons. Copyright © by 2016, the American Society of Anesthesiologists, Inc. Wolters Kluwer Health, Inc. All Rights Reserved. Source


Tinti L.,Jan Kochanowski University | Florkowski W.,Jan Kochanowski University | Florkowski W.,Polish Academy of Sciences
Physical Review C - Nuclear Physics | Year: 2014

The earlier projection method introduced for boost-invariant and cylindrically symmetric systems is used to introduce a new formulation of anisotropic hydrodynamics that allows for three substantially different values of pressure acting locally in three different directions. Our considerations are based on the Boltzmann kinetic equation with the collision term treated in the relaxation-time approximation and the momentum anisotropy is included explicitly in the leading term of the distribution function. A novel feature of our work is the complete analysis of the second moment of the Boltzmann equation, in addition to the zeroth and first moments that have been analyzed in earlier studies. We define the final equations of anisotropic hydrodynamics in the leading order as a subset of the analyzed moment equations (and their linear combinations) which agree with the Israel-Stewart theory in the case of small pressure anisotropies. © 2014 American Physical Society. Source


Nopoush M.,Kent State University | Nopoush M.,Polish Academy of Sciences | Ryblewski R.,Kent State University | Strickland M.,Kent State University
Physical Review C - Nuclear Physics | Year: 2014

We derive a system of moment-based dynamical equations that describe the 1+1d space-time evolution of a cylindrically symmetric massive gas undergoing boost-invariant longitudinal expansion. Extending previous work, we introduce an explicit degree of freedom associated with the bulk pressure of the system. The resulting form generalizes the ellipsoidal one-particle distribution function appropriate for massless particles to massive particles. Using this generalized form, we obtain a system of partial differential equations that can be solved numerically. In order to assess the performance of this scheme, we compare the resulting anisotropic hydrodynamics solutions with the exact solution of the 0+1d Boltzmann equation in the relaxation-time approximation. We find that the inclusion of the bulk degree of freedom improves the agreement between anisotropic hydrodynamics and the exact solution for a massive gas. © 2014 American Physical Society. Source


Nasalski W.,Polish Academy of Sciences
Applied Physics B: Lasers and Optics | Year: 2014

Reformulation of conventional beam definitions into their bidirectional versions and use of Hertz potentials make beam fields exact vector solutions to Maxwell's equations. This procedure is applied to higher-order elegant Laguerre-Gaussian beams of transverse magnetic and transverse electric polarization. Their vortex and anti-vortex co-axial compositions of equal and opposite topological charges are given in a closed analytic form. Polarization components of the composed beams are specified by their radial and azimuthal indices. The longitudinal components are common for beam compositions of both types; meanwhile, their transverse components are different and comprise two - nonparaxial and paraxial - separate parts distinguished by a paraxial parameter and its inverse, respectively. The new solutions may appear useful in modeling and tailoring of arbitrary vector beams. © 2014 The Author(s). Source


Bozek P.,Polish Academy of Sciences | Bozek P.,University of Rzeszow
Acta Physica Polonica B | Year: 2012

The hydrodynamic model for the expansion of the fireball in relativistic heavy-ion collisions is presented. Calculations using relativistic hydrodynamics of a fluid with small viscosity yield a satisfactory description of the experimental data on the particle spectra, the elliptic flow or the interferometry radii. Source


Korzynski M.,Polish Academy of Sciences
Classical and Quantum Gravity | Year: 2014

We discuss the continuum limit of the initial data for a vacuum, closed cosmological model with black holes as the only sources of the gravitational field. The model we consider is an exact solution of the constraint equations and represents a vacuum universe with a number of black holes placed on a spatial slice of S3 topology considered at the moment of its largest expansion when the black holes are momentary at rest. We explain how and under what conditions the Friedmann-Lemaître-Robertson-Walker (FLRW) metric arises as the continuum limit when the number of black holes contained in the model goes to infinity. We also discuss the relation between the effective cosmological parameters of the model, inferred from the large scale geometry of the spacetime, and the masses of individual black holes. In particular, we prove an estimate for the difference between the total effective mass of the system and the sum of the masses of all black holes, thus quantifying the effects of the inhomogeneities in the matter distribution or the cosmological backreaction. © 2014 IOP Publishing Ltd. Source


Meissner M.,Polish Academy of Sciences
Acta Physica Polonica A | Year: 2014

The paper presents a theoretical basis of calculations of the sound intensity in enclosed spaces and shows results of numerical visualization of the active intensity in a room with absorptive walls formed by two coupled rectangular subrooms. The study was focused on the low-frequency range, therefore to describe the active and reactive intensities, the modal theory of room acoustics was applied. Space distribution of eigenfunctions, modal frequencies and modal damping coeffcients were calculated numerically using the forced oscillator method (FOM) and the finite difierence time-domain (FDTD) method. Based on theoretical and numerical results, the computer program has been developed to simulate the active intensity vector field when the room is excited by a harmonic point source. Calculation data have shown that the active intensity was extremely sensitive to position of the source since at a fixed source frequency, different source locations always generate different distributions of characteristic objects of the active sound field such as energy vortices and stagnation points. Because of complex room shape, the vortex centers are in most cases positioned irregularly inside the room. Almost regular arrangement of vortices was found only in the case when the source frequency was tuned to the frequencies of modes which were strongly localized in one of the subrooms. Source


The Carpathians belong to the main elements of the European Alpine System and have an important biogeographical location between the Balkan ranges in the South, the Alps in the West and the Scandinavian range in the North. However, until recently this area was rarely included in detailed phylogeographical studies that could bring insights into its biogeographical history, links with other mountain ranges and contemporary genetic structure of populations. Here, available phylogeographical studies on high-mountain plants that include data concerning the Carpathians are reviewed in order to (1) discuss regional phylogeographical structure and divergence of the Carpathian populations from those in other European mountain ranges, and (2) outline further perspectives of the Carpathian phylogeography. Analysis of available studies revealed the complexity of the biogeographical history of high-mountain plants. The studies show a deep phylogeographical structure in the Carpathians, mostly concurring with classical biogeographical boundaries, and suggesting a long-term isolation and restricted gene flow between the main Carpathian regions. For some species, though, recent dispersal events among isolated mountain ranges were detected. Such contrasting patterns were found at a larger geographical scale as well (e.g., between the Carpathians and the Alps). Several examples suggest the importance of the Carpathians in migration of arctic-alpine plants from the East and towards the North. In most reviewed studies, however, the Carpathians are only marginally represented and detailed intraspecific studies based on dense population coverage in all disjunct areas of species' ranges are clearly needed to obtain reliable information and confirm the preliminary phylogeographical patterns emerging from the overview presented here. Source


Erdmann V.A.,Free University of Berlin | Barciszewski J.,Polish Academy of Sciences
Angewandte Chemie - International Edition | Year: 2011

On May 27, 1961 Nirenberg and Matthaei performed an in vitro translation experiment in which bacterial ribosomes were supplemented with a fraction of low-molecular-weight RNAs; they demonstrated that polyuridilic acid codes for polyphenylalanine-the first information on the genetic code. This Essay recalls the major achievements prior to the discovery of the genetic code, the experiments leading to its identification, and the developments in the field of molecular biology thereafter. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source


Cinal M.,Polish Academy of Sciences
Journal of Chemical Physics | Year: 2010

It is found that for closed-l-shell atoms, the exact local exchange potential vx(r) calculated in the exchange-only Kohn-Sham (KS) scheme of the density functional theory (DFT) is very well represented within the region of every atomic shell by each of the suitably shifted potentials obtained with the nonlocal Fock exchange operator for the individual Hartree-Fock (HF) orbitals belonging to this shell. This newly revealed property is not related to the well-known steplike shell structure in the response part of vx (r), but it results from specific relations satisfied by the HF orbital exchange potentials. These relations explain the outstanding proximity of the occupied HF and exchange-only KS orbitals as well as the high quality of the Krieger-Li-Iafrate and localized HF (or, equivalently, common-energy- denominator) approximations to the DFT exchange potential vx (r). Another highly accurate representation of vx (r) is given by the continuous piecewise function built of shell-specific exchange potentials, each defined as the weighted average of the shifted orbital exchange potentials corresponding to a given shell. The constant shifts added to the HF orbital exchange potentials, to map them onto vx (r), are nearly equal to the differences between the energies of the corresponding KS and HF orbitals. It is discussed why these differences are positive and grow when the respective orbital energies become lower for inner orbitals. © 2010 American Institute of Physics. Source


Cieplak M.,Polish Academy of Sciences | Robbins M.O.,Johns Hopkins University
PLoS ONE | Year: 2013

A coarse-grained model is used to study the mechanical response of 35 virus capsids of symmetries T = 1, T = 2, T = 3, pseudo T = 3, T = 4, and T = 7. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the Cα atoms associated with each amino acid. The number of these atoms ranges between 8 460 (for SPMV - satellite panicum mosaic virus) and 135 780 (for NBV - nudaureli virus). Nanoindentation by a broad AFM tip is modeled as compression between two planes: either both flat or one flat and one curved. Plots of the compressive force versus plate separation show a variety of behaviors, but in each case there is an elastic region which extends to a characteristic force Fc. Crossing Fc results in a drop in the force and irreversible damage. Across the 35 capsids studied, both Fc and the elastic stiffness are observed to vary by a factor of 20. The changes in mechanical properties do not correlate simply with virus size or symmetry. There is a strong connection to the mean coordination number 〈z〉, defined as the mean number of interactions to neighboring amino acids. The Young's modulus for thin shell capsids rises roughly quadratically with 〈z〉-6, where 6 is the minimum coordination for elastic stability in three dimensions. © 2013 Cieplak, Robbins. Source


Goyeneche D.,University of Concepcion | Zyczkowski K.,Jagiellonian University | Zyczkowski K.,Polish Academy of Sciences
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

A pure quantum state of N subsystems with d levels each is called k-multipartite maximally entangled state, which we call a k-uniform state, if all its reductions to k qudits are maximally mixed. These states form a natural generalization of N-qudit Greenberger-Horne-Zeilinger states which belong to the class 1-uniform states. We establish a link between the combinatorial notion of orthogonal arrays and k-uniform states and prove the existence of several classes of such states for N-qudit systems. In particular, known Hadamard matrices allow us to explicitly construct 2-uniform states for an arbitrary number of N>5 qubits. We show that finding a different class of 2-uniform states would imply the Hadamard conjecture, so the full classification of 2-uniform states seems to be currently out of reach. Furthermore, we establish links between the existence of k-uniform states and classical and quantum error correction codes and provide a graph representation for such states. © 2014 American Physical Society. Source


Szymczak P.,University of Warsaw | Cieplak M.,Polish Academy of Sciences
Journal of Physics Condensed Matter | Year: 2011

Experimental and numerical results pertaining to flow-induced effects in proteins are reviewed. Special emphasis is placed on shear-induced unfolding and on the role of solvent mediated hydrodynamic interactions in the conformational transitions in proteins. © 2011 IOP Publishing Ltd. Source


Derendarz D.,Polish Academy of Sciences
Nuclear Physics A | Year: 2014

The measurement of the azimuthal anisotropy of charged particles produced in lead-lead collisions at √SNN=2.76TeV is reported. The Fourier coefficients vn of the azimuthal angle distribution are obtained using multi-particle cumulants. The results on the transverse momentum and centrality dependence of the elliptic flow (v2) obtained from two-, four-, six- and eight-particle cumulants are presented. Higher-order harmonics, v3 and v4, are also derived using two- and four-particle cumulants and shown as a function of centrality and transverse momentum. A reduction of contributions from correlations not related to the collective flow are discussed. Event-by-event fluctuations of the flow harmonics are also presented as a function of transverse momentum and the collision centrality. © 2014 CERN. Source


Carstensen J.,University of Aarhus | Weydmann A.,Polish Academy of Sciences
Ambio | Year: 2012

Arctic ecosystems have experienced and are projected to experience continued large increases in temperature and declines in sea ice cover. It has been hypothesized that small changes in ecosystem drivers can fundamentally alter ecosystem functioning, and that this might be particularly pronounced for Arctic ecosystems. We present a suite of simple statistical analyses to identify changes in the statistical properties of data, emphasizing that changes in the standard error should be considered in addition to changes in mean properties. The methods are exemplified using sea ice extent, and suggest that the loss rate of sea ice accelerated by factor of *5 in 1996, as reported in other studies, but increases in random fluctuations, as an early warning signal, were observed already in 1990. We recommend to employ the proposed methods more systematically for analyzing tipping points to document effects of climate change in the Arctic. © 2012 Royal Swedish Academy of Sciences. Source


Wilk K.,Polish Academy of Sciences
Mycotaxon | Year: 2011

Caloplaca atroalba, C. dichroa, C. marmorata, C. oasis, and C. pseudofulgensia are reported as new to Poland. Two other taxa: C. albopruinosa and C. pusilla are discussed in view of modern approaches. The species reported here were mainly collected in the Polish Carpathians. Additionally, C. atroalba is reported as new to Ukraine. Detailed taxonomic descriptions and comments are provided for the treated taxa. © 2011. Mycotaxon, Ltd. Source


Bajer K.,University of Warsaw | Mizerski K.,Polish Academy of Sciences
Physical Review Letters | Year: 2013

We demonstrate that arbitrarily weak magnetic field may cause violent instability of an anticyclonic, recirculating flow with uniform mean angular velocity. This magnetohydrodynamic instability would trigger turbulence in the cores of vortices where neither centrifugal, exchange instability, nor magnetorotational instability is effective. In the accretion disk vortices this can be an important mechanism of enhanced outward transport of angular momentum. © 2013 American Physical Society. Source


Carinena J.F.,University of Zaragoza | De Lucas Araujo J.,Polish Academy of Sciences
Journal of Geometric Mechanics | Year: 2011

A superposition rule is a particular type of map that enables one to express the general solution of certain systems of first-order ordinary di erential equations, the so-called Lie systems, out of generic families of particular solutions and a set of constants. The first aim of this work is to propose various generalisations of this notion to second-order di erential equations. Next, several results on the existence of such generalisations are given and relations with the theories of Lie systems and quasi-Lie schemes are found. Finally, our methods are used to study second-order Riccati equations and other second-order di erential equations of mathematical and physical interest. © American Institute of Mathematical Sciences. Source


Bednarska A.J.,Polish Academy of Sciences
Integrated environmental assessment and management | Year: 2013

We discuss the importance of selected natural abiotic and biotic factors in ecological risk assessment based on simplistic laboratory bioassays. Although it is impossible to include all possible natural factors in standard lower-tier ecotoxicological testing, neglecting them is not an option. Therefore, we try to identify the most important factors and advocate redesigning standard testing procedures to include theoretically most potent interactions. We also point out a few potentially important factors that have not been studied enough so far. The available data allowed us to identify temperature and O2 depletion as the most critical factors that should be included in ecotoxicity testing as soon as possible. Temporal limitations and fluctuations in food availability also appear important, but at this point more fundamental research in this area is necessary before making decisions on their inclusion in risk assessment procedures. We propose using specific experimental designs, such as Box-Behnken or Central Composite, which allow for simultaneous testing of 3 or more factors for their individual and interactive effects with greater precision and without increasing the effort and costs of tests dramatically. Factorial design can lead to more powerful tests and help to extend the validity of conclusions. Finally, ecological risk assessment procedures should include information on animal behavior, especially feeding patterns. This requires more basic studies, but already at this point adequate mechanistic effect models can be developed for some species. Copyright © 2013 SETAC. Source


Derzsi M.,University of Warsaw | Piekarz P.,Polish Academy of Sciences | Grochala W.,University of Warsaw
Physical Review Letters | Year: 2014

Most late transition metal (LTM) monoxides crystallize in other than a rock salt structure, which is so common in the earlier transition metal monoxides. Here we present theoretical evidence based on density functional theory that an electron-phonon coupling involving a single soft mode in the cubic cell is responsible for the onset of the experimentally observed structures of the late transition metal monoxides. © 2014 American Physical Society. Source


Castillo O.,Tijuana Institute of Technology | Melin P.,Tijuana Institute of Technology | Pedrycz W.,Polish Academy of Sciences
Applied Soft Computing Journal | Year: 2011

In this paper, we offer a new design methodology of type-2 fuzzy models whose intent is to effectively exploit the uncertainty of non-numeric membership functions. A new performance index, which guides the development of the fuzzy model, is used to navigate the construction of the fuzzy model. The underlying idea is that an optimal granularity allocation throughout the membership functions used in the fuzzy model leads to the best design. In contrast to the commonly utilized criterion where one strives for the highest accuracy of the model, the proposed index is formed in such a way so that the type-2 fuzzy model produced intervals, which "cover" the experimental data and at the same time are made as narrow (viz. specific) as possible. Genetic algorithm is proposed to automate the design process and further improve the results by carefully exploiting the search space. Experimental results show the efficiency of the proposed design methodology. © 2011 Elsevier B.V. All rights reserved. Source


Krolikowska M.,Polish Academy of Sciences
Astronomy and Astrophysics | Year: 2014

Context. The dynamical evolution of near-parabolic comets strongly depends on the starting values of the orbital elements derived from the positional observations. In addition, when drawing conclusions about the origin of these objects, it is crucial to control the uncertainties of orbital elements at each stage of the dynamical evolution. Aims. I apply a completely homogeneous approach to determine the cometary orbits and their uncertainties. The resulting catalogue is suitable for the investigation of the origin and future of near-parabolic comets. Methods. First, osculating orbits were determined on the basis of positional data. Second, the dynamical calculations were performed backwards and forwards up to 250 au from the Sun to derive original and future barycentric orbits for each comet. In the present investigation of dynamical evolution, the numerical calculations for a given object start from the swarm of virtual comets constructed using the previously determined osculating (nominal) orbit. In this way, the uncertainties of orbital elements were derived at the end of numerical calculations. Results. Homogeneous sets of orbital elements for osculating, original and future orbits are given. The catalogue of 119 cometary orbits constitutes about 70 per cent of all the first class so-called Oort spike comets discovered during the period 1801-2010 and about 90 per cent of those discovered in 1951-2010, for which observations were completed at the end of 2013. Non-gravitational (NG) orbits are derived for 45 comets, including asymmetric NG solution for six of them. Additionally, the new method for cometary orbit-quality assessment is applied for all these objects. © ESO, 2014. Source


Wolczynski W.S.,Polish Academy of Sciences
International Journal of Thermodynamics | Year: 2010

A general theory for the lamella → rod transformation is presented. The analysis has been developed in two steps: first, taking into account the condition of minimum Gibbs' free energy, next, using the criterion of minimum entropy production together with the concept of marginal stability. The present theory provides a justification for theoretical determination of a threshold growth rate at which solidification begins to form a rod-like structure instead of a lamellar one. Additionally, the so-called operating range for transformation is justified by the oscillation between the trajectory of minimum entropy production and the trajectory of marginal stability. A model of the evolution of the mechanical equilibrium is introduced to satisfy some changes of the curvature of the solid / liquid interface with increasing growth rate. A consideration associated with the Gibbs' free energy allows to formulate a new criterion which predicts whether the lamellar structure is the stable form or a rod-like structure is the stable form (for a given phase diagram). An application of the criterion of minimum entropy production, together with a model of the instability of the solid/liquid interface (referred to as marginal stability), allows for determining a/ a trajectory at which a regular structure is forming and b/ a trajectory of marginal stability at which the maximum destabilization of the s/l interface of the non-faceted phase is observed together with the faceted phase branching. Source


Broniowski W.,Jan Kochanowski University | Broniowski W.,Polish Academy of Sciences | Ruiz Arriola E.,University of Granada
Physical Review Letters | Year: 2014

We argue that relativistic nuclear collisions may provide experimental evidence of α clustering in light nuclei. A light α-clustered nucleus has a large intrinsic deformation. When collided against a heavy nucleus at very high energies, this deformation transforms into the deformation of the fireball in the transverse plane. The subsequent collective evolution of the fireball leads to harmonic flow reflecting the deformation of the initial shape, which can be measured with standard methods of relativistic heavy-ion collisions. We illustrate the feasibility of the idea by modeling the C12-Pb208 collisions and point out that very significant quantitative and qualitative differences between the α-clustered and uniform C12 nucleus occur in such quantities as the triangular flow, its event-by-event fluctuations, or the correlations of the elliptic and triangular flows. The proposal offers a possibility of studying low-energy nuclear structure phenomena with "snapshots" made with relativistic heavy-ion collisions. © 2014 American Physical Society. Source


Garcia-Martin R.,Complutense University of Madrid | Kaminski R.,Polish Academy of Sciences | Pelaez J.R.,Complutense University of Madrid | De Elvira J.R.,Complutense University of Madrid
Physical Review Letters | Year: 2011

We use our latest dispersive analysis of ππ scattering data and the very recent Kℓ4 experimental results to obtain the mass, width, and couplings of the two lightest scalar-isoscalar resonances. These parameters are defined from their associated poles in the complex plane. The analytic continuation to the complex plane is made in a model-independent way by means of once- and twice-subtracted dispersion relations for the partial waves, without any other theoretical assumption. We find the f0(600) pole at (457-13+14)-i(279-7+11)MeV and that of the f0(980) at (996±7)-i(25-6+10)MeV, whereas their respective couplings to two pions are 3.59-0.13+0.11 and 2.3±0.2GeV. © 2011 American Physical Society. Source


Skarzynski D.J.,Polish Academy of Sciences
Society of Reproduction and Fertility supplement | Year: 2010

The bovine corpus luteum (CL) grows very fast and regresses within a few days at luteolysis. Mechanisms controlling development and secretory function of the bovine CL may involve many factors that are produced both within and outside the CL. In the cow, luteolysis is initiated by uterine prostaglandin (PG)F2alpha released at the late luteal stage. It can also be induced by injection of exogenous PGF2alpha given at the mid luteal stage. Luteolysis consists of a phase of rapid decrease in progesterone (P4) production by the CL, followed by a phase of structural regression. Although uterine PGF2alpha is known to be the main luteolytic factor, its direct action on the CL is mediated by the products of accessory luteal cells: immune cells, endothelial cells, pericytes and fibroblasts. There are studies showing that beside endothelin-1, cytokines (tumor necrosis factor-alpha, interferons) and nitric oxide play critical roles in functional and structural luteolysis in cattle by stimulating leukotrienes and PGF2alpha', decreasing P4 secretion and apoptosis induction. Because of luteal blood flow and P4 concentrations decrease in parallel during both spontaneous and PGF2alpha-induced luteolysis, a decrease in luteal blood flow resulting in hypoxia has been proposed as one of the main luteolytic mechanisms in the cow. Hypoxia inhibits P4 synthesis in luteal cells by inhibiting the steroidogenic enzymes and promotes apoptosis of luteal cells by increasing pro-apoptotic proteins. Although reduction of luteal blood flow and hypoxia contribute to the late events of luteolysis, little is known about the physiological relevance and the cause of the transient increase in luteal blood flow and reactive oxygen species during the initial step of luteolysis. Source


Chmura J.,University School of Physical Education in Wroclaw | Nazar K.,Polish Academy of Sciences
International Journal of Psychophysiology | Year: 2010

During aerobic exercise with increasing intensities choice reaction time (CRT) progressively shortens up to 60-80% of maximal workload, and then it rapidly increases. The aim of this study was to determine whether workload associated with the shortest CRT operationally called "the psychomotor fatigue threshold" is related to the metabolic response to exercise. Thirteen male soccer players (aged 23.3 ± 1.0 yrs) participated in this study. Before and after 6 weeks of training in the pre-competition period they underwent treadmill test at 0 grade with running speed increasing every 3 min by 2 km/h starting from 6 km/h until exhaustion. At each stage of exercise CRT, heart rate, respiratory gas exchange and blood lactate [LA] were measured and the workload corresponding to [LA] of 4 mmol/l (OBLA) was recorded. After training, CRT was significantly shortened at rest (from m ± SEM = 345 ± 12 to 317 ± 12 ms) and during exercise (from 304 ± 10 to 285 ± 11 ms at the psychomotor fatigue threshold and from 359 ± 13 to 331 ± 13 ms, p < 0.001at the last stage). Both OBLA and the psychomotor fatigue threshold were shifted towards greater running velocities (by 0.92 ± 0.26 and 0.85 ± 0.22 km/h, respectively). The psychomotor fatigue threshold exceeded OBLA both before and after training. Significant correlations were ascertained between OBLA and psychomotor fatigue threshold (r = 0.97) and between the changes in OBLA occurring during training and those in psychomotor fatigue threshold (r = 0.88). It is concluded that endurance training not only increases exercise tolerance due to its influence on metabolism but also facilitates psychomotor performance during heavy exercise. © 2010 Elsevier B.V. All rights reserved. Source


Sikora M.,Polish Academy of Sciences | Begelman M.C.,U.S. National Institute of Standards and Technology | Begelman M.C.,University of Colorado at Boulder
Astrophysical Journal Letters | Year: 2013

We argue that the magnetic flux threading the black hole (BH), rather than BH spin or Eddington ratio, is the dominant factor in launching powerful jets and thus determining the radio loudness of active galactic nuclei (AGNs). Most AGNs are radio quiet because the thin accretion disks that feed them are inefficient in depositing magnetic flux close to the BH. Flux accumulation is more likely to occur during a hot accretion (or thick disk) phase, and we argue that radio-loud quasars and strong emission-line radio galaxies occur only when a massive, cold accretion event follows an episode of hot accretion. Such an event might be triggered by the merger of a giant elliptical galaxy with a disk galaxy. This picture supports the idea that flux accumulation can lead to the formation of a so-called magnetically choked accretion flow. The large observed range in radio loudness reflects not only the magnitude of the flux pressed against the BH, but also the decrease in UV flux from the disk, due to its disruption by the "magnetosphere" associated with the accumulated flux. While the strongest jets result from the secular accumulation of flux, moderate jet activity can also be triggered by fluctuations in the magnetic flux deposited by turbulent, hot inner regions of otherwise thin accretion disks, or by the dissipation of turbulent fields in accretion disk coronae. These processes could be responsible for jet production in Seyferts and low-luminosity AGNs, as well as jets associated with X-ray binaries. © 2013. The American Astronomical Society. All rights reserved.. Source


Wilbik A.,Polish Academy of Sciences | Wilbik A.,University of Missouri | Keller J.M.,University of Missouri
IEEE Transactions on Fuzzy Systems | Year: 2013

In this paper, we consider the problem of evaluating the similarity of two sets of linguistic summaries of sensor data. Huge amounts of available data cause a dramatic need for summarization. In continuous monitoring, it is useful to compare one time interval of data with another, for example, to detect anomalies or to predict the onset of a change from a normal state. Assuming that summaries capture the essence of the data, it is sufficient to compare only those summaries, i.e., they are descriptive features for recognition. In previous work, we developed a similarity measure between two individual summaries and proved that the associated dissimilarity is a metric. Additionally, we proposed some basic methods to combine these similarities into an aggregate value. Here, we develop a novel parameter free method, which is based on fuzzy measures and integrals, to fuse individual similarities that will produce a closeness measurement between sets of summaries. We provide a case study from the eldercare domain where the goal is to compare different nighttime patterns for change detection. The reasons for studying linguistic summaries for eldercare are twofold: First, linguistic summaries are the natural communication tool for health care providers in a decision support system, and second, due to the extremely large volume of raw data, these summaries create compact features for an automated reasoning for detection and prediction of health changes as part of the decision support system. © 2012 IEEE. Source


Zielinski T.G.,Polish Academy of Sciences
Journal of the Acoustical Society of America | Year: 2015

This paper presents a methodology for the inverse characterization of sound absorbing rigid porous media, based on standard measurements of the surface acoustic impedance of a porous sample. The model parameters need to be normalized to have a robust identification procedure which fits the model-predicted impedance curves with the measured ones. Such a normalization provides a substitute set of dimensionless (normalized) parameters unambiguously related to the original model parameters. Moreover, two scaling frequencies are introduced, however, they are not additional parameters and for different, yet reasonable, assumptions of their values, the identification procedure should eventually lead to the same solution. The proposed identification technique uses measured and computed impedance curves for a porous sample not only in the standard configuration, that is, set to the rigid termination piston in an impedance tube, but also with air gaps of known thicknesses between the sample and the piston. Therefore, all necessary analytical formulas for sound propagation in double-layered media are provided. The methodology is illustrated by one numerical test and by two examples based on the experimental measurements of the acoustic impedance and absorption of porous ceramic samples of different thicknesses and a sample of polyurethane foam. © 2015 Acoustical Society of America. Source


Smak J.,Polish Academy of Sciences
Acta Astronomica | Year: 2016

Light curves of superhumps and their evolution during superoutbursts are analyzed by decomposing them into their Fourier components, including the fundamental mode and the first three overtones. The amplitudes of the fundamental mode are found to decrease significantly during superoutburst while those of the overtones remain practically constant. The phases of maxima of the fundamental mode increase systematically during superoutburst while those of the overtones - systematically decrease. The combination of the two effects is responsible for the characteristic evolution of superhump light curves: the appearance and growth of the secondary humps and the spurious phase jumps in the (O-C) diagrams. Two intrepretations are possible. Either that instead of just one superhump period Psh there are four periods Pk which resemble - but are significantly different from - the fundamental mode and the first three overtones of Psh. Or - more likely - that those time-dependent phase shifts are genuine. Source


The aim of the present study was to investigate whether the growth promoted transition to puberty in lambs involved changes in the effects of testicular hormones on somatostatin in hypothalamic neurons and GH secretion. The study was performed in infants (9-week-old) testis-intact (TEI) and orchidectomized (ORCHX) at the sixth week of age, and pubertal lambs (16-week-old) TEI and ORCHX at the 12th week of age (n = 20). In TEI lambs, the changes included a pubertal increase in immunoreactive somatostatin in the periventricular nucleus and median eminence with simultaneous neuropeptide depletion in the median eminence, and a decrease in the percentage of the hypophyseal area (PA) occupied by GH-immunoreactive cells (P < 0.05). The mean concentration of GH in the peripheral blood plasma was greater (P < 0.001) in early infancy (5 wk), because of the greater (P < 0.0001) pulse amplitude, and then uniformly low until puberty. The postnatal increase in the body weight (BW) was prominent (P < 0.01) in middle-late infancy (9-12 wk) because of the large daily live-weight gain. After orchidectomy somatostatin was abundant. This effect on nerve terminals in the median eminence was greater (P < 0.01) in infancy and lesser (P < 0.05) in puberty. Conversely, the PA occupied by GH cells was lower in the ORCHX pubertal lambs compared to TEI lambs (P < 0.05). The GH concentration and pulse characteristics were less (P < 0.05) in the infantile and pubertal ORCHX lambs compared to the TEI lambs. However, this effect was weak (P < 0.05) until middle infancy because of no influence on the GH basal concentration, and strong (P < 0.001) after late infancy. The BW did not differ (P > 0.05) between TEI and ORCHX lambs. Findings suggest activation of GH negative autofeedback loop in middle infancy. Testicular factors may play an inhibitory role in regulating somatostatin accumulation and a stimulatory role in GH secretion until puberty. The start of puberty is related to an attenuation in the stimulatory role of gonadal factors in regulating somatostatin depletion in nerve terminals associated with an intensification of the stimulatory role of gonadal factors in regulating GH secretion. From a somatic perspective of growth rate, these mechanisms do not seem to be important. Thus, testicular factors modulate mechanisms within the somatostatin-GH system to integrate somatotropic and gonadotropic functions at the time of growth-promoted sexual maturation in sheep. © 2012 Elsevier Inc. Source


Wegrzyn G.,University of Gdansk | Licznerska K.,University of Gdansk | Wegrzyn A.,Polish Academy of Sciences
Advances in Virus Research | Year: 2012

Bacteriophage λ, rediscovered in the early 1950s, has served as a model in molecular biology studies for decades. Although currently more complex organisms and more complicated biological systems can be studied, this phage is still an excellent model to investigate principles of biological processes occurring at the molecular level. In fact, very few other biological models provide possibilities to examine regulations of biological mechanisms as detailed as performed with λ. In this chapter, recent advances in our understanding of mechanisms of bacteriophage λ development are summarized and discussed. Particularly, studies on (i) phage DNA injection, (ii) molecular bases of the lysis-versus-lysogenization decision and the lysogenization process itself, (iii) prophage maintenance and induction, (iv), λ DNA replication, (v) phage-encoded recombination systems, (vi) transcription antitermination, (vii) formation of the virion structure, and (viii) lysis of the host cell, as published during several past years, will be presented. © 2012 Elsevier Inc. Source


Los M.,University of Gdansk | Los M.,Polish Academy of Sciences | Wegrzyn G.,University of Gdansk
Advances in Virus Research | Year: 2012

Pseudolysogeny can be defined as the stage of stalled development of a bacteriophage in a host cell without either multiplication of the phage genome (as in lytic development) or its replication synchronized with the cell cycle and stable maintenance in the cell line (as in lysogenization), which proceeds with no viral genome degradation, thus allowing the subsequent restart of virus development. This phenomenon is usually caused by unfavorable growth conditions for the host cell (such as starvation) and is terminated with initiation of either true lysogenization or lytic growth when growth conditions improve. Pseudolysogeny has been known for tens of years; however, its role has often been underestimated. Currently, it is being considered more often as an important aspect of phage-host interactions. The reason for this is mostly an increased interest in phage-host interactions in the natural environment. Pseudolysogeny seems to play an important role in phage survival, as bacteria in a natural environment are starved or their growth is very slow. This phenomenon can be an important aspect of phage-dependent bacterial mortality and may influence the virulence of some bacterial strains. © 2012 Elsevier Inc. Source


Lundberg M.,Uppsala University | Borowski T.,Polish Academy of Sciences
Coordination Chemistry Reviews | Year: 2013

Mononuclear non-heme iron enzymes perform a wide range of chemical reactions. Still, the catalytic mechanisms are usually remarkably similar, with formation of a key oxoferryl (Fe(IV)O) intermediate through two well-defined steps. First, two-electron reduction of dioxygen occurs to form a peroxo species, followed by OO bond cleavage. Even though the peroxo species have different chemical character in various enzyme families, the analogies between different enzymes in the group make it an excellent base for investigating factors that control metal-enzyme catalysis. We have used density-functional theory to model the complete chemical reaction mechanisms of several enzymes, e.g., for aromatic and aliphatic hydroxylation, chlorination, and oxidative ring-closure. Reactivity of the Fe(IV)O species is discussed with focus on electronic and steric factors determining the preferred reaction path. Various spin states are compared, as well as the two reaction channels that stem from involvement of different frontier molecular orbitals of Fe(IV)O. Further, the two distinctive species of Fe(IV)O, revealed by Mössbauer spectroscopy, and possibly relevant for specificity of aliphatic chlorination, can be identified. The stability of the modeling results have been analyzed using a range of approaches, from active-site models to multi-scale models that include classical free-energy contributions. Large effects from an explicit treatment of the protein matrix (∼10kcal/mol) can be observed for O 2 binding, electron-transfer and product release. © 2012 Elsevier B.V.. Source


This paper provides diagnostic drawings for selected Oriental genera and species, to complement the existing scanty literature. The following 16 new species are described: Bavia kahariana sp.n. (♂ ♀), B. suhartoi sp.n. (♂ ♀), Cytaea semengohi sp.n. (♂), C. sepakuensis sp.n. (♀), C. trusmadii sp.n. (♂), Echeclus sokoli sp.n. (♂ ♀), Euryattus kinabalus sp.n. (♂ ♀), E. koomeni sp.n. (♂ ♀), E. pengi sp.n. (♂), Onomastus danum sp.n. (♂ ♀), Pancorius petoti sp.n. (♀), Poecilorchestes logunovi sp.n. (♂), Sobasina platnicki sp.n. (♂ ♀), Sertinius onoi sp.n. (♂ ♀), Vailimia bakoensis sp.n. (♂) and V. jianyuae sp.n. (♂). One new species is described from New Guinea Euryattus ventralis sp.n. (♀). New female is added to Donoessus striatus Simon, 1902. Complementary, comparative drawings are given to 10 species: Bianor incitatus Thorell, 1890, Euryattus venustus (Doleschall, 1859), E. bleekeri (Doleschall, 1859), E. porcellus Thorell, 1881, E. venustus (Doleschall, 1859), Onomastus complexipalpis Wanless, 1980, O. kaharian Benjamin, 2010, O. simoni-abka, 1985, Pancorius dentichelis (Simon, 1899), Vailimia masinei (Peckham et Peckham, 1907). Genus name Orissania Prószynski, 1992 syn.n. is synonymised with the genus name Pancorius Simon, 1902 and a new combination Pancorius daitaricus (Prószyński, 1992) comb.n. ex Orissania daitarica Prószyński, 1992 is established. Three nominal species of Plotius: P. breviusculus Simon, 1902, P. celebensis Merian, 1911, P. leopoldi Roewer, 1938, are transferred back from Euryattus. Comments on subfamily Euophryinae are added. © ARTHROPODA SELECTA, 2013. Source


Zielinski T.G.,Polish Academy of Sciences
Journal of the Acoustical Society of America | Year: 2015

This paper proposes and discusses an approach for the design and quality inspection of the morphology dedicated for sound absorbing foams, using a relatively simple technique for a random generation of periodic microstructures representative for open-cell foams with spherical pores. The design is controlled by a few parameters, namely, the total open porosity and the average pore size, as well as the standard deviation of pore size. These design parameters are set up exactly and independently, however, the setting of the standard deviation of pore sizes requires some number of pores in the representative volume element (RVE); this number is a procedure parameter. Another pore structure parameter which may be indirectly affected is the average size of windows linking the pores, however, it is in fact weakly controlled by the maximal pore-penetration factor, and moreover, it depends on the porosity and pore size. The proposed methodology for testing microstructure-designs of sound absorbing porous media applies the multi-scale modeling where some important transport parameters - responsible for sound propagation in a porous medium - are calculated from microstructure using the generated RVE, in order to estimate the sound velocity and absorption of such a designed material. © 2015 Acoustical Society of America. Source


Swiatek B.J.,Polish Academy of Sciences
Cytokine and Growth Factor Reviews | Year: 2012

The clinical outcome of hepatitis C virus (HCV) infection varies between individuals - from spontaneous viral clearance and persistence without complication, to chronic hepatitis, cirrhosis and hepatocellular carcinoma. Also patterns of response to interferon-based anti-HCV therapy are different from person to person. This diversity may be affected by host genetic factors, including alterations in genes encoding cytokines. Interleukin-10, as an anti-inflammatory cytokine and immune response modulator, may influence on HCV infection susceptibility as well as spontaneous and treatment-induced HCV eradication. Moreover, it is stated that IL-10 has antifibrotic properties and play a role in progression of liver disease. This review summarized studies on interleukin-10 gene polymorphisms (mainly promoter SNPs at positions -1082(G/A), -819(C/T) and -592(C/A)), which may determine IL-10 production, regarding susceptibility to HCV infection, course of HCV-related liver disease (fibrosis, cirrhosis, hepatocellular carcinoma, ALT abnormalities), spontaneous viral elimination as well as hepatitis C treatment outcomes. Analysis of hereby summarized studies shows that it is difficult to unambiguously determine the importance of IL-10 polymorphism as a predictor of clinical outcome of hepatitis C and response to anti-HCV therapy before its beginning. Thus, future larger studies need to address these issues. Continuation of studies on interleukin-10 polymorphisms as well as identification of other candidate predictive markers in HCV infection has important practical implications and there is a chance that may contribute to reduce the scale of hepatitis C problem. © 2012 Elsevier Ltd. Source


Holdynski M.,Polish Academy of Sciences
Journal of physics. Condensed matter : an Institute of Physics journal | Year: 2012

A study of phase and electrical behaviour in the bismuth niobate, Bi(4)NbO(8.5), using x-ray and neutron powder diffraction, thermogravimetric analysis (TGA), x-ray photoelectron spectroscopy (XPS) and ac impedance spectroscopy is presented. Two polymorphs were identified in this composition, a tetragonal phase (type III), which can appear at temperatures above 800 °C and a pseudo-cubic phase (type II) evident at lower temperatures. The defect structure analysis of the type II phase is consistent with the existence of chains of niobate polyhedra, which facilitate electronic conduction at low temperatures. The appearance of the type III phase is strongly dependent on experimental conditions and TGA and XPS measurements suggest a likely association with change in oxygen stoichiometry. Source


Slowicka A.M.,Polish Academy of Sciences
The Journal of chemical physics | Year: 2012

Dynamics of single flexible non-Brownian fibers, tumbling in a Poiseuille flow between two parallel solid plane walls, is studied with the use of the HYDROMULTIPOLE numerical code, based on the multipole expansion of the Stokes equations, corrected for lubrication. Fibers, which are closer to a wall, more flexible (less stiff) or longer, deform more significantly and, for a wide range of the system parameters, they faster migrate towards the middle plane of the channel. For the considered systems, fiber velocity along the flow is only slightly smaller than (and can be well approximated by) the Poseuille flow velocity at the same position. In this way, the history of a fiber migration across the channel is sufficient to determine with a high accuracy its displacement along the flow. © 2012 American Institute of Physics Source


Puchala Z.,Polish Academy of Sciences
Quantum Information Processing | Year: 2013

We give a criterion that is sufficient for controllability of multipartite quantum systems. We generalize the graph infection criterion to the quantum systems that cannot be described with the use of a graph theory. We introduce the notation of hypergraphs and reformulate the infection property in this setting. The introduced criterion has a topological nature and therefore it is not connected to any particular experimental realization of quantum information processing. © 2012 The Author(s). Source


Salamonczyk G.M.,Polish Academy of Sciences
Tetrahedron Letters | Year: 2011

The efficient synthesis of new dendrimeric polyesters up to generation 3 that consist of 1,3,5-benzenetricarboxylic acid building blocks with potential applications in drug delivery is described. The dendrimers possess hydroxy or allyl functional groups on the surface and were prepared through a divergent approach using readily available 2-(hydroxymethyl)-2-ethylpropan-1,3-diol and 1,3,5-benzenetrimethanol as central cores, with 3,5-bis[(allyloxy)methyl]benzoic acid being an essential unit of the dendrimer. The latter compound was synthesized, in high yield, from 1,3,5-benzenetricarboxylic acid, applying selective hydrolysis of the corresponding triester as the key step. © 2010 Elsevier Ltd. All rights reserved. Source


Pedrycz W.,University of Alberta | Pedrycz W.,Polish Academy of Sciences | Song M.,University of Alberta
IEEE Transactions on Fuzzy Systems | Year: 2011

In group decision making, one strives to reconcile differences of opinions (judgments) expressed by individual members of the group. Fuzzy-decision-making mechanisms bring a great deal of flexibility. By admitting membership degrees, we are offered flexibility to exploit different aggregation mechanisms and navigate a process of interaction among decision makers to achieve an increasing level of consistency within the group. While the studies reported so far exploit more or less sophisticated ways of adjusting/transforming initial judgments (preferences) of individuals, in this paper, we bring forward a concept of information granularity. Here, information granularity is viewed as an essential asset, which offers a decision maker a tangible level of flexibility using some initial preferences conveyed by each individual that can be adjusted with the intent to reach a higher level of consensus. Our study is concerned with an extension of the well-known analytic hierarchy process to the group decision-making scenario. More specifically, the admitted level of granularity gives rise to a granular matrix of pairwise comparisons. The granular entries represented, e.g., by intervals or fuzzy sets, supply a required flexibility using the fact that we select the most suitable numeric representative of the reciprocal matrix. The proposed concept of granular reciprocal matrices is used to optimize a performance index, which comes as an additive combination of two components. The first one expresses a level of consistency of the individual pairwise comparison matrices; by exploiting the admitted level of granularity, we aim at the minimization of the corresponding inconsistency index. The second part of the performance index quantifies a level of disagreement in terms of the individual preferences. The flexibility offered by the level of granularity is used to increase the level of consensus within the group. Given an implicit nature of relationships between the realizations of the granular pairwise matrices and the values of the performance index, we consider using particle swarm optimization as an optimization vehicle. Two scenarios of allocation of granularity among decision makers are considered, namely, a uniform allocation of granularity and nonuniform distribution of granularity, where the levels of allocated granularity are also subject to optimization. A number of numeric studies are provided to illustrate an essence of the method. © 2011 IEEE. Source


Andrychowski J.,Polish Academy of Sciences
European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society | Year: 2012

Erysipelas is an animal disease caused by Gram-positive bacteria Erysipelothrix rhusiopathiae. Among the domestic animals, domestic pig (Sus scrofa f. domestica) suffers most frequently from the disease in human environment. This is a typical animal-borne disease observed mainly in occupational groups employed in agriculture, farming (of animals and birds), fishing and manufacturing industry. We are presenting the clinical course of infection (E. rhusiopathiae) and discuss clinical forms. E. rhusiopathiae in humans may have the following clinical course: mild form of skin infection diagnosed as local erythema (erysipeloid), disseminated form of skin infection and the most serious form of infection of systemic course (endocarditis and sepsis). Mild skin infection and local erythema are the most common forms. Very rare case of animal-borne infection course has been presented in which after initial phase the disease was generalised to the abscesses formation in paravertebral space, spondylitis and empyema formation in spinal canal. In the presented clinical case, the patient was suffering from diabetes. It was probably an additional risk factor of the disease generalisation. Patient underwent drainage of empyema in spinal canal, after which his neurological status gradually improved. Antibiotic therapy was implemented and continued for 8 weeks. Such course of erysipelas was not previously described in the literature. After therapy neurological status was improved. In follow MRI control exam empyema and spondylitis was successfully eliminated. Various complications of the disease, such as endocarditis and heart valves disturbances, are well known and are the most severe complications of the generalised infection. Proper targeted and long-term antibiotic therapy is crucial. Source


Piskozub J.,Polish Academy of Sciences | McKee D.,University of Strathclyde
Optics Express | Year: 2011

The propagation of light through turbid media is of fundamental interest in a number of areas of optical science including atmospheric and oceanographic science, astrophysics and medicine amongst many others. The angular distribution of photons after a single scattering event is determined by the scattering phase function of the material the light is passing through. However, in many instances photons experience multiple scattering events and there is currently no equivalent function to describe the resulting angular distribution of photons. Here we present simple analytic formulas that describe the angular distribution of photons after multiple scattering events, based only on knowledge of the single scattering albedo and the single scattering phase function. © 2011 Optical Society of America. Source


Sobkowski M.,Polish Academy of Sciences
Collection of Czechoslovak Chemical Communications | Year: 2010

Application of the pivaloyl group as a protection for the N3 position of thymidine and uridine was investigated. Pivaloylation of thymidine is a very rapid reaction proceeding under mild conditions with excellent regioselectivity for sugar or thymine moiety, depending on the amines used. Several pivaloylated thymidine derivatives were obtained by treatment of unprotected thymidine with pivaloyl chloride under various experimental conditions. Stability of the N3-pivaloyl protecting group under basic and acidic conditions was evaluated and the conditions for its selective removal were found. © 2010 Institute of Organic Chemistry and Biochemistry. Source


Cieplak M.,Polish Academy of Sciences | Robbins M.O.,Johns Hopkins University
Journal of Chemical Physics | Year: 2010

A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the Cα atoms. Nanoindentation by a large tip is modeled as compression between parallel plates. Plots of the compressive force versus plate separation for CCMV are qualitatively consistent with continuum models and experiments, showing an elastic region followed by an irreversible drop in force. The mechanical response of CPMV has not been studied, but the molecular model predicts an order of magnitude higher stiffness and a much shorter elastic region than for CCMV. These large changes result from small structural changes that increase the number of bonds by only 30% and would be difficult to capture in continuum models. Direct comparison of local deformations in continuum and molecular models of CCMV shows that the molecular model undergoes a gradual symmetry breaking rotation and accommodates more strain near the walls than the continuum model. The irreversible drop in force at small separations is associated with rupturing nearly all of the bonds between capsid proteins in the molecular model, while a buckling transition is observed in continuum models. © 2010 American Institute of Physics. Source


Zaleski T.A.,Polish Academy of Sciences | Polak T.P.,Adam Mickiewicz University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

We discuss a system of dilute Bose gas confined in a layered structure of stacked square lattices (slab geometry). A derived phase diagram reveals a nonmonotonic dependence of the ratio of tunneling to on-site repulsion on the artificial magnetic field applied to the system. The effect is reduced when more layers are added, which mimics a two- to quasi-three-dimensional geometry crossover. Furthermore, we establish a correspondence between anisotropic infinite (quasi-three-dimensional) and isotropic finite (slab geometry) systems that share exactly the same critical values, which can be an important clue for choosing experimental setups that are less demanding, but still leading to the identical results. Finally, we show that the properties of the ideal Bose gas in a three-dimensional optical lattice can be closely mimicked by finite (slab) systems when the number of two-dimensional layers is larger than 10 for isotropic interactions, or even less when the layers are weakly coupled. © 2011 American Physical Society. Source


Maciula R.,Polish Academy of Sciences | Szczurek A.,University of Rzeszow
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

We discuss inclusive production of open charm in proton-proton scattering at LHC. The calculation is performed within the kt-factorization approach. Different models of unintegrated gluon distributions (UGDFs) from the literature are used. The theoretical transverse momentum as well as (pseudo)rapidity distributions of charmed mesons are compared with recent experimental data of the ATLAS, ALICE, and LHCb Collaborations. Only the calculation with Kimber-Martin-Ryskin UGDF gives results comparable to experimental ones. All other popular models of UGDF significantly underpredict experimental data. Several sources of uncertainties of the theoretical predictions are also studied in detail. In addition, we discuss correlations between D and D̄ mesons. Good description of experimental distribution in invariant mass and in relative azimuthal angle between D and D̄ mesons is achieved for the Kimber-Martin-Ryskin UGDF. The considered correlation observables measured by the LHCb experiment were not discussed in other approaches in the literature © 2013 American Physical Society. Source


Gorzelak P.,Polish Academy of Sciences | Salamon M.A.,University of Silesia | Baumiller T.K.,University of Michigan
Proceedings of the National Academy of Sciences of the United States of America | Year: 2012

Sea urchins are a major component of recent marine communities where they exert a key role as grazers and benthic predators. However, their impact on past marine organisms, such as crinoids, is hard to infer in the fossil record. Analysis of bite mark frequencies on crinoid columnals and comprehensive genus-level diversity data provide unique insights into the importance of sea urchin predation through geologic time. These data show that over the Mesozoic, predation intensity on crinoids, as measured by bite mark frequencies on columnals, changed in step with diversity of sea urchins. Moreover, Mesozoic diversity changes in the predatory sea urchins show a positive correlation with diversity of motile crinoids and a negative correlation with diversity of sessile crinoids, consistent with a crinoid motility representing an effective escape strategy. We contend that the Mesozoic diversity history of crinoids likely represents a macroevolutionary response to changes in sea urchin predation pressure and that it may have set the stage for the recent pattern of crinoid diversity in which motile forms greatly predominate and sessile forms are restricted to deep-water refugia. Source


Ovarian progesterone induces essential changes leading to a temporary state of uterine receptivity for conceptus implantation. Estrogens secreted by the porcine conceptus on days 11 and 12 of pregnancy provide the initial signal for maternal recognition of pregnancy and maintenance of a functional corpus luteum (CL) for continued production of progesterone. As prostaglandins F 2α(PGF 2α) and E 2 (PGE 2) exert opposing actions on the CL, a tight control over their synthesis and secretion is critical either for the initiation of luteolysis or maintenance of pregnancy. One of the supportive mechanisms by which conceptus inhibits luteolysis is changing PG synthesis in favor of luteoprotective PGE 2. Conceptus PGE 2 could be amplified by PGE 2 feedback loop in the endometrium. In pigs, as in other species, implantation and establishment of pregnancy is associated with upregulation of expression of proinflammatory factors, which include cytokines, growth factors, and lipid mediators. The conceptus produces inflammatory mediators: interferon γ and interferon δ, interleukins IL1B and IL6, and PGs, which probably activate inflammatory pathways in the endometrium. The endometrium responds to these embryonic signals by enhancing further progesterone-induced uterine receptivity. Understanding the mechanisms of pregnancy establishment is required for translational research to increase reproductive efficiencies and fertility in humans and animals. © 2011 Society for Reproduction and Fertility. Source


Chmielarz P.,Polish Academy of Sciences
Cryo-Letters | Year: 2010

We evaluated the sensitivity of orthodox seeds of black alder (Alnus glutinosa (L.) Gaertn.) to extreme desiccation and/or to the ultra-low temperature of liquid nitrogen (LN; -196°C). The critical water content (WC) of desiccated seeds and the high-moisture freezing limit of seeds desiccated or imbibed to various WCs and frozen for 24 h or up to two years in LN was determined. Germination tests revealed that desiccation to 0.03 g H 2O.g-1 dry mass was not detrimental to these seeds. Seeds tolerated LN freezing when the WC was 0.03-0.18 g H2O g-1 dm (nuts). Seeds desiccated to this WC and stored in LN for two years showed similar germination as seeds stored at -3°C for two years. Therefore, long-term cryopreservation of A. glutinosa seeds in genebanks is feasible. © CryoLetters. Source


Nopoush M.,Kent State University | Ryblewski R.,Polish Academy of Sciences | Strickland M.,Kent State University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

We derive the equations of motion for a system undergoing boost-invariant longitudinal and azimuthally symmetric transverse "Gubser flow" using leading-order anisotropic hydrodynamics. This is accomplished by assuming that the one-particle distribution function is ellipsoidally symmetric in the momenta conjugate to the de Sitter coordinates used to parametrize the Gubser flow. We then demonstrate that the SO(3)q symmetry in de Sitter space further constrains the anisotropy tensor to be of spheroidal form. The resulting system of two coupled ordinary differential equations for the de Sitter-space momentum scale and anisotropy parameter are solved numerically and compared to a recently obtained exact solution of the relaxation-time-approximation Boltzmann equation subject to the same flow. We show that anisotropic hydrodynamics describes the spatiotemporal evolution of the system better than all currently known dissipative hydrodynamics approaches. In addition, we prove that anisotropic hydrodynamics gives the exact solution of the relaxation-time approximation Boltzmann equation in the ideal, η/s→0, and free-streaming, η/s→?, limits. © 2015 American Physical Society. Source


Stefanski P.,Polish Academy of Sciences
Journal of Physics Condensed Matter | Year: 2013

A system composed of two quantum dots, i.e. a strongly interacting Kondo dot and a noninteracting one, placed in the arms of the Aharonov-Bohm ring, is investigated theoretically. The ring is coupled to normal leads. This configuration is mapped on the system of a correlated impurity embedded in a host with energy and flux dependent density of states. Additionally, the presence of the Rashba field allows a spin selective opening of the pseudogap in the density of states of the host, when the level of the noninteracting dot is tuned to the Fermi energy. This selectively diminishes electron correlations in the Kondo dot and creates resultant spin polarization at the Fermi level. It is shown that this polarization arises in the absence of any exchange field. Interestingly, this Rashba-correlation-induced spin polarization reaches its maximum for the position of the Kondo dot level corresponding to the Kondo temperature of the Anderson impurity in the host with constant density of states. © 2013 IOP Publishing Ltd. Source


White D.J.,Geological Survey of Canada | Malinowski M.,Polish Academy of Sciences
Geophysics | Year: 2012

A methodology was demonstrated for the 3D interpretation of networks of 2D seismic profiles in conjunction with other 3D geological constraints. The methodology employs 3D migration of 2D seismic data as a means of directly correlating reflections with out-of-plane geology, followed by ray-trace modeling of interpreted 3D geological surfaces. The proposed interpretation workflow was demonstrated with examples taken from 2D seismic profiles that were recently acquired for VMS ore exploration within the Flin Flon mining camp, Canada. In each example, the utility of the method was demonstrated and the resulting inferences were validated by comparison with a true 3D seismic survey acquired over a subset of the same area. © 2012 Society of Exploration Geophysicists. Source


Huy Phan A.,RIKEN | Cichocki A.,Polish Academy of Sciences
Neurocomputing | Year: 2011

Parallel factor analysis (PARAFAC) is a tensor (multiway array) factorization method which allows to find hidden factors (component matrices) from a multidimensional data. Most of the existing algorithms for the PARAFAC, especially the alternating least squares (ALS) algorithm need to compute Khatri-Rao products of tall factors and multiplication of large matrices, and due to this require high computational cost and large memory and are not suitable for very large-scale-problems. Hence, PARAFAC for large-scale data tensors is still a challenging problem. In this paper, we propose a new approach based on a modified ALS algorithm which computes Hadamard products, instead Khatri-Rao products, and employs relatively small matrices. The new algorithms are able to process extremely large-scale tensors with billions of entries. Extensive experiments confirm the validity and high performance of the developed algorithm in comparison with other well-known algorithms. © 2011 Elsevier B.V. Source


Kaczmarczyk B.,Polish Academy of Sciences
Journal of Molecular Structure | Year: 2013

A series of aromatic polyazomethines synthesized from reactions between selected aromatic diamines and either terephthalaldehyde or 4,4'- diformyltriphenylamine were characterized using infrared spectroscopy. In this report the influence of diamine structure on the C=N stretching frequency and the conjugation of π-electrons in polymers are discussed. The results of infrared spectroscopy were confirmed by analyzing the 1H NMR spectra of the relevant compounds. Special attention was given to the conjugation in the polyimines and model compounds with ortho-substituted alkyl groups to the amine phenyl rings. For the model compounds geometry optimizations were calculated. © 2013 Elsevier B.V. All rights reserved. Source


Wincel H.,Polish Academy of Sciences
Journal of the American Society for Mass Spectrometry | Year: 2012

Hydration reactions of sodiated and potassiated nucleic acid bases (uracil, thymine, cytosine, and adenine) produced by electrospray have been studied in a gas phase using the pulsed ionbeam high-pressure mass spectrometer. The thermochemical properties, ΔHo n, ΔS o n, and ΔGo n, for the hydrated systems were obtained from hydration equilibrium measurement. The structural aspects of the hydrated complexes are discussed in conjunction with available literature data. The correlation between water binding energies in the hydrated complexes and the corresponding metal ion affinities of nucleobases suggests that a significant (if not dominant) amount of the canonical structure of cytosine undergoes tautomerization during electrospray ionization, and the thermochemical values for cationized cytosine probably correspond to a mixture of tautomeric complexes. © The Author(s), 2012. Source


Smak J.,Polish Academy of Sciences
Acta Astronomica | Year: 2010

The mass transfer rate in SS Cyg at quiescence, estimated from the observed luminosity of the hot spot, is logMtr· = 16.8±0.3. This is safely below the critical mass transfer rates of logMcrit ·= 18.1 (corresponding to logTcrit 0 = 3.88) or logMcrit· = 17.2 (corresponding to the "revised" value of log Tcrit 0 = 3.65). The mass transfer rate during outbursts is strongly enhanced. Source


Krasinski A.,Polish Academy of Sciences
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

This is a supplement to an earlier paper, where those shearfree normal cosmological models were identified, in which all light rays have repeatable paths. All of them are conformally flat, but less general than the Stephani model and more general than Robertson-Walker. In this paper, their defining feature is identified: in each of them, in comoving coordinates, the time dependence factors out so that the cofactor is a static metric. An example is given of a congruence of test observers and sources in the Minkowski spacetime that displays nonrepeatable light paths. © 2012 American Physical Society. Source


Banski J.,Polish Academy of Sciences | Wesolowska M.,Maria Curie Sklodowska University
Landscape and Urban Planning | Year: 2010

The analysis presented here concerns the influence of housing construction on spatial systems and the physiognomy of rural settlements serving various economic functions. In addition, the study offers an assessment of the influence new construction is having on the living conditions experienced by country-dwellers and the appearance and aesthetics characterising rural settlements. Particular attention is paid to modern housing construction, which only began to flourish in Poland in the period of economic transformation. A basis for the work has been provided by detailed research (field surveys, questionnaires and interviews) carried out in 15 villages located in Lublin voivodeship, eastern Poland. Changes in the spatial structure of villages under the influence of the new building are presented by reference to three villages representative of the residential, tourist-recreational and agricultural functional types. The post-1989 process of economic transformation has magnified spatial differences as regards the kind of new housing construction taking place in rural areas. The intensity at which new building is taking place is very much a function of the size of the adjacent urban centre and the area's distance from it. Housing construction concentrates close to the main transport arteries, along which a belt of enhanced economic activity is to be found. Pressure from new investors is giving rise to a transformation of the natural environment, as well to the appearance of new conflicts between agriculture and housing. The development of new styles of building has led to changes in traditional configuration of villages. © 2009 Elsevier B.V. All rights reserved. Source


Kaczanowski S.,Polish Academy of Sciences
Physical Biology | Year: 2016

Programmed cell death is a basic cellular mechanism. Apoptotic-like programmed cell death (called apoptosis in animals) occurs in both unicellular and multicellular eukaryotes, and some apoptotic mechanisms are observed in bacteria. Endosymbiosis between mitochondria and eukaryotic cells took place early in the eukaryotic evolution, and some of the apoptotic-like mechanisms of mitochondria that were retained after this event now serve as parts of the eukaryotic apoptotic machinery. Apoptotic mechanisms have several functions in unicellular organisms: they include kin-selected altruistic suicide that controls population size, sharing common goods, and responding to viral infection. Apoptotic factors also have non-apoptotic functions. Apoptosis is involved in the cellular aging of eukaryotes, including humans. In addition, apoptosis is a key part of the innate tumor-suppression mechanism. Several anticancer drugs induce apoptosis, because apoptotic mechanisms are inactivated during oncogenesis. Because of the ancient history of apoptosis, I hypothesize that there is a deep relationship between mitochondrial metabolism, its role in aerobic versus anaerobic respiration, and the connection between apoptosis and cancer. Whereas normal cells rely primarily on oxidative mitochondrial respiration, most cancer cells use anaerobic metabolism. According to the Warburg hypothesis, the remodeling of the metabolism is one of the processes that leads to cancer. Recent studies indicate that anaerobic, non-mitochondrial respiration is particularly active in embryonic cells, stem cells, and aggressive stem-like cancer cells. Mitochondrial respiration is particularly active during the pathological aging of human cells in neurodegenerative diseases. According to the reversed Warburg hypothesis formulated by Demetrius, pathological aging is induced by mitochondrial respiration. Here, I advance the hypothesis that the stimulation of mitochondrial metabolism leads to pathological aging. © 2016 IOP Publishing Ltd. Source


Krasinski A.,Polish Academy of Sciences | Bolejko K.,University of Oxford
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

The notion of an apparent horizon (AH) in a collapsing object can be carried over from the Lemaître-Tolman to the quasispherical Szekeres models in three ways: 1. Literally by the definition-the AH is the boundary of the region, in which every bundle of null geodesics has negative expansion scalar. 2. As the locus, at which null lines that are as nearly radial as possible are turned toward decreasing areal radius R. These lines are in general nongeodesic. The name "absolute apparent horizon" (AAH) is proposed for this locus. 3. As the boundary of a region, where null geodesics are turned toward decreasing R. The name "light collapse region" is proposed for this region (which is three-dimensional in every space of constant t); its boundary coincides with the AAH. The AH and AAH coincide in the Lemaître-Tolman models. In the quasispherical Szekeres models, the AH is different from (but not disjoint with) the AAH. Properties of the AAH and light collapse region are investigated, and the relations between the AAH and the AH are illustrated with diagrams using an explicit example of a Szekeres metric. It turns out that an observer who is already within the AH is, for some time, not yet within the AAH. Nevertheless, no light signal can be sent through the AH from the inside. The analogue of the AAH for massive particles is also considered. © 2012 American Physical Society. Source


Rozynski G.,Polish Academy of Sciences
Ocean Engineering | Year: 2010

The paper analyses long-term variability of wave climate near Poland for the 1958-2002 period. With spectral and cross-spectral analysis, linear regression and singular spectrum analysis the modes of long-term variability were quantified for the most energetic months (November-February). For monthly indices of North Atlantic Oscillation from 1950 until 2006, it was established that the long-term trends of NAO and significant wave height demonstrate a gentle coupling. For Januaries this relationship is strongest and dates back to 1960, for Februaries a certain consistency appears since 1975. For Novembers and Decembers no statistically discernible coupling was found. Thus, the Baltic Sea appears to be the easternmost NAO-affected region, despite its separation from the Atlantic. The hydrodynamic variability also includes a non-trivial oscillation in the January wave energy records with T=8 years. The same periodicity was identified with the multi-channel SSA technique in the long-term shoreline data of a neighboring beach. The study shows that even almost entirely isolated water bodies are becoming exposed to global climatic phenomena and accelerated erosion of sandy beaches, typical for the South Baltic region. On the other hand, the 8-year hydrodynamic cycle can be viewed as the driver of long-term shoreline evolution. © 2009 Elsevier Ltd. All rights reserved. Source


Pawelaa L.,Polish Academy of Sciences | Sladkowski J.,University of Silesia
Physica D: Nonlinear Phenomena | Year: 2013

Coordination and cooperation are among the most important issues of game theory. Recently, the attention turned to game theory on graphs and social networks. Encouraged by interesting results obtained in quantum evolutionary game analysis, we study cooperative Parrondo's games in a quantum setup. The game is modeled using multidimensional quantum random walks with biased coins. We use the GHZ and W entangled states as the initial state of the coins. Our analysis shows that an apparent paradox in cooperative quantum games and some interesting phenomena can be observed. © 2013 Elsevier B.V. Source