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Krakow, Poland

The Jagiellonian University is a research university founded in 1364 by Casimir III the Great in Kazimierz . It is the oldest university in Poland, the second oldest university in Central Europe and one of the oldest universities in the world. It was positioned by QS World University Rankings as the best Polish university among the world's top 500 and the ARWU as second-best Polish higher-level institution.The university fell upon hard times when the occupation of Kraków by Austria-Hungary during the Partitions of Poland threatened its existence. In 1817, soon after the creation of the Duchy of Warsaw the university renamed as Jagiellonian University to commemorate Poland's Jagiellonian dynasty, which first revived the Kraków University in the past. In 2006, The Times Higher Education Supplement ranked Jagiellonian University as Poland's top university. Wikipedia.


Bizon P.,Jagiellonian University | Bizon P.,Max Planck Institute for Physics | Friedrich H.,Max Planck Institute for Physics
Classical and Quantum Gravity | Year: 2013

We consider a massless scalar field propagating on the exterior of the extreme Reissner-Nordström black hole. Using a discrete conformal symmetry of this spacetime, we draw a one-to-one relationship between the behavior of the field near the future horizon and near future null infinity. In particular, we show that the polynomial growth of the second and higher transversal derivatives along the horizon, recently found by Aretakis, reflects well-known facts about the retarded time asymptotics at null infinity. We also observe that the analogous relationship holds true for an axially symmetric massless scalar field propagating on the extreme Kerr-Newman background. © 2013 IOP Publishing Ltd.


Krompiec S.,University of Silesia | Penkala M.,University of Silesia | Szczubialka K.,Jagiellonian University | Kowalska E.,University of Silesia
Coordination Chemistry Reviews | Year: 2012

A comprehensive review of the reports concerning the synthesis of symmetrical and, particularly, mixed acetals and orthoesters with transition metal compounds and complexes as catalysts is presented. The following methods for the synthesis of symmetric and mixed acetals are discussed: acetalization of aldehydes or ketones with alcohols or diols; transacetalization; synthesis from vinyl and allyl ethers; synthesis via intra- or intermolecular addition of OH group to a triple bond; oxidation of primary alcohols; tetrahydropyranylation of alcohols or phenols; synthesis from epoxides and aldehydes or ketones; formation of 1,3-dioxanes by Prins cyclization of olefins with paraformaldehyde; oxidative cyclization-carbonylation of ynones; acetalization of ene-diol under Wacker-type catalysis. Reviewed is also the synthesis of mixed orthoesters via addition of alcohols and phenols to acrolein acetals. Presented are methods of the isolation of pure products, recycling of the catalysts (if applicable) and the advantages of the metal complexes compared to classical catalysts, Brønsted acids in particular. The relationship between the structure and reactivity was analyzed and the mechanisms of the reactions of acetal formation catalyzed by transition metal compounds and complexes were discussed. © 2012 Elsevier B.V.


Mlynarski J.,Jagiellonian University | Mlynarski J.,Polish Academy of Sciences | Bas S.,Polish Academy of Sciences
Chemical Society Reviews | Year: 2014

Asymmetric reactions in water and in aqueous solutions have become an area of fast growing interest recently. Although for a long time neglected as a medium for organic reactions, water has attracted attention as the most widely distributed solvent in the world. Indeed, water is the solvent used by nature for biological chemistry including aldol reactions being essential for glycolysis, gluconeogenesis and related processes. Consequently, artificial catalysts designed and used for aldol reactions in water can be promising for the synthesis of enantiopure molecules and are also important for the understanding of complex chemistry of life. This tutorial review summarizes recent developments in the area of aqueous asymmetric aldol reactions highlighting two fundamental directions-development of water compatible chiral Lewis acids and amine-based organocatalysts. © The Royal Society of Chemistry.


Binkowski L.J.,Pedagogical University of Cracow | Sawicka-Kapusta K.,Jagiellonian University
Chemosphere | Year: 2015

During the studies in 2003, high concentrations of cadmium (Cd) were noted among Mallards and Coots in Poland. Further research, five years later, showed the histopathological alterations in birds from the same area which were probably stimulated by Cd. This paper presents the analysis of Cd in ten different materials collected from these species (n=180) in years 2006-2009 in two areas, including southern - Zator and western Poland - Milicz. Similarly high concentrations to those from 2003 were noted only in kidneys of Mallards from the Zator area (up to 56.49μgg-1d.w.). Other comparable materials accumulated significantly lower concentration of Cd. Generally, lower concentrations occurred in birds from Milicz. Concentrations varied also between species and age groups. They correlated between liver and kidneys, brain and muscle and brain and spleen. Potential in vivo bioindicators (blood, feathers and excrements) did not seem to be useful as biomarkers in both areas. © 2014 Elsevier Ltd.


Chaloupka J.,Max Planck Institute for Solid State Research | Chaloupka J.,Masaryk University | Oles A.M.,Max Planck Institute for Solid State Research | Oles A.M.,Jagiellonian University
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

We investigate the ground state of the d1 spin-orbital model for triply degenerate t2g orbitals on a triangular lattice that unifies intrinsic frustration of spin and orbital interactions with geometrical frustration. Using full or Lanczos exact diagonalization of finite clusters, we establish that the ground state of the spin-orbital model that interpolates between superexchange and direct exchange interactions on the bonds is characterized by valence-bond correlations. In the absence of Hund's exchange the model describes a competition between various possible valence-bond states. By considering the clusters with open boundary conditions we demonstrate that orbital interactions are always frustrated, but this frustration is removed by pronounced spin singlet correlations that coexist with dimer orbital correlations supporting them. Such local configurations contribute to the disordered ground states found for the clusters with periodic boundary conditions that interpolate between a highly resonating, dimer-based, entangled spin-orbital liquid phase and a valence-bond state with completely static spin-singlet states. We argue that these states are also realized for the infinite lattice and anticipate that pronounced transitions between different regimes found for particular geometries will turn out to smooth crossovers in the properties of the spin-orbital liquid in the thermodynamic limit. Finally, we provide evidence that the resonating spin-orbital liquid phase involves entangled states on the bonds. In such a phase classical considerations based on the mean-field theory cannot be used, spin exchange interactions do not determine spin bond correlations, and quantum fluctuations play a crucial role in the ground states and magnetic transitions. © 2011 American Physical Society.


Bodaszewska-Lubas M.,Jagiellonian University
Postȩpy higieny i medycyny doświadczalnej (Online) | Year: 2012

In this paper, an attempt was made to evaluate the antibacterial potential of standard strains of lactic acid bacteria (LAB) producing bacteriocins of various classes, thus demonstrating various mechanisms of cell membrane damages against the Streptococcus agalactiae strains (Group B Streptococcus, GBS), depending on surface polysaccharides and surface alpha-like protein genes. Antimicrobial property of the strains of L. plantarum C 11, L. sakei DSMZ 6333, and L. lactis ATCC 11454 producing bacteriocins: JK and EF plantaricins, sakacin and nisin, respectively, against the GBS strains was evaluated. The chosen to the study GBS strains were represented by serotypes Ia, Ib, II, III, V and they had bca, epsilon, rib, alp2 or alp3 alpha-like protein genes. The experiment was conducted by means of suspension culture and the bacteria count was determined using the serial dilution method. A great ability of L. plantarum C 11 strain was proven to inhibit the GBS growth. The strain of L. sakei DSMZ 6333 did not demonstrate any ability to inhibit the growth of GBS, whereas L. lactis ATCC 11454 inhibited the growth of S. agalactiae indicator strains to a minor extent. Statistically significant differences were demonstrated between the GBS strains representing various serotypes against the antimicrobial activity of model LAB strains. The least sensitive to the activity of bacteriocins were the strains representing serotypes Ib and III, whereas the strains representing serotype II were the most sensitive. The sensitivity of the GBS strains to the antimicrobial activity of LAB was not dependent on alpha-like protein genes. Among the LAB standard strains producing bacteriocins, the strongest antimicrobial property was observed in the strain of L. plantarum C 11. Because of the generally known and verified strong antagonistic property of the strains of L. plantarum species against indicator bacteria, it is necessary to further pursue the research presented in this paper.


Abbott M.C.,University of Cape Town | Aniceto I.,Jagiellonian University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

We propose a number of modifications to the classical term in the dressing phase for integrable strings in AdS3×S3×S3×S1, and check these against existing perturbative calculations, crossing symmetry, and the semiclassical limit of the Bethe equations. The principal change is that the phase for different masses should start with a term Q1Q2, like the one-loop AdS3 dressing phase, rather than Q2Q3 as for the original AdS5 AFS phase. © 2015 The Authors.


Adam C.,University of Santiago de Compostela | Naya C.,University of Santiago de Compostela | Sanchez-Guillen J.,University of Santiago de Compostela | Vazquez R.,University of Santiago de Compostela | Wereszczynski A.,Jagiellonian University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

The BPS Skyrme model has been demonstrated already to provide a physically intriguing and quantitatively reliable description of nuclear matter. Indeed, the model has both the symmetries and the energy-momentum tensor of a perfect fluid, and thus represents a field theoretic realization of the "liquid droplet" model of nuclear matter. In addition, the classical soliton solutions together with some obvious corrections (spin-isospin quantization, Coulomb energy, proton-neutron mass difference) provide an accurate modeling of nuclear binding energies for heavier nuclei. These results lead to the rather natural proposal to try to describe also neutron stars by the BPS Skyrme model coupled to gravity. We find that the resulting self-gravitating BPS Skyrmions provide excellent results as well as some new perspectives for the description of bulk properties of neutron stars when the parameter values of the model are extracted from nuclear physics. Specifically, the maximum possible mass of a neutron star before black-hole formation sets in is a few solar masses, the precise value of which depends on the precise values of the model parameters, and the resulting neutron star radius is of the order of 10 km. © 2015 The Authors.


Bialas A.,Jagiellonian University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

It is shown that the transverse momentum distributions of particles emerging from the decay of statistical clusters, distributed according to a power law in their transverse energy, closely resemble those following from the Tsallis non-extensive statistical model. The experimental data are well reproduced with the cluster temperature T≈. 160 MeV. © 2015 The Author.


Gajos A.,Jagiellonian University
Acta Physica Polonica B | Year: 2015

This work presents prospects for conducting a novel direct test of timereversal symmetry at the KLOE-2 experiment. Quantum entanglement of neutral K meson pairs uniquely available at KLOE-2 allows to probe directly the time-reversal symmetry (T{script}) independently of C{script} violation. This is achieved by a comparison of probabilities for a transition between flavour and C{script}-definite states and its inverse obtained through exchange of initial and final states. As such, a test requires the reconstruction of the KL → 3π0 decay accompanied by KS → π±ℓ∓ν with good timing information, a new reconstruction method for this process is also presented which is capable of reconstructing the KL → 3π0 decay with decay time resolution of O{script}(1T{script}S). © 2015 ACTA PHYSICA POLONICA B.


Ficek F.,Jagiellonian University
Classical and Quantum Gravity | Year: 2015

In this paper I study the stationary, spherically symmetric accretion of fluids onto a charged black hole in the presence of a cosmological constant. For some isothermal equations of state it is possible to obtain analytic solutions. For the case of a radiation fluid I derive the relation between the locations of horizons and sonic (critical) points. In specific cases the solutions form closed, binocular-like trajectories in a phase diagram of the velocity versus radius. © 2015 IOP Publishing Ltd.


Strug B.,Jagiellonian University
Automation in Construction | Year: 2013

This paper contributes to the problem of assisting the designer in dealing with evaluating the quality of a design. Especially, spatial relationships and arrangements of components within a design are explicitly dealt with. Hierarchical graphs are used as the design representation to enable capturing different ways components can be related by taking into account the fact that a component can form a part of another one. As the human evaluation is often based on the experience gained from seeing and analyzing many designs a similar approach is proposed in this paper. This approach uses methods drawn from machine learning, in particular kernels for structured data. Kernel functions are used to calculate similarity of new designs to other designs for which the evaluation is known thus simulating the process of learning from experience. The proposed approach is illustrated by experimental results obtained for the task of floor layout design. © 2012 Elsevier B.V. All rights reserved.


Senderecka M.,Jagiellonian University
Biological Psychology | Year: 2016

The present study investigated the effect of emotion on response inhibition and error monitoring using event-related potentials. Participants performed an emotional stop-signal task that required response inhibition to briefly presented threatening and neutral visual stimuli. Negative, arousing pictures improved behavioral performance by decreasing the stop-signal reaction time and increasing the inhibitory rate, but had no enhancing effect on inhibitory processing at the electrophysiological level (N2-P3 complex). The perceptual processing of threatening stop-signals resulted in a larger and earlier N1 component. The Pe component, associated with conscious evaluation or affective processing of an error, was stronger in negative than in neutral trials. The stronger Pe correlated with superior task performance in the emotional condition. Prioritized perceptual processing of the stop-signal was associated with better conscious error monitoring. These results support the hypothesis that threatening, arousing stimuli improve behavioral inhibitory performance and error monitoring due to the enhancement of perceptual processing. © 2015 Elsevier B.V.


Gaweda L.,Medical University of Warsaw | Prochwicz K.,Jagiellonian University
European Psychiatry | Year: 2015

Background: The role of psychosis-related cognitive biases (e.g. jumping to conclusions) in a delusion continuum is well-established. Little is known about the role of types of cognitive biases. The aim of this study was to investigate the role of psychosis-related and "Beckian" (i.e. anxiety- and depression-related) cognitive biases assessed with a clinical questionnaire in the delusion continuum and its dimensions. Methods: Schizophrenia patients with (n=57) and without (n=35) delusions were compared to healthy subjects who had a low (n=53) and high (n=57) level of delusion-like experiences (DLEs) on the Cognitive Biases Questionnaire for Psychosis (CBQp). Delusion dimensions in the clinical sample were assessed with the semi-structured interview PSYRATS. DLEs were measured with the Peters Delusion Inventory (PDI). Results: High DLEs participants scored significantly higher than low DLEs, and patients with delusions scored higher than patients without delusions on the total scores of the CBQp. High DLEs participants scored significantly higher than low DLEs on catastrophisation and JTC. Schizophrenia patients with delusions scored significantly higher when compared to patients without delusions on intentionalising, dichotomous thinking, JTC and emotional reasoning. Patients with delusions and high DLEs participants scored similarly on JTC. Stepwise regression analysis revealed that catastrophising predicted total severity of clinical delusions and JTC predicted the cognitive dimension of clinical delusions. Both JTC and catastrophisation predicted the frequency and conviction associated with DLEs. Conclusions: Both "Beckian" and psychosis-related cognitive biases may underlie delusions. Different aspects of clinical delusions and delusion-like experiences may be related to different cognitive biases. © 2015 Elsevier Masson SAS. All rights reserved.


Zdziarski A.A.,Centrum Astronomiczne im. M. Kopernika | Stawarz L,Japan Aerospace Exploration Agency | Stawarz L,Jagiellonian University | Pjanka P.,Obserwatorium Astronomiczne Uniwersytetu Warszawskiego | Sikora M.,Centrum Astronomiczne im. M. Kopernika
Monthly Notices of the Royal Astronomical Society | Year: 2014

This is part one of our study of models of jets with distributed electron acceleration. We present here our assumptions, basic equations, and their solutions for the steady-state electron distribution. We assume the shape of the rate of electron acceleration and the dependences of its normalization and the magnetic field strength on the height along the jet. Our focus is on the hard spectral state of black hole binaries, for which we take into account that their typical radio spectra are flat. This appears to require a constant dissipation rate per unit logarithmic length and conservation of the magnetic energy flux. Our electron kinetic equation includes adiabatic and radiative losses and advection, and our photon radiative transfer equation includes synchrotron absorption and emission and Compton emission. Apart from the self-Compton process, we take into account Compton scattering of stellar and accretion photons and absorption of very high energy γ-rays by pair production on soft photons. We present a general solution of the kinetic equation with advection and radiative and adiabatic losses and an analytic solution in the case of dominant synchrotron losses in conical jets. In the following paper, we present detailed spectra resulting from our equations as applied to Cyg X-1. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Plachno B.J.,Jagiellonian University | Swiatek P.,University of Silesia
Protoplasma | Year: 2010

In most species of the Genlisea-Utricularia sister lineage, the organs arising directly after germination comprise a single leaf-like structure, followed by a bladder-trap/stolon, with the lack of an embryonic primary root considered a synapomorphic character. Previous anatomical work suggests that the most common recent ancestor of Utricularia possessed an embryo comprising storage tissue and a meristematic apical region minus lateral organs. Studies of embryogenesis across the Utricularia lineage suggest that multiple primary organs have only evolved in the viviparous Utricularia nelumbifolia, Utricularia reniformis, and Utricularia humboldtii within the derived Iperua/Orchidioides clade. All three of these species are specialized for growth as "aquatic epiphytes" in the tanks of bromeliads, with recent phylogenetic evidence suggesting the possibility that multiple primary organs may have evolved twice independently within this clade. The primary organs of viviparous Utricularia also possess epidermal surface glands, and our study suggests that these may function as root hairs for uptake of solutes from the external environment-a possible adaptation for the "aquatic-epiphytic" habitat. © Springer-Verlag 2009.


Kaminska D.,Jagiellonian University
Acta Physica Polonica B | Year: 2015

Study of semileptonic decays of neutral kaons allows to perform a test of discrete symmetries, as well as basic principles of the Standard Model. In this paper, a general review on dependency between charge asymmetry constructed for semileptonic decays of short- and long-lived kaons and C{script}T{script} symmetry is given. © 2015 ACTA PHYSICA POLONICA B.


Ma S.,University of Melbourne | Blasiak A.,Jagiellonian University | Olucha-Bordonau F.E.,University of Valencia | Verberne A.J.M.,University of Melbourne | Gundlach A.L.,University of Melbourne
Journal of Physiology | Year: 2013

Abstract The nucleus incertus (NI) of the rat hindbrain is a putative node in the ascending control of the septohippocampal system and hippocampal theta rhythm and is stress and arousal responsive. NI contains GABA neurons that express multiple neuropeptides, including relaxin-3 (RLN3) and neuropeptide receptors, including corticotrophin-releasing factor receptor-1 (CRF-R1), but the precise anatomical and physiological characteristics of NI neurons are unclear. Therefore, we examined the firing properties of NI neurons and their responses to CRF, the correlation of these responses with occurrence of relaxin-3, and NI neuron morphology in the rat. Most NI neurons excited by intracerebroventricular CRF infusion were RLN3-positive (9 of 10), whereas all inhibited cells were RLN3-negative (8 of 8). The spontaneous firing of RLN3 (n= 6) but not non-RLN3 neurons (n= 6) was strongly modulated and phase-locked with the initial ascending phase of hippocampal theta oscillations. In brain slices, the majority of recorded NI neurons (15 of 19) displayed excitatory responses to CRF, which uniformly increased action potential frequency and membrane potential depolarization in the presence of tetrodotoxin, indicating a direct, postsynaptic action of CRF on NI neurons. This excitation was associated with reduction in the slow component of afterhyperpolarization and a strong depolarization. Quantitative analysis in naïve rats of validated CRF-R1, RLN3 and neuronal nuclear antigen (NeuN) immunoreactivity revealed 52% of NI neurons as CRF-R1 positive, of which 53% were RLN3 positive, while 48% of NI neurons lacked CRF-R1 and RLN3. All RLN3 neurons expressed CRF-R1. CRF neurons that projected to the NI were identified in lateral preoptic hypothalamus, but not in paraventricular hypothalamus, bed nucleus of stria terminalis or central amygdala. Our findings suggest NI is an important site for CRF modulation of hippocampal theta rhythm via effects on GABA/RLN3 transmission. © 2013 The Physiological Society.


During severe hypoxia in the heart, impaired supply of ATP by oxidative phosphorylation could lead to a great drop in ATP turnover and heart work. Anaerobic glycolysis enables unchanged ATP turnover to be maintained, but leads to huge changes in metabolite (PCr, ATP, ADP, Pi) concentrations and to cytosol acidification. A computer model of heart energetics developed previously is used to analyze semi-quantitatively the effect of different processes/mechanisms that can partly counteract these effects. Down-regulation of ATP usage compromises cardiac output, but reduces changes in cytosolic pH and metabolite concentrations. AMP decomposition delays cytosol acidification but reduces metabolite homeostasis (concentration stability). An increase in the parallel activation of oxidative phosphorylation (OXPHOS) (a hypothetical mechanism involving direct activation of all OXPHOS complexes by a cytosolic factor, postulated to take place also during work increase) reduces cytosol acidification and elevates metabolite homeostasis. All these mechanisms can generate the post-ischemic PCr overshoot. © The Physiological Society of Japan and Springer 2011.


PURPOSE:: To analyze the spontaneous closure mechanisms, retinal layer regeneration, and best corrected visual acuity (BCVA) in the full-thickness macular hole (FMTH). METHODS:: Ten eyes of 10 patients were studied. The measured outcomes included the time of persisting clinical symptoms and spontaneous closure of FTMH, BCVA, and spectral domain optical coherence tomography (SD-OCT) of vitreomacular interface. RESULTS:: In a follow-up period, all eyes showed closure of FTMH (closure range: 3–64 weeks). The “bridging” phenomenon was a main mechanism of a spontaneous FMTH closure. Additionally, posterior vitreous detachment with the release of vitreomacular traction was observed in 4 eyes (40%). The statistical analysis showed that shorter the duration of symptoms, shorter the duration of the spontaneous FTMH closure (r = 0 673, P < 0 05). No significant association was observed between the time of spontaneous closure FTMH, the age of patients, and BCVA. The regeneration of the outer nuclear layer (ONL) and external limiting membrane (ELM) was confirmed in 10 and 9 eyes, respectively. In six eyes, connections between inner and outer segments of photoreceptors were rebuilt; in these cases, the final BCVA was the best. None of the eyes showed the regeneration of the connections between the outer segments of photoreceptor and retinal pigment epithelium (RPE). CONCLUSION:: The main mechanism leading to a spontaneous closure of FTMH is the “bridging” phenomenon. Vitreous detachment and vitreomacular traction release are not necessary conditions promoting the closure of FTMH. Shorter duration of symptoms and regeneration of photoreceptors IS/OS interface provide a better final BCVA. © 2016 by Ophthalmic Communications Society, Inc.


Nrf2 transcription factor plays a crucial role in protection of cells against oxidative stress. Under normal conditions Nrf2 is sequestered in cytoplasm by a cytoskeletal protein, Keapl. Situation is changed under stressful conditions,when electrophiles and/or reactiveoxygen species (ROS) cause dissociation of Nrf2 from Keap1. As a consequence, Nrf2 is translocated to the nucleus, that leads to activation of cytoprotective genes involved in electrophile conjugation, excretion of xenobiotics, ROS scavenging and stabilization of cellular redox potential. Amongst xenobiotics, there are many mutagenic and cancerogenic factors. Phase I and II enzymes are responsible for inactivation and removal of such compounds. It has been shown that induction of phase II enzymes confers protection upon insult by reactive metabolites of cancerogens or ROS. Since Nrf2 is an inductor of those enzymes it can be considered as a potential target for cancer chemoprevention. Similarly, in case of neurodegenerative disorders, which pathogenesis is connected to oxidative stress, Nrf2 may be important for therapeutical and preventive strategies


Salat R.,Warsaw University of Life Sciences | Salat K.,Jagiellonian University
Computer Methods and Programs in Biomedicine | Year: 2013

Drug interactions are an important issue of efficacious and safe pharmacotherapy. Although the use of drug combinations carries the potential risk of enhanced toxicity, when carefully introduced it enables to optimize the therapy and achieve pharmacological effects at doses lower than those of single agents. In view of the development of novel analgesic compounds for the neuropathic pain treatment little is known about their influence on the efficacy of currently used analgesic drugs.Below we describe the preliminary evaluation of support vector machine in the regression mode (SVR) application for the prediction of maximal antiallodynic effect of a new derivative of dihydrofuran-2-one (LPP1) used in combination with pregabalin (PGB) in the streptozocin-induced neuropathic pain model in mice. Based on SVR the most effective doses of co-administered LPP1 (4. mg/kg) and PGB (1. mg/kg) were predicted to cause the paw withdrawal threshold at 6.7. g in the von Frey test. In vivo for the same combination of doses the paw withdrawal was observed at 6.5. g, which confirms good predictive properties of SVR. © 2013 Elsevier Ireland Ltd.


Odrzywolek A.,Jagiellonian University | Plewa T.,Florida State University
Astronomy and Astrophysics | Year: 2011

Aims. We present neutrino light curves and energy spectra for two representative type Ia supernova explosion models: a pure deflagration and a delayed detonation. Methods. We calculate the neutrino flux from β processes using nuclear statistical equilibrium abundances convoluted with approximate neutrino spectra of the individual nuclei and the thermal neutrino spectrum (pair+plasma). Results. Although the two considered thermonuclear supernova explosion scenarios are expected to produce almost identical electromagnetic output, their neutrino signatures appear vastly different, which allows an unambiguous identification of the explosion mechanism: a pure deflagration produces a single peak in the neutrino light curve, while the addition of the second maximum characterizes a delayed-detonation. We identified the following main contributors to the neutrino signal: (1) weak electron neutrino emission from electron captures (in particular on the protons 55Co and 56Ni) and numerous β-active nuclei produced by the thermonuclear flame and/or detonation front, (2) electron antineutrinos from positron captures on neutrons, and (3) the thermal emission from pair annihilation. We estimate that a pure deflagration supernova explosion at a distance of 1 kpc would trigger about 14 events in the future 50 kt liquid scintillator detector and some 19 events in a 0.5 Mt water Cherenkov-type detector. Conclusions. While in contrast to core-collapse supernovae neutrinos carry only a very small fraction of the energy produced in the thermonuclear supernova explosion, the SN Ia neutrino signal provides information that allows us to unambiguously distinguish between different possible explosion scenarios. These studies will become feasible with the next generation of proposed neutrino observatories. © 2011 ESO.


The aim of the study was to determine to what extent cervical intraepithelial neoplasia and cervical cancer surgery affect a woman's mental state and how does it affect her interpersonal relationships, sexual activity, family life, and her professional and social activity. The clinical material consisted of 153 women aged 20 and 47, who were diagnosed and treated by the Chair of Gynaecology and Obstetrics, Jagiellonian University Medical College in Kraków between 2006 and 2010, and were confirmed to have CIN3 and cervical carcinoma stage IA. An oryginally constructed survey form consisting of 108 questions and divided into 5 research stages was implemented. H.J. Eysenck's Personality Questionnaire, and Physical and Mental State Questionnaire KS-40. RESULTS: The diagnosis generated a change in the patients' self-images: prior to the diagnosis, 74.6% considered themselves to be completely healthy, whereas after the diagnosis was given 40.5% of respondents had the feeling of illness, and 33.3% of the moderately illness. CONCLUSIONS: The diagnosis of CIN and microinvasive cervical cancer, and surgical procedure, invokes a feeling of being unwell in a woman who previously felt completely healthy, and significantly impedes quality of life. The diagnostic-therapeutic management induces general anxiety, worry about preservation of the generative organ, sexual intercourse, fertility, changes in the dynamics of the family and in the professional field, as well as changes in interpersonal relationships.


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

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


Romanczukiewicz T.,Jagiellonian University | Shnir Y.,Durham University | Shnir Y.,Belarusian National Technical University
Physical Review Letters | Year: 2010

We present a numerical study of the process of production of kink-antikink pairs in the collision of particlelike states in the one-dimensional 1/4 model. It is shown that there are 3 steps in the process: The first step is to excite the oscillon intermediate state in the particle collision, the second step is a resonance excitation of the oscillon by the incoming perturbations, and, finally, the soliton-antisoliton pair can be created from the resonantly excited oscillon. It is shown that the process depends fractally on the amplitude of the perturbations and the number of perturbations. We also present the effective collective coordinate model for this process.


Kaminska-Winciorek G.,Center for Cancer Prevention and Treatment | Spiewak R.,Jagiellonian University
Postepy Dermatologii i Alergologii | Year: 2013

Nevus comedonicus (NC) is a very rare, benign hamartoma characterised by the occurrence of dilated, comedo-like openings, typically on the face, neck, upper arms, chest or abdomen. In uncertain cases, histopathological examination confirms the diagnosis. The authors suggest dermoscopy as a rapid and useful method of initial diagnosis of nevus comedonicus based upon its distinctive dermoscopic features. The dermoscopy reveals numerous lightand dark-brown, circular or barrel-shaped, homogenous areas with prominent keratin plugs.


Casner K.L.,University of California at Davis | Pyrcz T.W.,Jagiellonian University
Ecography | Year: 2010

Species distributions are a product of contemporary and historical forces. Using phylogenetic and geographic data, we explore the timing of and barriers to the diversification of the Andean butterfly genus Lymanopoda (Nymphalidae, Satyrinae). Clade and species level diversification is coincident with Andean orogeny and Pleistocene glaciation cycles. Lymanopoda has primarily diversified within elevational bands, radiating horizontally throughout the Andes with occasional speciation across elevational boundaries, often associated with ecotones. Narrow elevational ranges and infrequent speciation into adjacent elevational strata suggest that expansion across elevational gradients is relatively difficult. These results are similar to those found in studies of other Andean taxa. © 2010 The Authors. Journal compilation © 2010 Ecography.


The aim of this paper is a critical analysis of ecophilosophy and pro-ecologial politics. I present the arguments of the supporters of liberal capitalism on the basis of Vaclav Klaus's opinions; and the arguments of traditional humanism on the basis of the views of Luc Ferry. My analysis will demonstrate that Klaus's polemics with the supporters of the so called 'environmentalism' is based on a misunderstanding. Whereas Luc Ferry's critical arguments fail to take into account the historical development of humanism. In conclusion I demonstrate that, contrary to what Ferry claims, pro-ecological politics does not involve a breach with the humanistic tradition, it only requires a reform of that tradition. In a new phase of development of humanism, which we may call the 'humanism of tomorrow', human improvement does not entail a breach with Nature, or a conquest of Nature, it entails a new pact with Nature that will be realized by means of sustainable development.


Spiewak R.,Jagiellonian University
Current Opinion in Allergy and Clinical Immunology | Year: 2012

Purpose of review: Both atopy and diseases from the spectrum of dermatitis and eczema are among the most frequent clinical problems worldwide; nevertheless, they are still poorly defined and too frequently misdiagnosed. In the present review, studies pertinent to this topic were systematized and critically assessed with particular attention to definitions of relevant diseases. Recent finding: The overall message from the research done to date is that various types of dermatitis frequently coexist. Atopy and contact allergy seem independent, while there is insufficient data to state upon the relationship between atopy and allergic contact dermatitis. Furthermore, it seems at present that atopy does not, whereas atopic eczema does constitute a risk factor for irritant contact dermatitis. Summary: The interplay between atopy and diseases from the spectrum of dermatitis and eczema is not fully understood; nevertheless, their coexistence and overlapping are not rare. Therefore, every patient with eczema - regardless of age, sex or atopic status - should undergo an extensive diagnostic programme including each atopic eczema, irritant contact dermatitis, allergic contact dermatitis, and protein contact dermatitis. Better definitions and well designed studies are necessary to achieve detailed information on the complex relationships between each atopy, atopic eczema, and the three contact dermatitides. © 2012 Wolters Kluwer Health | Lippincott Williams & Wilkins.


Autschbach J.,State University of New York at Buffalo | Srebro M.,Jagiellonian University
Accounts of Chemical Research | Year: 2014

ConspectusKohn-Sham theory (KST) is the "workhorse" of numerical quantum chemistry. This is particularly true for first-principles calculations of ground- and excited-state properties for larger systems, including electronic spectra, electronic dynamic and static linear and higher order response properties (including nonlinear optical (NLO) properties), conformational or dynamic averaging of spectra and response properties, or properties that are affected by the coupling of electron and nuclear motion.This Account explores the sometimes dramatic impact of the delocalization error (DE) and possible benefits from the use of long-range corrections (LC) and "tuning" of functionals in KST calculations of molecular ground-state and response properties. Tuning refers to a nonempirical molecule-specific determination of adjustable parameters in functionals to satisfy known exact conditions, for instance, that the energy of the highest occupied molecular orbital (HOMO) should be equal to the negative vertical ionization potential (IP) or that the energy as a function of fractional electron numbers should afford straight-line segments. The presentation is given from the viewpoint of a chemist interested in computations of a variety of molecular optical and spectroscopic properties and of a theoretician developing methods for computing such properties with KST. In recent years, the use of LC functionals, functional tuning, and quantifying the DE explicitly have provided valuable insight regarding the performance of KST for molecular properties.We discuss a number of different molecular properties, with examples from recent studies from our laboratory and related literature. The selected properties probe different aspects of molecular electronic structure. Electric field gradients and hyperfine coupling constants can be exquisitely sensitive to the DE because it affects the ground-state electron density and spin density distributions. For π-conjugated molecules, it is shown how the DE manifests itself either in too strong or too weak delocalization of localized molecular orbitals (LMOs). Optical rotation is an electric-magnetic linear response property that is calculated in a similar fashion as the electric polarizability, but it is more sensitive to approximations and can benefit greatly from tuning and small DE. Hyperpolarizabilities of π-conjugated "push-pull" systems are examples of NLO properties that can be greatly improved by tuning of range-separated exchange (RSE) functionals, in part due to improved charge-transfer excitation energies. On-going work on band gap predictions is also mentioned. The findings may provide clues for future improvements of KST because different molecular properties exhibit varying sensitivity to approximations in the electronic structure model. The utility of analyzing molecular properties and the impact of the DE in terms of LMOs, representing "chemists orbitals" such as individual lone pairs and bonds, is highlighted. © 2014 American Chemical Society.


The aim of the study was to construct the model forecasting the birch pollen season characteristics in Cracow on the basis of an 18-year data series. The study was performed using the volumetric method (Lanzoni/Burkard trap). The 98/95 % method was used to calculate the pollen season. The Spearman's correlation test was applied to find the relationship between the meteorological parameters and pollen season characteristics. To construct the predictive model, the backward stepwise multiple regression analysis was used including the multi-collinearity of variables. The predictive models best fitted the pollen season start and end, especially models containing two independent variables. The peak concentration value was predicted with the higher prediction error. Also the accuracy of the models predicting the pollen season characteristics in 2009 was higher in comparison with 2010. Both, the multi-variable model and one-variable model for the beginning of the pollen season included air temperature during the last 10 days of February, while the multi-variable model also included humidity at the beginning of April. The models forecasting the end of the pollen season were based on temperature in March-April, while the peak day was predicted using the temperature during the last 10 days of March. © 2012 The Author(s).


Malec E.,Jagiellonian University | Xie N.,Fudan University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

We discuss the relation between the concentration of the Brown-York mass and the formation of trapped surfaces in nonspherical massive systems. In particular, we formulate and prove a precise version of the Thorne hoop conjecture in conformally flat three-geometries sliced by equipotential foliation leaves. An intriguing relationship between the total rest mass and the Brown-York mass is shown. This is a further investigation of the previous work on the Brown-York mass hoop conjecture in spherical symmetry. © 2015 American Physical Society.


Eilmes A.,Jagiellonian University
Theoretical Chemistry Accounts | Year: 2014

Solvent-induced shifts in the absorption spectrum of N,N-diethyl-4-nitroaniline were studied by quantum-chemical methods in water, dimethylsulfoxide, acetonitrile and acetone. TDDFT methodology and semiempirical ZINDO/S and PM6-CIS approaches were used to calculate excitation energies. Solvent effect was modeled in implicit solvent model by different variants of the PCM approach. Classical molecular dynamics was applied to obtain solute-solvent geometries used in explicit solvent modeling. Most implicit solvent models fail to reproduce the sequence of solvatochromic shifts for four studied solvents, usually yielding too small effect for water. The best result of the PCM method was obtained with SMD atomic radii. Semiempirical quantum-chemical methods in explicit solvent model did not provide satisfactory description of solvatochromic shifts with the largest disagreement to experiment observed for water. TDDFT explicit solvent calculations performed the best in modeling of spectral shifts. Problems with reproduction of experimental data were attributed to specific interactions. © 2014 The Author(s).


Michalczyk L.,Jagiellonian University | Kaczmarek L.,Adam Mickiewicz University
Journal of Limnology | Year: 2013

In this paper we present the Tardigrada Register (www.tardigrada.net/register): a free, comprehensive, and standardised online data repository for tardigrade taxonomy. We outline key problems of the modern tardigrade systematics and we propose the Register as a potential solution to some of them. We then describe the idea, structure and works of the service and discuss challenges it may face. However, most importantly, we hope to convince fellow Tardigradologists that sharing their data via the Register will benefit the entire community of the contemporary and future tardigrade researchers.


Undas A.,Jagiellonian University | Undas A.,Center for Research and Medical Technology
Seminars in Thrombosis and Hemostasis | Year: 2016

Fibrin formed from fibrinogen is the main component of thrombi. Clot structure is characterized by fiber thickness and pore size, which differs within a given clot and between individuals. Plasma clot architecture is largely determined by the quantity and quality of fibrinogen. Plasma fibrinogen concentrations are most commonly measured in citrated plasma using the Clauss method. However, several factors, including instrument type and reagent, may affect results. Other approaches to express the ability of fibrinogen to clot involve prothrombin time-derived or clottable protein assays, while fibrinogen antigen levels in clinical settings are measured using immunological or precipitation assays. Fibrin clot permeability (reflected by the Darcy constant, K s) being proportional to a buffer volume percolating through a clot under a given hydrostatic pressure is now the most commonly used measure of clot structure. Low K s values indicating tightly packed fibrin structure have been shown to be associated with venous and arterial thrombotic complications, while high K s might contribute to bleeding disorders. The measurement of K s, however, is not standardized and validated. This review summarizes the current knowledge on practical aspects of the measurement of fibrinogen levels and K s in patients. © 2016 by Thieme Medical Publishers, Inc.


Horsch P.,Max Planck Institute for Solid State Research | Oles A.M.,Max Planck Institute for Solid State Research | Oles A.M.,Jagiellonian University
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

We present a model for typical charged defects in weakly doped Y 1-xCa xVO 3 perovskites and study how they influence the magnetic and orbital order. Starting from a multiband Hubbard model, we show that the charge carriers introduced by doping are bound to the Ca defects with large binding energy of ≈1 eV at small doping, and give rise to the in-gap absorption band observed in the optical spectroscopy. The central position of a generic Ca defect with eight equidistant vanadium neighbors implies a partly filled defect band and permits activated transport due to Coulomb disorder. We explore the effect of bound charge carriers on the dynamics of the {yz,zx} orbital and spin degrees of freedom in the context of a spin-orbital t-J model. After deriving the superexchange interactions around the doped hole, we show that the transition from G-type to C-type antiferromagnetic (AF) order is triggered by the kinetic energy of doped holes via the double-exchange mechanism. The defect states lead to local modification of orbital correlations within ferromagnetic chains along the c axis; some of them contain hole defects, while the charge-orbital coupling suppresses locally {yz,zx} orbital fluctuations in the others. Thereby, Ca defects provide a physical mechanism for spin-orbital dimerization along the ferromagnetic bonds, suggesting that, in the C-AF phase of weakly doped Y 1-xCa xVO 3, dimerization increases with doping. © 2011 American Physical Society.


The smooth (Lissotriton vulgaris) and Carpathian (L. montandoni) newts are sister species. These are separated by a moderate genetic distance, but exhibit striking morphological differences, especially in male epigamic traits. In the areas where they co-occur, they readily mate with each other and produce viable hybrids. However, a high level of pre-zygotic isolation with an unknown behavioral basis has been reported. The complex courtship of newts consists of at least three types of modality: chemical, visual, and tactile. The relative significance of these in mate choice is unclear, but it is commonly accepted that pheromones are an important communication channel. The goal of this study was to determine whether the females of L. vulgaris and L. montandoni exhibit preferences for conspecific extracts from the pheromone-producing abdominal (dorsal) glands. Females of both species spent more time in proximity to the source of the abdominal gland extracts of their own species when a liver extract was presented as an alternative. In a second trial, females were simultaneously confronted with conspecific and heterospecific abdominal gland extracts. Asymmetric preferences were found. Lissotriton vulgaris females were not selective, whereas L. montandoni females preferred the conspecific abdominal gland extract. This finding is consistent with the results of earlier experiments on mate choice in these species. The results strongly indicate that pheromones play a crucial role in courtship and species recognition in this pair of closely related, hybridizing species. © 2012 Zoological Society of Japan.


1. In two partridge species, the grey partridge (Perdix perdix) and chukar (Alectoris chukar), from hatching up to 120 d, the growth rate and development of body mass, wing, tarsus, and bill length were measured and fitted by Gompertz equations.2. As a typical precocial species, partridges hatched with relatively well developed legs and bills, and wing growth followed a gradual development of thermoregulation.3. Gompertz growth constants for body mass growth were 0·039 and 0·038 for grey partridges and chukars, respectively.4. The allometric relationship between tarsus length and body mass followed a geometric similarity (1/3 power) in both grey partridges and chukars. © 2012 Copyright Taylor and Francis Group, LLC.


Kaczmarczyk J.,Jagiellonian University | Spalek J.,AGH University of Science and Technology
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

The coexistence of antiferromagnetism with superconductivity is studied theoretically within the t-J model with the Zeeman term included. The strong electron correlations are accounted for by means of the extended Gutzwiller projection method within a statistically consistent approach proposed recently. The phase diagram on the band filling-magnetic field plane is shown, and subsequently the system properties are analyzed for the fixed band filling n=0.97. In this regime, the results reflect principal qualitative features observed recently in selected heavy-fermion systems, namely, (i) with the increasing magnetic field the system evolves from coexisting antiferromagnetic-superconducting phase through antiferromagnetic phase toward polarized paramagnetic state and (ii) the onset of superconducting order suppresses partly the staggered moment. The superconducting gap has both the spin-singlet and the staggered-triplet components, a direct consequence of a coexistence of the superconducting state with antiferromagnetism. © 2011 American Physical Society.


Kopera I.,Jagiellonian University
European journal of histochemistry : EJH | Year: 2010

The aim of this study was to show whether the connexin43 (Cx43) expression in gonads is affected by an anti-androgen action. To test this, pigs were prenatally (on gestational days 20-28 and 80-88; GD20, GD80), and postnatally (on days 2-10 after birth; PD2) exposed to flutamide that was given in five doses, every second day and its effect was observed in prepubertal gilts and boars. Morphology and expression of Cx43 was investigated in testes and ovaries by means of routine histology, immunohistochemistry, Western blotting, and RT-PCR, respectively. Qualitative analysis of immunohistochemical staining for Cx43 was confirmed by quantitative image analysis in which the staining intensity was expressed as relative optical density of diaminobenzidine deposits. There were statistically significant differences in Cx43 signal intensity between interstitial tissue of control and GD20 pigs (p less than 0.01), between seminiferous tubules of control and PD2 boars (p less than 0.01), between granulosa cells of preantral follicles of control and GD20 and PD2 pigs (p less than 0.01 and p less than 0.05, respectively), and between theca cells of control and GD80 and PD2 gilts (p less than 0.01). In Western blotting Cx43 appeared as a band of 43 kDa, whereas the size of the PCR-amplified product was 232 bp in all gonad tissue samples. Since we demonstrated changes in gonad morphology and in the expression of Cx43 at the level of protein of prepubertal boars and gilts, it seems possible that flutamide through blocking androgen action, causes delayed gonadal maturation in later postnatal life and, among other factors, may be involved in the regulation of Cx43 gene expression in pig gonads.


Kobylarz K.,Jagiellonian University
Anaesthesiology intensive therapy | Year: 2014

As any complex surgical procedure, separation of conjoined twins requires complex anaesthesia management that is a prerequisite of performing the operation, while complex postoperative care is a decisive factor in the survival of the patients. The paper describes the anaesthetic management for surgical operations in ten sets of conjoined twins in the Children's Hospital of Cracow during 1977-2005. The anaesthetic technique and associated problems are summarized.


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.


Kersevan B.P.,University of Ljubljana | Kersevan B.P.,Jozef Stefan Institute | Richter-Was E.,Jagiellonian University
Computer Physics Communications | Year: 2013

The AcerMC Monte Carlo generator is dedicated to the generation of Standard Model background processes which were recognised as critical for the searches at LHC, and generation of which was either unavailable or not straightforward so far. The program itself provides a library of the massive matrix elements (coded by MADGRAPH) and native phase space modules for generation of a set of selected processes. The hard process event can be completed by the initial and the final state radiation, hadronisation and decays through the existing interface with either PYTHIA, HERWIG or ARIADNE event generators and (optionally) TAUOLA and PHOTOS. Interfaces to all these packages are provided in the distribution version. The phase-space generation is based on the multi-channel self-optimising approach using the modified Kajantie-Byckling formalism for phase space construction and further smoothing of the phase space was obtained by using a modified ac-VEGAS algorithm. An additional improvement in the recent versions is the inclusion of the consistent prescription for matching the matrix element calculations with parton showering for a select list of processes. © 2012 Elsevier B.V. All rights reserved.


OBJECTIVE:: To test if posterior retroperitoneoscopic adrenalectomy (PRA) is superior to lateral transperitoneal laparoscopic adrenalectomy (LTLA).BACKGROUND:: Most popular LTLA has been recently challenged by an increasing popularity of PRA, which is believed by many surgeons (not evidence-based) as superior to LTLA in the treatment of small and benign adrenal tumors.METHODS:: Participants were assigned randomly to PRA or LTLA and followed for 5 years after surgery. The primary endpoint was the duration of surgery. Secondary endpoints were blood loss, conversion rate, postoperative recovery, morbidity, and costs.RESULTS:: Sixty-five patients were included, of whom 61 (PRA 30, LTLA 31) completed the 5-year follow-up. The following differences were identified in favor of PRA vs LTLA: shorter duration of surgery (50.8 vs 77.3 minutes), lower intraoperative blood loss (52.7 vs 97.8 mL), diminished pain intensity within 48 hours postoperatively, lower prevalence of shoulder-tip pain (3.0% vs 37.5%), shorter time to oral intake (4.4 vs 7.3 hours), shorter time to ambulation (6.1 vs 11.5 hours), shorter length of hospital stay, and lower cost (1728 &OV0556; vs 2315 &OV0556;), respectively (P < 0.001 for all). No differences were noted in conversion rate or morbidity except for herniation occurring more often after LTLA than PRA (16.1% vs 0%, P = 0.022) and need for hernia repair (12.9% vs 0%, P = 0.050), respectively.CONCLUSIONS:: Both approaches were equally safe. However, outcomes of PRA operations were superior to LTLA in terms of shorter surgery duration, lower blood loss, lower postoperative pain, faster recovery, improved cost-effectiveness, and abolished risk of surgical access site herniation. Registration number: NCT01959711 (http://www.clinicaltrials.gov). © 2014 by Lippincott Williams & Wilkins.


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2010

The molecular communication system in the resolution of the basis functions χ = {χX} contributed by the molecule constituent atoms {X}, the key concept of the Orbital Communication Theory (OCT) of the chemical bond, is introduced and its information-theoretic (IT) bond descriptors are summarized. The additive and non-additive components of these molecular information channels are identified. The former involve only the internal (one-center) communications {X → X} between the basis functions χX of each bonded atom X, determined by the associated (diagonal) block P(χX{pipe}χX) of the molecular conditional probabilities, which are responsible for the intra-atom promotion to its effective valence state. The latter accordingly involve only the external (two-center) communications between the contributed AO of each pair of bonded atoms, {Y → X and X → Y}, generated by the off-diagonal blocks of conditional probabilities P(χX{pipe}χY) and P(χY{pipe}χX),X ≠ Y, respectively, which are responsible for the inter-atomic bonding effects in the molecule. Both these probability scatterings ultimately determine the resultant multiplicities of the system chemical bonds. The input-ensemble average value of the channel conditional-entropy, which measures its communication "noise" due to electron delocalization via all chemical bonds, measures the IT-covalency in the molecule, while the complementary descriptor of the ensemble average value of the network mutual-information (information-capacity) reflects the electron localization effects and measures the system IT-ionic component. The illustrative example of the localized chemical bond originating from the interaction between two atomic orbitals is reexamined in some detail and the bond-weighted ensemble approach to chemical interactions in diatomic molecular fragments is discussed within the standard Restricted Hartree-Fock theory. In diatomic systems such treatment exactly reproduces the familiar bond index of Wiberg and provides its resolution into the complementary IT-covalent and IT-ionic components. The operator formulation of the probability-scattering phenomena in molecules is given and the probability-amplitude channel defined by the first-order density matrix is introduced. The AIM internal and external eigenvalue problems of this Charge-and-Bond-Order matrix are introduced and a similar approach to probability propagation matrices/operators is suggested. © 2009 Springer Science+Business Media, LLC.


Bryniarski K.,Jagiellonian University
Folia biologica | Year: 2013

To evaluate the influence of natural regulatory CD8+ T cells on macrophages we investigated in vitro production of cytokines, reactive oxygen intermediates (ROIs) and expression of CD80 surface costimulatory molecules by macrophages (MF) of wild type (WT) B10PL and syngeneic knock-out (KO) strains, TCRalpha-/-, beta2m-/- and CD1d-/- mice. MF of TCR alpha-/- (CD4- and CD8-) and beta2m-/- (CD8-) animals produced higher levels ofTNF-a, IL-6, IL-12 and ROIs and showed increased expression of CD80 costimulatory molecules in comparison to MF of WT or CD1d-/- (NKT-) mice. When MF of these strains were conjugated with TNP hapten and injected i.v. into WT mice to test either induction of contact sensitivity (CS) or tolerance, only TNP-MF of TCRalpha-/- and beta2m-/- animals induced a significant CS reaction, while cells of WT and CD1d-/- strains were tolerogenic. MF of the tested strains can be classified functionally as resembling either proinflammatory (TCRalpha-/- and beta2m-/-mice) or immunosuppressive (WT and CD1d-/-) phenotypes. We suggest the presence of an in vivo regulatory loop in which innate CD8+ Treg cells control the transition between MF phenotypes and thus adjust the magnitude of the inflammatory response to strictly local requirements.


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

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


Stencel A.,Jagiellonian University | Crespi B.,Simon Fraser University
Molecular Ecology | Year: 2013

The field of genomics is expanding rapidly, yet the meanings of the word 'genome' have yet to be conceptualized in explicit, coherent and useful frameworks. We develop and apply an evolutionary conceptualization of the genome, which represents a logical extension of the evolutionary definition of a gene developed by George C. Williams. An evolutionary genome thus represents a set of genetic material, in a lineage, that due to common interests tends to favour the same or similar phenotypes. This conceptualization provides novel perspectives on genome functions, boundaries and evolution, which should help to guide theoretical and empirical genomics research. © 2013 John Wiley & Sons Ltd.


Eilmes A.,Jagiellonian University
Theoretical Chemistry Accounts | Year: 2010

Transition energies for a ketocyanine dye and its complexes with Li+ and Mg2+ ions with an implicit solvent have been studied. Molecular Dynamics simulations have been used to prepare structures of the dye in acetonitrle solution of lithium or magnesium perchlorate. TDDFT methodology has been used to calculate the transition energies for dye and dye-ion complexes solvated by an increasing number of acetonitrile molecules. Results have been compared to the predictions of the continuous solvation model. Evolution of the spectrum with the number of explicit solvent molecules has been observed and the solvent-induced shifts have been determined. It has been found that the explicit solvation model may predict sequence of transitions and their parentage different than that resulting from implicit solvation. Effect of the perchlorate counterion for the dye-cation spectrum has been also analyzed. © 2010 The Author(s).


Kasza A.,Jagiellonian University
Cytokine | Year: 2013

This review focuses on the mechanisms by which the expression of specific genes is regulated by two proteins that are important in inflammation and cancer, namely the pro-inflammatory cytokine interleukin (IL)-1β and epidermal growth factor (EGF). In the review the receptors that recognize factors that cause inflammation are described with main focus on the receptors associated with activation of IL-1β. The function of IL-1β and pathways leading to activation of transcription factors, particularly NFκB and Elk-1 are analyzed. Then the mechanisms of EGF action, with particular emphasis of the activation of Elk-1 are illustrated. The link between aberrant signaling of EGF receptor family members and cancer development is explained. The relationship between inflammation and tumorigenesis is discussed. © 2013 Elsevier Ltd.


Rams M.M.,Los Alamos National Laboratory | Rams M.M.,Jagiellonian University | Damski B.,Los Alamos National Laboratory
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

We study ground-state fidelity defined as the overlap between two ground states of the same quantum system obtained for slightly different values of the parameters of its Hamiltonian. We focus on the thermodynamic regime of the XY model and the neighborhood of its critical points. We describe extensively fidelity when it is dominated by the universal contribution reflecting the quantum criticality of the phase transition. We show that proximity to the multicritical point leads to anomalous scaling of fidelity. We also discuss fidelity in a regime characterized by pronounced oscillations resulting from the change in either the system size or the parameters of the Hamiltonian. Moreover, we show when fidelity is dominated by non-universal contributions, study fidelity in the extended Ising model, and illustrate how our results provide additional insight into dynamics of quantum phase transitions. Special attention is given to studies of fidelity from the momentum space perspective. All our main results are obtained analytically. They are in excellent agreement with numerics. © 2011 American Physical Society.


Undas A.,Jagiellonian University | Brummel-Ziedins K.,University of Vermont | Mann K.G.,University of Vermont
Journal of Thrombosis and Haemostasis | Year: 2014

It is well established that aspirin, an irreversible inhibitor of platelet cyclooxygenase activity, is effective in secondary prevention of arterial thromboembolic events. The pooled results of the recent randomized, multicenter WARFASA and ASPIRE aspirin trials showed a 32% reduction in the rate of recurrence of venous thromboembolism (VTE) in patients receiving aspirin following VTE. These clinical data support evidence that platelets contribute to the initiation and progression of venous thrombosis and aspirin inhibits thrombin formation and thrombin-mediated coagulant reactions. In addition to the known acetylation of serine 529 residue in platelet cyclooxygenase-1, the postulated mechanisms of aspirin-induced antithrombotic actions also involve the acetylation of other proteins in blood coagulation, including fibrinogen, resulting in more efficient fibrinolysis. This review summarizes current knowledge on the aspirin-induced antithrombotic effects that potentially explain clinical studies showing reduced rates of VTE events in aspirin-treated subjects. © 2014 International Society on Thrombosis and Haemostasis.


Bas B.,AGH University of Science and Technology | Bas S.,Jagiellonian University
Electrochemistry Communications | Year: 2010

This work describes a novel type of working electrode for use in voltammetry and polarography - the renewable silver liquid amalgam film-modified silver solid amalgam annular band electrode (AgLAF-AgSAE). The electrode is produced by mechanically refreshing the silver liquid amalgam film (AgLAF) before each measurement. The main constituents of the electrode are: a specially constructed silver solid amalgam annular band electrode (AgSAE), two silicon O-rings, silver liquid amalgam and a polypropylene electrode body. Contaminants from the analyzed solution are removed and the AgSAE surface is covered with a thick layer of fresh amalgam while pulling the AgSAE into the sensor body. During movement in the reverse direction AgLAF is formed and homogenized. The time needed to refresh the film is less than 1 s. The electrode is characterized by excellent surface repeatability (∼ 1%) and long-term stability (over ten thousand measurement cycles). © 2010 Elsevier B.V. All rights reserved.


Rutherford A.W.,Imperial College London | Osyczka A.,Jagiellonian University | Rappaport F.,University Pierre and Marie Curie
FEBS Letters | Year: 2012

The energy-converting redox enzymes perform productive reactions efficiently despite the involvement of high energy intermediates in their catalytic cycles. This is achieved by kinetic control: with forward reactions being faster than competing, energy-wasteful reactions. This requires appropriate cofactor spacing, driving forces and reorganizational energies. These features evolved in ancestral enzymes in a low O 2 environment. When O 2 appeared, energy-converting enzymes had to deal with its troublesome chemistry. Various protective mechanisms duly evolved that are not directly related to the enzymes' principal redox roles. These protective mechanisms involve fine-tuning of reduction potentials, switching of pathways and the use of short circuits, back-reactions and side-paths, all of which compromise efficiency. This energetic loss is worth it since it minimises damage from reactive derivatives of O 2 and thus gives the organism a better chance of survival. We examine photosynthetic reaction centres, bc 1 and b 6f complexes from this view point. In particular, the evolution of the heterodimeric PSI from its homodimeric ancestors is explained as providing a protective back-reaction pathway. This "sacrifice-of- efficiency-for-protection" concept should be generally applicable to bioenergetic enzymes in aerobic environments. © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.


Ejsmond M.J.,Jagiellonian University | Babik W.,Polish Academy of Sciences | Radwan J.,Polish Academy of Sciences
BMC Evolutionary Biology | Year: 2010

Background: The extreme polymorphism that is observed in major histocompatibility complex (MHC) genes, which code for proteins involved in recognition of non-self oligopeptides, is thought to result from a pressure exerted by parasites because parasite antigens are more likely to be recognized by MHC heterozygotes (heterozygote advantage) and/or by rare MHC alleles (negative frequency-dependent selection). The Ewens-Watterson test (EW) is often used to detect selection acting on MHC genes over the recent history of a population. EW is based on the expectation that allele frequencies under balancing selection should be more even than under neutrality. We used computer simulations to investigate whether this expectation holds for selection exerted by parasites on host MHC genes under conditions of heterozygote advantage and negative frequency-dependent selection acting either simultaneously or separately. Results: In agreement with simple models of symmetrical overdominance, we found that heterozygote advantage acting alone in populations does, indeed, result in more even allele frequency distributions than expected under neutrality, and this is easily detectable by EW. However, under negative frequency-dependent selection, or under the joint action of negative frequency-dependent selection and heterozygote advantage, distributions of allele frequencies were less predictable: the majority of distributions were indistinguishable from neutral expectations, while the remaining runs resulted in either more even or more skewed distributions than under neutrality. Conclusions: Our results indicate that, as long as negative frequency-dependent selection is an important force maintaining MHC variation, the EW test has limited utility in detecting selection acting on these genes. © 2010 Ejsmond et al; licensee BioMed Central Ltd.


Korona R.,Jagiellonian University
Current Opinion in Biotechnology | Year: 2011

Genome-wide mutagenesis studies indicate that up to about 90% of genes in bacteria and 80% in eukaryotes can be inactivated individually leaving an organism viable, often seemingly unaffected. Several strategies are used to learn what these apparently dispensable genes contribute to fitness. Assays of growth under hundreds of physical and chemical stresses are among the most effective experimental approaches. Comparative studies of genomic DNA sequences continue to be valuable in discriminating between the core bacterial genome and the more variable niche-specific genes. The concept of the core genome appears currently unfeasible for eukaryotes but progress has been made in understanding why they contain numerous gene duplicates. © 2011 Elsevier Ltd.


Dziedzic T.,Jagiellonian University
Expert Review of Neurotherapeutics | Year: 2015

Acute systemic inflammatory reaction superimposed on chronic low-grade inflammation accompanies acute ischemic stroke. Elevated blood levels of systemic inflammatory markers such as IL-6 or C-reactive protein are associated with an unfavorable functional outcome and increased mortality after stroke. Animal studies have demonstrated a causal relationship between systemic inflammation and ischemic brain damage. The mechanisms linking systemic inflammation with poor outcome include increased neutrophil infiltration of cerebral cortex, disruption of the blood-brain barrier, impaired tissue reperfusion, increased platelet activation and microvascular coagulation and complement-dependent brain injury. Non-selective (e.g., by statins) or selective (e.g., by inhibition of IL-6) attenuation of systemic inflammation, enhancement of systemic anti-inflammatory response (e.g., by infusion of IL-1 receptor antagonist), prevention of infections that exacerbate systemic inflammation or inhibition of neuronal pathways triggering inflammatory reaction are potential therapeutic targets in stroke patients. This review discusses the relationship between systemic inflammation, cerebral ischemia and prognosis in the context of therapeutic strategies. © 2015 Informa Uk, Ltd.


McLerran L.,Brookhaven National Laboratory | McLerran L.,Central China Normal University | Praszalowicz M.,Jagiellonian University | Schenke B.,Brookhaven National Laboratory
Nuclear Physics A | Year: 2013

The CMS experiment at the Large Hadron Collider has recently presented data on the average transverse momentum of protons, kaons and pions as a function of particle multiplicity. We relate the particle multiplicity to saturation momentum using recently published computations of the interaction radius determined from the theory of the Color Glass Condensate. We show that the pp and the pA experimental data scale in terms of these saturation momenta. Computing transverse momentum spectra for identified particles using Boltzmann-type distributions and relating different associated multiplicities using geometric scaling, these simple distributions reproduce the observed dependence of the mean transverse momentum on particle multiplicities seen in both pp and pA interactions for pions to good accuracy, and to fair agreement for protons and kaons. © 2013 Elsevier B.V.


Kobylarz K.,Jagiellonian University
Anaesthesiology Intensive Therapy | Year: 2014

Conjoined twinning is one of the most uncommon congenital anomalies. Maintenance in an intensive care setting during this time allows for close monitoring, stabilisation, and nutritional supplementation of the infants as necessary to optimise preoperative growth and development. The birth of conjoined twins is a very difficult and dramatic moment for parents. It is also a very difficult situation for the team of physicians, nurses and other required hospital staff to carry out treatment and care of these specific developmental anomalies. The diagnostics and treatment in this extraordinary situation requires close cooperation of the multidisciplinary medical team, which includes their personal experience and medical knowledge, with a team of intensive care unit nurses. This report presents the rules in cease of conjoined twins during their intensive care unit stay with special reference to the proceedings before and after complete separation.


Kobylarz K.,Jagiellonian University
Anaesthesiology Intensive Therapy | Year: 2014

Conjoined twins have been a source of fascination to the public and the medical profession for centuries. Their birth was initially viewed as an ominous sign of impending disaster. Since Middle Ages into the 19th century they were regarded as monstrosities and were exhibited at circuses and sideshows. The frequency of conjoined twins is approximately 1 in 50,000 gestation, but many of them die in utero, are terminated or stillborn. The true incidence is estimated to be 1 in 200,000 live births. This article gives an overview of Siamese twins and of the prenatal diagnosis in assessing the prognosis, anaesthetic and post-natal surgical management and outcome. Anaesthesia for conjoined twins surgery, whether prior to or for separation, is an enormous challenge to the anaesthesiologist. The site and complexity of the conjunction affect management of the airway, an intravenous access, the extent of blood and number of surgical specialties involved. Preoperative assessment and planning with interdisciplinary communication and cooperation is vital to the success of the operations. Meticulous attention to detail, monitoring and vigilance are mandatory.


Hoffmann N.A.,Structural and Computational Biology Unit | Jakobi A.J.,Structural and Computational Biology Unit | Jakobi A.J.,Hamburg Unit | Moreno-Morcillo M.,Structural and Computational Biology Unit | And 7 more authors.
Nature | Year: 2015

Transcription of genes encoding small structured RNAs such as transfer RNAs, spliceosomal U6 small nuclear RNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet structurally least characterized eukaryotic RNA polymerase. Here we present the cryo-electron microscopy structures of the Saccharomyces cerevisiae Pol III elongating complex at 3.9 Å resolution and the apo Pol III enzyme in two different conformations at 4.6 and 4.7 Å resolution, respectively, which allow the building of a 17-subunit atomic model of Pol III. The reconstructions reveal the precise orientation of the C82-C34-C31 heterotrimer in close proximity to the stalk. The C53-C37 heterodimer positions residues involved in transcription termination close to the non-template DNA strand. In the apo Pol III structures, the stalk adopts different orientations coupled with closed and open conformations of the clamp. Our results provide novel insights into Pol III-specific transcription and the adaptation of Pol III towards its small transcriptional targets. © 2015 Macmillan Publishers Limited. All rights reserved.


Chmielnicki W.,Jagiellonian University | Stacpor K.,Silesian University of Technology
Neurocomputing | Year: 2012

There are two standard approaches to the classification task: generative, which use training data to estimate a probability model for each class, and discriminative, which try to construct flexible decision boundaries between the classes. An ideal classifier should combine these two approaches. In this paper a classifier combining the well-known support vector machine (SVM) classifier with regularized discriminant analysis (RDA) classifier is presented. The hybrid classifier is used for protein structure prediction which is one of the most important goals pursued by bioinformatics. The obtained results are promising, the hybrid classifier achieves better result than the SVM or RDA classifiers alone. The proposed method achieves higher recognition ratio than other methods described in the literature. © 2011 Elsevier B.V..


Klimek B.,Jagiellonian University
Bulletin of Environmental Contamination and Toxicology | Year: 2012

The aim of the study was to compare the effects of stress (contamination trials) on the microorganisms in zinc-polluted soil (5,018 mg Zn kg-1 soil dry weight) and unpolluted soil (141 mg Zn kg-1 soil dw), measured as soil respiration rate. In the laboratory, soils were subjected to copper contamination (0, 500, 1,500 and 4,500 mg kg-1 soil dw), and then a bactericide (oxytetracycline) combined with a fungicide (captan) along with glucose (10 mg g-1 soil dw each) were added. There was a highly significant effect of soil type, copper treatment and oxytetracycline/ captan treatment. The initial respiration rate of chronically zinc-polluted soil was higher than that of unpolluted soil, but in the copper treatment it showed a greater decline. Microorganisms in copper-treated soil were more susceptible to oxytetracycline/captan contamination. After the successive soil contamination trials the decline of soil respiration was greater in zinc-polluted soil than in unpolluted soil. © Springer Science+Business Media, LLC 2012.


Krajewska B.,Jagiellonian University
Journal of Molecular Catalysis B: Enzymatic | Year: 2011

Evidence has been collected that H2O2 resulting from redox reactions taking place in some inhibitor systems, is responsible for the inactivation of urease. Accordingly, in this study the inactivation by H 2O2 exogenously added to urease (jack bean) was investigated. The reaction accountable for the inactivation was the oxidation of the enzyme thiol groups. The reaction was studied at pHs over 6.2-8.2. At each pH, the first-order kinetics was obeyed, the resulting dependences of k obs on H2O2 concentration being hyperbolic. Analyzed with Kitz-Wilson method, the kinact appeared to be invariant with pH, while the inhibitor binding constant KI decreased with increasing pH. Consequently, the process grew faster with an increase in pH, the second-order rate constants increasing from 0.0032 M-1 s -1 at pH 6.2 to 0.0615 M-1 s-1 at pH 8.2, consistent with higher susceptibility of thiolate anions to oxidation by H 2O2 compared to reduced thiols. The reactions always resulted in irreversible inactivation of urease, indicative of the oxidation of thiol groups to either sulfinic or sulfonic acid, independent of the extent of inactivation. Analysis of the numbers of urease thiol groups modified with H2O2 revealed that for the complete inactivation, out of 36 thiols/molecule available under non-denaturating conditions, the rapid oxidation of 30 highly reactive -SH groups was responsible for a 50% loss in enzyme activity, and the slower oxidation of the remaining six -SH groups, for the other 50%. The enzyme was protected by active-site binding inhibitors, boric acid and fluoride, from the inactivation, suggesting that the six thiols are the active-site flap Cys-592s. For comparison with other urease inhibitors, the IC50 was determined for 20 min incubation with H2O 2, its value changing from 242 mM at pH 6.2 to 11 mM at pH 8.2. © 2010 Elsevier B.V. All rights reserved.


Kolarz M.,Jagiellonian University
RAIRO - Theoretical Informatics and Applications | Year: 2010

We consider directed figures defined as labelled polyominoes with designated start and end points, with two types of catenation operations. We are especially interested in codicity verification for sets of figures, and we show that depending on the catenation type the question whether a given set of directed figures is a code is decidable or not. In the former case we give a constructive proof which leads to a straightforward algorithm. © 2011 EDP Sciences.


Trembecka-Lucas D.O.,Jagiellonian University
Nucleus (Austin, Tex.) | Year: 2013

Heterochromatin protein 1 (HP1), a small non-histone chromosomal protein, was recently shown to form a complex in vivo with Proliferating Cell Nuclear Antigen (PCNA), a key factor in DNA replication. The complex, which requires HP1β in a form of a dimer, is engaged in DNA repair and replication. We now provide further evidence based on FRET-FLIM live cell studies confirming the association and close proximity between HP1β and PCNA in the complex. We also demonstrate using FRAP, that although HP1β-PCNA complexes are highly mobile in nonreplicating nuclei, when engaged in DNA replication, they become bound and do not exchange with the mobile pool. These observations are in agreement with a notion that a subpopulation of HP1 molecules interact with PCNA in vivo during DNA replication. Similarly, HP1β which is associated with PCNA in regions of DNA repair, is bound and does not exchange with the mobile pool, suggesting that HP1β in association with PCNA may be a component of a DNA repair complex.


Marcinkiewicz J.,Jagiellonian University | Kontny E.,Institute of Rheumatology
Amino Acids | Year: 2014

Taurine (2-aminoethanesulfonic acid) is the most abundant free amino acid in humans and plays an important role in several essential biological processes such as bile acid conjugation, maintenance of calcium homeostasis, osmoregulation and membrane stabilization. Moreover, attenuation of apoptosis and its antioxidant activity seem to be crucial for the cytoprotective effects of taurine. Although these properties are not tissue specific, taurine reaches particularly high concentrations in tissues exposed to elevated levels of oxidants (e.g., inflammatory cells). It suggests that taurine may play an important role in inflammation associated with oxidative stress. Indeed, at the site of inflammation, taurine is known to react with and detoxify hypochlorous acid generated by the neutrophil myeloperoxidase (MPO)-halide system. This reaction results in the formation of less toxic taurine chloramine (TauCl). Both haloamines, TauCl and taurine bromamine (TauBr), the product of taurine reaction with hypobromous acid (HOBr), exert antimicrobial and anti-inflammatory properties. In contrast to a well-documented regulatory role of taurine and taurine haloamines (TauCl, TauBr) in acute inflammation, their role in the pathogenesis of inflammatory diseases is not clear. This review summarizes our current knowledge concerning the role of taurine, TauCl and TauBr in the pathogenesis of inflammatory diseases initiated or propagated by MPO-derived oxidants. The aim of this paper is to show links between inflammation, neutrophils, MPO, oxidative stress and taurine. We will discuss the possible contribution of taurine and taurine haloamines to the pathogenesis of inflammatory diseases, especially in the best studied example of rheumatoid arthritis. © 2012 The Author(s).


A combined temperature-pH study of urease kinetics was performed with the primary objective to assign the observed pKa values to the ionizable groups of the enzyme active site involved in the reaction. This was done in view of the fact that the identity of the groups detected by pH studies reported in the literature has never been conclusively resolved. Accordingly, herein the urease kinetic parameters KM and vmax were measured at eight pHs between 5.0 and 8.3 in noninteracting biological buffers (MES and HEPES), at each pH at five temperatures between 15 and 35 °C. The determined values of pKas and of the enthalpies of ionizationΔHiono allowed the ionizable groups to have the pKas assigned. Unlike previously assumed to have pKa ≈ 6.5, the determined acidic pK2 ≈ 5.0 was assigned to a histidine residue (most likely His320 by Klebsiella aerogenes numbering). By contrast, the basic pK1 ≈ 8.8 was assigned to the Ni-Ni bridging hydroxyl ion, a feature that supports the mechanism operative in the urease activity in which this hydroxyl is a general acid. Further, the pH-dependent analysis of the obtained KM and vmax values revealed that even though both the thermodynamic and activation parameters of the urease reaction were little pH-dependent, their values indicated that the most favorable conditions for the substrate binding are at pH 5.5-6.0, and those for the catalytic step, at pH 6.5-7.0. Taken together, the work brings in new mechanistic information of significance to the understanding of the activity of urease. © 2015 Elsevier B.V. All rights reserved.


Lisowska M.,Jagiellonian University
Environmental Monitoring and Assessment | Year: 2011

Dynamics of epiphytic lichen distribution and diversity in the town of Skawina, one of the major industrial centres of southern Poland, over the last 30 years, was documented in relation to air quality changes. Fieldwork was conducted in 2006-2007. A total of 34 species were recorded at 202 sites, which is similar to the historical data, however, significant qualitative changes occurred. Nitrogen- and dust-tolerant species have expanded and dominate, while some acidophytes, such as Lecanora conizaeoides, are in decline. Lichens have recolonised the former 'lichen desert' in the town centre. Species richness at study sites has increased; and an improvement in the health of lichen thalli was noted. These trends reflect air quality improvement, mainly SO 2 decline in the last few decades and transport-related compounds, mainly NO x and dust that have became the main pollutants. Host tree species and diameter diversity also contribute significantly to lichen species diversity in the study area. The recolonisation process seems far from complete and further changes in the lichen distribution and diversity in the study area are expected. © 2010 The Author(s).


Bialas A.,Polish Academy of Sciences | Bialas A.,Jagiellonian University | Peschanski R.,CEA Saclay Nuclear Research Center
Physical Review C - Nuclear Physics | Year: 2011

The possibility that particle production in high-energy collisions is a result of two asymmetric hydrodynamic flows is investigated using the Khalatnikov form of the (1+1)-dimensional approximation of hydrodynamic equations. The general solution is discussed and applied to the physically appealing "generalized in-out cascade" where the space-time and energy-momentum rapidities are equal at initial temperature but boost invariance is not imposed. It is demonstrated that the two-bump structure of the entropy density, characteristic of the asymmetric input, changes easily into a single broad maximum compatible with data on particle production in symmetric processes. A possible microscopic QCD interpretation of asymmetric hydrodynamics is proposed. © 2011 American Physical Society.


In this article various ways to recognize the concept of quality of life are presented. The author attempted to show what factors may influence quality of life, and how this issue is recognized in the context of medicine and psychology. Attention was also paid to the subjective and objective aspects of quality of life. The author attempted to demonstrate that the patient's quality of life, especially in the context of rheumatology, cannot be considered one-dimensional, only in the field of medicine or psychology. Evaluation and planning of activities designed to improve and maintain the patient's quality of life require an eclectic approach, taking into account psychological and medical aspects of the patient's life. The text is divided into three parts: quality of life in medical science, quality of life and happiness in psychological approaches, and quality of life in rheumatology.


Dimitrow P.P.,Jagiellonian University
Polskie Archiwum Medycyny Wewnetrznej | Year: 2014

Aortic stenosis (AS) represents the most common type of acquired valvular heart disease. Its incidence increases with age; therefore, from 3% to 9% of adults over 75 years of age develop AS. The pathophysiological mechanisms and role of biomarkers in the prediction of AS have been extensively studied. Progression of AS is characterized by a number of abnormalities in calcification regulation, inflammation/ adipokine dysregulation, prothrombic state, and altered von Willebrand factor function. The current understanding of the mechanisms of AS involves a complex role of the multiple cell types, in particular myofibroblasts and macrophages. The introduction of transcatheter aortic valve implantation provides invaluable opportunities for periprocedural and long-term monitoring of the changes in the biomarker profile. Effective pharmacological treatment, especially in the early stage of AS, is largely unknown. The current review discusses not only the pathophysiology of AS but also attempts at pharmacological treatment. Copyright © 2014 Medycyna Praktyczna All rights reserved.


Koziel J.,Jagiellonian University
Current rheumatology reports | Year: 2014

Porphyromonas gingivalis is a leading pathogen in chronic periodontitis, a disease process involving progressive destruction of the tissues that support the teeth. Recently, the organism has been reported to produce a unique bacterial enzyme, P. gingivalis peptidyl-arginine deiminase (PPAD), which has the ability to convert arginine residues in proteins to citrulline. Protein citrullination alters protein structure and function; hence, PPAD may be involved in deregulation of the host's signalling network and immune evasion. Further, accumulating evidence suggests a role for autoimmunity against citrullinated proteins in the development of rheumatoid arthritis (RA). As inflammatory conditions in the lungs of cigarette smokers contribute to the breakdown of immune tolerance to citrullinated epitopes, chronic exposure to citrullinated proteins at periodontitis sites may also predispose susceptible individuals to the development of autoantibodies and the initiation of RA. In this review, we discuss evidence that PPAD may represent a mechanistic link between periodontitis and RA, diseases that are known to be significantly associated at the epidemiological level.


Larsen D.T.,Jagiellonian University
Journal of Physics: Conference Series | Year: 2016

The NA61/SHINE programme on strong interactions covers the study of the onset of deconfinement and aims to discover the critical point of strongly interacting matter by performing an energy and system-size scan over the full CERN SPS momentum range. So far the scans of p+p, 7Be+9Be, as well as Ar+Sc have been completed. Results from p+p and Be+Be collisions are now emerging, in particular the energy dependence of hadron spectra and yields. Status and preliminary results from this effort will be presented.


Holko P.,Centrum HTA | Kawalec P.,Jagiellonian University
Expert Review of Anticancer Therapy | Year: 2014

The objective is to examine the cost-utility of sipuleucel-T immunotherapy in asymptomatic or minimally symptomatic castration-resistant prostate cancer patients. The addition of sipuleucel-T immunotherapy to standard treatment led to a gain of 0.37 quality-adjusted life-year (QALY) at an additional cost of US 104,536. The incremental cost-utility ratio was US 283,000 per QALY saved. Threshold sensitivity analyses indicated that a price reduction of at least 53%, or application in a group of patients resulting in the relative reduction in the mortality rate of at least 39%, ought to augment the economic value of this regimen. Sipuleucel-T immunotherapy treatment at the current price with 96.5% certainty is not cost-effective. The specific group of patients who will benefit more from the treatment should be revealed and treated, or the cost of the vaccine should be lowered significantly to increase its economic value. Accounting for crossover treatment in control patients improves sipuleucel-T's value (US 132,000 per QALY saved) although further investigation is necessary. © 2014 Informa UK, Ltd.


Walczynska A.,Jagiellonian University
Bulletin of Entomological Research | Year: 2012

The current case study concerns evaluation of the life history of an insect species living in a demanding habitat, namely a xylem-feeder Aredolpona rubra (Linnaeus) (Coleoptera: Cerambycidae) representing the wood-feeding guild. Growth rate, development time and body size at maturity were studied at different temperature regimes with discreteness of insect growth pattern, associated with moultings, taken into account. Moreover, the temperature effect on reproductive strategy of females was tested, and the general life history was compared with available data within the wood-feeding guild. The results show that: (i) the growth of A. rubra is slow but compensated by prolonged development; (ii) size dimorphism is probably caused by the longer development time of females; (iii) fecundity is at least partly determined by the temperature experienced during the egg-laying period; and (iv) interspecific comparisons reveal that the life strategy of a wood-feeder depends on the niche occupied within the tree, whilst its breeding strategy (whether capital or income) is controlled at a taxonomic level. Control of all the main life history traits at one time provided a unique opportunity to understand the selection pressures on A. rubra species. Moreover, comparison within a feeding guild broadens this context and identifies the sources of heterogeneity in the â ̃inside-woodâ™ habitat. The knowledge so gathered may be applied to pest control in forestry science, as well as to the conservation of rare and endangered insect species living within trees. © 2012 Cambridge University Press.


Loboda A.,Jagiellonian University
Molecules and cells | Year: 2010

Hypoxia inducible factor (HIF)-1 and HIF-2 are heterodimeric transcription factors mediating the cellular response to hypoxia. Recent data indicate that not only ubiquitous HIF-1 alpha, but also more cell-specific HIF-2 alpha, is an important regulator of the hypoxia response. Although both alpha subunits are highly conservative at protein level, share similar domain structure, heterodimerize with HIF-1 beta, and bind to the same DNA sequence called hypoxia responsive element (HRE), their effect on the expression of some genes may vary. In this review we stressed the differences between the isoforms, their structure and expression pattern. Moreover, we described diversity of coactivators and proteins which interact with HIFs, and which are responsible for the specificity of their action. Finally, recent data showing link between HIFs and specific microRNA have been presented.


Rak-Mardyla A.,Jagiellonian University
Journal of physiology and pharmacology : an official journal of the Polish Physiological Society | Year: 2013

Based on the available data, it was shown that ghrelin is involved in a series of physiological processes such as regulation of food intake, body weight, and cardiovascular or immune function. Recent studies have shown that ghrelin also plays an important role in the regulation of female reproduction. Information exists that its functional receptor, GHSR type 1a (GHS-R1a), is expressed in the hypothalamic-pituitary-ovarian axis. Ghrelin is synthesized locally in the hypothalamus, pituitary and ovaries of many species and has autocrine and/or paracrine effects. Most research indicates that ghrelin has inhibitory effect on gonadotropin secretion. Ghrelin also participates in the direct regulation of different ovarian functions such as steroid secretion, cell proliferation and apoptosis; these functions appear to be species-specific. Moreover, the importance of GHS-R1a or MAPK/IP3 pathway activation in ghrelin action in the ovary has been described. The article summarizes results of a series of recent studies on the effect of ghrelin on the hypothalamic-pituitary-ovarian axis, as well as on ovarian physiology with an indication that ghrelin via its biological functions such as energy metabolism and food intake could also be a key signal between animal energy status and control of ovarian function.


Tarnopolski M.,Jagiellonian University
Astrophysics and Space Science | Year: 2015

Two classes of GRBs have been identified thus far without doubt and are prescribed to different physical scenarios—NS-NS or NS-BH mergers, and collapse of massive stars, for short and long GRBs, respectively. The existence of two distinct populations was inferred through a bimodal distribution of the observed durations T90$T_{90}$, and the commonly applied 2s$2~\mbox{s}$ limit between short and long GRBs was obtained by fitting a parabola between the two peaks in binned data from BATSE 1B. Herein, by means of a maximum likelihood (ML) method a mixture of two Gaussians is fitted to the datasets from BATSE, Swift, BeppoSAX, and Fermi in search for a local minimum that might serve as a new, more proper, limit for the two GRB classes. It is found that Swift and BeppoSAX distributions are unimodal, hence no local minimum is present, Fermi is consistent with the conventional limit, whereas BATSE gives the limit significantly longer (equal to 3.38±0.27s$3.38\pm 0.27~\mbox{s}$) than 2s$2~\mbox{s}$. These new values change the fractions of short and long GRBs in the samples examined, and imply that the observed T90$T_{90}$ durations are detector dependent, hence no universal limiting value may be applied to all satellites due to their different instrument specifications. Because of this, and due to the strong overlap of the two-Gaussian components, the straightforward association of short GRBs to mergers and long ones to collapsars is ambiguous. © 2015, The Author(s).


Kozieradzka-Kiszkurno M.,University of Gdansk | Plachno B.J.,Jagiellonian University
Protoplasma | Year: 2012

It is believed that there is symplastic isolation between the embryo (new sporophyte) and the endosperm (maternal-parental origin tissue, which nourishes the embryo) in angiosperms. However, in embryological literature there are rare examples in which plasmodesmata between the embryo suspensor and endosperm cells have been recorded (three species from Fabaceae). This study was undertaken in order to test the hypothesis that plasmodesmata between the embryo suspensor and the endosperm are not so rare but also occur in other angiosperm families; in order to check this, we used the Crassulaceae family because embryogenesis in Crassulaceae has been studied extensively at an ultrastructure level recently and also we tread members of this family as model for suspensor physiology and function studies. These plasmodesmata even occurred between the basal cell of the two-celled proembryo and endosperm cells. The plasmodesmata were simple at this stage of development. During the development of the embryo proper and the suspensor, the structure of plasmodesmata changes. They were branched and connected with electron-dense material. Our results suggest that in Crassulaceae with plasmodesmata between the endosperm and suspensor, symplastic connectivity at this cell-cell boundary is still reduced or blocked at a very early stage of embryo development (before the globular stage). The occurrence of plasmodesmata between the embryo suspensor and endosperm cells suggests possible symplastic transport between these different organs, at least at a very early stage of embryo development. However, whether this transport actually occurs needs to be proven experimentally. A broader analysis of plants from various families would show whether the occurrence of plasmodesmata between the embryo suspensor and the endosperm are typical embryological characteristics and if this is useful in discussions about angiosperm systematic and evolution. © 2011 The Author(s).


Wycech S.,National Center for Nuclear Studies | Krzemien W.,Jagiellonian University
Acta Physica Polonica B | Year: 2014

Collisions in a system of two particles at energies close to a bound state in different channels are discussed. Next, the bound state decays into a third coupled channel. A phenomenological approach to dd → π-p 3He reaction is presented.


Czarnobilska E.,Jagiellonian University
Przegla̧d lekarski | Year: 2010

BACKGROUND: Contact allergy is the most frequent type of allergy, affecting 26-40% of all adults and 21-36% children. The gold standard in the diagnosis of contact allergy is patch test. OBJECTIVE: To study the influence of the range and composition of patch test series on the efficacy of the diagnostic procedure. MATERIAL AND METHODS: Retrospective analysis of the frequency of positive reactions among patients diagnosed with patch tests at our Department during 2 periods: From December 2003 to March 2005, patients were tested with a series of 9 substances plus white petrolatum as the negative control. From April 2005 to July 2008, the series was expanded to 21 substances, while petrolatum was removed. RESULTS: In the analyzed period, 1379 patients were tested with 9 substances plus petrolatum (group referred to as "G9") and 682 patients with 21 substances ("G21"). In G9, at least one positive reaction was observed in 343 (24.9%, 95% CI: 22.6-27.2%) patients, as compared to 376 (55.1%; 95% CI: 51.4-58.7%) in G21 (p < 0.0001). The increase in the number of tested substances from 9 to 21 led to significant increase in the mean number of positive reactions per one patient (0.34 in G9 versus 0.90 in G21; p < 0.0001). We have not observed any positive reaction to white petrolatum. CONCLUSIONS: Patch testing with more extensive test series increases the chance for the detection of patient's sensitizations. As we have not observed any positive reaction to white petrolatum, using the vehicle as negative control does not seem to offer any advantage.


Korzeniewski B.,Jagiellonian University
Journal of Applied Physiology | Year: 2014

The regulation of oxidative phosphorylation (OXPHOS) during work transitions in skeletal muscle and heart is still not well understood. Different computer models of this process have been developed that are characterized by various kinetic properties. In the present research-polemic theoretical study it is argued that models belonging to one group (Model A), which predict that among OXPHOS complexes complex III keeps almost all of the metabolic control over oxygen consumption (VO2) and involve a strong complex III activation by inorganic phosphate (Pi), lead to the conclusion that an increase in Pi is the main mechanism responsible for OXPHOS activation (feedback-activation mechanism). Models belonging to another group (Model B), which were developed to take into account an approximately uniform distribution of metabolic control over VO2 among particular OXPHOS complexes (complex I, complex III, complex IV, ATP synthase, ATP/ADP carrier, phosphate carrier) encountered in experimental studies in isolated mitochondria, predict that all OXPHOS complexes are directly activated in parallel with ATP usage and NADH supply by some external cytosolic factor/mechanism during rest-to-work or low-to-high work transitions in skeletal muscle and heart ("each-stepactivation" mechanism). Model B demonstrates that different intensities of each-step activation can account for the very different (slopes of) phenomenological VO2-ADP relationships observed in various skeletal muscles and heart. Thus they are able to explain the differences in the regulation of OXPHOS during work transitions between skeletal muscle (where moderate changes in ADP take place) and intact heart in vivo (where ADP is essentially constant). Copyright © 2014 the American Physiological Society.


Despite new diagnostic methods, including novel laboratory parameters and imaging techniques, and growing knowledge on pathogenesis of acute pancreatitis, early assessment of severity remains the main factor influencing prognosis in the disease. The aim of the study was the evaluation of diagnostic accuracy of interleukins (IL): 6 and 18 and acute phase proteins: C-reactive protein (CRP) and serum amyloid A (SAA), together with Glasgow prognostic score during first 48 hours after diagnosing acute pancreatitis in a group of 40 patients treated in the I-st Department of General and Gastrointestinal Surgery University Hospital in Cracow. All the studied inflammatory markers were significantly higher in patients with moderate and severe acute pancreatitis versus patients with mild form of the disease on the first 48 hours of the disease. Expanding Glasgow score with IL-6, IL-18, SAA or CRP determinations resulted in better accuracy for diagnosing severe clinical course of acute pancreatitis.


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.


Gora-Marek K.,Jagiellonian University
Vibrational Spectroscopy | Year: 2010

The migration of Co2+ cations in zeolite CoY was studied by IR spectroscopy. It has been found, that in the presence of water, ammonia, and pyridine Co2+ cations migrated from hexagonal prisms and/or cubooctahedra to supercages and were able to form complexes with H2O, NH3 or pyridine as ligands. The evidence of cations migration was the formation of mononitroslyl or dinitrosyl adducts if NO was sorbed in zeolite with preadsorbed H2O, NH3 or pyridine (without preadsorbed molecules Co2+ hidden in hexagonal prisms and/or cubooctahedra were inaccessible to NO). IR experiments suggested also that not all Co2+ could migrate. H2O and NH3 were able to withdraw only ca. 20-30% of Co2+, pyridine was more efficient and has withdrawn ca. 50% of all Co2+. Co2+ ions withdrawn by preadsorbed H2O, NH3 or pyridine to supercages can also form carbonyl adducts with CO (without preadsorbed molecules Co2+ ions were inaccessible to CO). The stretching frequencies of CO (in carbonyl adducts) or NO (in mononitrosyl adducts) for CO and NO interacting with Co2+ which bonds preadsorbed H2O, NH3 or pyridine were distinctly lower than if CO or NO interacted with Co2+ solo without preadsorbed molecules. This was explained by the transfer of electrons from electrondonor H2O, NH3 or pyridine molecules via Co2+ to antibonding π* orbitals of CO and NO. © 2009 Elsevier B.V. All rights reserved.


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2010

The joint/conditional "probability" measures of simultaneous many-orbital events in chemical bonds, which involve several basis functions, are derived within standard SCF LCAO MO description of molecular systems. These generalized projection/overlap quantities satisfy the symmetry properties and sum rules of the ordinary probabilities, but can exhibit negative values. The associated information-theoretic descriptors of chemical bonds for a general case of several (dependent) orbital probability schemes are examined. The many-orbital theory extends the range of applications of the orbital communication theory to many classical issues in the theory of molecular electronic structure and chemical reactivity. Such probabilities are required in several molecular scenarios, e. g., bimolecular and catalytic reactivity, directing influence of ligands/substituents, the three-centre bonds, etc., which are also identified. Such an approach implies the effect of the IT-ionic activation of the chemisorbed reactants in catalytic systems. © 2009 Springer Science+Business Media, LLC.


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2010

The information coupling between chemical bonds in molecular fragments, e. g., distinct parts of a single molecule or reactants in the bimolecular system, is investigated within the orbital communication theory. The relevant overlap measures of the joint/conditional "probabilities" of simultaneous two-orbital probability scatterings on different sites are established within the standard restricted Hartree-Fock (SCF LCAO MO) theory and the associated entropy/information descriptors of the chemical interactions between the bond/reactivity phenomena in such molecular subsystems are explored. The relevant four-orbital bond-projections measure the external dependencies between the associated intra-fragment communications between atomic orbitals on each fragment, thus effectively accounting for the external communication couplings between the internal chemical bonds in each subsystem. © 2009 Springer Science+Business Media, LLC.


The entropic principles of information theory are used for defining molecular fragments. The additive and non-additive components of the entropy-deficiency and Fisher-information functionals are introduced. The implications of the adopted constraints for predicted in situ charge sensitivities of molecular fragments in donor-acceptor systems are examined and the exhaustive, local partitioning of the molecular electron/probability density into atomic pieces is discussed as an illustration. The alternative information principles using the free-atom references, which define the atomic "promolecule", formulated in terms of the local electron density/probability of bonded atoms and their share/enhancement factors, are shown to give rise the stockholder partitioning of Hirshfeld. It is alternatively characterized by the common (subsystem independent), molecular local enhancements for each bonded atom or by the equality of the molecular and promolecular share factors. This unbiased division is shown to exactly remove the non-additive component of the missing-information of electron probabilities; in the conditional probability representation the entropy-deficiency of stockholder atoms is shown to generate the exactly vanishing additive component. The additivity of information contributions in the hypothetical (non-interacting) Kohn-Sham (KS) system in the resolution defined by the KS molecular orbitals (MO) is stressed and their non-additivity in the atomic-orbital (AO) resolution is emphasized. The non-additive Fisher information of the real (interacting) molecular system in both the MO and AO resolutions is then examined: the former is linked to the electron localization function (ELF) while the latter defines the so called contra-gradience(CG) criterion for localizing chemical bonds in the molecule. The bonding basins of the negative CG density in the valence-shell identify regions of an increased electron delocalization due to formation of the chemical bond. Representative plots of these local probes of the molecular electron distributions are presented and discussed. © 2009 Springer Science+Business Media, LLC.


Piprek R.P.,Jagiellonian University
Results and Problems in Cell Differentiation | Year: 2016

Current knowledge on gonadal development and sex determination is the product of many decades of research involving a variety of scientific methods from different biological disciplines such as histology, genetics, biochemistry, and molecular biology. The earliest embryological investigations, followed by the invention of microscopy and staining methods, were based on histological examinations. The most robust development of histological staining techniques occurred in the second half of the nineteenth century and resulted in structural descriptions of gonadogenesis. These first studies on gonadal development were conducted on domesticated animals; however, currently the mouse is the most extensively studied species. The next key point in the study of gonadogenesis was the advancement of methods allowing for the in vitro culture of fetal gonads. For instance, this led to the description of the origin of cell lines forming the gonads. Protein detection using antibodies and immunolabeling methods and the use of reporter genes were also invaluable for developmental studies, enabling the visualization of the formation of gonadal structure. Recently, genetic and molecular biology techniques, especially gene expression analysis, have revolutionized studies on gonadogenesis and have provided insight into the molecular mechanisms that govern this process. The successive invention of new methods is reflected in the progress of research on gonadal development. © Springer International Publishing Switzerland 2016.


The radiolarian fauna from deep-water settings in the Umbria-Marche and the Outer Carpathian basins of the Western Tethys is used for biostratigraphic purpose and interpretation of environmental changes during the late Cenomanian through the Early Turonian time interval. The frequency of 184 recognized species, thirteen of them newly described, has been processed and analyzed. Three radiolarian biozones and one subzone are distinguished based on radiolarian datum events, correlated with the chrono stratigraphic scale through the S C curve. The whole radiolarian set has been subdivided into six super groups, including 25 groups related to specific water masses. The assembled species represented various feeding preferences and ecological strategies. An increase of radiolarian total number in the sediments related to the Bonarelli Level (BL) displays a positive correlation with an increase of phosphorus (P) content, and with a significant decrease in radiolarian diversity. Most of radiolarian species avoided levels with high P content, in contrast, some species as H. barbui and C. conara increased significantly in number of specimens. Diversified radiolarian assemblages appeared at levels, directly preceded by a notable P increase, marking a period when the water system was saturated in relation to nitrogen. The radiolarian abundance in the sediments was strongly related to their preservation during sinking in the water column and at the water/sediment interface, increasing significantly at levels, marked by high pellet production. Thus, pelletization played an important role in the transport of radiolarian skeletons and their further preservation, irrespective to conditions of radio larians growth. Radiolarians experienced and responded to environmental changes during the 1.8 Ma around the Bonarelli Interval (BI). The Cenomanian-Turonian press extinction event - a period of unquestionable eutrophication represented by the BI, did not result in great radiolarian extinction and turnovers. The radiolarian radiation preceded the BI by over 330 ka. The extinction, directly connected with the OAE2 started ca. 240 ka before the end of the organic-rich sedimentation, coinciding with the onset of enhanced diatom frustules deposition, recorded in the siliceous part of the BI. Since this period, a step-wise radiolarian extinction continued through the Early Turonian. Many of the radiolarian species previously considered as terminating during the BI, in fact outlived up to "post-Bonarelli" times, having their last occurrence after the BI or even in the Early Turonian. In the case of the radiolarian fauna, the Bonarelli period caused the disappearance of many Lazarus taxa, which returned in almost their initial state during 940 ka after the BI. The current radiolarian study sheds light on the biological effects of anoxic events, indicating the role of the mesopelagic zone and oceanic circulation in nutrient exchange, which modulates and controls the OAE2. The mesopelagic zone played an important role in P sequestration and was responsible for the release of the most of P, leading to enhanced eutrophication of water column.


The study presents the results of the analysis of antibiotic consumption and its direct costs in selected neonatal units. Data were collected retrospectively (the year 2007) in five hospitals, during the pilot phase of the Polish Neonatal Network . Antibiotic consumption was assessed using the Defined Daily Dose (DDD). The costs were assessed as the costs of purchase of one DDD. The study included 11 922 children hospitalized in the period from 1.01 to 31.12.2007. In this group, 731 infants have birth weight < 1500 grams (from 2.2% to 64.2% in individual units, median--7.3%). The mean consumption of antibacterial drugs was 48.52 DDD/1 000 person-days (P-D) of stay among the entire study population (median--42,52), and varied from 23.13 to 85.82 DDD/1,000 P-D. However, this difference has not been statistically significant. The most commonly used group of antibiotics were beta-lactams--in four out of five units the percentage of its usage ranged from 48.71% to 74.67%. Next group were aminoglicosides--in one unit its usage reached 56.97% and in other ranged from 5.01% to 22.53%. Glycopeptides and macrolides were also used in every unit of the studied group. The usage of glycopeptides ranged from 1.7% to 10.81% and of macrolides from 1.32% to 15.71%. Different kinds of antibiotics were used occasionally. The differences of costs of purchase of one DDD between hospitals were greater and varied from 17,64 PLN/ DDD to 84,58 PLN/ DDD (average costs). A considerable range of costs index values was also noted for different groups of antibiotics. The costs of purchase of one DDD of beta-lactams varied from 19.54 PLN/ DDD to 68.35 PLN/ DDD; for aminoglicosides the cost varied from 4.61 PLN/ DDD to 122.9 PLN/ DDD, for glycopeptides--from 31.40 PLN/ DDD to 283.13 PLN/ DDD and in case of macrolides: from 12.05 PLN/ DDD to 90.77 PLN/ DDD. This differentiation of the cost of purchasing a single defined daily dose, taking into account the specific groups of antibiotics, did not have the characteristics of statistical significance. As expected, the antibiotic regimens in the studied wards were similar. This is due to a homogeneous population of hospitalized patients. However, the differences of costs of purchase of antibiotics observed in the study, indicate the considerable variety of the treatment patterns in Polish neonatology units and the need to develop and implement recommendations of effective pharmacotherapy for patients in intensive neonatal care units and the implementation of a unified model of infections surveillance.


Uzarowicz L.,Warsaw University of Technology | Skiba S.,Jagiellonian University
Geoderma | Year: 2011

Technogenic soils (Technosols) containing iron sulphides, developed on mine spoils located in three abandoned industrial sites in Poland (the "Siersza" hard coal mine in Trzebinia, "Staszic" pyrite mine in Rudki, and pyrite mines in Wieściszowice), were investigated in order to identify the most important mineral transformations occurring in the soils. The X-ray diffraction (XRD), scanning electron microscope-energy dispersive spectrometry (SEM-EDS) techniques, and selective extraction methods were applied in the examination of soil mineralogy. The soils studied represented weakly developed soil formations in which organic matter accumulation increasing with age was observed, along with intense weathering of parent materials containing iron sulphides. The degree of sulphide transformations is age-dependent. In young soils from Trzebinia and Rudki, poorly weathered iron sulphides occurred, whereas in old soils from Wieściszowice, iron sulphides were almost entirely transformed. The main products of sulphide weathering are iron oxides and sulphate minerals (gypsum and jarosite group minerals mainly). Inherited phyllosilicates and pedogenic clay minerals (smectite, vermiculite, kaolinite, and mixed-layer minerals) were present in the soils studied. The development of Al-hydroxy interlayers and the possibility of the formation of poorly crystalline Al phases were also documented. The processes seem to be pH-dependent and occur at pH ranging from 4.3 to 4.4. The development of iron oxides and sulphate minerals in the process of sulphide weathering, as well as phyllosilicate transformations (e.g. the development of swelling clay minerals at the expense of inherited mica and chlorite, and the formation of hydroxy interlayers in clay minerals) are the main mineralogical aspects of pedogenesis of technogenic soils developed on mine spoils containing iron sulphides. The WRB and Soil Taxonomy systems require more precise solutions concerning the classification of technogenic soils investigated. The thionic horizon (WRB) and sulfuric horizon (Soil Taxonomy) definitions, as well as the sulphidic material (WRB) and sulfidic material (Soil Taxonomy) definitions need to be supplemented. The paper suggests the introduction of the Sulfic Udorthents taxon in the Soil Taxonomy, as well as the introduction of "Thionic" suffix qualifier to the key to the Technosols in the WRB. © 2011 Elsevier B.V.


Iacobone M.,University of Padua | Jansson S.,Sahlgrenska University Hospital | Barczynski M.,Jagiellonian University | Goretzki P.,Lukaskrankenhaus Neuss
Langenbeck's Archives of Surgery | Year: 2014

Background: Multifocal papillary thyroid carcinoma (MPTC) has been reported in literature in 18-87 % of cases. This paper aims to review controversies in the molecular pathogenesis, prognosis, and management of MPTC. Methods: A review of English-language literature focusing on MPTC was carried out, and analyzed in an evidence-based perspective. Results were discussed at the 2013 Workshop of the European Society of Endocrine Surgeons devoted to surgery of thyroid carcinoma. Results: Literature reports no prospective randomized studies; thus, a relatively low level of evidence may be achieved. Conclusions: MPTC could be the result of either true multicentricity or intrathyroidal metastasis from a single malignant focus. Radiation and familial nonmedullary thyroid carcinoma are conditions at risk of MPTC development. The prognostic importance of multifocal tumor growth in PTC remains controversial. Prognosis might be impaired in clinical MPTC but less or none in MPTC <1 cm. MPTC can be diagnosed preoperatively by FNAB and US, with low sensitivity for MPTC <1 cm. Total or near-total thyroidectomy is indicated to reduce the risk of local recurrence. Prophylactic central node dissection should be considered in patients with total tumor diameter >1 cm, or in cases with high number of cancer foci. Completion thyroidectomy might be necessary when MPTC is diagnosed after less than near-total thyroidectomy. Radioactive iodine ablation should be considered in selected patients with MPTC at increased risk of recurrence or metastatic spread. © 2013 Springer-Verlag.


Maliborski M.,Jagiellonian University
Physical Review Letters | Year: 2012

We consider a spherically symmetric self-gravitating massless scalar field enclosed inside a timelike worldtube R×S3 with a perfectly reflecting wall. Numerical evidence is given that arbitrarily small generic initial data evolve into a black hole. © 2012 American Physical Society.


Olszowska M.,Jagiellonian University
Polskie Archiwum Medycyny Wewnetrznej | Year: 2011

Aortic stenosis (AS) is themost common form of valvular heart disease. AS of degenerative etiology is predominant. It is apersistent disease associated with theactivation of 3 processes: lipid accumulation, inflammation, and calcification. Recent studies suggest that valve calcification is anactively regulated process that involves extracellular matrix remodeling, angiogenesis, and inflammation leading to bone formation. Many mechanisms and risk factors involved in thepathogenesis of AS are similar to those observed in atherosclerosis. The knowledge of these processes may play a significant role in adequate prevention and therapy of patients with AS, especially at an early stage. Copyright by Medycyna Praktyczna, Kraków 2011.


Dlotko P.,University of Pennsylvania | Dlotko P.,Jagiellonian University | Specogna R.,University of Udine
Computer Physics Communications | Year: 2013

The issue of computing (co)homology generators of a cell complex is gaining a pivotal role in various branches of science. While this issue may be rigorously solved in polynomial time, it is still overly demanding for large scale problems. Drawing inspiration from low-frequency electrodynamics, this paper presents a physics inspired algorithm for first cohomology group computations on three-dimensional complexes. The algorithm is general and exhibits orders of magnitude speed up with respect to competing ones, allowing to handle problems not addressable before. In particular, when generators are employed in the physical modeling of magneto-quasistatic problems, this algorithm solves one of the most long-lasting problems in low-frequency computational electromagnetics. In this case, the effectiveness of the algorithm and its ease of implementation may be even improved by introducing the novel concept of lazy cohomology generators. © 2013 Elsevier B.V. All rights reserved.


Lukowski T.,Jagiellonian University | Rej A.,Imperial College London | Velizhanin V.N.,RAS Petersburg Nuclear Physics Institute
Nuclear Physics B | Year: 2010

In this article we calculate the five-loop anomalous dimension of twist-two operators in the planar N = 4 SYM theory. Firstly, using reciprocity, we derive the contribution of the asymptotic Bethe ansatz. Subsequently, we employ the first finite-size correction for the AdS5 × S5 sigma model to determine the wrapping correction. The anomalous dimension found in this way passes all known tests provided by the NLO BFKL equation and double-logarithmic constraints. This result thus furnishes an infinite number of experimental data for testing the veracity of the recently proposed spectral equations for planar AdS/CFT correspondence. © 2010 Elsevier B.V. All rights reserved.


Grosso G.,University of Catania | Yang J.,Harvard University | Yang J.,Tufts University | Marventano S.,Section of Hygiene and Public Health | And 3 more authors.
American Journal of Clinical Nutrition | Year: 2015

Background: Recent pooled analyses supported a beneficial impact of nut consumption on health, but to our knowledge, whether nuts are associated with overall decreased mortality has not been previously reviewed. Objectives: We aimed to systematically review prospective studies that explored the effects of nut consumption on all-cause, cardiovascular disease (CVD), and cancer mortality and quantify the size effect through a meta-analysis. We also reviewed confounding factors associated with nut consumption to assess potential clustering with other covariates. Design: We searched PubMed and EMBASE for studies published up to June 2014. Study characteristics, HRs, and 95% CIs were generated on the basis of quantitative analyses. A dose-response analysis was performed when data were available. Results: Seven studies for all-cause mortality, 6 studies for CVD mortality, and 2 studies for cancer mortality were included in the meta-analysis with a total of 354,933 participants, 44,636 cumulative incident deaths, and 3,746,534 cumulative person-years. Nut consumption was associated with some baseline characteristics such as lower body mass index and smoking status as well as increased intakes of fruit, vegetables, and alcohol. One-serving of nuts per week and per day resulted in 4% (RR: 0.96; 95% CI: 0.93, 0.98) and 27% (RR: 0.73; 95% CI: 0.60, 0.88) decreased risk of all-cause mortality, respectively, and decreased risk of CVD mortality [RR: 0.93 (95% CI: 0.88, 0.99) and 0.61 (95% CI: 0.42, 0.91), respectively]. Effects were primarily driven by decreased coronary artery disease deaths rather than stroke deaths. Nut consumption was also associated with decreased risk of cancer deaths when highest compared with lowest categories of intake were compared (RR: 0.86; 95% CI: 0.75, 0.98), but no dose-effect was shown. Conclusion: Nut consumption is associated with lower risk of allcause, CVD, and cancer mortality, but the presence of confounding factors should be taken into account when considering such findings. © 2015 American Society for Nutrition.


Ciecholewski M.,Jagiellonian University
Journal of Signal Processing Systems | Year: 2014

Due to its precision, computed tomography (CT) is now generally used to image the liver and diagnose its diseases. Computer-assisted methods aimed at facilitating the extraction of organ shapes from medical images and helping to diagnose disease entities are rapidly developing. This study presents a new method of automatically segmenting the shape of the liver, both for cases free of lesions and those showing certain disease units, i.e. focused lesions like hemangiomas and hepatomas. For the 1,330 2D CT images of the abdominal cavity and liver analysed, the Dices similarity coefficient amounted to 81.3 %. The method proposed is to be used in an IT system supporting liver diagnostics. © 2013 The Author(s).


Walczynska A.,Jagiellonian University | Serra M.,University of Valencia
Hydrobiologia | Year: 2014

The strategy of decreasing size with increasing temperature operates at regional and phenotypic scale and presents a puzzle to researchers. In this work, we studied two aspects of the temperature-performance relationship along a temperature gradient, (i) comparing the population growth rates of three cryptic Brachionus species differing in adult size, and (ii) assessing the phenotypic plasticity of adult size, in one clone per species. The working hypotheses were that (i) the bigger the species the lower its optimal temperature for population growth, and (ii) the higher the temperature the smaller the individual within each focal species. The results showed that (i) the optimal temperature for population growth is related to species size in a manner foreseen by Bergmanns' rule for two of the three species (the third, biggest species, performed evenly well at all temperatures examined, what could be explained by its generally eurioic character), and that (ii) the strategy of body size adjustment to environmental temperature differs between species and may depend on the level of temperature specialization. This work demonstrated the usefulness of inter- and intraspecific comparisons for studying the role of growth strategies in adaptation to temperature. © 2014 Springer International Publishing Switzerland.


The studies on the influence of cholesterol on phospholipids accumulated in inner leaflet of membrane are performed rather rarely, especially in the presence of electrolytes, which are present in membrane environment. Therefore, in this work the interactions between cholesterol and saturated phosphatidylethanolamine (PE) and phosphatidylserine (PS) were studied in binary (phospholipid/cholesterol) and ternary (PS/PE/cholesterol) monolayers in the presence and absence of sodium and calcium ions. The composition of ternary films was estimated to reflect the proportion of PSs to PEs in inner layer of human erythrocyte membrane. The influence of electrolytes on pure PS and PE films was also analyzed. It was found that both sodium and calcium ions affect the condensation of DPPS films, and influence the interactions in DPPS/cholesterol monolayers. On the other hand, no effect of these ions on DPPE films as well as on DPPE/cholesterol interactions in the mixed systems was observed. The results obtained for ternary mixtures prove that in the presence of Na+ the interactions between the lipids are more favorable than in the absence of these ions. This is in contrast to the effect of Ca2+. All the results were thoroughly analyzed in the context of the structure of polar heads of the investigated phospholipids. © 2010 Elsevier B.V.


Copper(II), cobalt(II) and nickel(II) complexes incorporating 3-hydroxy-2-naphthoyl hydrazone (HLL) have been prepared: nanometer-sized metallopolymeric chains [Cu(μ-LL)2]n as well as octahedral monomers [Co(LL)2(L)2] (L = H2O, pyridine) and [Ni(LL)2(L)2] (L = H2O, thf). Their structural diversity both in the solid state and solution, evidenced by single-crystal X-ray diffraction and dynamic light scattering, fundamentally affects their electrochemical behavior. Contrary to monomeric nickel and cobalt complexes, 1-D polymeric copper complex forms aggregates (ca. 750 nm in size) in solution and undergoes a unique cathodic electropolymerization that results in the formation of a conducting film on Pt electrode. The plausible mechanism of its formation, based on the preorganization present in the 1-D structure of the copper(II) complex, is proposed. © 2012 Elsevier Ltd. All rights reserved.


The taxonomic position and distribution of Stipa tianschanica Roshev, a species new to the flora of Tajikistan (central Asia), are discussed. Its morphological characters are compared with other members of the S. tianschanica complex and information on their taxonomy and distribution are presented. The distinguishing features of S. tianschanica subsp. tianschanica, S. tianschanica subsp. gobica (Roshev.) D. F. Cui and S. klemenzii Roshev. are presented in a table, together with photographs of their lemma surfaces and a list of their synonyms. Analysis of the morphological characters of the taxa provides new information on their variability and a new combination, S. tianschanica subsp. gobica var. pubescens (Hanelt & Davažamc) M. Nobis comb. nov., is proposed. A key to the taxa of Stipa sect. Smirnovia Tzvel. occurring in Tajikistan (especially in the area of Pamirs), a description of S. tianschanica subsp. tianschanica and illustrations of the most important diagnostic characters of the taxon are included. © 2011 The Authors.


Lazewska D.,Jagiellonian University
Frontiers in bioscience (Scholar edition) | Year: 2012

Since 2000, when the histamine H4 receptor (H4R) was cloned, it has constituted an interesting target for drug development. Pharmacological studies suggest the potential utility of histamine H4R antagonists/inverse agonists in the treatment of inflammatory diseases, e.g. allergic rhinitis, asthma, atopic dermatitis, colitis, or pruritus. The first H4R ligands were non-selective compounds, but intensive chemical and pharmacological work has led to the discovery of highly potent and selective H4R antagonists (e.g. JNJ7777120, CZC-13788, PF-2988403, A-940894, A-987306). The first compound (UR-63325) has finally entered into clinical studies for the treatment of allergic respiratory diseases (completing the phase I ascending dose trial) and has been found to be safe and well tolerated. The number of scientific publications and patent applications in the H4 field is increasing annually. Among the diverse chemical structures of the H4R antagonists described a 2-aminopyrimidine scaffold is repeatedly found. This review looked at recent advances in the search for H4R antagonists as reflected in patent applications/patents and peer-reviewed publications over the last two years. The work concerns azines (mono-, di-, triazines) and their fused analogues. The chemistry and pharmacology has been described.


Jonsson P.,Malmo University | Bieron J.,Jagiellonian University
Journal of Physics B: Atomic, Molecular and Optical Physics | Year: 2010

Energy levels, fine-structure separations, specific mass shift parameters, isotope shifts, hyperfine interaction constants, Landé g J-factors and transition probabilities are reported for the 2s 22p2-2s2p3 transition array in N II, O III, F IV, Ne V and Ti XVII. Wavefunctions were determined using the multiconfiguration Dirac-Hartree-Fock method with account for valence, core-valence and core-core correlation effects. The transition energies and rates are compared with experimental data and with values from other calculations. © 2010 IOP Publishing Ltd.


Gadek A.,Jagiellonian University | Liszka H.,Hospital of the Ministry of Internal Affairs
Foot and Ankle International | Year: 2013

Background: The mini-invasive Mitchell-Kramer procedure is a new method of operative correction of mild to moderate hallux valgus deformity. The aim of this study was to describe the technique and evaluate the results of the procedure. Methods: We evaluated 54 patients who underwent mini-invasive distal metatarsal osteotomy of the first metatarsal with preservation of the lateral cortex of the distal fragment. We did percutaneous 2-mm K-wire stabilization of the osteotomy and did not use cast immobilization with postoperative offloading of the forefoot. We used anteroposterior and lateral foot standing X-rays, visual analog scale (VAS), and American Orthopaedic Foot and Ankle Society (AOFAS) hallux-metatarsophalangeal-interphalangeal scale for the clinical assessment at 18 months' follow-up. Results: Preoperatively, mean hallux valgus angle was 33.9 degrees; intermetatarsal angle, 14.8 degrees; VAS, 8.9; and AOFAS, 37.0. At follow-up period, hallux valgus angle was 14.2; intermetatarsal angle, 9.7; VAS, 2.6; and AOFAS, 90.7. The average first metatarsal shortening was 2.7 mm. No transfer metatarsalgia was noted at 18 months' follow-up. We found 1 superficial infection, but all patients were satisfied. Conclusions: The mini-invasive Mitchell-Kramer method was indicated in mild to moderate hallux valgus deformity. Cast immobilization was unnecessary, and full weightbearing was allowed early. Using the minioscillating saw allowed for reduced surgical exposure. The technique of the osteotomy also allowed for rotational stability of the osteotomy. © The Author(s) 2013.


Lipert M.,Jagiellonian University
Classical and Quantum Gravity | Year: 2010

Using mixed numerical and analytical methods we provide evidence that the (6+1)-dimensional Taub-NUT soliton is asymptotically nonlinearly stable against small perturbations preserving biaxial Bianchi IX symmetry. We also show that for sufficiently strong perturbations the soliton collapses to a warped black hole. Since this black hole solution is not known in closed form, for completeness of the exposition we prove its existence and determine its properties. In particular, the mass of the black hole is computed. © 2010 IOP Publishing Ltd.


Krafts K.,University of Minnesota | Hempelmann E.,University of Witwatersrand | Skorska-Stania A.,Jagiellonian University
Parasitology Research | Year: 2012

Malarial treatment is widely and readily available today. However, there was a time in the not-so-distant past when malaria was a deadly disease with no known cause or cure. In this article, we trace the origins of an antimalarial therapy from the discovery of the nature of the malarial parasite through the development of chloroquine. We dedicate this article to Johann "Hans" Andersag, the scientist who developed chloroquine, on the 110th anniversary of his birth, 16 February 1902. © 2012 Springer-Verlag.


Witala H.,Jagiellonian University | Glockle W.,Ruhr University Bochum
Journal of Physics G: Nuclear and Particle Physics | Year: 2010

In view of recent neutron-deuteron (nd) breakup data for neutron-neutron (nn) and neutron-proton (np) quasi-free-scattering (QFS) arrangements and the large discrepancy found between theoretical predictions and measured nn QFS cross sections, we analyze the sensitivity of the QFS cross sections to different partial wave components of the nucleon-nucleon (NN) interaction. We found that the QFS cross section is strongly dominated by the 1S 0 and 3S1-3D1 contributions. Because the standard three-nucleon force (3NF) only weakly influences the QFS region, we conjecture that it must be the nn 1S0 force component which is responsible for the discrepancy in the nn QFS peak. A stronger 1S0 nn force is required to bring theory and data into agreement. Such an increased strength of the nn interaction will, however, not help to explain the nd breakup symmetric-space-star (SST) discrepancy. Further experimental cross-checkings are required. © 2010 IOP Publishing Ltd.


Kotulski L.,AGH University of Science and Technology | Strug B.,Jagiellonian University
Advanced Engineering Informatics | Year: 2013

Different types of graphs has been successfully used to represent designs at different stages of the design process. Changes to a model representing a design during the process can be modelled by applying graph transformations. In many real life design tasks the changes/updates can be carried out simultaneously on different parts of the design. Hence a model based on graph transformations is coupled with a multiagent paradigm to enable the parallelisation of these transformations to mimic the real life approach. In this paper a hypergraph representation and transformation model is used as a basis for building a multiagent system supporting distribution and adaptation in computer aided design. This representation can be applicable throughout the lifecycle of the design. It is based on research in formal language theory, like graph grammars, and distributed models including multiagent systems. The motivation for the work presented here is given and possible applications are described. The application of the theoretical results in a graph distribution toolkit proposed as a multiagent framework is also considered. To assure the efficiency of the system it should be implemented as a parallel multiagent system. The hypergraph distribution and partial replication, allowing for its parts to be managed by agents, is also presented. The approach is illustrated by a case study from the domain of building design, where it is used to represent, modify and maintain building information.© 2012 Elsevier Ltd. All rights reserved.


Nobis M.,Jagiellonian University | Nowak A.,University of Opole
Polish Botanical Journal | Year: 2011

The paper presents distributional data for nine species new to the flora of the central Pamir Alai Mts in Tajikistan: Acalypha australis L., Azolla filiculoides Lam., Bidens frondosa L., Bromus willdenowii Knuth, Eragrostis virescens J. Presl, Galinsoga ciliata (Raf.) S. F. Blake, Nanorrhinum ramosissimum (Wall.) Betsche, Stipa gracilis Roshev. and Zygophyllum miniatum Cham. & Schlecht. Six species should be regarded as alien to the Tajik flora, expansively spreading or invasive in this part of Asia. The other three taxa are native elements of the flora of the Pamir Alai Mts. A list of localities of the species in the Tajik Pamir Alai Mts is given, and their habitat preferences are described. Their distribution is mapped and illustrations of some species are provided.


Rapala-Kozik M.,Jagiellonian University
Advances in Botanical Research | Year: 2011

Thiamine (vitamin B1) is essential for human metabolism and is particularly important for proper brain functioning. Plants, which are the best source of this vitamin for human nutrition, synthesize thiamine in three stages. The first of these involves the independent formation of thiazole and pyrimidine moieties. In the next phase, these are coupled together to form thiamine monophosphate. The final step results in the formation of the active form of vitamin B1, thiamine diphosphate, which functions as a major enzymatic cofactor. The biosynthesis of thiamine is regulated through feedback inhibition by the end product of the pathway, that is, thiamine diphosphate. This regulatory mechanism involves the binding of thiamine diphosphate by mRNA elements, riboswitches (THI-BOXes). The transport of thiamine and thiamine diphosphate between plant tissues and into cell compartments determines the proper functioning of major metabolic pathways such as the acetyl-CoA synthesis, the tricarboxylic acid cycle, the pentose phosphate pathway, Calvin-Benson cycle and isoprenoid biosynthesis pathway. The recently reported activation of thiamine production in plant cells under biotic or abiotic stress conditions also suggests a non-cofactor role of this vitamin as a stress alarmone or stress protectant to enable plants to survive in unfavourable environments. © 2011 Elsevier Ltd.


Hadasz L.,Jagiellonian University | Jaskolski Z.,Wroclaw University | Suchanek P.,Wroclaw University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2010

The modular matrix for the generic 1-point conformal blocks on the torus is expressed in terms of the fusion matrix for the 4-point blocks on the sphere. The modular invariance of the toric 1-point functions in the Liouville field theory with DOZZ structure constants is proved. © 2010 Elsevier B.V. All rights reserved.


Lis J.,Jagiellonian University
Acta Physica Polonica B | Year: 2010

The regularized signum-Gordon potential has a smooth minimum and is linear in the modulus of the field value for higher amplitudes. The Q-ball solutions in this model are investigated. Their existence for charges large enough is demonstrated. In three dimensions numerical solutions are presented and the absolute stability of large Q-balls is proved. It is also shown, that the solutions of the regularized model approach uniformly the solution of the unregularized signum-Gordon model. From the stability of Q-balls in the regularized model follows the stability of the solutions in the original theory.


Hadasz L.,Jagiellonian University | Jaskolski Z.,Wroclaw University | Suchanek P.,Wroclaw University
Journal of High Energy Physics | Year: 2010

The recursive relation for the 1-point conformal block on a torus is derived and used to prove the identities between conformal blocks recently conjectured by Poghossian in [1]. As an illustration of the efficiency of the recurrence method the modular invariance of the 1-point Liouville correlation function is numerically analyzed. © SISSA 2010.


Sosin Z.,Jagiellonian University
International Journal of Modern Physics E | Year: 2010

The equation of state (EOS) in a form suitable for calculation in the model of quantum molecular dynamics (QMD) is presented. Using the proposed form of the EOS, different properties of nuclei such as ground state energy, nuclear radii and neutron skin could be calculated. The preliminary results of calculations are compared with the experimental data. © 2010 World Scientific Publishing Company.


Hadasz L.,Jagiellonian University | Jaskolski Z.,Wroclaw University | Suchanek P.,Wroclaw University
Journal of High Energy Physics | Year: 2010

Using recursive relations satisfied by Nekrasov partition functions and by irregular conformal blocks we prove the AGT correspondence in the case of M = 2 superconformal SU(2) quiver gauge theories with N f = 0,1,2 antifundamental hypermultiplets.


Trzetrzelewski M.,Jagiellonian University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2010

We study spiky configurations of membranes in the SO (d) × SU (N) invariant matrix models. A class of exact solutions (analogous to plane-waves) of the corresponding Schrödinger equation for an arbitrary N is discussed. If the large N limit is performed so that the energy scales like N2, the N = ∞ wavefunctions reduce to the ground state of the d-dimensional harmonic oscillator. © 2010 Elsevier B.V. All rights reserved.


Mlyniec K.,Jagiellonian University
Current Neuropharmacology | Year: 2015

Depression is a serious psychiatric illness that affects millions of people worldwide. Weeks of antidepressant therapy are required to relieve depressive symptoms, and new drugs are still being extensively researched. The latest studies have shown that in depression, there is an imbalance between the main excitatory (glutamatergic) and inhibitory (GABAergic) systems. Administration of antagonists of the glutamatergic system, including zinc, has shown an antidepressant effect in preclinical as well as clinical studies. Zinc inhibits the NMDA receptor via its binding site located on one of its subunits. This is thought to be the main mechanism explaining the antidepressant properties of zinc. In the present review, a link between zinc and the glutamatergic system is discussed in the context of depressive disorder. © 2015 Bentham Science Publishers.


Dabrowski J.M.,Jagiellonian University | Arnaut L.G.,University of Coimbra | Arnaut L.G.,Luzitin SA
Photochemical and Photobiological Sciences | Year: 2015

Photodynamic therapy (PDT) requires a medical device, a photosensitizing drug and adequate use of both to trigger biological mechanisms that can rapidly destroy the primary tumour and provide long-lasting protection against metastasis. We present a multidisciplinary view of the issues raised by the development of PDT. We show how spectroscopy, photophysics, photochemistry and pharmacokinetics of photosensitizers determine the mechanism of cell death and clinical protocols. Various examples of combinations with chemotherapies and immunotherapies illustrate the opportunities to potentiate the outcome of PDT. Particular emphasis is given to the mechanisms that can be exploited to establish PDT as a systemic treatment of solid tumours and metastatic disease. © The Royal Society of Chemistry and Owner Societies 2015.


Dlotko P.,Jagiellonian University
Pattern Recognition Letters | Year: 2012

In this paper a fast algorithm to compute cohomology group generators of cellular decomposition of any orientable open or closed 2-manifold is described. The presented algorithm is a dual version of algorithm to compute homology generators presented by David Eppstein in "Dynamic generators of topologically embedded graphs" and developed by Jeff Erickson and Kim Whittlesey in "Greedy optimal homotopy and homology generators". Some parts of the paper bases on ideas presented in "Optimal discrete Morse functions for 2-manifolds" by Thomas Lewiner, Helio Lopes and Geovan Tavares. Extension of the algorithm to some non-manifold cases is provided. © 2011 Elsevier B.V. All rights reserved.


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2014

The quantum-generalized Information Theory is applied to explore molecular equilibrium states by using the resultant information content of electronic states, determind by the classical (probability based) measures and their non-classical (phase/current related) complements, in the extremum entropy/information principles. The "vertical" (probability-constrained) entropic rules are investigated within the familiar Levy and Harriman-Zumbach-Maschke constructions of Density Functional Theory. A close parallelism between the vertical maximum-entropy and minimum-energy principles in quantum mechanics and their thermodynamic analogs is emphasized and a relation between the probability and phase distributions in the "horizontal" (probability-unconstrained) phase-equilibria is examined. These solutions are shown to involve the spatial phase contribution related to the system electron density.The complete specification of the equilibrium states of molecular/promolecular fragments, including the subsystem density and the equilibrium phase of the system as a whole, is advocated and illustrated for bonded hydrogens in H2. Elements of the non-equilibrium thermodynamic description of molecular systems are formulated. They recognize the independent probability and phase state parameters, the associated currents, and their contributions to the quantum entropy density and its current. The phase and entropy continuity equations are explored and the local sources of these quantities are identified. © 2014 The Author(s).


Wronka I.,Jagiellonian University
Journal of Biosocial Science | Year: 2013

Adult height reflects long-term nutritional status and exposure to infectious diseases, both of which are influenced by socioeconomic factors. Very little research has been done on these inequalities from a longitudinal perspective. This paper explores the links between body height at different life stages and socioeconomic characteristics. Data were obtained from 1008 Polish schoolgirls aged 16-18 years for whom earlier data on height were available. The height of each subject was measured. Socioeconomic status and age at menarche were assessed based on information received from the surveyed girls. Girls' heights in early life were ascertained from medical records. All girls were measured by trained school nurses at 7, 9 and 14 years of age. Socioeconomic status was found to be related to body height, but not to the rate of height gain during childhood and adolescence. Girls of a higher socioeconomic status were taller than girls of a lower socioeconomic status. On dividing the research material into homogeneous groups by maturity status, the same relationship was observed. No significant relationships were found between socioeconomic status and rate of height gain between ages 7 and 16, 17, 18 years. The findings suggest that socioeconomic variation in height is the result of living conditions during the first years of life. Copyright © Cambridge University Press 2012.


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2015

The probability and phase/current facets of electronic states generate the classical and nonclassical information terms, respectively. The current-related supplements of the classical information measures and continuity equations for these degrees-of-freedom are summarized. The continuity of the resultant quantum entropy is also explored. This thermodynamic-like description is applied to discuss the temporal aspect of the promolecule-to-molecule transition in (Formula presented.). The Wiberg-type bond multiplicity concept is extended to cover the degenerate electronic states. They generally exhibit finite spatial phases and hence nonvanishing electronic currents, and thus also nonzero nonclassical contributions to the resultant content of the state entropy/information. Illustrative example of the excited configurations in the (Formula presented.)-electron ring of benzene is investigated using the complex framework of the (ground-state equivalent) molecular orbitals in Hückel approximation. To validate these generalized concepts, correlations between the (Formula presented.)-bond orders/multiplicities and orbital excitation energies are explored. © 2015, The Author(s).


Krasny M.W.,University Pierre and Marie Curie | Placzek W.,Jagiellonian University
Acta Physica Polonica B | Year: 2014

We construct a simple model of the Double Drell - Yan Process (DDYP) for proton - proton collisions and investigate its possible contribution to the background for the Higgs-boson searches at the LHC. We demonstrate that under the assumption of the predominance of short range, (0.1) fm, transverse-plane correlations of quark - antiquark pairs within the proton, this contribution becomes important and may even explain the observed excess of the four-lepton events at the LHC - the events interpreted as originating from the Higgs-boson decays: H → ZZ → 4l and H → WW → 2l2ν.


For detection of phenolic compounds a simple amperometric biosensor based on tyrosinase immobilized in titania solgel/ Nafion composite was employed. Titania sol-gel was mixed with Nafion (v/v) in ratios 1:1 (TiO 2/NF-1/1) and 2:1 (TiO2/NF-2/1), v/v. Morphology of immobilization composites was characterized by scanning electron microscopy. Analytical performance of biosensors with Nafion and based only on titania sol-gel (TiO2) was compared. Apart from sensitivity, linear range and detection limit also repeatability, reproducibility and storage stability were evaluated. The biosensor based on titania sol mixed with Nafion in ratio 1:1 (v/v) exhibited the best analytical parameters in terms of sensitivity: 2.84 μA L μmol-1, corresponding LOD, 0.056 μmol L-1, and the long-term stability within 20 days: it retained 80% of initial activity.


Gaweda L.,Medical University of Warsaw | Prochwicz K.,Jagiellonian University | Cella M.,Kings College London
Psychiatry Research | Year: 2015

Psychotic-like experiences (PLEs) are frequently reported in the general population. Healthy individuals reporting PLEs have a similar personality profile to people with psychosis; however, the mechanisms by which personality influences PLEs are unclear. This study tests the hypothesis that cognitive biases mediate the relationship between two dimensions of personality (i.e. temperament and character) and positive and negative PLEs. Two hundred and ninety-six healthy participants were assessed using the Community Assessment of Psychic Experiences scale, the Temperament and Character Inventory and the Davos Scale for Cognitive Biases. We performed multiple stepwise regression analysis and mediation analysis according to Baron and Kenny's method. Harm-avoidance and self-directedness personality dimensions significantly predicted PLEs frequency. High self-transcendence and lower cooperativeness predicted positive PLEs. Cognitive biases were significant mediators in relationships between temperament, character and both positive and negative PLEs. In particular, attention to threat and external attribution biases fully mediate the relationship between cooperativeness and positive PLEs. Other cognitive biases partially mediate the relationships between self-transcendence and positive PLEs and self-directedness, harm-avoidance and negative PLEs. Our study tentatively suggests that personality may influence PLEs via the cognitive bias pathway. © 2014 Elsevier Ireland Ltd.


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

In this paper, the Shapley value method is introduced to power allocation in cognitive radio (CR) networks. This concept is intended to maximize the information throughput sustained by each link over the network. In the traditional approach, game theory is used as a tool to model the interaction between several players and predict the outcome of the power allocation game. Our solution to this problem determines the participation of the players in the formed coalition of secondary users (SUs) in cognitive radio networks by using the Shapley value. The simulation results show the effectiveness of the proposed power control policy. © 2012 Springer-Verlag.


Knoevenagel condensation of barbituric acids with aromatic aldehydes containing one or two formyl groups was carried out. 5-Arylidenebarbituric acids underwent smooth hetero-Diels-Alder (HDA) reactions with enol ethers to afford cis and trans diastereoisomers of pyr-ano[2,3-d]pyrimidine-2,4-diones and 5,5′-(1,4-phenylene)-bis[2H-pyrano[2,3-d]pyrimidine-2,4(3H)-dione] derivatives in excellent yields (75-88%). Syntheses were realized by Knoevenagel condensation and HDA reaction in four different reaction conditions: Knoevenagel condensation in water and Diels-Alder reaction in methylene chloride solution, Knoevenagel condensation in water and Diels-Alder reaction without solvent, three-component one-pot reaction in methylene chloride solution, or three-component one-pot reaction in water. All reactions were carried out without catalyst at room temperature. The reactions of malononitrile with Knoevenagel condensation products of barbituric acids and heteroaromatic aldehydes or terephthalaldehyde were examined and did not provide corresponding pyranopyrimidines. © 2012 Springer-Verlag.


IR spectroscopic studies evidenced that Cu + ions coordinating basic molecules (ammonia, water, and pyridine) influenced both the CO and NO bond order. The significant downshift of the stretching frequency of the NO and CO bands indicates a considerable weakening of the multiple bonds. The effect was found to be the most important for pyridine as the molecule of the strongest electron donation properties. © 2011 Elsevier B.V. All rights reserved.


Baranski A.,Jagiellonian University
Journal of Chemical Education | Year: 2012

Numerous articles have been published that address problems encountered in teaching basic concepts of chemistry such as the atomic mass unit, Avogadro's number, and the mole. The origin of these problems is found in the concept definitions. If these definitions are adjusted for teaching purposes, understanding could be improved. In the present article, the definitions are discussed, and the following adjustments are suggested: (i) the feature that classifies carbon-12 for the definition as the standard be its abundance, (ii) Avogadro's number should refer directly to the standard nuclide sample, (iii) the definition of the mole be based on Avogadro's number, and (iv) the term amount of substance be replaced by the collection or quantity of microentities. It is also proposed that the definition of the mole is first presented for nuclides and then generalized for poly-isotopic elements and chemical compounds. A possible redefinition of kilogram as a multiple of the standard nuclide mass is also briefly discussed. Copyright © 2011 American Chemical Society and Division of Chemical Education, Inc.


The Orbital Communication Theory of the chemical bond, in which molecules are treated as information systems transmitting "signals" of electron allocations to Atomic Orbitals, is extended to cover the local resolution level of electron distributions and the Configuration-Interaction (CI, multi-determinantal) description of molecular states. These communication systems generate the information-theoretic measures of both the absolute and relative multiplicities of chemical bonds, as well as the bond covalent (communication-noise) and ionic (information-flow) components. The orbital/local communications via the CI ensembles of the occupied molecular orbitals in such generalized molecular states are investigated. Illustrative two-orbital model and its prototype Valence-Bond structures are examined in a more detail. © 2013 The Author(s).


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2014

The role of phases in local Communication Theory of the Chemical Bond is investigated. Probability amplitudes of such molecular (fine-grained) information systems originate from the superposition principle of quantum mechanics involving the projection onto the bond system defined by the subspace of the state occupied Molecular Orbitals. They are explicitly phase-dependent, thus being capable of interference effects. The phase factors of the local direct and indirect (bridge, cascade) channels are examined and the associated amplitude/probability sum rules are established. The entropic descriptors of the local channels, providing the system "covalent" (communication-noise) and "ionic" (information-flow) components, are investigated using prototype one-electron systems. The competition between these information-theoretic measures of the chemical bond covalency (electron delocalization) and ionicity (electron localization) is illustrated in H2 + and H2. © 2013 The Author(s).


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2014

Several concepts of information theory (IT) are extended to cover the complex probability amplitudes (wave functions) of molecular quantum mechanics. The classical and non-classical aspects of the electronic structure are revealed by the electronic probability and phase distributions, respectively. The information terms due to the probability and current distributions are accounted for in the complementary Shannon and Fisher measures of the resultant information content of quantum states. Similar generalization of the information-distance descriptors is also established. The superposition principle (SP) of quantum mechanics, which introduces the conditional probabilities between quantum states, is used to generate a network of quantum communications in molecules, and to identify the non-additive contributions to physical and information quantities. The phase-relations in two-orbital model are explored. The orbital communication theory of the chemical bond introduces the entropic bond multiplicities and their partition into IT covalent/ionic components. The conditional probabilities between atomic orbitals, propagated via the network of the occupied molecular orbitals, which define the bond system and orbital communications in molecules, are generated from the bond-projected SP. In the one-determinantal representation of the molecular ground state the communication amplitudes are then related to elements of the charge and bond-order matrix. Molecular equilibria are reexamined and parallelism between the vertical (density-constrained) energy or entropy/information principles of IT and the corresponding thermodynamic criteria is emphasized. © 2014 The Author(s).


Dybiec B.,Jagiellonian University
Journal of Physics A: Mathematical and Theoretical | Year: 2010

Within a continuous time random walk scenario we consider a motion of a complex of particles which moves coherently. The motion of every particle is characterized by the waiting time and jump length distributions which are of the power-law type. Due to the interactions between particles it is assumed that the waiting time is adjusted to the shortest or to the longest waiting time. Analogously, the jump length is adjusted to the shortest or to the longest jump length. We show that adjustment to the shortest waiting time can suppress the subdiffusive behavior even in situations when the exponent characterizing the waiting time distribution assures subdiffusive motion of a single particle. Finally, we demonstrate that the characteristic of the motion depends on the number of particles building a complex. © 2010 IOP Publishing Ltd.


Jachimska B.,Polish Academy of Sciences | Lapczynska M.,Polish Academy of Sciences | Zapotoczny S.,Jagiellonian University
Journal of Physical Chemistry C | Year: 2013

Dynamic light scattering (DLS) was used to measure the electrophoretic mobility and diffusion coefficients of sixth-generation poly(amido amine), G6 PAMAM, dendrimers in an aqueous solution. The measurements were used to determine the effective charge and the hydrodynamic radius of PAMAM molecules. The physicochemical measurements were supplemented with dynamic viscosity measurements. From these data, the intrinsic viscosity of the PAMAM solutions was determined. The viscosity behavior was discussed in terms of the core/shell dendrimer structure postulated in the literature. Additional information about the structure of the dendrimers was obtained using atomic force microscopy (AFM) and a quartz crystal microbalance (QCM). The latter was used to study the adsorption of G6 PAMAM from aqueous solution on a Au-coated surface. The QCM measurements indicate that the adsorbed dendrimer molecules significantly change their conformation and viscoelastic properties in response to variations in ionic strength and solution pH. We demonstrated that the QCM method detects the reversible swelling of dendrimer molecules in the film due to its adoption of an extended conformation upon the protonation of the dendrimer's amine groups. © 2012 American Chemical Society.


Recognition of pathogens by innate immune cells is mediated by pattern recognition receptors (PRR), which include the class A scavenger receptors (SR), SR-A/CD204 and MARCO. It seems that in addition to activating innate immune responses, phagocytosis and inflammation, this initial, PRR-mediated recognition also determines polarization of adaptive immune responses (Th1, Th2, Th17 or Treg). It has been demonstrated that class A SR are major PRR mediating opsonin-independent phagocytosis. SR-A- or MARCO-deficient mice exhibit impaired ability to control bacterial infections, resulting in increased mortality. Our results suggest that in addition to impaired bacterial destruction by macrophages, dysregulation of immune responses may contribute to defective antibacterial defense in class A SR-deficient mice. Using specific receptor ligation with antibodies, we showed that SR-A and MARCO regulate in an opposite manner production of IL-12 in macrophages, the cytokine playing a crucial role in Th1/Th2 polarization of adaptive immune responses. Together with the observation that expression of MARCO is increased by different Th1-polarizing factors and decreased by Th2-polarizing factors, these results suggest that changes in relative expression levels of SR-A and MARCO may be a mechanism of sustained polarization of adaptive immune responses.


Staszel P.,Jagiellonian University
Acta Physica Polonica B | Year: 2010

The Compressed Baryonic Matter (CBM) project at the future accelerator center FAIR will be a dedicated heavy-ion experimental operating in fixed target mode at beam energies from 8 to 45AGeV. The ultimate goal of the research program is to explore the QCD phase diagram in the range of moderate temperature but the highest net-baryon densities. The CBM detector concept aims to obtain feasibility of measurement of hadronic, leptonic and photonic observables at interaction rates up to 10MHz. It will allow to detect extremely rare probes such as charm near its production threshold. The CBM experiment will enter a new era with diagnostic probes never accessible before in the FAIR energy range, and thus has a unique research potential.


Zuzel G.,Jagiellonian University
Acta Physica Polonica B | Year: 2010

The GERDA experiment has been designed to search for neutrinoless double beta decay of 76Ge. Observation of such a process would imply that the neutrino is a Majorana particle, and that the lepton number is not conserved. Establishing the half-life of the decay would also allow to estimate the effective neutrino mass. The installation of the experiment in the Gran Sasso underground laboratory of INFN/Italy has been recently completed. Deployment of the first non-enriched Ge detectors is scheduled for spring 2010.


Nalewajski R.F.,Jagiellonian University
Structure and Bonding | Year: 2012

Selected concepts and techniques of Information-Theory (IT) are summarized and their use in probing the molecular electronic structure is advocated. The electron redistributions accompanying formation of chemical bonds, relative to the (molecularly placed) free atoms of the corresponding "promolecule, " generate the associated displacements in alternative measures of the amount of information carried by electrons. The latter are shown to provide sensitive probes of information origins of the chemical bonds, allow the spatial localization of bonding regions in molecules, and generate attractive entropy/ information descriptors of the system bond multiplicities. Information-theoretic descriptors of both the molecule as a whole and its diatomic fragments can be extracted. Displacements in the molecular Shannon entropy and entropy deficiency, relative to the promolecular reference, are investigated. Their densities provide efficient tools for detecting the presence of the direct chemical bonds and for monitoring the promotion/hybridization changes the bonded atoms undergo in a molecular environment. The nonadditive Fisher information density in the Atomic Orbital (AO) resolution is shown to generate an efficient Contra-Gradience (CG) probe for locating the bonding regions in molecules. Rudiments of the Orbital Communication Theory (OCT) of the chemical bond are introduced. In this approach molecules are treated as information systems propagating "signals" of electron allocations to basis functions, from AO "inputs" to AO "outputs." The conditional probabilities defining such an information network are generated using the bond-projected superposition principle of quantum mechanics. They are proportional to squares of the corresponding elements of the first-order density matrix in AO representation. Therefore, they are related to Wiberǵs quadratic index of the chemical bond multiplicity. Such information propagation in molecules exhibits typical communication "noise" due to the electron delocalization via the system chemical bonds. In describing this scattering of electron probabilities throughout the network of chemical bonds, due to the system occupied Molecular Orbitals (MO), the OCT uses the standard entropy/information descriptors of communication devices. They include the average communication noise (IT covalency) and information flow (IT ionicity) quantities, reflected by the channel conditional entropy and mutual information characteristics, respectively. Recent examples of applying these novel tools in an exploration of the electronic structure and bonding patterns of representative molecules are summarized. This communication perspective also predicts the "indirect" (through-bridge) sources of chemical interactions, due to the "cascade" probability propagation realized via AO intermediates. It supplements the familiar through-space mechanism, due to the constructive interference between the interacting AO, which generates the "direct" communications between bonded atoms. Such bridge "bonds" effectively extend the range of chemical interactions in molecular systems. Representative examples of the p systems in benzene and butadiene are discussed in a more detail and recent applications of the information concepts in exploring the elementary reaction mechanisms are mentioned. © Springer-Verlag Berlin Heidelberg 2012.


Pacyna G.,Jagiellonian University
Acta Palaeobotanica | Year: 2013

The Lower Jurassic plant macrofossils of Poland are poorly known. Relatively rich sources of fossils are found in only a few outcrops in the Holy Cross Mountains. Other described plant remains come from drill cores taken from most areas of Poland, but as a rule these are single specimens. The only professional descriptions of Lower Jurassic macroflora are papers by Raciborski, Makarewiczówna, and a team of researchers consisting of Reymanówna, Barbacka, Ziaja, and Wcisło-Luraniec. Raciborski's fossil collection is still available for research and revision. Such work is in progress. The collection described by Makarewiczówna contained many interesting specimens but unfortunately the majority of them are now missing. Stratigraphic research by geologists has provided some new specimens from drill cores and outcrops in the Holy Cross Mountains but these have not been subjected to detailed palaeobotanical analysis. The palynology of the Lower Jurassic was focused on biostratigraphy from the outset of that research. As an outcome it provided spore-pollen and megaspore zonations for Lower Jurassic strata in Poland. The Polish Lower Jurassic flora is comprised of ferns (very numerous), lycopsids, sphenopsids, cycadaleans, bennettitaleans, gnetaleans, ginkgoaleans, and conifers. This flora is taxonomically poorer than the equally old and geographically close floras of Denmark, Sweden, and Germany. Macrofloristic data have been used by geologists as an important source of information for assessing the age of Lower Jurassic formations, particularly in the Holy Cross Mountains. Hence the need for the old collections to be taxonomically revised and for new material from outcrops and drill cores to be examined and described.


Argasinski K.,Jagiellonian University
Journal of Theoretical Biology | Year: 2012

Classical formalizations of the Fisherian theory of sex ratio evolution are based on the assumption that the number of grand offspring of a female serves as a measure of fitness. However, the classical population genetics approach also considers the contribution of male individuals to gene proliferation. The difference between the predictions of phenotypic and genetic models is that the phenotypic approach describes the primary sex ratio of 0.5 as the ESS value, while genetic models describe the stable state of a population by a combination of the stable states of the male and female subpopulations. In this paper, we formulate an alternative model of sex ratio evolution that is focused on the dynamics and quantitative properties of this process and that combine a rigorous genetic approach with a game theoretic strategic analysis. In the new model, females are the strategic agents and males are the passive carriers on unexpressed genes. Fitness functions in the new model are derived with respect to a "fitness exchange" effect, i.e. the contribution of male individuals to female fitness and vice versa. This new model shows that the dynamics of this system are complex and consist of two phases. The first, rapid, phase converges the system to a stable manifold (termed the male subpopulation equilibrium-MSE) where the male subpopulation state is in equilibrium, conditional on the current state of the female subpopulation. Double phase dynamics occur when the population state is not compatible with the current strategic composition of the population (determined by the value of the primary sex ratio) which can be caused by ecological factors. The trajectory of convergence to the MSE can be very complicated and may contain a dramatic change in the primary sex ratio. Thus, the primary sex ratio of 0.5 is unstable for perturbations of gene frequencies among male carriers. Therefore, the new model supports predictions of genetic models that the evolutionary stability of the sex ratio should be characterized by a combination of a stable value of the primary sex ratio and the male subpopulation equilibrium. © 2012 Elsevier Ltd.


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2011

The atomic orbitals (AO) contributed by bonded atoms of molecular systems emit or receive the "signals" of electronic allocations to these basis functions, thus acting as the signal source (input) or receiver (output), respectively, in the associated communication network. Each orbital simultaneously participates in both the through-space and through-bridge probability propagations: the former involve direct communications between two AO while the latter are realized indirectly via orbital intermediates. This work examines the interference effects of the amplitudes of molecular probability scatterings, and introduces the operator representation of AO communications. The eigenvalue problem of the associated Hermitian operator combining the forward and reverse information propagations defines the stationary modes ("standing" waves) of the molecular propagation of electronic conditional probabilities. The combined effect of interference between the multiple (direct and indirect) information scatterings, which establishes the stationary distribution of electronic probabilities, is probed. The wave-superposition principle for the conditional-probability amplitudes of the generalized through-bridge information propagation is linked to the idempotency relations of the system density matrix. It explicitly demonstrates that the resultant effect of the probability propagations involving bridges containing all basis functions, at arbitrary bridge orders indeed generates the (stationary) molecular distribution of conditional probabilities. © 2010 The Author(s).


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2011

The direct (through-space) and indirect (through-bridge) components of chemical interactions between atomic orbitals are identified in both the Wiberg bond-order formalism and the Orbital Communication Theory of the chemical bond. The illustrative examples using the Hückel description of the conjugated π-bonds in benzene and butadiene are given and the existence of the through-bridge bond between bridgehead carbons in small propellanes is conjectured. © 2010 The Author(s).


The problem of defining and determining the multi-conditional probabilities of many-orbital events in the chemical bond system of a molecule is addressed anew within theoretical framework of the one-determinantal orbital representation of molecular electronic structure. Its solution is vital for determining the information-theoretic indices of bond couplings between molecular fragments or the reactant/product subsystems in chemical reactions. The superposition principle of quantum mechanics, appropriately projected into the occupied subspace of molecular orbitals, is used to condition the atomic orbitals or general basis functions of the self-consistent-field calculations. The conditional probabilities between the subspaces of basis functions (atomic orbitals) are derived from an appropriate generalization of the bond-projected superposition principle. They are then used to define the triply-conditional probabilities, relating one conditional event to another. The resulting expression is shown to satisfy the relevant non-negativity and symmetry requirements. It is applied to probe the π-bond coupling in butadiene and benzene. © 2010 The Author(s).


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2011

The indirect components of chemical interactions between atomic orbitals are explored within the Orbital Communication Theory of the chemical bond. The conditional probabilities for such through-bridge probability propagation and the associated entropy/information measures of the bond covalency are examined. The illustrative example of the bridge components of the chemical bonds between bridgehead carbons in small propellanes is discussed using the hybrid-orbital model. The bridge π-bonds in benzene and butadiene from the inter-orbital communications involving the single intermediate atomic orbitals are probed within the Hückel description and selected higher-orders of orbital bridges, involving several orbital intermediaries, are investigated. © 2010 The Author(s).


Grzes I.M.,Jagiellonian University
European Journal of Soil Biology | Year: 2010

This study was designed to test whether the ant species Myrmica rubra had developed a tolerance to metal pollution. Larvae and workers, collected from seven sites located along a metal pollution gradient in the vicinity of Olkusz, Poland were exposed to a range of Zn concentrations in food, artificially contaminated in a laboratory experiment. The mortality of adults and larvae, as well as maximum larvae body mass, was recorded. The results of this study indicate that larvae mortality was independent of the site pollution, but decreased significantly with the Zn concentration in food. Opposite results were found for workers: irrespectively of Zn concentration in the food, the mortality decreased with site pollution, indicating enhanced metal tolerance in workers. Contrary to the expectations, the maximum larvae mass estimated with the von Bertalanffy curve, increased by the pollution gradient. Larvae were more sensitive to Zn than the adults, but their higher mass at the most polluted sites, may have enhanced tolerance to metal pollution. © 2009 Elsevier Masson SAS. All rights reserved.


Lukasik P.,Jagiellonian University
Behavioral Ecology | Year: 2010

Presence of alternative male morphologies within a species has traditionally been related to different reproductive behaviors of morphs, and sexually selected weapons, that is, structures often present in a major male morph of a species, have been associated exclusively with competition between males over females. In this study, I show that alternative male phenotypes of the acarid mite Sancassania berlesei, one of the model male dimorphic species, differ in their foraging behaviors and diets. When food is deficient, aggressive "fighter" males use their weapons-thickened and sharply clawed third pair of legs, to kill conspecific juveniles and females, as well as individuals from at least one other species, which are subsequently consumed. Unarmed and benign "scrambler" males have no means of feeding in this way. The ecological importance and evolutionary consequences of this trophic dimorphism are unknown, but it might play an important role in fitness trade-offs between alternative male morphologies and, therefore, in evolution of conditional strategies. It might also increase the species' potential for rapid diversification and speciation.


Jezierski A.,Polish Academy of Sciences | Szytula A.,Jagiellonian University
Journal of Solid State Chemistry | Year: 2016

The electronic structures and thermodynamic properties of LaPtIn and CePtIn are studied by means of ab-initio full-relativistic full-potential local orbital basis (FPLO) method within densities functional (DFT) methodologies. We have also examined the influence of hydrogen on the electronic structure and stability of CePtInH and LaPtInH systems. The positions of the hydrogen atoms have been found from the minimum of the total energy. Our calculations have shown that band structure and topology of the Fermi surfaces changed significantly during the hydrogenation. The thermodynamic properties (bulk modulus, Debye temperatures, constant pressure heat capacity) calculated in quasi-harmonic Debye-Grüneisen model are in a good agreement with the experimental data. We have applied different methods of the calculation of the equation of states (EOS) (Murnaghan, Birch-Murnaghan, Poirier-Tarantola, Vinet). The thermodynamic properties are presented for the pressure 0


Tarnopolski M.,Jagiellonian University
Romanian Reports in Physics | Year: 2014

The box counting dimension dC and the correlation dimension dG change with the number of numerically generated points forming the attractor. At a sufficiently large number of points the fractal dimension tends to a finite value. The obtained values are dC ≈ 1.43 and dG ≈ 1.38. © 2014 Romanian Reports in Physics. All rights reserved.


Janik R.A.,Jagiellonian University
Nuclear Physics A | Year: 2014

I give a brief introduction to the AdS/CFT correspondence targeted at heavy-ion physicists. I also review some insights into our understanding of the early stages of heavy-ion collisions coming from selected studies made using methods of the AdS/CFT correspondence. © 2014 Elsevier B.V.


Wronka I.,Jagiellonian University
Anthropologischer Anzeiger | Year: 2010

Objective: The study examines whether the differences in both average BMI values and the prevalence of the underweight, overweight and obesity between girls with early, average and late age at menarche depend on the socio-economic status. Subjects and methods: The data were obtained from 2694 female students aged 15-18 years. Height and weight were measured and used to calculate BMI. The girls were divided into three groups in terms of their socio-economic status. Each girl was also classified as early, on time or late maturing based on the age at menarche. Results: The inverse correlation between BMI values and age at menarche was observed. In groups of the same socio-economic status the highest BMI value was always observed in girls with early age at menarche and the lowest in those with late age at menarche. The maturation rate had also statistically significant effect on the prevalence of underweight, overweight and obesity. The early maturing girls presented a lower prevalence of underweight and higher prevalence of overweight and obesity than average and late maturing girls. This relationship was evident for both the entire sample material and in socio-economic groups. Conclusion: The relationship between BMI and age at menarche occurs regardless of socio-economic status. © 2010 E. Schweizerbart'sche Verlagsbuchhandlung, Stuttgart, Germany.


Adam C.,University of Santiago de Compostela | Naya C.,University of Santiago de Compostela | Sanchez-Guillen J.,University of Santiago de Compostela | Wereszczynski A.,Jagiellonian University
Physical Review C - Nuclear Physics | Year: 2013

Recently, within the space of generalized Skyrme models, a submodel with a Bogomol'nyi-Prasad-Sommerfield (BPS) bound was identified that reproduces some bulk properties of nuclear matter already on a classical level and, as such, constitutes a promising field theory candidate for the detailed and reliable description of nuclei and hadrons. Here we extend and further develop these investigations by applying the model to the calculation of nuclear binding energies. Concretely, we calculate these binding energies by including the classical soliton energies, the excitation energies from the collective coordinate quantization of spin and isospin, the electrostatic Coulomb energies, and a small explicit isospin symmetry breaking, which accounts for the mass difference between proton and neutron. The integrability properties of the BPS Skyrme model allow, in fact, for an analytical calculation of all contributions, which may then be compared with the semi-empirical mass formula. We find that for heavier nuclei, where the model is expected to be more accurate on theoretical grounds, the resulting binding energies are already in excellent agreement with their physical values. This result provides further strong evidence for the viability of the BPS Skyrme model as a distinguished starting point and lowest-order approximation for the detailed quantitative investigation of nuclear and hadron physics. © 2013 American Physical Society.


Turcza P.,AGH University of Science and Technology | Duplaga M.,Jagiellonian University
IEEE Journal of Biomedical and Health Informatics | Year: 2013

This paper presents the design of a hardware-efficient, low-power image processing system for next-generation wireless endoscopy. The presented system is composed of a custom CMOS image sensor, a dedicated image compressor, a forward error correction (FEC) encoder protecting radio transmitted data against random and burst errors, a radio data transmitter, and a controller supervising all operations of the system. The most significant part of the system is the image compressor. It is based on an integer version of a discrete cosine transform and a novel, low complexity yet efficient, entropy encoder making use of an adaptive Golomb-Rice algorithm instead of Huffman tables. The novel hardware-efficient architecture designed for the presented system enables on-the-fly compression of the acquired image. Instant compression, together with elimination of the necessity of retransmitting erroneously received data by their prior FEC encoding, significantly reduces the size of the required memory in comparison to previous systems. The presented system was prototyped in a single, low-power, 65-nm field programmable gate arrays (FPGA) chip. Its power consumption is low and comparable to other application-specific-integrated- circuits-based systems, despite FPGA-based implementation. © 2013 IEEE.


Urban S.,Jagiellonian University | Roland C.M.,U.S. Navy
Journal of Non-Crystalline Solids | Year: 2011

Liquid crystals (LC) are the state of matter intermediate between isotropic liquids and the crystalline state. LC-forming molecules have strongly anisotropic shapes (rod-like in most cases). This leads to an interaction potential that consists of distance-dependent and orientation-dependent parts. Rotational dynamics of LC molecules falls into two frequency regions. Rotations about the short axes are strongly hindered by the potential barrier and thus coupled to fluctuations of the molecular centers of mass. This in turn causes these longitudinal or "flip-flop" motions, characterized by a relatively large relaxation time τ||, to exhibit considerable temperature, pressure and volume dependences. Experimental relaxation times determined to date for various LC phases (nematic, smectic A, C, and E) for different thermodynamic conditions (isobaric, isothermal and isochoric) are discussed herein, adopting the formulae applied for characterization of the structural relaxation times of glass-formers (GF). This analysis appears fruitful; in particular, the strength parameter characterizing the steepness of the interaction potential can be determined from the relaxation times, and τ|| is independent of temperature and pressure along the nematic-isotropic transition line, similar to the behavior of the structural relaxation time along certain transitions in GFs. © 2010 Elsevier B.V.All rights reserved.


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2014

Information theory (IT) is applied to explore electronic phase-equilibria in molecules. The modulus and phase parts of electronic states, giving rise to the particle probability and current densities, respectively, delineate two basic degrees-offreedom in the generalized (quantum) IT treatment of molecular states. The classical and non-classical contributions to the resultant information content are accounted for in the complementary Shannon and Fisher measures. These quantum descriptors are then applied in the "vertical" information principles, which determine the density-constrained molecular equilibria. A close parallelism between the vertical maximum-entropy and minimum-energy principles of quantum mechanics and their thermodynamic analogs is emphasized. The relation between the probability and phase distributions in the "horizontal" (probability-unconstrained) equilibria is examined and solutions of the (energy-unconstrained) orbital variational rules for the extremum entropy/information are shown to involve the spatial phase related to electron density. Selected properties of such molecular equilibrium states are explored. © Springer Science+Business Media New York 2013.


Zuk A.,Jagiellonian University
International journal of nanomedicine | Year: 2011

The main function of red blood cells is to transport oxygen to all parts of the body with the help of hemoglobin. Other proteins of the cell membrane can attach xenobiotics (eg, drugs) from the blood and transport them throughout the body. Only drugs able to bind to the membrane of the red blood cell can modify its structure and elastic properties. The morphology and local elastic properties of living red blood cells incubated with drug solutions commonly used in the treatment of severe asthma were studied by atomic force microscopy and nanoindentation with an atomic force microscopy tip. The elasticity modules of native red blood cells, as well as those incubated with two types of drugs, ie, aminophylline and methylprednisolone, were determined from experimentally measured nanoindentation curves. The elasticity modules of erythrocytes incubated with aminophylline were substantially higher than those obtained for nonincubated native, ie, healthy, red blood cells. The increase of the elasticity module obtained for aminophylline can reduce the cell's ability to bind oxygen and transport it through capillaries.


Zalewska-Galosz J.,Jagiellonian University
Nordic Journal of Botany | Year: 2011

Because the name Potamogeton ×babingtonii has been synonymised with P. ×angustifolius, no valid binominal exists for the hybrid P. lucens×praelongus. A morphological and anatomical study presented here demonstrates that specimens regarded by Hagström as Potamogeton ×babingtonii f. danicus really represent the hybrid between P. lucens and P. praelongus. As a consequence, a new binominal for this hybrid is introduced and its basionym Potamogeton ×babingtonii f. danicus is lectotypified. Morphological and anatomical characters of Potamogeton ×jutlandicus nom. nov. (=P. lucens×praelongus) are provided and its taxonomic delimitation is discussed. © 2011 The Authors.


Hadasz L.,Jagiellonian University | Jaskolski Z.,Wroclaw University
Journal of High Energy Physics | Year: 2014

The AGT motivated relation between the tensor product of the N = 1 super-Liouville field theory with the imaginary free fermion (SL) and a certain projected tensor product of the real and the imaginary Liouville field theories (LL) is analyzed. Using conformal field theory techniques we give a complete proof of the equivalence in the NS sector. It is shown that the SL-LL correspondence is based on the equivalence of chiral objects including suitably chosen chiral structure constants of all the three Liouville theories involved. © The Authors.


Undas A.,Jagiellonian University | Ariens R.A.S.,University of Leeds
Arteriosclerosis, Thrombosis, and Vascular Biology | Year: 2011

The formation of fibrin clots that are relatively resistant to lysis represents the final step in blood coagulation. We discuss the genetic and environmental regulators of fibrin structure in relation to thrombotic disease. In addition, we discuss the implications of fibrin structure for treatment of thrombosis. Fibrin clots composed of compact, highly branched networks with thin fibers are resistant to lysis. Altered fibrin structure has consistently been reported in patients with several diseases complicated by thromboembolic events, including patients with acute or prior myocardial infarction, ischemic stroke, and venous thromboembolism. Relatives of patients with myocardial infarction or venous thromboembolism display similar fibrin abnormalities. Low-dose aspirin, statins, lowering of homocysteine, better diabetes control, smoking cessation, and suppression of inflammatory response increase clot permeability and susceptibility to lysis. Growing evidence indicates that abnormal fibrin properties represent a novel risk factor for arterial and venous thrombotic events, particularly of unknown etiology in young and middle-aged patients. © 2011 American Heart Association, Inc.


Stipa ×brozhiana M. Nobis nothosp. nov. (Poaceae) is described and illustrated. The taxon belongs to sect. Smirnovia Tzvel. and originated from the hybridization of species belonging to sect. Smirnovia and Barbatae Junge. Stipa ×brozhiana is morphologically close to Stipa lipskyi Roshev., but is easily distinguished by its much shorter hairs on the seta, thinner, uni- or indistinctly bigeniculate awns, differently shaped callus and longer ligules of vegetative shoots. Characters distinguishing S. ×brozhiana from the parental species and other similar hybrid taxa belonging to sect. Smirnovia and occurring in the Pamir Alai Mts are discussed. In addition, the taxonomical status of S. ×tzvelevii Ikonn. pro sp., another taxon that has originated from hybridization between species belonging to sect. Smirnovia and Barbatae, is discussed. The taxon was originally described as a distinct species, but is now considered to be the hybrid S. caucasica×S. orientalis. The main characters distinguishing S. ×tzvelevii from parental species are given. © 2011 The Authors.


Praszalowicz M.,Jagiellonian University
Physical Review Letters | Year: 2011

We show that geometrical scaling exhibited by the pT spectra measured by the CMS Collaboration at the LHC is substantially improved if the exponent λ of the saturation scale depends on pT. This dependence is shown to be the same as the dependence of small x exponent of F2 structure function in deep inelastic scattering taken at the scale pTQ/2. © 2011 American Physical Society.


Dorey P.,Durham University | Dorey P.,University Pierre and Marie Curie | Mersh K.,Durham University | Romanczukiewicz T.,Jagiellonian University | Shnir Y.,Durham University
Physical Review Letters | Year: 2011

We study kink-antikink collisions in the one-dimensional nonintegrable scalar 6 model. Although the single-kink solutions for this model do not possess an internal vibrational mode, our simulations reveal a resonant scattering structure, thereby providing a counterexample to the standard belief that the existence of such a mode is a necessary condition for multibounce resonances in general kink-antikink collisions. We investigate the two-bounce windows in detail, and present evidence that this structure is caused by the existence of bound states in the spectrum of small oscillations about a combined kink-antikink configuration. © 2011 American Physical Society.


Nowobilski R.,Jagiellonian University
Polskie Archiwum Medycyny Wewnetrznej | Year: 2010

Multiplicity and variety of chest physical therapy (CPT) methods for increasing bronchial clearance in patients with chronic obstructive pulmonary disease (COPD) require an assessment of validity and reliability of the available clinical evidence. The aim of the review was to evaluate publications on CPT in COPD patients and to establish the basis (objective criteria) on which given methods and techniques are recommended or refuted. Systematic reviews, narrative reviews, and clinical practice guidelines, published in English between January 1, 2000 and July 1, 2010, were identified from the PubMed/MEDLINE and Cochrane (DARE, CRD, The Cochrane Airways Review Group Register) databases. The PEDro and SIGN scales were used to assess the quality and grade of recommendations for selected papers. Generally, the papers that we identified were based on small studies, limited to short-term outcomes, mostly using crossover designs, and rarely including sham therapy. Recommendations from clinical guidelines were mainly grade C or D. Health-related quality-of-life analyses, including working and exercise capacity, are lacking. The evidence from the studies in patients with cystic fibrosis cannot be directly extrapolated to COPD subjects. Despite the lack of convincing evidence, clinical practice supports the value of CPT in COPD. However, when making a clinical decision, potential side effects should be considered.


Ambjorn J.,Copenhagen University | Jordan S.,University Utrecht | Jurkiewicz J.,Jagiellonian University | Loll R.,University Utrecht
Physical Review Letters | Year: 2011

Causal dynamical triangulations are a concrete attempt to define a nonperturbative path integral for quantum gravity. We present strong evidence that the lattice theory has a second-order phase transition line, which can potentially be used to define a continuum limit in the conventional sense of nongravitational lattice theories. © 2011 American Physical Society.


Kasza A.,Jagiellonian University
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms | Year: 2013

Elk-1 was regarded as a transcription factor engaged mainly in the regulation of cell growth, differentiation, and survival. Recent findings show the engagement of Elk-1 in the control of expression of genes encoding proteins involved in transcript turnover, such as MCPIP1/ZC3H12A and tristetraprolin (TTP/ZFP36). Thus, Elk-1 plays an important role in the control of gene expression not only through the stimulation of expression of transcription factors, but also through regulation of transcript half-live. Moreover, Elk-1 is engaged in the regulation of expression of genes encoding proteins that control proteolytic activity, such as inhibitor of plasminogen activator-1 (PAI-1) and metalloproteinases-2 and -9 (MMP-2 and MMP-9). This review summarizes the biological roles of proteins with expression regulated by Elk-1, involved in transcripts turnover or in cell migration. The broad range of function of these proteins illustrates the complex role of Elk-1 in the regulation of cancer and inflammation. © 2013 Elsevier B.V.


Praszalowicz M.,Jagiellonian University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

We analyze geometrical scaling (GS) of negative pion multiplicity p T distributions at NA61/SHINE energies. We show that even though NA61/SHINE energies are low, one may expect to find GS in the particle spectra. We argue that qualitative behavior of ratios of multiplicities at different energies is in agreement with a simple picture of GS which is violated for pT smaller than some nonperturbative scale Λ and when larger Bjorken x of one of the scattering patrons crosses xmax above which a gluonic cloud becomes dilute and quark degrees of freedom become important. © 2013 American Physical Society.


Rams M.M.,Los Alamos National Laboratory | Rams M.M.,Jagiellonian University | Damski B.,Los Alamos National Laboratory
Physical Review Letters | Year: 2011

We study quantum fidelity, the overlap between two ground states of a many-body system, focusing on the thermodynamic regime. We show how a drop in fidelity near a critical point encodes universal information about a quantum phase transition. Our general scaling results are illustrated in the quantum Ising chain for which a remarkably simple expression for fidelity is found. © 2011 American Physical Society.


Zyczkowski K.,Jagiellonian University
Scientometrics | Year: 2010

A scheme of evaluating an impact of a given scientific paper based on importance of papers quoting it is investigated. Introducing a weight of a given citation, dependent on the previous scientific achievements of the author of the citing paper, we define the weighting factor of a given scientist. Technically the weighting factors are defined by the components of the normalized leading eigenvector of the matrix describing the citation graph. The weighting factor of a given scientist, reflecting the scientific output of other researchers quoting his work, allows us to define weighted number of citation of a given paper, weighted impact factor of a journal and weighted Hirsch index of an individual scientist or of an entire scientific institution. © 2010 Akadémiai Kiadó, Budapest, Hungary.


Nikiforuk A.,Polish Academy of Sciences | Popik P.,Polish Academy of Sciences | Popik P.,Jagiellonian University
Psychoneuroendocrinology | Year: 2011

Deficits in executive control associated with frontal lobe dysfunction have been reported in affective disorder, which is often precipitated by stressful life events. Here we examined the impact of repeated restraint stress (1. h daily for 7 days) on rats' performance in the attentional set-shifting task (ASST). To evaluate the persistence of cognitive deficits, the performance of separate groups of rats was assessed on the 4th, 7th, 14th and 21st day following stress cessation. Stressed rats exhibited unusually long-lasting extra-dimensional (ED) set-shifting impairments, since these deficits were demonstrated even 3 weeks following stress termination. An inhibitor of corticosterone synthesis, the drug metyrapone (50. mg/kg, IP) protected rats from the cognitive impairment suggesting an involvement of endogenous adrenal steroids in the debilitating effects of stress. Acute intraperitoneal administration of four different antidepressants (desipramine, nomifensine, fluoxetine and escitalopram) at the minimum effective doses of 3, 0.3, 1 and 1. mg/kg, respectively, reversed the deficits of ED set-shifting in stressed animals. Desipramine, nomifensine, fluoxetine and escitalopram at the minimum effective doses of 6, 1, 1 and 1. mg/kg, IP, respectively, promoted also cognitive flexibility in unstressed groups. We conclude that stress-induced long-term set-shifting impairment may represent a useful model mimicking clinically relevant aspects of depression, i.e., the persistence of executive dysfunction. The potential utility of antidepressants in treating frontal-like cognitive impairments is suggested. © 2010 Elsevier Ltd.


Wronka I.,Jagiellonian University
Pediatric Endocrinology, Diabetes and Metabolism | Year: 2011

Introduction: The pattern of development of obesity during childhood and adolescence is unclear, hindering preventive strategies. Aim of the study: The aim of this study was to investigate the differences in growth and tempo of maturation between overweight or obese and normal weight girls. Materials and methods: The data were obtained from 1008 schoolgirls aged 16-18 years for whom earlier data on weight and height were available. The height and body mass were measured and the BMI was calculated. Height and weight in early life were assessed by medical records review. Underweight, overweight and obesity were assessed using the international BMI cut points, defined by Cole et al. Results: Girls in higher BMI categories at 7 years had significantly higher values of BMI at 9, 14 and 16-18 years of age, however only 10% of them were also overweight or obese at youth. Overweight and obese girls tend to lose body weight after the puberty period, whereas normal weight children tend to gain body weight. Overweight and obese children were significantly taller than their peers at 7, 9 and 14 years. Those differences vanished after the puberty period. The rate of height gain between ages 7 and 16-18 years was lower in girls with higher BMI values at childhood. Girls, those who were overweight or obese at young age experience menarche at a younger age than normal weight girls. Conclusion: The obtained data show that overweight and obesity in childhood is associated with rapid tempo of growth and maturity.


Silarski M.,Jagiellonian University
Acta Physica Polonica B | Year: 2014

In this article, studies of the near threshold pp → ppK +K-A reaction conducted with the COSY-11 and the ANKE detectors are reviewed. In particular. recent investigations on the +K- final state interaction are revisited taking into account updated cross sections of the COSY-11 experiment. These studies resulted in the new value of K+K- effective range amounting to: Re(bK+K-) = -0:2+0:8stat+0:4sys -0:6stat-0:4sys fm and Im(bK+K-) = 1:2+0:5stat+0:3sys -0:3stat-0:3sys fm. The determined real and imaginary parts of the K+K- scattering length were estimated to be: |Re(a K+K-)| = 10+17stat -10stat fm and Im(a K+K-)=0+37stat -10stat fm.


Silarski M.,Jagiellonian University
Journal of Physics: Conference Series | Year: 2014

The KLOE experiment at the DAΦNE φ-factory located at the INFN Laboratory in Frascati, Italy collected data corresponding to 2.5 fb-1 of integrated luminosity. Neutral kaon pairs produced in φ-meson decays offer a unique possibility to perform tests of fundamental discrete symmetries. The entanglement of the two kaons is exploited to search for possible violation of CPT symmetry and Lorentz invariance in the context of the Standard-Model Extension (SME) framework. A new approach to the analysis of φ → KSKL → π+π-,π+π- events has been adopted allowing us to independently measure all four CPT violating parameters Δaμ appearing for neutral kaons in the SME. The final KLOE results on Δaμ will be presented. These are presently the most precise measurements in the quark sector of the SME. © Published under licence by IOP Publishing Ltd.


Basista K.,Jagiellonian University
International Journal of Occupational Medicine and Environmental Health | Year: 2012

The paper describes an atypical case of simultaneous airborne and direct contact dermatitis in a beekeeper from the Małopolska region. This is the third such case described in a beekeeper in the world and the first in Poland. I suggest that propolis should be regarded as both a direct and airborne contact allergen in beekeepers. © 2012 Versita Warsaw and Springer-Verlag Wien.


Kwolek P.,AGH University of Science and Technology | Szacilowski K.,AGH University of Science and Technology | Szacilowski K.,Jagiellonian University
Electrochimica Acta | Year: 2013

Highly crystalline powder of bismuth oxyiodide in the form of micro-platelets was synthesized by a microwave assisted hydrothermal process. Application of this novel and environmentally friendly technique in the synthesis of BiOI has never been reported before. Electronic structure of the obtained semiconducting compound was characterized by the spectroscopic methods, i.e. The reflectance and fluorescence spectroscopy as well as the electrochemical impedance spectroscopy. Mott-Schottky analysis of this material was performed for the first time and indicated the n-type conductivity of the sample. Photoelectrochemical properties were determined using the pulsed photocurrent spectroscopy technique which is also a novel approach in the case of BiOI. Bismuth oxyiodide exhibits the Photoelectrochemical Photocurrent Switching Effect. The anodic-to-cathodic photocurrent transition occurs at ca. 0.5 V vs. NHE. The switching effect arises due to the presence of oxygen dissolved in the electrolyte and makes this material promising from the point of view of optoelectronic applications. © 2012 Elsevier Ltd. All rights reserved.


Matuszko D.,Jagiellonian University
International Journal of Climatology | Year: 2012

This paper analyzes the influence of cloudiness and cloud genera on sunshine duration based on a very long (1884-2007) homogeneous daily nephological and sunshine duration data series for the City of Krakow. Quadratic regression was used to describe the relationship between sunshine duration and cloudiness. It has been shown that cloudiness affects sunshine duration the most in June and July, and the least in December, January and February. High clouds (Cirrus, Cirrostratus, Cirrocumulus) do not interrupt the recording of sunshine duration even when they completely cover the sky. Layered clouds such as Stratus and Nimbostratus, on the other hand, do not transmit solar radiation at all. The degree of influence of different cloud genera on sunshine duration changes very little from season to season and with respect to the position of the Sun over the horizon. When the Sun is positioned higher over the horizon, clouds are less able to weaken solar radiation, resulting in larger sunshine duration values. This is especially true with respect to the following clouds: Cirrus, Cirrostratus and Cumulus. It has been shown that daytime sunshine duration patterns can be a very good indicator of cloud type and cloudiness variability. © 2011 Royal Meteorological Society.


The Ociese{ogonek}ki Sand stone Formation represents the Holmia-Schmidtiellus and the Protolenus-Issafeniella zones. Seven ichnospecies of Rusophycus, including Rusophycus exsilius isp. nov, are recognized in this for ma tion. Moreover, Rusophycus ispp. A, B, C are recognized. The diagnoses for R. dispar, R. crebrus and R. magnus have been emended and the stratigraphic range of R. versans has been extended. The presence of Rusophycus dispar may suggest a palaeozoogeographical connection between the Małopolska Block, the Baltica palaeocontinent and the Laurentia palaeocontinent.


Silarski M.,Jagiellonian University
International Journal of Modern Physics A | Year: 2011

In this article we present studies of the near threshold pp → ppK +K- reaction in view of the K+K- final state interaction. The investigations include analysis of both the low-energy K+K- invariant mass distributions measured by COSY-11 collaboration at excess energies of Q = 10 MeV and Q = 28 MeV and the near threshold excitation function for the pp → ppK+K - reaction. As a result of these studies we have estimated the K +K- scattering length more precise compared to the previous analysis based only on the analysis of the differential cross sections. © 2011 World Scientific Publishing Company.


Wetzel A.,University of Basel | Uchman A.,Jagiellonian University
Developments in Sedimentology | Year: 2012

The bathyal and abyssal environments represent an extent benthic habitat. The deep-sea floor is a dynamic setting affected by fluctuations of organic-matter deposition, sedimentation rate (regulating burial of organic matter), bottom-water oxygenation, etc. In continuously accumulating deposits, the bioturbated zone exhibits tiered burrows; its vertical range increases with benthic-food content, as long as the bottom water is well oxygenated and the substrate is soft. The benthic-food content influences the burrowing activity of the benthic organisms that irrigate the sea-floor sediments. While the various ecologic factors are complexly interrelated, typical end-members are considered with respect to their trace-fossil content: (1) "red" oxidized, slowly accumulating deposits are completely bioturbated by in-average small-sized, shallow-penetrating organisms; (2) grayish-green sediments preserving organic matter are completely bioturbated by in-average large, deep-burrowing organisms; and (3) grayish-black organic-rich sediments are partly bioturbated by a fauna decreasing in size and diversity with decreasing oxygen availability. Examples from modern sediments and their fossil counterparts are given and the occurring trace fossils are briefly described. © 2012 Elsevier B.V.


Tomasik T.,Jagiellonian University
Medycyna wieku rozwojowego | Year: 2012

A report on dichorionic/diamniotic pregnancy in which only one, female, fetus was infected with cytomegalovirus and presented with severe congenital diseases at birth. Infection of the fetus occurred after recurrent maternal infection. The second, male, fetus did not have CMV infection. The cesarean section was performed at the 38th week of gestation. The birth weight of the infected girl was 1680g, the main symptoms, beside dystrophy, concerned the central nervous system: microcephaly, brain atrophy, hydrocephalus, corpus callosum agenesis. She also had Turner syndrome symptoms. The viral load was highest in the urine 81.2 x10^6/ml, in the cerebro-spinal fluid 15.4x10^6/ml and lower in blood 0.38 x10^5/ml. The concentration of specific IgG was 308 U/ml. Specific IgM was not detected. Throughout hospitalization, the infection maintained only one viral genotype gB2. Despite treatment with ganciclovir (10 weeks) and foscarnet (2 weeks), the girl died at the age of 8 months. Novel molecular diagnostic techniques (nested and real time PCR) confirmed the congenital infection and were helpful in the monitoring of the infection and treatment efficacy.


The preamble to the European Landscape Convention states, that the landscape is an important part of economic life, affecting culture, the environment and social issues. It is a basic component of the European natural and cultural heritage, building both national and local identities of society. The Convention also regards landscape as a key element of social well-being, meaning its protection and improvements to its quality and variety, yield economic value and depend on each of us. This conception of space provides a basis for building the sustainability in landscape, a challenging and multi-dimensional problem, whose foundations can be found in ecophilosophy. Therefore, this publication seeks to combine the world of philosophy and realistic spatial management in order to answer some fundamental questions about the nature of this relatively new idea. The author discusses the chances of this perspective gaining popularity and presents her understanding of the concepts of landscape and landscape sustainability.


The mineral energy sources, possessed by a certain state or remaining an object of interest for it, may form a basis for political activities, both oriented on usage either of the purely political (non-militarized) or militarized methods. The usage of these sources in the political context may have a natural impact on the essence of sustainable development, especially then if to juxtapose it with previous experiences of the mankind. The natural gas based energy policy seems to be the key factor for the above political activities of states with imperial ambitions, as the contemporary Russia. Referring to the shale gas, the syndrome as such concerns the monopolistic position of the USA in terms of the applied exploitation technologies. The size of coal mining and steel production at the turn of the 19th and 20th century, or oil fields' possession and their usage before and during WW II used to play such a role in the past. In both of these cases there were necessary prerequisites for planning the military campaigns in potential wars (envisaged as successful indeed). Fortunately such an extreme way of conducting political activities is not confirmed today. Following the same trace the policy of the possessed energy sources' usage, or taking over those being in possession of others, might ultimately lead towards maintaining an economic and perhaps political supremacy of ones over others. On the one hand it demonstrates the policy of pressure led by stronger, imperially oriented states against weaker and dependent ones. On the other one, it shows the results of the mutual antagonizing policy of the latter stimulated by the stronger state- and non-state-like entities, having their own interests. Due to some experiences, taken from the most recent past, one can speculate, if the possessed or desired energy sources may be utilized as a tool for unequivocally political decisions, also in the military sphere. It is hard to be optimistic bearing in mind the rule that history tends to repeat itself. Such scepticism is even deeper if we realize that the control over the water reserves remains a source of the future large-scale international conflicts.


Rygula R.,Polish Academy of Sciences | Papciak J.,Polish Academy of Sciences | Popik P.,Polish Academy of Sciences | Popik P.,Jagiellonian University
Neuropsychopharmacology | Year: 2013

Depressive disorder is often associated with cognitive biases. In this study, we took a unique opportunity to investigate whether trait pessimism could predict vulnerability to stress-induced anhedonia in an animal model of depression. In a series of ambiguous-cue interpretation (ACI) tests, we identified animals displaying 'pessimistic' and 'optimistic' traits. Subsequently, the rats were subjected to chronic restraint, and the trait differences in response to stress were investigated using sucrose preference and ACI tests before, during and after the stress regime. Although stress resulted in anhedonia in both subgroups, it occurred faster and lasted longer in the 'pessimistic' compared with the 'optimistic' animals. Chronic stress exposure also increased the negative judgment bias in rats, although this effect was not dependent on the 'pessimistic' trait. For the first time, we demonstrated a link between cognitive judgment bias and vulnerability to stress-induced anhedonia in an animal model. We also introduced a cognitive biomarker, which may be of value for etiological depression studies. © 2013 American College of Neuropsychopharmacology. All rights reserved.


Mach P.,Jagiellonian University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

The aim of this paper is to clarify the distinction between homoclinic and standard (global) Bondi-type accretion solutions in the Schwarzschild-anti-de Sitter space-time. The homoclinic solutions have recently been discovered numerically for polytropic equations of state. Here I show that they exist also for certain isothermal (linear) equations of state, and an analytic solution of this type is obtained. It is argued that the existence of such solutions is generic, although for sufficiently relativistic matter models (photon gas, ultrahard equation of state) there exist global solutions that can be continued to infinity, similarly to standard Michel's solutions in the Schwarzschild space-time. In contrast to that global solutions should not exist for matter models with a nonvanishing rest-mass component, and this is demonstrated for polytropes. For homoclinic isothermal solutions I derive an upper bound on the mass of the black hole for which stationary transonic accretion is allowed. © 2015 American Physical Society.


Coumbe D.N.,Jagiellonian University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

We present numerical evidence that fictitious diffusing particles in the causal dynamical triangulation (CDT) approach to quantum gravity exceed the speed of light on small distance scales. We argue this superluminal behavior is responsible for the appearance of dimensional reduction in the spectral dimension. By axiomatically enforcing a scale invariant speed of light we show that time must dilate as a function of relative scale, just as it does as a function of relative velocity. By calculating the Hausdorff dimension of CDT diffusion paths we present a seemingly equivalent dual description in terms of a scale dependent Wick rotation of the metric. Such a modification to the nature of time may also have relevance for other approaches to quantum gravity. © 2015 American Physical Society.


Matuszko D.,Jagiellonian University
International Journal of Climatology | Year: 2012

This paper aims to describe the influence of cloud cover, its extent and cloud genus, on solar radiation intensity measured at the Earth's surface. Solar radiation intensity values at varying degrees of cloudiness, based on observations and measurements performed between 2003 and 2007 in Krakow (Poland), are analysed in this paper. Analyses show that cloud cover impacts solar radiation intensity in two ways: usually weakening it, but intensifying in certain weather conditions. The greatest solar radiation intensity can be detected not when the sky is cloudless, but when it is partly cloudy (3/8-6/8), with convective clouds present. © 2011 Royal Meteorological Society.


Avigad D.,Hebrew University of Jerusalem | Gerdes A.,Goethe University Frankfurt | Morag N.,Hebrew University of Jerusalem | Bechstadt T.,Jagiellonian University
Gondwana Research | Year: 2012

U-Pb-Hf of detrital zircons from diverse Cambrian units in Morocco and Sardinia were investigated in order to clarify the sandstone provenance and how it evolved with time, to assess whether the detrital spectra mirror basement crustal composition and whether they are a reliable pointer on the ancestry of peri-Gondwanan terranes. Coupled with Hf isotopes, the detrital age spectra allow a unique perspective on crustal growth and recycling in North Africa, much of which is concealed below Phanerozoic sediments.In Morocco, the detrital signal of Lower Cambrian arkose records local crustal evolution dominated by Ediacaran (0.54-0.63Ga) and Late-Paleoproterozoic (1.9-2.2Ga; Eburnian) igneous activity. A preponderance of the Neoproterozoic detrital zircons possess positive ε Hf(t) values and their respective Hf model ages (T DM) concentrate at 1.15Ga. In contrast, rather than by Ediacaran, the Neoproterozoic detrital signal from the Moroccan Middle Cambrian quartz-rich sandstone is dominated by Cryogenian-aged detrital zircons peaking at 0.65Ga alongside a noteworthy early Tonian (0.95Ga) peak; a few Stenian-age (1.0-1.1Ga) detrital zircons are also distinguished. The majority of the Neoproterozoic zircons displays negative ε Hf(t), indicating the provenance migrated onto distal Pan-African terranes dominated by crustal reworking. Terranes such as the Tuareg Shield were a likely provenance. The detrital signal of quartz-arenites from the Lower and Middle Cambrian of SW Sardinia resembles the Moroccan Middle Cambrian, but 1.0-1.1Ga as well as ~2.5Ga detrital zircons are more common. Therefore, Cambrian Sardinia may have been fed from different sources possibly located farther to the east along the north Gondwana margin. 1.0-1.1Ga detrital zircons abundant in Sardinia generally display negative ε Hf(t) values while 0.99-0.95Ga detrital zircons (abundant in Morocco) possess positive ε Hf(t), attesting for two petrologically-different Grenvillian sources. A paucity of detrital zircons younger than 0.6Ga is a remarkable feature of the detrital spectra of the Moroccan and Sardinian quartz-rich sandstones. It indicates that late Cadomian orogens fringing the northern margin of North Africa were low-lying by the time the Cambrian platform was deposited. About a quarter of the Neoproterozoic-aged detrital zircons in the quartz-rich sandstones of Morocco (and a double proportion in Sardinia) display positive ε Hf(t) values indicating considerable juvenile crust addition in North Africa, likely via island arc magmatism. A substantial fraction of the remaining Neoproterozoic zircons which possess negative ε Hf(t) values bears evidence for mixing of old crust with juvenile magmas, implying crustal growth in an Andean-type setting was also significant in this region. © 2011 International Association for Gondwana Research.


Morycowa E.,Jagiellonian University
Annales Societatis Geologorum Poloniae | Year: 2012

The studied corals have been collected from cores of boreholes located in the central part of the Polish Carpathian Foreland in the Da{ogonek}browa Tarnowska-Szczucin area. The Jurassic complex in this area presents a continuous stratigraphic section from the Upper Callovian to Tithonian, locally passing to the Lower Cretaceous (Berriasian). Its thickness exceeds 1,100 m in this area. This complex is composed of marine, mainly shallow- water deposits. The corals occur within the upper part of the Upper Jurassic (Tithonian) deposits, almost entirely within the Swarzów Limestone Formation (= coral-algal limestone formation). This occurrence marks the northernmost extent of Tithonian shallow-water corals in Poland and one of the northernmost in Europe. 42 coral species (among them 14 in open nomenclature) were identified in deposits of this formation. They include two new species: Complexastrea magna and Complexastrea dabroviensis. All taxa, except one, belong to the order Scleractinia. The described assemblage displays a Late Jurassic character. The broader stratigraphic span is assigned to some species, which are quoted from the Middle Jurassic and some species lasted until the Early Cretaceous, Berriasian and/or Valanginian.


Oszczypko-Clowes M.,Jagiellonian University
Geologica Carpathica | Year: 2012

Studies, based on calcareous nannofossils, proved that the level of reworked microfossils had so far been underestimated. More recently detailed quantitative studies of calcareous nannoplankton of the Magura, Malcov, Zawada and Kremna formations from the Magura Nappe in Poland documented a degree of nannofossil recycling among those formations. In the Late Eocene-Early Oligocene pelagic Leluchów Marl Member of the Malcov Formation the level of redeposition is very low (0-3.80 %), however, in the flysch deposits of the Malcov Formation reworking increased to 31.4 %. Late Oligocene through Early Miocene "molasse" type deposits of the Zawada and Kremna formations contain 43.7-69.0 % of reworked nannofossils. Quantitative analyses of the reworked assemblages confirmed the domination of Paleogene nannofossil species over Cretaceous ones. The most abundant, reworked assemblages belong to the Early- Middle Eocene age..


Stachacz M.,Jagiellonian University
Annales Societatis Geologorum Poloniae | Year: 2012

Ten ichnogenera and seven ichnospecies are described from the Czarna Shale Formation, possibly representing the Terreneuvian and Cambrian Series 2 of the Holy Cross Mountains. Moreover, five other ichnotaxa are described in open nomenclature. Phycodes circinatus, Taenidium isp., Trichichnus linearis and Dictyodora isp. are described from the Cam brian of the Holy Cross Mountains for the first time. The stratigraphic ranges of Trichichnus linearis and Phycodes circinatus are extended. The trace fossil assemblage and associated, sedimentological features point to deposition in the upper and lower off shore. Periodic, anoxic events may have occurred on the sea bed.


Uchman A.,Jagiellonian University | Wetzel A.,University of Basel
Developments in Sedimentology | Year: 2012

Turbiditic depositional systems are characterized by diverse, pre- and post-depositional trace fossils dominated by pascichnia, fodinichnia, agrichnia, and chemichnia. They belong mostly to the Nereites Ichnofacies, which includes the Nereites subichnofacies (mostly in shale-dominated facies), the Paleodictyon subichnofacies (mostly in thin- to medium-bedded turbidites), and the Ophiomorpha rudis subichnofacies (mostly in thick-bedded sandstones). Individual turbiditic beds are first colonized by opportunistic pascichnia, later by stationary fodinichnia and agrichnia, while oxygen and food content within the sediment decrease. Changes of oxygenation, food content, sedimentation rate, and other factors can influence the trace-fossil diversity and ichnofabric over longer time intervals. The Nereites Ichnofacies assemblages evolved since their appearance in the Early Ordovician. Their diversity decreased since the Late Carboniferous through the Permian/Triassic boundary crisis, increased during the Triassic and Jurassic and dropped during Early Cretaceous. Then diversity reached a maximum during the Eocene, showing a high diversification of agrichnia. © 2012 Elsevier B.V.


Walczynska A.,Jagiellonian University
Bulletin of Entomological Research | Year: 2010

The generally accepted assumption on the low mortality pressure for inside-tree habitat was challenged in this study. To achieve this objective, the number of larval instars of xylem-feeding Aredolpona rubra (L.) (Coleoptera: Cerambycidae) was determined using multidimensional statistics, and the life table was constructed based on the head-width distribution of larvae taken from the field. The mean value of natural mortality of an average larva was then compared with data available for other wood-feeding species and contrasted with insects from other feeding guilds. The results show that larvae living in wood experience lower mortality rates than those from other habitats and that, among the wood-feeders, the mortality rate of larvae decreases while development time increases further inside the tree. Copyright © 2009 Cambridge University Press.


Cipora K.,Jagiellonian University | Nuerk H.-C.,University of Tubingen | Nuerk H.-C.,Knowledge Media Research Center
Quarterly Journal of Experimental Psychology | Year: 2013

The SNARC (spatial-numerical association of response codes) described that larger numbers are responded faster with the right hand and smaller numbers with the left hand. It is held in the literature that arithmetically skilled and nonskilled adults differ in the SNARC. However, the respective data are descriptive, and the decisive tests are nonsignificant. Possible reasons for this nonsignificance could be that in previous studies (a) very small samples were used, (b) there were too few repetitions producing too little power and, consequently, reliabilities that were too small to reach conventional significance levels for the descriptive skill differences in the SNARC, and (c) general mathematical ability was assessed by the field of study of students, while individual arithmetic skills were not examined. Therefore we used a much bigger sample, a lot more repetitions, and direct assessment of arithmetic skills to explore relations between the SNARC effect and arithmetic skills. Nevertheless, a difference in SNARC effect between arithmetically skilled and nonskilled participants was not obtained. Bayesian analysis showed positive evidence of a true null effect, not just a power problem. Hence we conclude that the idea that arithmetically skilled and nonskilled participants generally differ in the SNARC effect is not warranted by our data. © 2013 The Experimental Psychology Society.


Kotlarczyk J.,AGH University of Science and Technology | Uchman A.,Jagiellonian University
Palaeogeography, Palaeoclimatology, Palaeoecology | Year: 2012

The anoxic, mostly black or brown fine-grained sediments of the Menilite Formation (Oligocene-Early Miocene) in the Skole and Subsilesian nappes contain thin layers of bioturbated green or grey-green mudstones, some of which contain the trace fossils Halimedides annulata, Multina isp., Palaeophycus ?tubularis, ?Planolites isp., Rhizocorallium isp., Trichichnus isp. and Zoophycos isp. The Trichichnus-Palaeophycus-(Multina, Halimedides). -Rhizocorallium suite indicates an increase in oxygenation of sediments. The contribution of different ecological groups of fishes, including epipelagic, bathypelagic, benthopelagic, neritic and reef, and demersal taxa changes significantly through the Menilite Formation. The absence or reduction of bathypelagic fishes points to anoxia in the water column. The combination of ichnological and ichthyological data and incorporation of data on benthic foraminifers allowed a reconstruction of oxygenation changes in the sediment and water column during deposition of the Menilite Formation. Total anoxia at the sea floor and in the water column, attributed to a combination of thermo-stratification and extremely high organic productivity, occurred only during the period reflected by ichthyofaunal Zone IPM2 (middle part of the NP23 Zone). Anoxia restricted to the basin floor or upper slope, related in part to upwelling, occurred during sedimentation of the upper part of the Menilite Formation. © 2012 Elsevier B.V.


The sediments of Lake Kwiecko, located in the eastern part of the Bytowskie Lake District (part of the West-Pomeranian Lake District, Poland), were studied by pollen analysis. Holocene vegetation history was reconstructed from the beginning of the Preboreal to the Late Middle Ages. On the basis of the curves of selected taxa and the occurrence of plant indicators of the presence of man 6 settlement phases were distinguished and correlated with archaeological data. The investigations have shown that the first week palynological indications of human presence around the lake were connected with the Atlantic chronozone, while the strongest impact of man on vegetation was recorded in the Middle Ages and modern times.


Iron carbonate concretion horizons are characteristic features of the Bathonian (Middle Jurassic) claystone-mudstone succession at Gnaszyn. They occur in single horizons, which generally represent the same genetic type. The siderite concretions are the main type of iron carbonate concretions at Gnaszyn; a second type is represented by phosphate-siderite concretions. On the basis of the fieldwork, and their petrographical and mineralogical characteristics, the genesis of the concretions and their palaeoenvironmental significance is discussed. The results of this study (based on the localization, mode of occurrence, mineralogy of iron carbonate concretions and also the textural relationship between the concretions and host sediment layers) suggest an early diagenetic origin of the concretions. The preferential occurrence of the concretion horizons in single layers in the ambient sediments was associated with particular conditions of their deposition and early diagenesis, favored by a slower sedimentation rate and more intense bioturbation, and related primarily to the greater availability of reactive iron ions. From the viewpoint of physicochemical conditions the horizons with iron carbonate concretions in the study area reflect the redox boundary between oxic/bioturbated and anoxic/non-bioturbated zones. The conditions favoring the formation of such horizons was possibly due to longer periods of diminished sedimentation rate when the redox boundary remained in the same position within the sediment.


Qualitative and quantitative studies on calcareous nannofossils have been carried out on the Middle-Upper Bathonian succession of Gnaszyn (Kraków-Silesia Homocline, Cze{ogonek}stochowa region). The nannofossil assemblages are moderately or well-preserved and are dominated by Watznaueria britannica; also common are Staurolithites lumina and Zeugrhabdotus erectus. The presence of delicate nannofossil forms together with dissolution-resistant taxa shows that the changes in composition of some of the nannoplankton assemblages reflect original variations. The frequency and diversity changes of the calcareous nannofossil assemblages have been interpreted in relation to fluctuations of sedimentation rate versus changes in trophic conditions within the photic zone. The highest diversity assemblages contain a high percentage of palaeofertility indicators, and are impoverished in the genus Watznaueria. This is interpreted as a reflection of a lower sedimentation rate and more stable, possibly mesotrophic conditions within the photic zone. On the other hand, W. britannica-dominated assemblages with low species diversity may represent more unstable environments with a high influx of terrestrial material related to a high sedimentation rate and a high nutrient influx, i.e. eutrophic conditions in the photic zone.


Barto L.,McMaster University | Barto L.,Charles University | Kozik M.,Jagiellonian University
Proceedings of the Annual ACM Symposium on Theory of Computing | Year: 2012

An algorithm for a constraint satisfaction problem is called robust if it outputs an assignment satisfying at least (1-g(ε))-fraction of the constraints given a (1-ε)-satisfiable instance, where g(ε) → 0 as ε → 0, g(0)=0. Guruswami and Zhou conjectured a characterization of constraint languages for which the corresponding constraint satisfaction problem admits an efficient robust algorithm. This paper confirms their conjecture. © 2012 ACM.


Dlotko P.,Jagiellonian University | Specogna R.,University of Udine
Computer Methods in Applied Mechanics and Engineering | Year: 2013

The problem of computing cohomology generators of a cell complex is gaining more and more interest in various branches of science ranging from computational physics to biology. Focusing on engineering applications, cohomology generators are currently used in computer aided design (CAD) and in potential definition for computational electromagnetics and fluid dynamics.The aim of this paper is to introduce a novel technique to effectively compute cohomology generators focusing on the application involving the potential definition for h-oriented eddy-current formulations. This technique, which has been called Thinned Current Technique (TCT), is completely automatic, computationally efficient and general. The TCT runs in most cases in linear time and exhibits a speed up of orders of magnitude with respect to the best alternative documented implementation. © 2012 Elsevier B.V.


Kresge C.T.,Dow Chemical Company | Roth W.J.,Jagiellonian University | Roth W.J.,J. Heyrovsky Institute of Physical Chemistry
Chemical Society Reviews | Year: 2013

By the combination of prior knowledge, observation skills, and novel synthetic approaches, we discovered a family of mesoporous molecular sieves including discrete structures-MCM-41 (hexagonal), MCM-48 (cubic), and MCM-50 (lamellar). These materials were formed unlike that of our classical microporous structures involving reagent induced-macromolecular templating mechanism. Based on synthetic data and working with others, we were able to establish a predictive mechanism of formation and identify a broad class of templating reagents. These initial findings generated great interest and effort worldwide. It resulted in tremendous expansion of knowledge and skills with many new additional discoveries that established a new area of ordered mesoporous materials. They are integrated with zeolites (microporous materials) and based on surfactant inorganic chemistry. © The Royal Society of Chemistry 2013.


Konieczynska M.,John Paul II Hospital | Fil K.,John Paul II Hospital | Bazanek M.,John Paul II Hospital | Undas A.,Jagiellonian University
Thrombosis and Haemostasis | Year: 2014

It has been shown that type 2 diabetes (DM) is associated with enhanced thrombin generation and formation of denser fibrin clots of reduced lysability. We sought to investigate the impact of diabetes duration versus glycaemia control on fibrin clot phenotype and its determinants in type 2 diabetic patients. In 156 consecutive Caucasian patients with type 2 diabetes we investigated ex vivo thrombin generation, fibrinolytic proteins, along with plasma fibrin clot permeation (Ks), compaction, turbidity, and efficiency of tissue plasminogen activator (t-PA)-mediated fibrinolysis. Patients with longer diabetes duration (>5 years, median; n=68) had higher peak thrombin generation (+16.3%, p<0.001), plasminogen activator inhibitor-1 (PAI-1) antigen (+14.8%, p=0.001), t-PA antigen (+13.9%, p=0.002) compared with those with duration ≤5 years (n=88). No such differences were observed between patients with inadequate glycaemic control, defined as glycated haemoglobin (HbA1C) >6.5% (48 mmol/mol) (n=77), versus those with HbA1C≤6.5% (n=79). Fibrinogen, thrombin-activatable fibrinolysis inhibitor antigen, plasminogen and soluble thrombomodulin were unaffected by disease duration or glycaemia control. Lower clot permeability, longer clot lysis, and higher maximum D-dimer levels released from clots (all p<0.05 after adjustment for fibrinogen, age, body mass index, insulin, acetylsalicylic acid treatment, and HbA1c or diabetes duration) were also observed in patients with diabetes duration >5 years and those with HbA1C>6.5%. We conclude that prolonged duration of type 2 diabetes is associated with increased thrombin formation, hypofibrinolysis, and prothrombotic fibrin clot phenotype. The impact of disease duration on coagulation is different and stronger than that observed during inadequate glycaemia control. © Schattauer 2014.


Michorczyk P.,Cracow University of Technology | Pietrzyk P.,Jagiellonian University | Ogonowski J.,Cracow University of Technology
Microporous and Mesoporous Materials | Year: 2012

A series of Crx/SBA-1 cubic mesoporous catalysts with 1, 3, 5, 7, 10, and 15 wt.% content of Cr (Cr total) were obtained by incipient wetness impregnation of SBA-1. The obtained catalysts were characterized with various physicochemical techniques (chemical composition, low-temperature adsorption of N 2, H 2-TPR, XRD, UV-vis DRS, Raman, and EPR) and tested in dehydrogenation of propane to propene in the presence of CO 2. Various chromium species including Cr 6+, dispersed Cr 5+, and crystalline Cr 2O 3 were found in the calcined Crx/SBA-1 samples. Cr 6+ species were present mainly in the form of mono- and dichromates, despite the Cr loading. The presence of dispersed Cr 5+ species and crystalline α-Cr 2O 3 in the calcined catalysts depended on the total Cr total content. Cr 5+ species were found in the samples containing below 7 wt.% of Cr total, while particles of crystalline α-Cr 2O 3 were detected in the catalyst with Cr total content above 5 wt.%. All of the Crx/SBA-1 catalysts exhibited excellent catalytic activity and high selectivity in the dehydrogenation of propane to propene in the presence of CO 2 with the maximum propane conversion (37.7% at 550 °C) for ∼7 wt.% of Cr total. For higher Cr contents the conversion of propane remained almost constant which was connected with the formation of crystalline Cr 2O 3 which was inactive in the test reaction. Operando UV-vis DRS measurements performed during the dehydrogenation of propane, both in the presence and absence of CO 2 at 550 °C, indicated that the Cr 6+ species (main redox sites) were reduced rapidly to Cr 2+/Cr 3+ species already at the beginning of the process. The dispersed Cr 2+/Cr 3+ ions were the main sites available to the reactants under the dehydrogenation conditions in all of the studied feed compositions. © 2012 Elsevier Inc. All rights reserved.


Ogorzaly J.,Jagiellonian University
Journal of Elasticity | Year: 2016

In this paper we present results on existence, uniqueness and convergence of solutions to the Cauchy problem for abstract first order evolutionary inclusion which contains two operators depending on the history of the solution. These results are applicable to a dynamic contact problem for viscoelastic materials with a normal compliance contact condition with memory and a friction law in which the friction bound depends on the magnitude of the tangential displacement. The proofs are based on recent results for hemivariational inequalities and a fixed point argument. © 2016 The Author(s)


Strzalka W.,Jagiellonian University | Ziemienowicz A.,University of Lethbridge
Annals of Botany | Year: 2011

BackgroundPCNA (proliferating cell nuclear antigen) has been found in the nuclei of yeast, plant and animal cells that undergo cell division, suggesting a function in cell cycle regulation and/or DNA replication. It subsequently became clear that PCNA also played a role in other processes involving the cell genome.ScopeThis review discusses eukaryotic PCNA, with an emphasis on plant PCNA, in terms of the protein structure and its biochemical properties as well as gene structure, organization, expression and function. PCNA exerts a tripartite function by operating as (1) a sliding clamp during DNA synthesis, (2) a polymerase switch factor and (3) a recruitment factor. Most of its functions are mediated by its interactions with various proteins involved in DNA synthesis, repair and recombination as well as in regulation of the cell cycle and chromatid cohesion. Moreover, post-translational modifications of PCNA play a key role in regulation of its functions. Finally, a phylogenetic comparison of PCNA genes suggests that the multi-functionality observed in most species is a product of evolution.ConclusionsMost plant PCNAs exhibit features similar to those found for PCNAs of other eukaryotes. Similarities include: (1) a trimeric ring structure of the PCNA sliding clamp, (2) the involvement of PCNA in DNA replication and repair, (3) the ability to stimulate the activity of DNA polymerase δ and (4) the ability to interact with p21, a regulator of the cell cycle. However, many plant genomes seem to contain the second, probably functional, copy of the PCNA gene, in contrast to PCNA pseudogenes that are found in mammalian genomes. © 2011 The Author.


Nalewajski R.F.,Jagiellonian University
Journal of Mathematical Chemistry | Year: 2011

Information-theoretic (IT) indexing of the chemical bond multiplicities and their covalent/ionic contributions in the Orbital Communication Theory is reexamined. The molecules are interpreted as information channels in the Atomic Orbital (AO) resolution, in which the signals (probabilities) of the electron-allocation to AO events are propagated between the channel "inputs" and "outputs". The molecular conditional-entropy descriptor of such a probability network measures the average communication "noise" due to electron delocalization via the framework of all occupied molecular orbitals (MO) and provides a measure (in bits) of the bond IT-covalent component. The complementary IT-ionic bond multiplicity has been previously characterized by the channel average mutual-information (information-capacity, flow) descriptor, between the promolecular input and molecular output distributions, which reflects a degree of the deterministic character of such AO communications. The consistency of using this promolecule → molecule channel, reflecting the "history" of the bond formation process, as the stationary information network is validated using the classical cascade of the sequential molecular channels, effecting the multiple probability propagations. The "normalization" of the global bond descriptor of this channel to the sum of the molecular Shannon entropy and the information distance between the two compared AO distributions is demonstrated analytically and tested numerically. The promolecule (M0) → molecule (M) transition channel is formulated in the general basis set case and its overall bond multiplicity index is determined. The mixed channels are examined, with different sets of the input and output events. The displacement in the density matrix reflecting the M0→ M transition provides the AO representation of the corresponding difference between the molecular and promolecular density operators. Finally, the closed communication loops are proposed, consisting of the molecular and promolecular cascades, respectively, which generate the difference entropy/information descriptors of the system chemical bonds, between the corresponding molecular indices and their promolecular analogs, with the latter reflecting the internal communications in the isolated atoms. © 2011 The Author(s).


Araszkiewicz M.,Jagiellonian University
Proceedings of the International Conference on Artificial Intelligence and Law | Year: 2015

This paper shows how a complex legal doctrinal theory (the doctrine of causation in law) may be represented in a semi-formal, two-layered model of statutory interpretation. The content of the theory is clarified by the proposed knowledge representation. It is argued that doctrinal theories in the reading proposed here are a source of intermediate legal concepts and, in consequence, of rules that enable the judge to argue efficiently in complex cases without entering into wider considerations involving case-based reasoning structures. © 2015 ACM.


There is increasing evidence for the existence of an association between the presence of etoposide phenoxyl radicals and the development of treatment-related acute myeloid leukemia (t-AML), which occurs in a few percent of patients treated with this chemotherapeutic agent. The most common side effect caused by etoposide is myelosuppression, which limits the use of this effective drug. The goal of the study was to investigate the influence of antioxidant querectin on myelosuppression and oxidative DNA damage caused by etoposide. The influence of quercetin and/or etoposide on oxidative DNA damage was investigated in LT-12 cell line and bone marrow cells of rats via comet assay. The effect of quercetin on myelosuppression induced by etoposide was invetsigated by cytological analysis of bone marrow smears stained with May-Grünwald-Giemsa stain. Etoposide caused a significant increase in oxidative DNA damage in bone marrow cells and LT-12 cell line in comparison to the appropriate controls. Quercetin significantly reduced the oxidative DNA damage caused by etoposide both in vitro and in vivo. Quercetin also significantly protected against a decrease in the percentage of myeloid precursors and erythroid nucleated cells caused by etoposide administration in comparison to the group treated with etoposide alone. The results of the study indicate that quercetin could be considered a protectively acting compound in bone marrow cells during etoposide therapy.


Borratynska A.,Jagiellonian University
Blood Coagulation and Fibrinolysis | Year: 2016

Evidence indicates that hypercoagulability and impaired fibrinolysis have been observed in patients with obstructive sleep apnea syndrome (OSAS). It is unclear which factors determine prolonged fibrin clot lysis in OSAS. One hundred and sixty-five consecutive patients suspected of OSAS underwent overnight polysomnography. Prior to polysomnography, we determined plasma clot lysis time (CLT), plasminogen activator inhibitor (PAI)-1 antigen, activated thrombin-activatable fibrinolysis inhibitor (TAFIa), plasmin, and antiplasmin. OSAS was diagnosed in 110 (66.7%) patients, including 35 (31.8%) with severe OSAS, 26 (23.6%) with moderate OSAS, and 49 (44.6%) mild OSAS. Compared with 55 (33.3%) individuals in whom OSAS was not confirmed, OSAS patients had prolonged CLT (+12.8%), associated with higher PAI-1 antigen (+18.1%) (after adjustment for age, diabetes, and body mass index; both P?


Abstract A Monte Carlo simulation was used to determine geometry correction factors that increase accuracy of quantitative X-ray microanalysis of laterally semithick biological materials. A model composed of cellulose with homogeneously distributed biological elements and lateral dimensions between 0.5-25 μm was chosen. The specimen was exposed to 5, 10, and 15 keV electrons, the net intensities of characteristic X-rays registered for the elements, and presented as a function of the lateral dimensions of the model. This showed the double decay exponential function fitted the distribution of X-ray intensities in relation to the model size. The applicability of the function as a correction method was successfully tested for 30 specimens with varying composition and dimensions. The value of relative error decreased from ±60% to ±5% when the correction was applied. Moreover, the minimal lateral size of the material was defined, below which the correction is not required. The simulation also revealed that the difference of the weighted sum of Z /A between the unknown and the standard could reach 25% without significant influence on the quantitative results. The correction method could be helpful for accurate assessment of elemental composition in biological or organic matrices, when their lateral dimensions are smaller than the distribution range. Copyright © Microscopy Society of America 2013.


Undas A.,Jagiellonian University | Brummel-Ziedins K.E.,University of Vermont | Mann K.G.,University of Vermont
Thrombosis and Haemostasis | Year: 2014

There is evidence indicating that statins (3-hydroxy-methylglutaryl coenzyme A reductase inhibitors) may produce several cholesterol-independent antithrombotic effects. In this review, we provide an update on the current understanding of the interactions between statins and blood coagulation and their potential relevance to the prevention of venous thromboembolism (VTE). Anticoagulant properties of statins reported in experimental and clinical studies involve decreased tissue factor expression resulting in reduced thrombin generation and attenuation of pro-coagulant reactions catalysed by thrombin, such as fibrinogen cleavage, factor V and factor XIII activation, as well as enhanced endothelial thrombomodulin expression, resulting in increased protein C activation and factor Va inactivation. Observational studies and one randomized trial have shown reduced VTE risk in subjects receiving statins, although their findings still generate much controversy and suggest that the most potent statin rosuvastatin exerts the largest effect. © Schattauer 2014.


Zalewska-Galosz J.,Jagiellonian University
Annales Botanici Fennici | Year: 2010

The original material of Potamogeton × subrufus Hagstr. [= P. lucens L. × P. nodosus Poir.] and the herbarium material of the morphologically most similar hybrid, P. × fluitans Roth [= P. lucens L. × P. natans L.], were examined taxonomically. Approximately 45 characters were studied on 42 herbarium specimens of both taxa. The analysis shows that P. × subrufus displays several characters consistently different from those of P. × fluitans. Two new European localities of P. × subrufus found during the study are also provided and a morphological description of the hybrid, including distinguishing characters, is given. © Finnish Zoological and Botanical Publishing Board 2010.


This is an analytical study of magnetic fields effects on the conductance, the shot noise power, and the third charge-transfer cumulant for the Aharonov-Bohm rings and the Corbino disks in graphene. The two distinct physical mechanisms lead to very similar magnetotransport behaviors. Differences are unveiled when discussing the third-cumulant dependence on magnetic fields.


Andrzejak M.,Jagiellonian University | Witek H.A.,National Chiao Tung University
Theoretical Chemistry Accounts | Year: 2011

A systematic multi-reference perturbation theory investigation of the excitation energies and oscillator strengths for the lowest excited states of 2,2′-bithiophene unequivocally shows that its optical spectrum is produced by two 1B u states separated from each other by approximately 1 eV. This picture is confirmed by additional calculations with alternative quantum chemical methods. Our findings are in strong contrast with the previous CASPT2 results of Rubio et al. [J Chem Phys 102:3580 (1995) and Chem Phys Chem 4:1308 (2003)], who predicted that the two lowest 1B u states are quasi-degenerate. The methodological reasons responsible for the previous seemingly erroneous assignment of the optical spectrum of bithiophene are identified and explained in terms of unusually large coupling between the 1B u states introduced by dynamical correlation effects. A general discussion of applicable computational techniques is offered aiming at avoiding similar problems for other molecular systems. © 2011 The Author(s).


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.


Adam C.,University of Santiago de Compostela | Haberichter M.,University of Kent | Wereszczynski A.,Jagiellonian University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2016

There exists, in general, no unique definition of the size (volume, area, etc., depending on dimension) of a soliton. Here we demonstrate that the geometric volume (area etc.) of a soliton is singled out in the sense that it exactly coincides with the thermodynamical or continuum-mechanical volume. In addition, this volume may be defined uniquely for rather arbitrary solitons in arbitrary dimensions. © 2016 The Authors.


Szczygiel A.M.,Jagiellonian University
Pflügers Archiv : European journal of physiology | Year: 2012

Tumor necrosis factor alpha (TNF-α) is a critical cytokine that is involved in systemic inflammatory response and contributes to the activation of the pro-inflammatory phenotype of the endothelium. In the present study, effects of TNF-α on morphology and elasticity of endothelium in relation to the production of NO and actin fiber reorganization were analyzed in human dermal microvascular endothelial cells. The cells were incubated in MCDB medium solution and stimulated with [Formula: see text] of TNF-α. Atomic force microscopy measurements have enabled characterization of cell morphology and elastic properties in physiological conditions. The spectrophotometric Griess method was applied to estimate nitric oxide (NO) production of the cells. We demonstrated that TNF-α-induced changes in elasticity of endothelium anti-correlate with NO production and are associated with the reorganization of actin cytoskeleton.


Kowal G.,University of Wisconsin - Madison | Kowal G.,Jagiellonian University | Kowal G.,University of Sao Paulo | Lazarian A.,University of Wisconsin - Madison
Astrophysical Journal | Year: 2010

We study compressible magnetohydrodynamic turbulence, which holds the key to many astrophysical processes, including star formation and cosmic-ray propagation. To account for the variations of the magnetic field in the strongly turbulent fluid, we use wavelet decomposition of the turbulent velocity field into Alfvén, slow, and fast modes, which presents an extension of the Cho & Lazarian decomposition approach based on Fourier transforms. The wavelets allow us to follow the variations of the local direction of the magnetic field and therefore improve the quality of the decomposition compared to the Fourier transforms, which are done in the mean field reference frame. For each resulting component, we calculate the spectra and two-point statistics such as longitudinal and transverse structure functions as well as higher order intermittency statistics. In addition, we perform a Helmholtz-Hodge decomposition of the velocity field into incompressible and compressible parts and analyze these components. We find that the turbulence intermittency is different for different components, and we show that the intermittency statistics depend on whether the phenomenon was studied in the global reference frame related to the mean magnetic field or in the frame defined by the local magnetic field. The dependencies of the measures we obtained are different for different components of the velocity; for instance, we show that while the Alfvén mode intermittency changes marginally with the Mach number, the intermittency of the fast mode is substantially affected by the change. © 2010. The American Astronomical Society. All rights reserved. Printed in the U.S.A.


Madej K.A.,Jagiellonian University
TrAC - Trends in Analytical Chemistry | Year: 2010

This review covers methods for determination of medicines and drugs of abuse in three biological specimens - meconium, nails and tears - based on the literature since 1998. It starts with general descriptions of specimens, sample-collection methods and sample-preparation procedures. The key questions addressed relate to drug analysis in meconium, nails and tears. © 2010 Elsevier Ltd. All rights reserved.


Majewski P.,Jagiellonian University
The International journal of periodontics & restorative dentistry | Year: 2012

Soft and hard tissue defects pose a therapeutic challenge in modern implant dentistry. There are a multitude of surgical techniques available, and it is necessary to match the problem with the solution. This report describes the reconstruction of the alveolar ridge in the esthetic zone with the help of autogenous bone blocks harvested from the chin that were shaped to fit and stabilized at the recipient site. The procedures were performed using Piezosurgery, which made it possible to introduce surgical modifications and had a significant impact on the accuracy of the procedure. An observation period of 2 to 7 years showed positive stable results for treatment in terms of function and esthetics.


Brown A.J.,Texas A&M University | Pinkowicz D.,Jagiellonian University | Saber M.R.,Texas A&M University | Saber M.R.,Fayoum University | Dunbar K.R.,Texas A&M University
Angewandte Chemie - International Edition | Year: 2015

Given the recent advent of mononuclear single-molecule magnets (SMMs), a rational approach based on lanthanides with axially elongated f-electron charge cloud (prolate) has only recently received attention. We report herein a new SMM, [Li(THF)4[Er{N(SiMe3)2}3Cl] 2 THF, which exhibits slow relaxation of the magnetization under zero dc field with an effective barrier to the reversal of magnetization (ΔEeff/kB=63.3 K) and magnetic hysteresis up to 3 K at a magnetic field sweep rate of 34.6 Oe s-1. This work questions the theory that oblate or prolate lanthanides must be stabilized with the appropriate ligand framework in order for SMM behavior to be favored. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Szewczyk J.M.,Jagiellonian University | Schriefers H.,Radboud University Nijmegen
Brain Research | Year: 2011

Animacy is often conceived as a special semantic feature because of its relevance to thematic and syntactic processing. This study uses event-related brain potentials to investigate whether violations of the expected animacy value of a noun are processed differently from semantic violations which preserve the expected animacy value in a situation in which the animate/inanimate distinction has no consequences for thematic or syntactic processing. The language under test is Polish, a language in which the animate-inanimate distinction is reflected in the inflection of nouns. We constructed short stories such that either an animate direct object noun is highly expected in the story's final sentence, or an inanimate direct object. This noun appears in one of three conditions: (a) congruent, i.e. fitting the preceding context, (b) semantic violation without a violation of the expected animacy value, or (c) animacy violation, i.e. a violation of the expected animacy value. Semantic violations and animacy violations elicited a biphasic N400/P600 pattern. The N400 effect had the same amplitude for the two types of violation, while the P600 elicited by animacy violations had a significantly higher amplitude than the P600 elicited by semantic violations. These results indicate that animacy is processed differently from other semantic features even in syntactically and thematically unambiguous positions in a sentence. © 2010 Elsevier B.V. All rights reserved.


The flow cytometry is acquiring more and more clinical importance. Despite its wide application in diagnostics, it is not used commonly in the clinical toxicology. The goal of the current investigation was to evaluate the mechanism for cell death (apoptosis or necrosis) and its manifestation in circulating human lymphocytes exposed to toxic concentration of carbon monoxide (CO). Since the large subpopulation of leukocytes have undergone apoptosis the next step of the studies was to assess the mobilization of progenitor cells (CD 34+) occurring in the peripheral blood after CO intoxication. Data were compared with those of 25 healthy controls comparable in terms of age, gender and physical activity. The application of the method in clinical reasoning was also evaluated. Significantly increased apoptosis of the lymphocytes in research group compared to control individuals correlates with the poisoning severity but does not depend on hypoxia. Decreased number of leukocytes caused by the cytotoxic effect of CO, stimulates the release of the CD 34+ to the peripheral blood. Increased cell death seems to be the relevant mechanism in the pathophysiology of acute carbon monoxide poisoning--the delayed apoptosis as the consequence of the reoxygenation can influence the delayed neurological and cardiological sequelae in patients after acute CO poisoning. In order to improve the treatment and help choose best fitting therapy, there should be need to introduce the new diagnostic methods like flow cytometry or innovative imaging techniques to the standard diagnostics in clinical toxicology.


Korzeniewski B.,Jagiellonian University
PLoS ONE | Year: 2015

A computer model of oxidative phosphorylation (OXPHOS) in skeletal muscle is used to compare state 3, intermediate state and state 4 in mitochondria with rest and work in skeletal muscle. 'Idealized' state 4 and 3 in relation to various 'experimental' states 4 and 3 are defined. Theoretical simulations show, in accordance with experimental data, that oxygen consumption (V'O2), ADP and Pi are higher, while ATP/ADP and Δp are lower in rest than in state 4, because of the presence of basal ATP consuming reactions in the former. It is postulated that moderate and intensive work in skeletal muscle is very different from state 3 in isolated mitochondria. V'O2, ATP/ADP, Δp and the control of ATP usage over V'O2 are much higher, while ADP and Pi are much lower in the former. The slope of the phenomenological V'O2-ADP relationship is much steeper during the rest-work transition than during the state 4-state 3 transition. The work state in intact muscle is much more similar to intermediate state than to state 3 in isolated mitochondria in terms of ADP, ATP/ADP, Δp and metabolic control pattern, but not in terms of V'O2. The huge differences between intact muscle and isolated mitochondria are proposed to be caused by the presence of the eachstep activation (ESA) mechanism of the regulation of OXPHOS in intact skeletal muscle. Generally, the present study suggests that isolated mitochondria (at least in the absence of Ca2+) cannot serve as a good model of OXPHOS regulation in intact skeletal muscle. © 2015 PLOS ONE.


Szczerba M.,Polish Academy of Sciences | Rospondek M.J.,Jagiellonian University
Organic Geochemistry | Year: 2010

The thermodynamic stability of methylphenanthrene isomers and the kinetics of reactions involved in their natural destruction/formation have been studied via molecular modelling. The results were combined with published methylphenanthrene abundances in extracts of rocks containing Type III kerogen of a wide maturity range, to evaluate the utility of methylphenanthrene maturity parameters. These parameters track the isomer evolution toward equilibrium, leading to enrichment in the stable 2- and 3-methyl isomers relative to the less stable 9-, 1- and 4-methyl isomers. The pathways from kinetically to thermodynamically controlled distributions remain unclear but probably involve isomerisation, transmethylation and demethylation reactions. To understand the importance of each pathway, ab initio quantum chemical calculations (DFT) have been performed, leading to the identification of possible transition states and to the determination of activation energies for reactions in aqueous solutions. Acid catalysis significantly lowers modelled reaction barriers to an extent consistent with the changes observed in nature. The equilibration can start at very low maturation with acid catalysed 1,2-methyl shifts (isomerisations) regarding low energy barriers: 15.1. kcal/mol from 4- to 3-, 22.5. kcal/mol from 1- to 2- and 30.2. kcal/mol from 3- to 2-methylphenanthrene. Alternative isomerisation pathways through tertiary carbon centres are ineffective. For example the isomerisation between the 9- and 1-isomer requires 39.7. kcal/mol, which is ca. 7. kcal/mol more than for demethylation coupled with methyl transfer to another molecule (transmethylation). A reverse transmethylation, e.g. modelled methylations of phenanthrene with either a terpenoid alcohol with a gem-dimethyl or polymethyl aryl carotenoid moiety can preferentially lead to 9-methylphenanthrene due to a relatively lower energy barrier. The appearance of 9-methylphenanthrene at very early maturation stages suggests effective heterogenic catalysis by the mineral matrix. The reaction is however reversible, which means that 9-methylphenanthrene tends to demethylate with much higher rates than the other isomers but only when suitable methyl acceptors are available. In turn, free radical demethylation which is likely at advanced levels of maturity would not significantly influence relative proportions of the isomers due to very similar barriers for all the isomers. However the reverse reaction would produce all isomers thus equalising all isomer concentrations. The discussed reactions are only a few of many reactions in which phenanthrene and methylphenanthrenes are potentially involved in nature to mention only biotic (biodegradation) and abiotic methylphenanthrene demethylation, and that there is no a single reaction that determines the fate of these molecules. Therefore, the commonly applied maturity index MPI-1 does not entirely reflect thermal maturity but is instead a molecular expression of complex processes and is dependent partly on catalytic effects of the mineral matrix. Analysis of the published data on methylphenanthrene abundance in rocks containing Type III kerogens indicates that there is no inversion of the MPI-1 trend above Rr=1.35% as has been suggested previously. The maturity parameter MPR, defined as the 2-/1-MP ratio seems more closely dependant on thermal maturity than MPI-1. © 2010 Elsevier Ltd.


Musial J.,Jagiellonian University
Thrombosis Research | Year: 2012

Antiphospholipid syndrome is an autoimmune disease which combines vascular thrombosis and/or pregnancy complications with the presence of antiphospholipid antibodies. It could be a devastating and sometimes life-threatening condition. As vascular thrombosis presents as typical venous or arterial thromboembolism diagnosis is based on laboratory data. Therefore proper performance and interpretation of laboratory tests is crucial. Broader knowledge about clinical and laboratory aspects of the syndrome and their associations are essential for proper evaluation and management of the patients. © 2011 Elsevier Ltd. All rights reserved.


A positive representation for an arbitrary complex, gaussian weight is derived and used to construct a statistical formulation of gaussian path integrals directly in the Minkowski time. The positivity of Minkowski weights is achieved by doubling the number of real variables. The continuum limit of the new representation exists only if some of the additional couplings tend to infinity and are tuned in a specific way. The construction is then successfully applied to three quantum mechanical examples including a particle in a constant magnetic field — a simplest prototype of a Wilson line. Further generalizations are shortly discussed and an intriguing interpretation of new variables is alluded to. © 2016, The Author(s).


Volonteri M.,CNRS Paris Institute of Astrophysics | Volonteri M.,University of Michigan | Sikora M.,Nicolaus Copernicus Astronomical Center | Lasota J.-P.,CNRS Paris Institute of Astrophysics | And 2 more authors.
Astrophysical Journal | Year: 2013

Massive black holes (MBHs), in contrast to stellar mass black holes, are expected to substantially change their properties over their lifetime. MBH masses increase by several orders of magnitude over a Hubble time, as illustrated by Sołtan's argument. MBH spins also must evolve through the series of accretion and mergers events that increase the masses of MBHs. We present a simple model that traces the joint evolution of MBH masses and spins across cosmic time. Our model includes MBH-MBH mergers, merger-driven gas accretion, stochastic fueling of MBHs through molecular cloud capture, and a basic implementation of accretion of recycled gas. This approach aims at improving the modeling of low-redshift MBHs and active galactic nuclei (AGNs), whose properties can be more easily estimated observationally. Despite the simplicity of the model, it does a good job capturing the global evolution of the MBH population from z ∼ 6 to today. Under our assumptions, we find that the typical spin and radiative efficiency of MBHs decrease with cosmic time because of the increased incidence of stochastic processes in gas-rich galaxies and MBH-MBH mergers in gas-poor galaxies. At z = 0, the spin distribution in gas-poor galaxies peaks at spins 0.4-0.8 and is not strongly mass dependent. MBHs in gas-rich galaxies have a more complex evolution, with low-mass MBHs at low redshift having low spins and spins increasing at larger masses and redshifts. We also find that at z > 1 MBH spins are on average the highest in high luminosity AGNs, while at lower redshifts these differences disappear. © 2013. The American Astronomical Society. All rights reserved..


Mach P.,Jagiellonian University
Journal of Mathematical Physics | Year: 2012

All real solutions of the Lane-Emden equation for n = 5 are obtained in terms of Jacobian and Weierstrass elliptic functions. A new family of solutions is found. It is expressed by remarkably simple formulae involving Jacobian elliptic functions only. The general properties and discrete scaling symmetries of these new solutions are discussed. We also comment on their possible applications. © 2012 American Institute of Physics.


Plant sterols, which are well known dietary taken cholesterol lowering agents, can incorporate into erythrocyte membranes. However, the influence of these compounds on membrane properties seems to be unclear. Since the composition of erythrocytes undergoes changes, e.g., in pathological cases, in this work the relationship between the proportion of lipids in model membranes (Langmuir monolayers) and the effect of β-sitosterol was analyzed. The investigations were carried out for cholesterol/phosphatidylcholine (POPC)/sphingomyelin films differing in the proportion of cholesterol and containing the plant sterol in various concentrations. Additionally, the experiments based on systematic replacement of cholesterol in model membranes were performed. Based on the analysis of mean area and the excess area per molecule, compressional modulus and the excess free energy of mixing values as well as BAM images it was evidenced that the effect of the plant sterol depends on the composition of model membrane. However, it was also found that, in the investigated range of monolayer composition, the increase of total sterol content in the mixed film caused by the presence of β-sitosterol practically does not influence the molecular packing and interactions in the investigated monolayers. On the other hand, the replacement of cholesterol by β-sitosterol causes a decrease of condensation and weakens the interactions between molecules in the mixed film. These effects are the strongest for the systems of the highest content of cholesterol. The most important finding is that the variations in the composition of membranes, widely occurring in natural systems, may influence the effect of phytosterols. © 2011 Elsevier B.V.


In this work the properties of two ternary sphingomyelin/phosphatidylcholine/cholesterol monolayers imitating erythrocyte membrane were studied at various content of sterol. Phosphatidylcholines chosen for experiments differ in the length of sn-1 saturated chain in the molecule (1-stearoyl-2-oleoyl- sn-glycero-3-phosphocholine-SOPC vs. 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine - POPC). Langmuir monolayer experiments combined with Brewster Angle Microscopy prove that for both investigated systems the most favorable effect of cholesterol appears at 30% of sterol in the film. However, the interactions between molecules at 50% of sterol are only slightly weaker as compared to those for 1:1:1 films. It was also found that only at higher sterol concentration appear differences in the ordering effect of cholesterol on the systems containing PC molecules of various length of sn-1 saturated chain. Although the differences in the properties of POPC versus SOPC-containing monolayers were found, similarities in the morphology of the respective systems and stoichiometry of thermodynamically the most favorable mixture allow one to conclude that both SM/POPC/Chol as well as SM/SOPC/Chol monolayer can be used to mimic raft systems. © 2012 Elsevier B.V.


Dziarmaga J.,Jagiellonian University
Advances in Physics | Year: 2010

We review recent theoretical work on two closely related issues: excitation of an isolated quantum condensed matter system driven adiabatically across a continuous quantum phase transition or a gapless phase, and apparent relaxation of an excited system after a sudden quench of a parameter in its Hamiltonian. Accordingly, the review is divided into two parts. The first part revolves around a quantum version of the Kibble-Zurek mechanism including also phenomena that go beyond this simple paradigm. What they have in common is that excitation of a gapless many-body system scales with a power of the driving rate. The second part attempts a systematic presentation of recent results and conjectures on apparent relaxation of a pure state of an isolated quantum many-body system after its excitation by a sudden quench. This research is motivated in part by recent experimental developments in the physics of ultracold atoms with potential applications in the adiabatic quantum state preparation and quantum computation. © 2010 Taylor & Francis.


The covering of the eggs in Russian sturgeon Acipenser gueldenstaedtii consists of three envelopes (the vitelline envelope, chorion and extrachorion) and is equipped with multiple micropyles. The most proximal to the oocyte is the vitelline envelope that consists of four layers of filamentous and trabecular material. The structural components of this envelope are synthesized by the oocyte (primary envelope). The chorion encloses the vitelline envelope. The extrachorion covers the external surface of the egg. Examination of the arrangement of layers that comprise the egg envelopes together with the ultrastructure of follicular cells revealed that the chorion and extrachorion are secondary envelopes. They are secreted by follicular cells and are built of homogeneous material. During formation of egg envelopes, the follicular cells gradually diversify into three morphologically different populations: 1) cells covering the animal oocyte region (cuboid), (2) main body cells (cylindrical) and (3) micropylar cells. The apical surfaces of follicular cells from the first two populations form processes that remain connected with the oocyte plasma membrane by means of gap junctions. Micropylar cells are located at the animal region of the oocyte. Their apical parts bear projections that form a barrier to the deposition of materials for egg envelopes, resulting in the formation of the micropylar canal. © 2010 The Author. Journal compilation © 2010 The Fisheries Society of the British Isles.


Krzysciak P.,Jagiellonian University
Wiadomości parazytologiczne | Year: 2010

Rhodotorula sp. have emerged as opportunistic pathogens, particularly in immunocompromised patients. Knowledge about the susceptibility of Rhodotorula strains to the common antifungal drugs is essential for the treatment of such new infections. The 68 isolates identified as: Rhodotorula mucilaginosa (47 strains; 69%), R. minuta (14; 21%) and R. glutinis (7; 10%) obtained from various sources (feces, skin and nails, vagina and hospital environment) were tested for susceptibility to 5-fluorocytosine (5FC), amphotericin B (AMB), fluconazole (FLC) and itraconazole (ITR). All of the isolates had low MICs for AMB and 5FC. For ITR, the R. minuta isolates had the lowest MICs within a range 0.125-0.25 mg/l and for FLC all isolates affected within the range 2-64 mg/l. The majority of R. mucilaginosa isolates (82.2%) had MICs in the range 64-128 mg/l for FLC and 95.6% of isolates had MICs above or equal to 2 mg/1 for ITR.


Kostrakiewicz K.,Jagiellonian University
Polish Journal of Ecology | Year: 2011

The disturbances defined as an external factor causing biomass removal are a key component of all ecosystems. In phytocenoses with a continuous vegetation cover and a large proportion of perennial plants the fine-scale disturbances create gaps, which are the temporary competitor-free microsites suitable for plant recruitment. The investigations of natural colonization of different size gaps in Molinietum caeruleae meadows were carried out in patches dominated by small species creating delicate, erect or procumbent stems (MC), prevailed by large-tussock grasses (GR), and overgrown by willows (SA). Each patch was represented by ten plots, divided into four square subplots of 0.16 m2, 0.09 m2, 0.04 m2 and 0.01 m2. In each of them the aboveground parts of plants were clipped and removed with the litter. The seedlings recruitment was observed in 2007-2009. The highest species richness in gaps was observed in the MC patch and might be caused by week competition for light from neighbouring plants with delicate, procumbent stems and narrow leaves. The smaller rate of recruitment in SA and GR patches could be caused by overshading willows as well as by the competition from large and dense tussocks of Deschampsia caespitosa and Molinia caerulea. At all patches species richness declined with the decreasing gap size. The developed seedling pool represented both species occurring in the surrounding canopy and such which were not found there. However, their contribution varied between particular patches. Regardless gap size, the MC seedling pool was dominated by species which did not occur in the established vegetation, whereas in GR gaps both groups were represented by similar numbers of taxa and the SA gaps become dominated by species present in the surrounding canopy. Irrespective of patch character, in each subplot the medium-seeded species were represented most abundantly. The recruitment of genets of large-seeded species decreased, while the abundance of individuals of small-seeded taxa increased with the increasing gap size. In the light of the performed study, one might suggest that extent-controlled disturbances can be used as an effective way of the conservation of Molinietum caeruleae patches dominated by small meadow species being outcompeted by large-tussock grasses and over-shaded by willows.


In the present study the natural orbitals for chemical valence (NOCVs) combined with the energy decomposition scheme (ETS) were used to characterize bonding in various clusters of ammonia borane (borazane): dimer D, trimer TR, tetramer TE, and the crystal based models: nonamer N and tetrakaidecamer TD. ETS-NOCV results have shown that shortening of the B-N bond (by ∼0.1 Å) in ammonia borane crystal (as compared to isolated borazane molecule) is related to the enhancement of donation (by 6.5 kcal/mol) and electrostatic (by 11.3 kcal/mol) contributions. This, in turn, is caused solely by the electrostatic dipole-dipole interaction between ammonia borane units; dihydrogen bonding, BH•••HN, formed between borazane units exhibits no direct impact on B-N bond contraction. On the other hand, formation of dihydrogen bonding appeared to be very important in the total stabilization of single borazane unit, namely, ETS-based data indicated that it leads to significant electronic stabilization λE orb = -17.5 kcal/mol, which is only slightly less important than the electrostatic term, λE elstat = -19.4 kcal/mol. Thus, both factors contribute to relatively high melting point of the borazane crystal. Deformation density contributions (λρ i) obtained from NOCVs allowed