CABS-flex predictions of protein flexibility compared with NMR ensembles

Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting of protein regions that undergo conformational changes and the extent of such changes

Use of the UNB_TopoDens model for local modelling of chosen gravity field parameters in the Western Carpathians

The latest, global density model of topographical masses (UNB TopoDms model) was used to determine complete Bouguer anomalies and the differences between geoid undulations and height anomalies in an area of the Western Carpathians, within the Polish-Slovak-Czech border region. The ranges of the calculated values are between approximately -74 and +23 mGal for Bouguer anomalies and -10 and +5 cm for differences between geoid and quasigeoid heights. Calculations were also performed for constant densities of topographical masses (2200, 2500 and 2670 kg/m(3)). The results show significant differences due to the various densities adopted for the calculations. For example, differences between the version using densities from the UNB TopoDens model and the version using a constant density of 2670 kg/m(3) ranged between -3.4 mGal and +37.5 mGal, for Bouguer anomalies, and between -0.5 cm and +7.4 cm for differences between geoid undulation and height anomalies. It has also been shown that, for high mountain areas, differences between geoid and quasigeoid height should be determined on the basis of exact formula (not on the basis of Bouguer anomalies).Web of Science17111811

Hranidbeni čimbenici kao podrška imunom odgovoru u životinja

The immune system in animals and in humans as well, is a “specific network of specialized organs, tissues and cells” and different intrinsic biochemical substances that protect the host organism against invasions and unfavourable effects of pathogenic microorganisms. It plays the essential role in maintaining the resistance to disease. It is also known that some groups of specific nutrients can affect, positively or negatively the immune response of animals. In present review some connections between nutrition and immune response will be discussed.Imuni sustav u životinja kao i u ljudi je "specifična mreža specijaliziranih organa, tkiva i stanica" te različitih važnih biokemijskih tvari koje štite organizam domaćina od napada i nepovoljnog djelovanja patogenih mikroorganizama. On ima bitnu ulogu u održavanju otpornosti na bolesti. Isto tako je poznato da neke skupine hranjivih tvari mogu djelovati pozitivno ili negativno na imuni odgovor životinja. U ovom radu raspravlja se o povezanosti između hranjivih tvari i imunog odgovora

Zespół Joubert i schorzenia pokrewne

The cerebellum plays a role not only in motor control but also in motor learning and cognition. Joubert syndrome is a rare heterogeneous inherited genetic disorder characterized by ataxia, hypotonia, developmental delay, and at least one of the following features: neonatal respiratory disturbances or abnormal eye movement. The estimated frequency of Joubert syndrome in the United States is around 1 : 100 000. The term Joubert syndrome and related disorders (JSRD) has been recently coined to describe all disorders presenting with molar tooth sign on brain neuroimaging. Joubert syndrome is believed to be a representative of a new group of disorders named ciliopathies. The identification of seven causal genes (NPHP1, AHI1, CEP290, RPGRIP1L, TMEM67/MKS3, ARL13B, CC2D2A) has led to substantial progress in the understanding of the genetic basis of Joubert syndrome. The authors focus on clinical presentation of JSRD, differential diagnosis and molecular background.Móżdżek odgrywa istotną rolę w kontroli nie tylko funkcji ruchowych, ale także procesów poznawczych. Zespół Joubert jest rzadkim heterogennym schorzeniem uwarunkowanym genetycznie, charakteryzującym się występowaniem ataksji, hipotonii, opóźnienia rozwoju psychoruchowego, a także jednej z następujących cech: zaburzeń oddychania w okresie noworodkowym lub nieprawidłowych ruchów gałek ocznych. Szacowana częstość występowania zespołu Joubert i zespołów pokrewnych w USA wynosi ok. 1 : 100 000. Zespół Joubert i zespoły pokrewne obejmują schorzenia, w których występuje obraz „zęba trzonowego” w badaniu obrazowym układu nerwowego. Zespół Joubert stanowi przykład nowej grupy chorób nazywanych ciliopatiami. Identyfikacja 7 genów (NPHP1, AHI1, CEP290, RPGRIP1L, TMEM67/MKS3, ARL13B, CC2D2A) poczyniła znaczący postęp w zrozumieniu genetycznych podstaw zespołu Joubert. Autorzy prezentują objawy kliniczne zespołu Joubert i schorzeń pokrewnych, diagnostykę różnicową i podłoże genetyczne

Asynchronous communication in spectral-element and discontinuous Galerkin methods for atmospheric dynamics – a case study using the High-Order Methods Modeling Environment (HOMME-homme_dg_branch)

The scalability of computational applications on current and next-generation supercomputers is increasingly limited by the cost of inter-process communication. We implement non-blocking asynchronous communication in the High-Order Methods Modeling Environment for the time integration of the hydrostatic fluid equations using both the spectral-element and discontinuous Galerkin methods. This allows the overlap of computation with communication, effectively hiding some of the costs of communication. A novel detail about our approach is that it provides some data movement to be performed during the asynchronous communication even in the absence of other computations. This method produces significant performance and scalability gains in large-scale simulations.publishedVersio

A Study of Transport Behaviour of Academic Communities

n important challenge to achieving sustainable university campuses is ensuring that the academic community makes sustainable transport choices. The objective of this study was to investigate the daily commuting patterns, identify the potential for change, and determine the factors and criteria affecting the transport decisions of academic communities of two universities located in Gdansk, Poland. This paper summarizes the results of trip generation measurements and a comprehensive online survey of 3678 respondents, including the universities&rsquo staff and students. Analysis of survey results revealed clear differences between students and university staff in terms of travel patterns and factors that influence their choices. Staff usually (57%) choose the car for daily commutes with students opting for public transport (59%). The choice of travel mode in particular groups is determined mostly by car availability, trip origin location, and accessibility. The choices also depend on transport user individual requirements such as trip quality, costs, or ecology. With approximately 1400 trips daily per 1000 students, the universities are large traffic generators. Thus, how the staff and students behave determines the effect the universities have on the urban transport system. Understanding the behaviour can help to estimate whether it can be changed and how. Document type: Articl

Validation of differential pulse polarographic method of ascorbic acid assay in food – Comparison with the chromatographic reference method

The objective of the study was to demonstrate the applicability of differential pulse polarography (DPP) technique of the ascorbic acid (AA) assay for the analysis of food samples with various matrices. The following validation parameters were determined: selectivity, linearity, precision, accuracy, limit of detection, and limit of quantification. The limits of detection and quantification were 0.17 and 0.5 mg ascorbic acid per 100 g food, respectively. The average recovery of added ascorbic acid from all matrices was 96.3–103.6%. The values of the coefficient of variation calculated on the basis of AA contents for food matrices were in the range 2–9.26% and Horrat values were 0.37–1.10. Ascorbic acid values of the samples obtained from the polarographic method were compared with those obtained from high-performance liquid chromatography with diode-array detection (HPLC-DAD) used as the reference method. The analytical parameters determined showed that the polarographic method was equivalent to the chromatographic method. Validation of the polarographic method of ascorbic acid assay indicates that it can be applied for the analysis of ascorbic acid concentration in food products that do not contain isoascorbic acid. This means that the method can be recommended for routine determinations