Cities and Disturbed Areas as Man-made Shelters for Orchid Communities

Many species from the family Orchidaceae spread in anthropogenic habitats and numerous studies documenting this process are known. Unfortunately, such data are scattered throughout various papers and reports, sometimes fragmentary and hard to reach (the ‘grey literature’). Scientific elaboration on this topic still lacks a comprehensive review and summary of the scale of this phenomenon. Therefore, the main aim of this study was to gather, review and analyse such data, seeking the answer to the question whether the man-made habitats can be considered as refugee for orchids. The paper summarises data on the occurrence of orchid species in man-made habitats in Europe originating from published and unpublished sources. The particular emphasis was placed in urban habitats. For this purpose, the floristically data from 42 European cities were used. The conducted studies showed that the apohytism phenomenon in the family Orchidaceae was more widespread than had been previously reported. As a result, 70 species of orchids in the distinguished man-made habitats were found. The majority of the species grow on sand and clay pits. The most common species were Epipactis helleborine and Dactylorhiza majalis. The gathered data have confirmed that man-made habitats become refugee for many orchid species in the aftermath of the loss of their natural habitats. Thus, protection of sites transformed by man with orchid occurrence should be taken into consideration. These sites can become a source of very useful information for biogeographically and phylo-geographically analyses of many valuable and endangered species

Modeling of Multivariate Longitudinal Phenotypes in Family Genetic Studies with Bayesian Multiplicity Adjustment

Genetic studies often collect data on multiple traits. Most genetic association analyses, however, consider traits separately and ignore potential correlation among traits, partially because of difficulties in statistical modeling of multivariate outcomes. When multiple traits are measured in a pedigree longitudinally, additional challenges arise because in addition to correlation between traits, a trait is often correlated with its own measures over time and with measurements of other family members. We developed a Bayesian model for analysis of bivariate quantitative traits measured longitudinally in family genetic studies. For a given trait, family-specific and subject-specific random effects account for correlation among family members and repeated measures, respectively. Correlation between traits is introduced by incorporating multivariate random effects and allowing time-specific trait residuals to correlate as in seemingly unrelated regressions. The proposed model can examine multiple single-nucleotide variations simultaneously, as well as incorporate familyspecific, subject-specific, or time-varying covariates. Bayesian multiplicity technique is used to effectively control false positives. Genetic Analysis Workshop 18 simulated data illustrate the proposed approach\u27s applicability in modeling longitudinal multivariate outcomes in family genetic association studies

Tako-tsubo cardiomyopathy after administration of ergometrine following elective caesarean delivery: a case report

<p>Abstract</p> <p>Introduction</p> <p>Tako-tsubo cardiomyopathy (stress-induced cardiomyopathy or transient left ventricular ballooning) is characterized by clinical suspicion of an acute myocardial infarction with transient apical or midventricular dyskinesia of the left ventricle without significant coronary stenosis on angiography. The etiology of this disease remains obscure. One of the possible causes is myocardial ischemia induced by coronary vasospasm due to sympathetic activation. It has been hypothesized that the application of ergometrine could induce tako-tsubo cardiomyopathy.</p> <p>Case presentation</p> <p>We report the case of a 28-year-old Turkish woman who developed tako-tsubo cardiomyopathy after administration of ergometrine for release of placenta and prevention of bleeding during the post-partum phase in the course of an elective caesarean delivery. Tako-tsubo cardiomyopathy was diagnosed by echocardiography and urgent cardiac magnetic resonance imaging. A coronary angiography was not performed because of the absence of myocardial necrosis or ischemia and signs of myocarditis on cardiac magnetic resonance imaging.</p> <p>Conclusion</p> <p>This life-threatening disease should be excluded in the differential diagnosis by comparing the symptoms with those of typical heart failure, particularly after use of ergometrine.</p

Impact of Population Stratification on Family-Based Association in an Admixed Population

Population substructure is a well-known confounder in population-based case-control genetic studies, but its impact in familybased studies is unclear. We performed population substructure analysis using extended families of admixed population to evaluate power and Type I error in an association study framework. Our analysis shows that power was improved by 1.5% after principal components adjustment. Type I error was also reduced by 2.2% after adjusting for family substratification. The presence of population substructure was underscored by discriminant analysis, in which over 92% of individuals were correctly assigned to their actual family using only 100 principal components. This study demonstrates the importance of adjusting for population substructure in family-based studies of admixed populations

Viral AlkB proteins repair RNA damage by oxidative demethylation

Bacterial and mammalian AlkB proteins are iron(II)- and 2-oxoglutarate-dependent dioxygenases that reverse methylation damage, such as 1-methyladenine and 3-methylcytosine, in RNA and DNA. An AlkB-domain is encoded by the genome of numerous single-stranded, plant-infecting RNA viruses, the majority of which belong to the Flexiviridae family. Our phylogenetic analysis of AlkB sequences suggests that a single plant virus might have acquired AlkB relatively recently, followed by horizontal dissemination among other viruses via recombination. Here, we describe the first functional characterization of AlkB proteins from three plant viruses. The viral AlkB proteins efficiently reactivated methylated bacteriophage genomes when expressed in Escherichia coli, and also displayed robust, iron(II)- and 2-oxoglutarate-dependent demethylase activity in vitro. Viral AlkB proteins preferred RNA over DNA substrates, and thus represent the first AlkBs with such substrate specificity. Our results suggest a role for viral AlkBs in maintaining the integrity of the viral RNA genome through repair of deleterious methylation damage, and support the notion that AlkB-mediated RNA repair is biologically relevant

Active target TPC for study of photonuclear reactions at astrophysical energies

A setup designed to study photonuclear reactions at astrophysical energies - an active target Time Projection Chamber was developed and constructed at the Faculty of Physics, University of Warsaw. The device was successfully employed in two experiments at the Institute of Nuclear Physics Polish Academy of Sciences in Cracow, in which {\gamma}- and neutron-induced reactions with CO2 gas target were measured. The reaction products were detected and their momenta reconstructed. Preliminary results are shown.Comment: Presented at Zakopane Conference on Nuclear Physics 202

Polarization and spectral energy distribution in OJ 287 during the 2016/17 outbursts

We report optical photometric and polarimetric observations of the blazar OJ 287 gathered during 2016/17. The high level of activity, noticed after the General Relativity Centenary flare, is argued to be part of the follow-up flares that exhibited high levels of polarization and originated in the primary black hole jet. We propose that the follow-up flares were induced as a result of accretion disk perturbations, travelling from the site of impact towards the primary SMBH. The timings inferred from our observations allowed us to estimate the propagation speed of these perturbations. Additionally, we make predictions for the future brightness of OJ 287. © 2017 by the authors

Patterns for High Performance Multiscale Computing

We describe our Multiscale Computing Patterns software for High Performance Multiscale Computing. Following a short review of Multiscale Computing Patterns, this paper introduces the Multiscale Computing Patterns Software, which consists of description, optimisation and execution components. First, the description component translates the task graph, representing a multiscale simulation, to a particular type of multiscale computing pattern. Second, the optimisation component selects and applies algorithms to find the most suitable mapping between submodels and available HPC resources. Third, the execution component which a middleware layer maps submodels to the number and type of physical resources based on the suggestions emanating from the optimisation part together with infrastructure-specific metrics such as queueing time and resource availability. The main purpose of the Multiscale Computing Patterns software is to leverage the Multiscale Computing Patterns to simplify and automate the execution of complex multiscale simulations on high performance computers, and to provide both application-specific and pattern-specific performance optimisation. We test the performance and the resource usage for three multiscale models, which are expressed in terms of two Multiscale Computing Patterns. In doing so, we demonstrate how the software automates resource selection and load balancing, and delivers performance benefits from both the end-user and the HPC system level perspectives

Specific Sequences in the N-terminal Domain of Human Small Heat Shock Protein HSPB6 Dictate Preferential Heterooligomerization with the Orthologue HSPB1

Small heat-shock proteins (sHSPs) are a conserved group of molecular chaperones with important roles in cellular proteostasis. Although sHSPs are characterized by their small monomeric weight, they typically assemble into large polydisperse oligomers that vary in both size and shape but are principally composed of dimeric building blocks. These assemblies can include different sHSP orthologues, creating additional complexity that may affect chaperone activity. However, the structural and functional properties of such hetero-oligomers are poorly understood. We became interested in hetero-oligomer formation between human heat-shock protein family B (small) member 1 (HSPB1) and HSPB6, which are both highly expressed in skeletal muscle. When mixed in vitro, these two sHSPs form a polydisperse oligomer array composed solely of heterodimers, suggesting preferential association that is determined at the monomer level. Previously, we have shown that the sHSP N-terminal domains (NTDs), which have a high degree of intrinsic disorder, are essential for the biased formation. Here we employed iterative deletion mapping to elucidate how the NTD of HSPB6 influences its preferential association with HSPB1 and show that this region has multiple roles in this process. First, the highly conserved motif RLFDQXFG is necessary for subunit exchange among oligomers. Second, a site ∼20 residues downstream of this motif determines the size of the resultant hetero-oligomers. Third, a region unique to HSPB6 dictates the preferential formation of heterodimers. In conclusion, the disordered NTD of HSPB6 helps regulate the size and stability of hetero-oligomeric complexes, indicating that terminal sHSP regions define the assembly properties of these proteins