Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data

Selectoscope is a web application which combines a number of popular tools used to infer positive selection in an easy to use pipeline. A set of homologous DNA sequences to be analyzed and evaluated are submitted to the server by uploading protein-coding gene sequences in the FASTA format. The sequences are aligned and a phylogenetic tree is constructed. The codeml procedure from the PAML package is used first to adjust branch lengths and to find a starting point for the likelihood maximization, then FastCodeML is executed. Upon completion, branches and positions under positive selection are visualized simultaneously on the tree and alignment viewers. Run logs are accessible through the web interface. Selectoscope is based on the Docker virtualization technology. This makes the application easy to install with a negligible performance overhead. The application is highly scalable and can be used on a single PC or on a large high performance clusters. The source code is freely available at https://github.com/anzaika/selectoscope

Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.

The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes. We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group. This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei

Coupled-mode equations and gap solitons in a two-dimensional nonlinear elliptic problem with a separable periodic potential

We address a two-dimensional nonlinear elliptic problem with a finite-amplitude periodic potential. For a class of separable symmetric potentials, we study the bifurcation of the first band gap in the spectrum of the linear Schr\"{o}dinger operator and the relevant coupled-mode equations to describe this bifurcation. The coupled-mode equations are derived by the rigorous analysis based on the Fourier--Bloch decomposition and the Implicit Function Theorem in the space of bounded continuous functions vanishing at infinity. Persistence of reversible localized solutions, called gap solitons, beyond the coupled-mode equations is proved under a non-degeneracy assumption on the kernel of the linearization operator. Various branches of reversible localized solutions are classified numerically in the framework of the coupled-mode equations and convergence of the approximation error is verified. Error estimates on the time-dependent solutions of the Gross--Pitaevskii equation and the coupled-mode equations are obtained for a finite-time interval.Comment: 32 pages, 16 figure

Chern-Simons Theory for Magnetization Plateaus of Frustrated J1J_1-J2J_2 Heisenberg model

The magnetization curve of the two-dimensional spin-1/2 $J_1$-$J_2$ Heisenberg model is investigated by using the Chern-Simons theory under a uniform mean-field approximation. We find that the magnetization curve is monotonically increasing for $J_2/J_1 < 0.267949$, where the system under zero external field is in the antiferromagnetic N\'eel phase. For larger ratios of $J_2/J_1$, various plateaus will appear in the magnetization curve. In particular, in the disordered phase, our result supports the existence of the $M/M_{\rm sat}=1/2$ plateau and predicts a new plateau at $M/M_{\rm sat}=1/3$. By identifying the onset ratio $J_2/J_1$ for the appearance of the 1/2-plateau with the boundary between the N\'eel and the spin-disordered phases in zero field, we can determine this phase boundary accurately by this mean-field calculation. Verification of these interesting results would indicate a strong connection between the frustrated antiferromagnetic system and the quantum Hall system.Comment: RevTeX 4, 4 pages, 3 EPS figure

Magnetic fields in supernova remnants and pulsar-wind nebulae

We review the observations of supernova remnants (SNRs) and pulsar-wind nebulae (PWNe) that give information on the strength and orientation of magnetic fields. Radio polarimetry gives the degree of order of magnetic fields, and the orientation of the ordered component. Many young shell supernova remnants show evidence for synchrotron X-ray emission. The spatial analysis of this emission suggests that magnetic fields are amplified by one to two orders of magnitude in strong shocks. Detection of several remnants in TeV gamma rays implies a lower limit on the magnetic-field strength (or a measurement, if the emission process is inverse-Compton upscattering of cosmic microwave background photons). Upper limits to GeV emission similarly provide lower limits on magnetic-field strengths. In the historical shell remnants, lower limits on B range from 25 to 1000 microGauss. Two remnants show variability of synchrotron X-ray emission with a timescale of years. If this timescale is the electron-acceleration or radiative loss timescale, magnetic fields of order 1 mG are also implied. In pulsar-wind nebulae, equipartition arguments and dynamical modeling can be used to infer magnetic-field strengths anywhere from about 5 microGauss to 1 mG. Polarized fractions are considerably higher than in SNRs, ranging to 50 or 60% in some cases; magnetic-field geometries often suggest a toroidal structure around the pulsar, but this is not universal. Viewing-angle effects undoubtedly play a role. MHD models of radio emission in shell SNRs show that different orientations of upstream magnetic field, and different assumptions about electron acceleration, predict different radio morphology. In the remnant of SN 1006, such comparisons imply a magnetic-field orientation connecting the bright limbs, with a non-negligible gradient of its strength across the remnant.Comment: 20 pages, 24 figures; to be published in SpSciRev. Minor wording change in Abstrac

Ethnic and gender differences in applicants' decision-making processes: An application of the theory of reasoned action

Contains fulltext : 54483.pdf (publisher's version ) (Closed access)11 p

Quantum magnetism in two dimensions: From semi-classical N\'eel order to magnetic disorder

This is a review of ground-state features of the s=1/2 Heisenberg antiferromagnet on two-dimensional lattices. A central issue is the interplay of lattice topology (e.g. coordination number, non-equivalent nearest-neighbor bonds, geometric frustration) and quantum fluctuations and their impact on possible long-range order. This article presents a unified summary of all 11 two-dimensional uniform Archimedean lattices which include e.g. the square, triangular and kagome lattice. We find that the ground state of the spin-1/2 Heisenberg antiferromagnet is likely to be semi-classically ordered in most cases. However, the interplay of geometric frustration and quantum fluctuations gives rise to a quantum paramagnetic ground state without semi-classical long-range order on two lattices which are precisely those among the 11 uniform Archimedean lattices with a highly degenerate ground state in the classical limit. The first one is the famous kagome lattice where many low-lying singlet excitations are known to arise in the spin gap. The second lattice is called star lattice and has a clear gap to all excitations. Modification of certain bonds leads to quantum phase transitions which are also discussed briefly. Furthermore, we discuss the magnetization process of the Heisenberg antiferromagnet on the 11 Archimedean lattices, focusing on anomalies like plateaus and a magnetization jump just below the saturation field. As an illustration we discuss the two-dimensional Shastry-Sutherland model which is used to describe SrCu2(BO3)2.Comment: This is now the complete 72-page preprint version of the 2004 review article. This version corrects two further typographic errors (three total with respect to the published version), see page 2 for detail

A review of spatial causal inference methods for environmental and epidemiological applications

The scientific rigor and computational methods of causal inference have had great impacts on many disciplines, but have only recently begun to take hold in spatial applications. Spatial casual inference poses analytic challenges due to complex correlation structures and interference between the treatment at one location and the outcomes at others. In this paper, we review the current literature on spatial causal inference and identify areas of future work. We first discuss methods that exploit spatial structure to account for unmeasured confounding variables. We then discuss causal analysis in the presence of spatial interference including several common assumptions used to reduce the complexity of the interference patterns under consideration. These methods are extended to the spatiotemporal case where we compare and contrast the potential outcomes framework with Granger causality, and to geostatistical analyses involving spatial random fields of treatments and responses. The methods are introduced in the context of observational environmental and epidemiological studies, and are compared using both a simulation study and analysis of the effect of ambient air pollution on COVID-19 mortality rate. Code to implement many of the methods using the popular Bayesian software OpenBUGS is provided

National identity predicts public health support during a global pandemic

Changing collective behaviour and supporting non-pharmaceutical interventions is an important component in mitigating virus transmission during a pandemic. In a large international collaboration (Study 1, N = 49,968 across 67 countries), we investigated self-reported factors associated with public health behaviours (e.g., spatial distancing and stricter hygiene) and endorsed public policy interventions (e.g., closing bars and restaurants) during the early stage of the COVID-19 pandemic (April-May 2020). Respondents who reported identifying more strongly with their nation consistently reported greater engagement in public health behaviours and support for public health policies. Results were similar for representative and non-representative national samples. Study 2 (N = 42 countries) conceptually replicated the central finding using aggregate indices of national identity (obtained using the World Values Survey) and a measure of actual behaviour change during the pandemic (obtained from Google mobility reports). Higher levels of national identification prior to the pandemic predicted lower mobility during the early stage of the pandemic (r = −0.40). We discuss the potential implications of links between national identity, leadership, and public health for managing COVID-19 and future pandemics.publishedVersio