SU(2) Cosmological Solitons

We present a class of numerical solutions to the SU(2) nonlinear $\sigma$-model coupled to the Einstein equations with cosmological constant $\Lambda\geq 0$ in spherical symmetry. These solutions are characterized by the presence of a regular static region which includes a center of symmetry. They are parameterized by a dimensionless ``coupling constant'' $\beta$, the sign of the cosmological constant, and an integer ``excitation number'' $n$. The phenomenology we find is compared to the corresponding solutions found for the Einstein-Yang-Mills (EYM) equations with positive $\Lambda$ (EYM$\Lambda$). If we choose $\Lambda$ positive and fix $n$, we find a family of static spacetimes with a Killing horizon for $0 \leq \beta < \beta_{max}$. As a limiting solution for $\beta = \beta_{max}$ we find a {\em globally} static spacetime with $\Lambda=0$, the lowest excitation being the Einstein static universe. To interpret the physical significance of the Killing horizon in the cosmological context, we apply the concept of a trapping horizon as formulated by Hayward. For small values of $\beta$ an asymptotically de Sitter dynamic region contains the static region within a Killing horizon of cosmological type. For strong coupling the static region contains an ``eternal cosmological black hole''.Comment: 20 pages, 6 figures, Revte

AN OPTIMIZED PROTOCOL FOR IN VACUO MOLECULARDYNAMICS SIMULATION AND TRAJECTORYANALYSIS OF MODIFIED DNA DUPLEXES

This paper presents an optimized protocol for in vacuo molecular dynamics studies of short DNAduplexes containing modified nucleosides. The example studied is an 11 base pair DNA duplex modifiedwith l,N6-ethenodeoxyadenosine (dεA) located opposite deoxyguanosine. A complex moleculardynamics trajectory was subjected to statistical cluster analysis. Groups (clusters) of similarconformations, which can be statistically identified after energy minimization of the trajectory results,have been analyzed with particular regard to the estimation of intrinsic stability of the duplex (hydrogenbonding and base stacking). The modified residue was found to form two hydrogen bonds within thed ε A / d G base pair, which stabilize the duplex, thus allowing its conformation to remain close to regularB-DNA.Pozna

New, extended hairpin form of the TAR-2 RNA domain points to the structural polymorphism at the 5′ end of the HIV-2 leader RNA

The HIV-2 TAR RNA domain (TAR-2) plays a key role in the trans-activation of HIV-2 transcription as it is the target for the Tat-2 protein and several cell factors. Here, we show that the TAR-2 domain exists in vitro in two global, alternative forms: a new, extended hairpin form with two conformers and the already proposed branched hairpins form. This points strongly to the structural polymorphism of the 5′ end of the HIV-2 leader RNA. The evidence comes from the non-denaturing PAGE mobility assay, 2D structure prediction, enzymatic and Pb(2+)- or Mg(2+)-induced RNA cleavages. Existence of the TAR-2 extended form was further proved by the examination of engineered TAR-2 mutants stabilized either in the branched or extended structure. The TAR-2 extended form predominates with an increasing magnesium concentration. Gel retardation assays reveal that both TAR-2 wt and its mutant, unable to form branched structure, bind Tat-2 protein with comparable, high affinity, while RNA hairpins I and II, derived from TAR-2 branched structure model, show much less protein binding. We propose that an internal loop region of the TAR-2 extended hairpin form is a potential Tat-2 binding site

Diagnostic Laparoscopy for Small Intestinal Intussusception in a Horse

Laparoscopy is a low-invasive diagnostic and surgical technique for examining and performing surgical procedures in the equine peritoneal cavity. This article is a case study of a horse with weakly expressed, irregular symptoms of colic occurring over a period of four weeks. Diagnostic laparoscopy was performed, and liver and spleen tissue samples were collected for a histopathological analysis. An endoscopic examination of the abdominal cavity ruled out small intestinal intussusception, and a histopathological analysis supported the identification of the causes of colic

Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape

H9N2 avian influenza virus is a major cause of poultry production loss across Asia leading to the wide use of vaccines. Efficacy of vaccines is often compromised due to the rapid emergence of antigenic variants. To improve the effectiveness of vaccines in the field, a better understanding of the antigenic epitopes of the major antigen, hemagglutinin, is required. To address this, a panel of nine monoclonal antibodies were generated against a contemporary Pakistani H9N2 isolate, which represents a major Asian H9N2 viral lineage. Antibodies were characterized in detail and used to select a total of 26 unique ‘escape’ mutants with substitutions across nine different amino acid residues in hemagglutinin including seven that have not been described as antigenic determinants for H9N2 viruses before. Competition assays and structural mapping revealed two novel, discrete antigenic sites “H9-A” and “H9-B”. Additionally, a second subset of escape mutants contained amino acid deletions within the hemagglutinin receptor binding site. This constitutes a novel method of escape for group 1 hemagglutinins and could represent an alternative means for H9N2 viruses to overcome vaccine induced immunity. These results will guide surveillance efforts for arising antigenic variants as well as evidence based vaccine seed selection and vaccine design

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

Background: Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description: RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl webcite. Conclusions: RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field

Global analysis of polarized DIS & SIDIS data with improved small-xx helicity evolution

We analyze the world polarized deep-inelastic scattering (DIS) and semi-inclusive DIS (SIDIS) data at low values of $x < 0.1$, using small-$x$ evolution equations for the flavor singlet and nonsinglet helicity parton distribution functions (hPDFs). The hPDFs for quarks, antiquarks, and gluons are extracted and evolved to lower values of $x$ to make predictions for the future Electron-Ion Collider (EIC). We improve on our earlier work by employing the more realistic large-$N_c\, \& N_f$ limit of the revised small-$x$ helicity evolution, and incorporating running coupling corrections along with SIDIS data into the fit. We find an anti-correlation between the signs of the gluon and $C$-even quark hPDFs as well as the $g_1$ structure function. While the existing low-$x$ polarized DIS and SIDIS data are insufficient to constrain the initial conditions for the polarized dipole amplitudes in the helicity evolution equations, future EIC data will allow more precise predictions for hPDFs and the $g_1$ structure function for $x$ values beyond those probed at the EIC. Using the obtained hPDFs, we discuss the contributions to the proton spin from quark and gluon spins at small $x$.Comment: 42 Pages, 21 Figures

Airbnb and crime in Barcelona (Spain): testing the relationship using a geographically weighted regression

The existence of works proving the possible relationship empirically that Airbnb lodgings could have with crime in Spain is not known. This research analyzes the relationship between Airbnb lodgings and crimes against the properties and people in Barcelona’s neighbourhoods. To achieve this, we use an ordinary least squares regression model and a geographically weighted regression model. The results show a significant and positive relationship between the higher density of Airbnb lodgings and the higher crime rates in the neighbourhoods, especially of patrimonial nature. Divided by type of leased space, the Airbnb homes, in which the guest shares a room with other guests, show a higher relationship with crimes against property and people. The results of the local model show a spatial heterogeneity in all variables used, indicating the need to address non-stationary spatial processes that reveal hidden patterns. However, the only variable that shows statistically significant local variability is the total Airbnb lodgings variable. Finally, we discussed some unexpected results, proposing some future lines of research. © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Nanjing Normal University

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling. The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a ‘dot-bracket’ notation. The algorithm searching for the requested 3D RNA fragments is very efficient. As of August 2007, the database contains: (i) RNA sequences and secondary structures, in the ‘dot-bracket’ notation, derived from 1065 protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures, (iii) calculated RNA torsion angles and sugar pucker parameters and (iv) information about base pairs. Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters. The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs. The RNA FRABASE is automatically, monthly updated and is freely accessible at http://rnafrabase.ibch.poznan.pl (mirror at http://cerber.cs.put.poznan.pl/rnadb)