A vortex model for transport in the polar stratosphere

A semi-empirical model based on a Gaussian vorticity distribution was developed for determining eddy diffusivity and wind transport distributions in the polar stratosphere. The model uses as input data pressure surface heights measured at periods of the year when the stratospheric polar vortex exhibits nearly circular patterns around the pole. The components of the polar wind velocities that result from a Prandtl eddy viscosity distribution are found to be in general agreement with those obtained by other investigators

Gramene QTL database: development, content and applications

Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene-phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research

Vertex Cover Kernelization Revisited: Upper and Lower Bounds for a Refined Parameter

An important result in the study of polynomial-time preprocessing shows that there is an algorithm which given an instance (G,k) of Vertex Cover outputs an equivalent instance (G',k') in polynomial time with the guarantee that G' has at most 2k' vertices (and thus O((k')^2) edges) with k' <= k. Using the terminology of parameterized complexity we say that k-Vertex Cover has a kernel with 2k vertices. There is complexity-theoretic evidence that both 2k vertices and Theta(k^2) edges are optimal for the kernel size. In this paper we consider the Vertex Cover problem with a different parameter, the size fvs(G) of a minimum feedback vertex set for G. This refined parameter is structurally smaller than the parameter k associated to the vertex covering number vc(G) since fvs(G) <= vc(G) and the difference can be arbitrarily large. We give a kernel for Vertex Cover with a number of vertices that is cubic in fvs(G): an instance (G,X,k) of Vertex Cover, where X is a feedback vertex set for G, can be transformed in polynomial time into an equivalent instance (G',X',k') such that |V(G')| <= 2k and |V(G')| <= O(|X'|^3). A similar result holds when the feedback vertex set X is not given along with the input. In sharp contrast we show that the Weighted Vertex Cover problem does not have a polynomial kernel when parameterized by the cardinality of a given vertex cover of the graph unless NP is in coNP/poly and the polynomial hierarchy collapses to the third level.Comment: Published in "Theory of Computing Systems" as an Open Access publicatio

Molecular genetic evidence for the place of origin of the Pacific rat, Rattus exulanso

Commensal plants and animals have long been used to track human migrations, with Rattus exulans (the Pacific rat) a common organism for reconstructing Polynesian dispersal in the Pacific. However, with no knowledge of the homeland of R. exulans, the place of origin of this human-commensal relationship is unknown. We conducted a mitochondrial DNA phylogeographic survey of R. exulans diversity across the potential natural range in mainland and Island Southeast Asia in order to establish the origin of this human-commensal dyad. We also conducted allozyme electrophoresis on samples from ISEA to obtain a perspective on patterns of genetic diversity in this critical region. Finally, we compared molecular genetic evidence with knowledge of prehistoric rodent faunas in mainland and ISEA. We find that ISEA populations of R. exulans contain the highest mtDNA lineage diversity including significant haplotype diversity not represented elsewhere in the species range. Within ISEA, the island of Flores in the Lesser Sunda group contains the highest diversity in ISEA (across all loci) and also has a deep fossil record of small mammals that appears to include R. exulans. Therefore, in addition to Flores harboring unusual diversity in the form of Homo floresiensis, dwarfed stegodons and giant rats, this island appears to be the homeland of R. exulans.Vicki Thomson, Ken P. Aplin, Alan Cooper, Susan Hisheh, Hitoshi Suzuki, Ibnu Maryanto, Grace Yap, Stephen C. Donnella

Structural, thermal, and optical analysis of zinc boro-aluminosilicate glasses containing different alkali and alkaline modifier ions

In this article, structural, thermal, and optical properties of zinc boro-aluminosilicate glasses with addition of different alkali (Li, Na, and K) and alkaline oxides (Mg, Ca, Sr, and Ba) have been reported. 10 mol% of alkali and alkaline oxides were incorporated into Zinc boro-aluminosilicate glasses and all these glasses possess high optical quality. Samples were characterized using X-ray diffraction (XRD), scanning electron microscopy and energy dispersive X-ray analysis (SEM-EDAX), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, Raman spectroscopy, thermo-gravimetric analysis (TGA), differential scanning calorimetry (DSC), and optical absorption spectroscopy. The XRD and SEM measurements demonstrated the amorphous origin for all the prepared glasses and EDAX confirms that all the elements are presented in the prepared glasses. The presence of various functional groups such as triangular and tetrahedral-borate (BO3 and BO4) was confirmed by ATR-FTIR and Raman spectra, and both of the ATR-FTIR and Raman spectra show lower phonon energy for H3 (K2O) in alkali series, and H7 (BaO) for alkaline. From TGA analysis we found a lower weight loss < 0.1% in K2O, MgO, and BaO; and from the DSC profiles the glass transition temperature (Tg), onset crystallization temperature (Tx), crystallization temperature (Tc), and melting temperature (Tm) were identified and related different thermal parameters are evaluated. Alkali and alkaline influenced Zinc boro-aluminosilicate glasses demonstrate excellent glass stability. From the optical absorption spectra, we calculated cut-off wavelength and it shows spectral shifting to longer wavelength with alkali (Li → Na → K), and alkaline (Mg → Ca → Sr → Ba) modifiers. We investigated optical band gap energy also for allowed transitions in UV–visible region using three methods; direct, indirect, and absorption spectrum fitting (ASF)

A Cryogenic Silicon Interferometer for Gravitational-wave Detection

The detection of gravitational waves from compact binary mergers by LIGO has opened the era of gravitational wave astronomy, revealing a previously hidden side of the cosmos. To maximize the reach of the existing LIGO observatory facilities, we have designed a new instrument that will have 5 times the range of Advanced LIGO, or greater than 100 times the event rate. Observations with this new instrument will make possible dramatic steps toward understanding the physics of the nearby universe, as well as observing the universe out to cosmological distances by the detection of binary black hole coalescences. This article presents the instrument design and a quantitative analysis of the anticipated noise floor

Kinetic regulation of multi-ligand binding proteins

Background: Second messengers, such as calcium, regulate the activity of multisite binding proteins in a concentration-dependent manner. For example, calcium binding has been shown to induce conformational transitions in the calcium-dependent protein calmodulin, under steady state conditions. However, intracellular concentrations of these second messengers are often subject to rapid change. The mechanisms underlying dynamic ligand-dependent regulation of multisite proteins require further elucidation. Results: In this study, a computational analysis of multisite protein kinetics in response to rapid changes in ligand concentrations is presented. Two major physiological scenarios are investigated: i) Ligand concentration is abundant and the ligand-multisite protein binding does not affect free ligand concentration, ii) Ligand concentration is of the same order of magnitude as the interacting multisite protein concentration and does not change. Therefore, buffering effects significantly influence the amounts of free ligands. For each of these scenarios the influence of the number of binding sites, the temporal effects on intermediate apo- and fully saturated conformations and the multisite regulatory effects on target proteins are investigated. Conclusions: The developed models allow for a novel and accurate interpretation of concentration and pressure jump-dependent kinetic experiments. The presented model makes predictions for the temporal distribution of multisite protein conformations in complex with variable numbers of ligands. Furthermore, it derives the characteristic time and the dynamics for the kinetic responses elicited by a ligand concentration change as a function of ligand concentration and the number of ligand binding sites. Effector proteins regulated by multisite ligand binding are shown to depend on ligand concentration in a highly nonlinear fashion

Steering hyper-giants' traffic at scale

Large content providers, known as hyper-giants, are responsible for sending the majority of the content traffic to consumers. These hyper-giants operate highly distributed infrastructures to cope with the ever-increasing demand for online content. To achieve 40 commercial-grade performance of Web applications, enhanced end-user experience, improved reliability, and scaled network capacity, hyper-giants are increasingly interconnecting with eyeball networks at multiple locations. This poses new challenges for both (1) the eyeball networks having to perform complex inbound traffic engineering, and (2) hyper-giants having to map end-user requests to appropriate servers. We report on our multi-year experience in designing, building, rolling-out, and operating the first-ever large scale system, the Flow Director, which enables automated cooperation between one of the largest eyeball networks and a leading hyper-giant. We use empirical data collected at the eyeball network to evaluate its impact over two years of operation. We find very high compliance of the hyper-giant to the Flow Director’s recommendations, resulting in (1) close to optimal user-server mapping, and (2) 15% reduction of the hyper-giant’s traffic overhead on the ISP’s long-haul links, i.e., benefits for both parties and end-users alike.EC/H2020/679158/EU/Resolving the Tussle in the Internet: Mapping, Architecture, and Policy Making/ResolutioNe

Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci.

Genetic and environmental components as well as their interaction contribute to the risk of schizophrenia, making it highly relevant to include environmental factors in genetic studies of schizophrenia. This study comprises genome-wide association (GWA) and follow-up analyses of all individuals born in Denmark since 1981 and diagnosed with schizophrenia as well as controls from the same birth cohort. Furthermore, we present the first genome-wide interaction survey of single nucleotide polymorphisms (SNPs) and maternal cytomegalovirus (CMV) infection. The GWA analysis included 888 cases and 882 controls, and the follow-up investigation of the top GWA results was performed in independent Danish (1396 cases and 1803 controls) and German-Dutch (1169 cases, 3714 controls) samples. The SNPs most strongly associated in the single-marker analysis of the combined Danish samples were rs4757144 in ARNTL (P=3.78 × 10(-6)) and rs8057927 in CDH13 (P=1.39 × 10(-5)). Both genes have previously been linked to schizophrenia or other psychiatric disorders. The strongest associated SNP in the combined analysis, including Danish and German-Dutch samples, was rs12922317 in RUNDC2A (P=9.04 × 10(-7)). A region-based analysis summarizing independent signals in segments of 100 kb identified a new region-based genome-wide significant locus overlapping the gene ZEB1 (P=7.0 × 10(-7)). This signal was replicated in the follow-up analysis (P=2.3 × 10(-2)). Significant interaction with maternal CMV infection was found for rs7902091 (P(SNP × CMV)=7.3 × 10(-7)) in CTNNA3, a gene not previously implicated in schizophrenia, stressing the importance of including environmental factors in genetic studies

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13