bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vertex coloring of graphs via phase dynamics of coupled oscillatory networks
Authors: Parihar Abhinav , Shukla Nikhil , Jerry Matthew , Datta Suman , Raychowdhury Arijit 
Published: April 2017

AbstractWhile Boolean logic has been the backbone of digital information processing, there exist classes of computationally hard problems wherein this paradigm is fundamentally inefficient. Vertex coloring of graphs, belonging to the class of combinatorial optimization, represents one such problem. It is well studied for its applications in data sciences, life sciences, social sciences and technology, and hence, motivates alternate, more efficient non-Boolean pathways towards its solution. Here we demonstrate a coupled relaxation oscillator based dynamical system that exploits insulator-metal transition in Vanadium Dioxide (VO2) to efficiently solve vertex coloring of graphs. Pairwise coupled VO2 oscillator circuits have been analyzed before for basic computing operations, but using complex networks of VO2 oscillators, or any other oscillators, for more complex tasks have been challenging in theory as well as in experiments. The proposed VO2 oscillator network harnesses the natural analogue between optimization problems and energy minimization processes in highly parallel, interconnected dynamical systems to approximate optimal coloring of graphs. We further indicate a fundamental connection between spectral properties of linear dynamical systems and spectral algorithms for graph coloring. Our work not only elucidates a physics-based computing approach but also presents tantalizing opportunities for building customized analog co-processors for solving hard problems efficiently.
Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array
Authors: Ma Qing , Liu Xuexue , Pan Jianfei , Ma Lina , Ma Yuehui , He Xiaohong , Zhao Qianjun , Pu Yabin , Li Yingkang , Jiang Lin 
Published: April 2017

AbstractCopy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs. Subsequently, ten novel CNVRs were randomly chosen for further quantitative real-time PCR (qPCR) confirmation, and eight were successfully validated. Gene functional enrichment revealed that these CNVRs cluster into Gene Ontology (GO) categories of homeobox and embryonic skeletal system morphogenesis. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. We constructed a Chinese indigenous sheep genomic CNV map based on the Illumina Ovine SNP 600 K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep.
Molecular diagnostic assays based on cpn60 UT sequences reveal the geographic distribution of subgroup 16SrXIII-(A/I)I phytoplasma in Mexico
Authors: Pérez-López Edel , Rodríguez-Martínez Douglas , Olivier Chrystel Y. , Luna-Rodríguez Mauricio , Dumonceaux Tim J. 
Published: April 2017

AbstractGeographically diverse samples from strawberry exhibiting symptoms of Strawberry Green Petal (SbGP), periwinkle plants with virescence, and blackberry, blueberry, and raspberry plants displaying yellowing and inedible fruits, were assayed for the presence of phytoplasma DNA. PCR targeting the 16S rRNA-encoding gene and chaperonin-60 (cpn60) showed that the plants were infected with phytoplasma subgroup16SrXIII-(A/I)I (SbGP/MPV). To examine the geographic distribution of this pathogen in Mexico, we designed an array ofcpn60-targeted molecular diagnostic assays for SbGP/MPV phytoplasma. A fluorescent microsphere hybridization assay was designed that was capable of detecting SbGP/MPV phytoplasma in infected plant tissues, successfully differentiating it from other known phytoplasmacpn60 UT sequences, while identifying a double infection with SbGP/MPV and aster yellows (16SrI) phytoplasma. Two quantitative assays, quantitative real-time PCR (qRT-PCR) and droplet digital PCR (ddPCR), gave similar results in infected samples. Finally, a loop-mediated isothermal amplification (LAMP) assay provided rapid detection of SbGP/MPV phytoplasma DNA. Application of these assays revealed that SbGP/MPV phytoplasma is widely distributed in Central Mexico, with positive samples identified from eleven localities within three states separated by hundreds of kilometres. These results also provide tools for determining the presence and geographic distribution of this pathogen in plant and insect samples in other localities.
Light penetration-coupled photoisomerization modeling for photodeformation of diarylethene single crystal: upscaling isomerization to macroscopic deformation
Authors: Kim Muyoung , Yun Jung-Hoon , Cho Maenghyo 
Published: April 2017

AbstractDiarylethene is one of the photo-responsive materials that show rapid and reversible changes in their color/electrochemical properties and macroscopic deformations in the crystalline phase by light irradiation. Photoisomerization is the main cause of the photo reactivity of diarylethene, and we established a statistical model based on the density matrix formalism, which predicts quantitative isomerization progress as a population term. The model reflects photo-switching properties of the target molecule, which were characterized by first principle calculations, and external stimulus factors (light irradiation conditions and temperature). By merging light penetration physics with the model, we derived light penetration depth dependent isomerization progress to theoretically investigate photodeformation of single crystal. The model well reproduced in-plane shear deformation under ultraviolet light irradiation which would provide guideline for photoactuator design. In addition, the statistical model addressed crucial findings (primary stimuli and molecular design parameter for increasing the isomerization rate, external stimuli enhancing fluorescence performance) itself.
Flow virometry analysis of envelope glycoprotein conformations on individual HIV virions
Authors: Arakelyan Anush , Fitzgerald Wendy , King Deborah F. , Rogers Paul , Cheeseman Hannah M. , Grivel Jean-Charles , Shattock Robin J. , Margolis Leonid 
Published: April 2017

AbstractHIV-1 envelope proteins (Envs) play a critical role in HIV infection. In a correct trimeric conformation, Env mediates virus–cell binding and fusion. Malfunctioning of this machinery renders virions incapable of infecting cells. Each HIV-1 virion carries 10–14 Envs, and therefore a defective Env may not necessarily render a HIV virion non-infectious, since other Env on the same virion may still be functional. Alternatively, it is possible that on a given virion either all the spikes are defective or all are functional. Here, we investigate Env conformations on individual virions using our new nanotechnology, “flow virometry”, and a panel of antibodies that discriminate between various Env conformations. We found that the majority of HIV-1 virions carry either only trimeric (“functional”) or only defective spikes. The relatively small subfraction of virions that carry both functional and nonfunctional Envs contributes little to HIV infection of human lymphoid tissue ex vivo. The observation that the majority of virions exclusively express either functional or nonfunctional forms of Env has important implications for understanding the role of neutralizing and non-neutralizing antibodies in the immune control of HIV infection as well as for the development of effective prophylactic strategies.
Improving superconductivity in BaFe2As2-based crystals by cobalt clustering and electronic uniformity
Authors: Li L. , Zheng Q. , Zou Q. , Rajput S. , Ijaduola A. O. , Wu Z. , Wang X. P. , Cao H. B. , Somnath S. , Jesse S. , Chi M. , Gai Z. , Parker D. , Sefat A. S. 
Published: April 2017

AbstractQuantum materials such as antiferromagnets or superconductors are complex in that chemical, electronic, and spin phenomena at atomic scales can manifest in their collective properties. Although there are some clues for designing such materials, they remain mainly unpredictable. In this work, we find that enhancement of transition temperatures in BaFe2As2-based crystals are caused by removing local-lattice strain and electronic-structure disorder by thermal annealing. While annealing improves Néel-ordering temperature in BaFe2As2 crystal (T
N
= 132 K to 136 K) by improving in-plane electronic defects and reducing overall a-lattice parameter, it increases superconducting-ordering temperature in optimally cobalt-doped BaFe2As2 crystal (Tc = 23 to 25 K) by precipitating-out the cobalt dopants and giving larger overall a-lattice parameter. While annealing improves local chemical and electronic uniformity resulting in higher T
N
in the parent, it promotes nanoscale phase separation in the superconductor resulting in lower disparity and strong superconducting band gaps in the dominant crystal regions, which lead to both higher overall T
c
and critical-current-density, J
c
.
In vivo dynamics of AAV-mediated gene delivery to sensory neurons of the trigeminal ganglia
Authors: Dang Chung H. , Aubert Martine , De Silva Feelixge Harshana S. , Diem Kurt , Loprieno Michelle A. , Roychoudhury Pavitra , Stone Daniel , Jerome Keith R. 
Published: April 2017

AbstractThe ability to genetically manipulate trigeminal ganglion (TG) neurons would be useful in the study of the craniofacial nervous system and latent alphaherpesvirus infections. We investigated adeno-associated virus (AAV) vectors for gene delivery to the TG after intradermal whiskerpad delivery in mice. We demonstrated that AAV vectors of serotypes 1, 7, 8, and 9 trafficked from the whiskerpad into TG neurons and expressed transgenes within cell bodies and axons of sensory neurons in all three branches of the TG. Gene expression was highest with AAV1, and steadily increased over time up to day 28. Both constitutive and neuronal-specific promoters were able to drive transgene expression in TG neurons. Levels of vector genomes in the TG increased with input dose, and multiple transgenes could be co-delivered to TG neurons by separate AAV vectors. In conclusion, AAV1 vectors are suitable for gene delivery to TG sensory neurons following intradermal whiskerpad injection.
The glycogen synthase kinase MoGsk1, regulated by Mps1 MAP kinase, is required for fungal development and pathogenicity in Magnaporthe oryzae
Authors: Zhou Tengsheng , Dagdas Yasin F. , Zhu Xiaohan , Zheng Shiqin , Chen Liqiong , Cartwright Zachary , Talbot Nicholas J. , Wang Zonghua 
Published: April 2017

AbstractMagnaporthe oryzae, the causal agent of blast disease, is one of the most destructive plant pathogens, causing significant yield losses on staple crops such as rice and wheat. The fungus infects plants with a specialized cell called an appressorium, whose development is tightly regulated by MAPK signaling pathways following the activation of upstream sensors in response to environmental stimuli. Here, we show the expression of the Glycogen synthase kinase 3 (GSK3) MoGSK1 in M. oryzae is regulated by Mps1 MAP kinase, particularly under the stressed conditions. Thus, MoGSK1 is functionally characterized in this study. MoGsk1 is functionally homologues to the Saccharomyces cerevisiae GSK3 homolog MCK1. Gene replacement of MoGSK1 caused significant delay in mycelial growth, complete loss of conidiation and inability to penetrate the host surface by mycelia-formed appressorium-like structures, consequently resulting in loss of pathogenicity. However, the developmental and pathogenic defects of Δmogsk1 are recovered via the heterologous expression of Fusarium graminearum GSK3 homolog gene FGK3, whose coding products also shows the similar cytoplasmic localization as MoGsk1 does in M. oryzae. By contrast, overexpression of MoGSK1 produced deformed appressoria in M. oryzae. In summary, our results suggest that MoGsk1, as a highly conservative signal modulator, dictates growth, conidiation and pathogenicity of M. oryzae.
Recovery of Alumina Nanocapacitors after High Voltage Breakdown
Authors: Belkin A. , Bezryadin A. , Hendren L. , Hubler A. 
Published: April 2017

AbstractBreakdown of a dielectric material at high electric fields significantly limits the applicability of metal-dielectric-metal capacitors for energy storage applications. Here we demonstrate that the insulating properties of atomic-layer-deposited Al2O3thin films in Al/Al2O3/Al trilayers can recover after the breakdown. The recovery has been observed in samples with the dielectric thickness spanning from 4 to 9 nm. This phenomenon holds promise for a new generation of capacitors capable of restoring their properties after the dielectric breakdown. Also, if employed in capacitor banks, the recovery process will ensure that the bank remains operational even if a breakdown occurs.
Predicting the potential distribution in China of Euwallacea fornicatus (Eichhoff) under current and future climate conditions
Authors: Ge Xuezhen , Jiang Chao , Chen Linghong , Qiu Shuang , Zhao Yuxiang , Wang Tao , Zong Shixiang 
Published: April 2017

AbstractEuwallacea fornicatus(Eichhoff) is an important forest pest that has caused serious damage in America and Vietnam. In 2014, it attacked forests ofAcer trialatumin the Yunnan province of China, creating concern in China’s Forestry Bureau. We used the CLIMEX model to predict and compare the potential distribution forE. fornicatesin China under current (1981–2010) and projected climate conditions (2011–2040) using one scenario (RCP8.5) and one global climate model (GCM), CSIRO-Mk3-6-0. Under both current and future climate conditions, the model predictedE. fornicatesto be mainly distributed in the south of China. Comparing distributions under both climate conditions showed that the area of potential distribution was projected to increase (mainly because of an increase in favourable habitat) and shift to the north. Our results help clarify the potential effect of climate change on the range of this forest pest and provide a reference and guide to facilitate its control in China.
Transcriptomic analysis reveals a previously unknown role for CD8+ T-cells in rVSV-EBOV mediated protection
Authors: Menicucci Andrea R. , Sureshchandra Suhas , Marzi Andrea , Feldmann Heinz , Messaoudi Ilhem 
Published: April 2017

AbstractEbola virus (EBOV) poses a significant threat to human health as highlighted by the recent epidemic in West Africa. Data from animal studies and a ring vaccination clinical trial conducted in Guinea during the recent epidemic demonstrated that a recombinant VSV where G protein is replaced with EBOV GP (rVSV-EBOV) is safe and highly efficacious. We previously established that antibodies are essential for rVSV-EBOV mediated protection against EBOV; however, the mechanisms by which this vaccine induces a humoral response and the role of T-cells in rVSV-EBOV mediated protection remain poorly understood. Since this is the only vaccine platform that has completed Phase III clinical studies, it is imperative to gain a better understanding of its mechanisms of protection. Therefore, we performed a longitudinal gene expression analysis of samples collected from controls and T-cell-depleted macaques after rVSV-EBOV vaccination and EBOV challenge. We show that rVSV-EBOV vaccination induces gene expression changes consistent with anti-viral immunity and B-cell proliferation. We also report a previously unappreciated role for CD8+ T-cells in mediating rVSV-EBOV protection. Finally, limited viral transcription in surviving animals may boost protective responses after EBOV challenge by maintaining transcriptional changes. This study presents a novel approach in determining mechanisms of vaccine efficacy.
Direct recognition of LPS drive TLR4 expressing CD8+ T cell activation in patients with rheumatoid arthritis
Authors: Tripathy Archana , Khanna Shweta , Padhan Prasanta , Smita Shuchi , Raghav Sunil , Gupta Bhawna 
Published: April 2017

AbstractAberrant immune responses characterize autoimmune disorders like Rheumatoid Arthritis (RA) wherein lymphocytes are recognized as key players. Role of CD8+T cells in RA has been less defined however we found that these cells are activated in RA patients with increased expression of cytolytic granules and inflammatory mediators thereby modulating immune responses contributing to disease severity. Though unconventional expression of different Toll Like Receptors (TLRs) on CD8+T cells has been proposed but their expression and role in T cell activation and differentiation in RA still remains obscure. Herein we report, for the first time, an increased expression of TLR4 on peripheral CD8+T cells of RA patients and its role in skewing CD8+T cells towards activated and inflammatory phenotype thereby playing a significant role in pathogenesis and progression of RA. We found that the surface expression of TLR4 on CD8+T cells directly correlates with disease severity. Moreover, these CD8+T cells respond to the TLR4 ligand LPS and express robust amounts of cytotolytic and inflammatory molecules including TNFα and IFNγ. Our study hence identifies an important role for CD8+T cells in orchestrating RA through TLR4 mediated activation and differentiation.
The Time Course of Spatial Attention Shifts in Elementary Arithmetic
Authors: Liu Dixiu , Cai Danni , Verguts Tom , Chen Qi 
Published: April 2017

AbstractIt has been proposed that elementary arithmetic induces spatial shifts of attention. However, the timing of this arithmetic-space association remains unknown. Here we investigate this issue with a target detection paradigm. Detecting targets in the right visual field was faster than in the left visual field when preceded by an addition operation, while detecting targets in the left visual field was faster than in the right visual field when preceded by a subtraction operation. The arithmetic-space association was found both at the end of the arithmetic operation and during calculation. In contrast, the processing of operators themselves did not induce spatial biases. Our results suggest that the arithmetic-space association resides in the mental arithmetic operation rather than in the individual numbers or the operators. Moreover, the temporal course of this effect was different in addition and subtraction.
The role of the brown adipose tissue in β3-adrenergic receptor activation-induced sleep, metabolic and feeding responses
Authors: Szentirmai Éva , Kapás Levente 
Published: April 2017

AbstractBrown adipose tissue (BAT) is regulated by the sympathetic nervous system via β3-adrenergic receptors (β3-AR). Here we tested the hypothesis that pharmacological stimulation of β3-ARs leads to increased sleep in mice and if this change is BAT dependent. In wild-type (WT) animals, administration of CL-316,243, a selective β3-AR agonist, induced significant increases in non-rapid-eye movement sleep ﻿(NREMS) lasting for 4–10 h. Simultaneously, electroencephalographic slow-wave activity (SWA) was significantly decreased and body temperature was increased with a delay of 5–6 h. In uncoupling protein 1 (UCP-1) knockout mice, the middle and highest doses of the β3-AR agonist increased sleep and suppressed SWA, however, these effects were significantly attenuated and shorter-lasting as compared to WT animals. To determine if somnogenic signals arising from BAT in response to β3-AR stimulation are mediated by the sensory afferents of BAT, we tested the effects of CL-316,243 in mice with the chemical deafferentation of the intra-scapular BAT pads. Sleep responses to CL-316,243 were attenuated by ~50% in intra-BAT capsaicin-treated mice. Present findings indicate that the activation of BAT via β3-AR leads to increased sleep in mice and that this effect is dependent on the presence of UCP-1 protein and sleep responses require the intact sensory innervation of BAT.
Network-assisted analysis of GWAS data identifies a functionally-relevant gene module for childhood-onset asthma
Authors: Liu Y. , Brossard M. , Sarnowski C. , Vaysse A. , Moffatt M. , Margaritte-Jeannin P. , Llinares-López F. , Dizier M. H. , Lathrop M. , Cookson W. , Bouzigon E. , Demenais F. 
Published: April 2017

AbstractThe number of genetic factors associated with asthma remains limited. To identify new genes with an undetected individual effect but collectively influencing asthma risk, we conducted a network-assisted analysis that integrates outcomes of genome-wide association studies (GWAS) and protein-protein interaction networks. We used two GWAS datasets, each consisting of the results of a meta-analysis of nine childhood-onset asthma GWASs (5,924 and 6,043 subjects, respectively). We developed a novel method to compute gene-level P-values (fastCGP), and proposed a parallel dense-module search and cross-selection strategy to identify an asthma-associated gene module. We identified a module of 91 genes with a significant joint effect on childhood-onset asthma (P < 10−5). This module contained a core subnetwork including genes at known asthma loci and five peripheral subnetworks including relevant candidates. Notably, the core genes were connected to APP (encoding amyloid beta precursor protein), a major player in Alzheimer’s disease that is known to have immune and inflammatory components. Functional analysis of the module genes revealed four gene clusters involved in innate and adaptive immunity, chemotaxis, cell-adhesion and transcription regulation, which are biologically meaningful processes that may underlie asthma risk. Our findings provide important clues for future research into asthma aetiology.
Treatment of donor corneal tissue with immunomodulatory cytokines: a novel strategy to promote graft survival in high-risk corneal transplantation
Authors: Tahvildari Maryam , Emami-Naeini Parisa , Omoto Masahiro , Mashaghi Alireza , Chauhan Sunil K. , Dana Reza 
Published: April 2017

AbstractAntigen-presenting cells (APCs) play an important role in transplant rejection and tolerance. In high-risk corneal transplantation, where the graft bed is inflamed and vascularized, immature APCs in the donor corneal stroma quickly mature and migrate to lymphoid tissues to sensitize host T cells. In this study, using a mouse model of corneal transplantation, we investigated whether enrichment of tolerogenic APCs (tolAPCs) in donor corneas can enhance graft survival in corneal allograft recipients with inflamed graft beds. Treatment of donor corneas with interleukin-10 (IL-10) and transforming growth factor-β1 (TGFβ1) altered the phenotype and function of tissue-residing APCs. Transplantation of these tolAPC-enriched corneas decreased frequencies of interferon gamma (IFNγ)+ effector T cells (Teffs), as well as allosensitization in the hosts, diminished graft infiltration of CD45+ and CD4+ cells, and significantly improved corneal allograft survival compared to saline-injected controls. These data provide a novel approach for tolAPC-based immunotherapy in transplantation by direct cytokine conditioning of the donor tissue.