bluuebunny/crossref_metadata_2025_split huggingface dataset:
M2BP inhibits HIV-1 virion production in a vimentin filaments-dependent manner
Authors: Wang Qin , Zhang Xiaolin , Han Yuling , Wang Xinlu , Gao Guangxia 
Published: September 2016

AbstractM2BP (also called 90K) is an interferon-stimulated gene product that is upregulated in HIV-1 infection. A recent study revealed that M2BP reduces the infectivity of HIV-1 by inhibiting the processing of the viral envelope protein. Here we report that in addition to reducing viral infectivity, M2BP inhibits HIV-1 virion production. We provide evidence showing that M2BP inhibits HIV-1 Gag trafficking to the plasma membrane in a vimentin-dependent manner. When vimentin filaments were collapsed by treating cells with acrylamide or by overexpression of a dominant-negative mutant of vimentin, M2BP inhibition of HIV-1 virion production was significantly relieved. We further show that M2BP interacts with both HIV-1 Gag and vimentin and thereby mediates their interactions. We propose that M2BP traps HIV-1 Gag to vimentin filaments to inhibit the transportation of HIV-1 Gag to the plasma membrane. These findings uncover a novel mechanism by which a host antiviral factor inhibits HIV-1 virion production.
Circulating plant miRNAs can regulate human gene expression in vitro
Authors: Pastrello Chiara , Tsay Mike , McQuaid Rosanne , Abovsky Mark , Pasini Elisa , Shirdel Elize , Angeli Marc , Tokar Tomas , Jamnik Joseph , Kotlyar Max , Jurisicova Andrea , Kotsopoulos Joanne , El-Sohemy Ahmed , Jurisica Igor 
Published: September 2016

AbstractWhile Brassica oleracea vegetables have been linked to cancer prevention, the exact mechanism remains unknown. Regulation of gene expression by cross-species microRNAs has been previously reported; however, its link to cancer suppression remains unexplored. In this study we address both issues. We confirm plant microRNAs in human blood in a large nutrigenomics study cohort and in a randomized dose-controlled trial, finding a significant positive correlation between the daily amount of broccoli consumed and the amount of microRNA in the blood. We also demonstrate that Brassica microRNAs regulate expression of human genes and proteins in vitro, and that microRNAs cooperate with other Brassica-specific compounds in a possible cancer-preventive mechanism. Combined, we provide strong evidence and a possible multimodal mechanism for broccoli in cancer prevention.
Chemical exposure-response relationship between air pollutants and reactive oxygen species in the human respiratory tract
Authors: Lakey Pascale S. J. , Berkemeier Thomas , Tong Haijie , Arangio Andrea M. , Lucas Kurt , Pöschl Ulrich , Shiraiwa Manabu 
Published: September 2016

AbstractAir pollution can cause oxidative stress and adverse health effects such as asthma and other respiratory diseases, but the underlying chemical processes are not well characterized. Here we present chemical exposure-response relations between ambient concentrations of air pollutants and the production rates and concentrations of reactive oxygen species (ROS) in the epithelial lining fluid (ELF) of the human respiratory tract. In highly polluted environments, fine particulate matter (PM2.5) containing redox-active transition metals, quinones, and secondary organic aerosols can increase ROS concentrations in the ELF to levels characteristic for respiratory diseases. Ambient ozone readily saturates the ELF and can enhance oxidative stress by depleting antioxidants and surfactants. Chemical exposure-response relations provide a quantitative basis for assessing the relative importance of specific air pollutants in different regions of the world, showing that aerosol-induced epithelial ROS levels in polluted megacity air can be several orders of magnitude higher than in pristine rainforest air.
miR-502 medaited histone methyltransferase SET8 expression is associated with outcome of esophageal squamous cell carcinoma
Authors: Wang Cuiju , Wu Jianhua , Zhao Yue , Guo Zhanjun 
Published: September 2016

AbstractThe histone methyltransferase SET8, whose expression is regulated by miR-502 though the binding site in the 3′ UTR of SET8, implicated in cancer development. Single nucleotide polymorphism (SNP) of rs16917496 located in the miR-502 and SET8 binding site was analyzed in esophageal squamous cell carcinoma (ESCC) patients, the SET8 C/C genotype was independently associated with longer post-operative survival by multivariate analysis (relative risk, 2.250; 95% CI, 1.041–4.857; p = 0.039). Moreover, the reduced SET8 expression mediated by SET8 C/C genotype was associated with longer ESCC survival. Functional assay indicated that the SET8 knock down could inhibit proliferation and promote apoptosis of ESCC cells. The subsequent assay also showed the markedly inhibition of ESCC cell migration and invasion by SET8 knock down. Our data suggested that the altering SET8 expression, which is mediated at least partly by miR-502 through changing the binding affinity between miR-502 and SET8 3′ UTR, could modify the ESCC outcome by inhibiting the proliferation and invasion as well as promoting the apoptosis of ECSS cell. Our data indicated that SET8 was a new target for ESCC therapy.
Mapping the complete glycoproteome of virion-derived HIV-1 gp120 provides insights into broadly neutralizing antibody binding
Authors: Panico Maria , Bouché Laura , Binet Daniel , O’Connor Michael-John , Rahman Dinah , Pang Poh-Choo , Canis Kevin , North Simon J. , Desrosiers Ronald C. , Chertova Elena , Keele Brandon F. , Bess Julian W. , Lifson Jeffrey D. , Haslam Stuart M. , Dell Anne , Morris Howard R. 
Published: September 2016

AbstractThe surface envelope glycoprotein (SU) of Human immunodeficiency virus type 1 (HIV-1), gp120SU plays an essential role in virus binding to target CD4+ T-cells and is a major vaccine target. Gp120 has remarkably high levels of N-linked glycosylation and there is considerable evidence that this “glycan shield” can help protect the virus from antibody-mediated neutralization. In recent years, however, it has become clear that gp120 glycosylation can also be included in the targets of recognition by some of the most potent broadly neutralizing antibodies. Knowing the site-specific glycosylation of gp120 can facilitate the rational design of glycopeptide antigens for HIV vaccine development. While most prior studies have focused on glycan analysis of recombinant forms of gp120, here we report the first systematic glycosylation site analysis of gp120 derived from virions produced by infected T lymphoid cells and show that a single site is exclusively substituted with complex glycans. These results should help guide the design of vaccine immunogens.
Effect of land use and hydrological processes on Escherichia coli concentrations in streams of tropical, humid headwater catchments
Authors: Rochelle-Newall Emma J. , Ribolzi Olivier , Viguier Marion , Thammahacksa Chanthamousone , Silvera Norbert , Latsachack Keooudone , Dinh Rinh Pham , Naporn Piyapong , Sy Hai Tran , Soulileuth Bounsamay , Hmaimum Nikom , Sisouvanh Pem , Robain Henri , Janeau Jean-Louis , Valentin Christian , Boithias Laurie , Pierret Alain 
Published: September 2016

AbstractLack of access to clean water and adequate sanitation continues to be a major brake on development. Here we present the results of a 12-month investigation into the dynamics of Escherichia coli, a commonly used indicator of faecal contamination in water supplies, in three small, rural catchments in Laos, Thailand and Vietnam. We show that land use and hydrology are major controlling factors of E. coli concentrations in streamwater and that the relative importance of these two factors varies between the dry and wet seasons. In all three catchments, the highest concentrations were observed during the wet season when storm events and overland flow were highest. However, smaller peaks of E. coli concentration were also observed during the dry season. These latter correspond to periods of intense farming activities and small, episodic rain events. Furthermore, vegetation type, through land use and soil surface crusting, combined with mammalian presence play an important role in determining E. coli loads in the streams. Finally, sampling during stormflow revealed the importance of having appropriate sampling protocols if information on maximum contamination levels is required as grab sampling at a fixed time step may miss important peaks in E. coli numbers.
Strong coupling of Asian Monsoon and Antarctic climates on sub-orbital timescales
Authors: Chen Shitao , Wang Yongjin , Cheng Hai , Edwards R. Lawrence , Wang Xianfeng , Kong Xinggong , Liu Dianbing 
Published: September 2016

AbstractThere is increasing evidence that millennial-scale climate variability played an active role on orbital-scale climate changes, but the mechanism for this remains unclear. A 230Th-dated stalagmite δ18O record between 88 and 22 thousand years (ka) ago from Yongxing Cave in central China characterizes changes in Asian monsoon (AM) strength. After removing the 65°N insolation signal from our record, the δ18O residue is strongly anti-phased with Antarctic temperature variability on sub-orbital timescales during the Marine Isotope Stage (MIS) 3. Furthermore, once the ice volume signal from Antarctic ice core records were removed and extrapolated back to the last two glacial-interglacial cycles, we observe a linear relationship for both short- and long-duration events between Asian and Antarctic climate changes. This provides the robust evidence of a link between northern and southern hemisphere climates that operates through changes in atmospheric circulation. We find that the weakest monsoon closely associated with the warmest Antarctic event always occurred during the Terminations. This finding, along with similar shifts in the opal flux record, suggests that millennial-scale events play a key role in driving the deglaciation through positive feedbacks associated with enhanced upwelling and increasing CO2.
CollagenVI-Cre mice: A new tool to target stromal cells in secondary lymphoid organs
Authors: Prados Alejandro , Kollias George , Koliaraki Vasiliki 
Published: September 2016

AbstractStromal cells in secondary lymphoid organs (SLOs) are non-hematopoietic cells involved in the regulation of adaptive immune responses. Three major stromal populations have been identified in adult SLOs: fibroblastic reticular cells (FRCs), follicular dendritic cells (FDCs) and marginal reticular cells (MRCs). The properties of these individual populations are not clearly defined, mainly due to the lack of appropriate genetic tools, especially for MRCs. Here, we analyzed stromal cell targeting in SLOs from a transgenic mouse strain that expresses Cre recombinase under the CollagenVI promoter, using lineage tracing approaches. We show that these mice target specifically MRCs and FDCs, but not FRCs in Peyer’s patches and isolated lymphoid follicles in the intestine. In contrast, stromal cells in lymph nodes and the spleen do not express the transgene, which renders ColVI-cre mice ideal for the specific targeting of stromal cells in the gut-associated lymphoid tissue (GALT). This funding further supports the hypothesis of organ-specific stromal precursors in SLOs. Interestingly, in all tissues analyzed, there was also high specificity for perivascular cells, which have been proposed to act as FDC precursors. Taken together, ColVI-Cre mice are a useful new tool for the dissection of MRC- and FDC-specific functions and plasticity in the GALT.
Important Variation in Vibrational Properties of LiFePO4 and FePO4 Induced by Magnetism
Authors: Seifitokaldani Ali , Gheribi Aïmen E. , Phan Anh Thu , Chartrand Patrice , Dollé Mickaël 
Published: September 2016

AbstractA new thermodynamically self-consistent (TSC) method, based on the quasi-harmonic approximation (QHA), is used to obtain the Debye temperatures of LiFePO4 (LFP) and FePO4 (FP) from available experimental specific heat capacities for a wide temperature range. The calculated Debye temperatures show an interesting critical and peculiar behavior so that a steep increase in the Debye temperatures is observed by increasing the temperature. This critical behavior is fitted by the critical function and the adjusted critical temperatures are very close to the magnetic phase transition temperatures in LFP and FP. Hence, the critical behavior of the Debye temperatures is correlated with the magnetic phase transitions in these compounds. Our first-principle calculations support our conjecture that the change in electronic structures, i.e. electron density of state and electron localization function, and consequently the change in thermophysical properties due to the magnetic transition may be the reason for the observation of this peculiar behavior of the Debye temperatures.
Loss of Tau protein affects the structure, transcription and repair of neuronal pericentromeric heterochromatin
Authors: Mansuroglu Zeyni , Benhelli-Mokrani Houda , Marcato Vasco , Sultan Audrey , Violet Marie , Chauderlier Alban , Delattre Lucie , Loyens Anne , Talahari Smail , Bégard Séverine , Nesslany Fabrice , Colin Morvane , Souès Sylvie , Lefebvre Bruno , Buée Luc , Galas Marie-Christine , Bonnefoy Eliette 
Published: September 2016

AbstractPericentromeric heterochromatin (PCH) gives rise to highly dense chromatin sub-structures rich in the epigenetic mark corresponding to the trimethylated form of lysine 9 of histone H3 (H3K9me3) and in heterochromatin protein 1α (HP1α), which regulate genome expression and stability. We demonstrate that Tau, a protein involved in a number of neurodegenerative diseases including Alzheimer’s disease (AD), binds to and localizes within or next to neuronal PCH in primary neuronal cultures from wild-type mice. Concomitantly, we show that the clustered distribution of H3K9me3 and HP1α, two hallmarks of PCH, is disrupted in neurons from Tau-deficient mice (KOTau). Such altered distribution of H3K9me3 that could be rescued by overexpressing nuclear Tau protein was also observed in neurons from AD brains. Moreover, the expression of PCH non-coding RNAs, involved in PCH organization, was disrupted in KOTau neurons that displayed an abnormal accumulation of stress-induced PCH DNA breaks. Altogether, our results demonstrate a new physiological function of Tau in directly regulating neuronal PCH integrity that appears disrupted in AD neurons.
Surgical Management of Hiatal Hernia in Children with Asplenia Syndrome
Authors: Fukumoto Koji , Yamoto Masaya , Nouso Hiroshi , Kaneshiro Masakatsu , Koyama Mariko , Urushihara Naoto , Miyake Hiromu 
Published: September 2016

Purpose Patients with asplenia syndrome (AS) are likely to have upper gastrointestinal tract malformations such as hiatal hernia. This report discusses the treatment of such conditions.
Methods Seventy-five patients with AS underwent initial palliation in our institution between 1997 and 2013. Of these, 10 patients had hiatal hernia. Of the patients with hiatal hernia, 6 had brachyesophagus and 7 had microgastria.
Results Of the 10 patients with hiatal hernia, 9 underwent surgery in infancy (7 before Glenn operation, 2 after Glenn operation). Two underwent typical Toupet fundoplication, and the other 7 underwent atypical repair including reduction of the stomach. Two patients with atypical repair showed recurrence of hernia and required reoperation. Three patients required reoperation due to duodenal obstruction. Duodenal obstruction occurred due to preduodenal portal vein or abnormal vessels compressing the duodenum. Obstructive symptoms were not seen in any cases preoperatively.
Conclusions In patients with hiatal hernia, typical fundoplication is often difficult because most have concomitant brachyesophagus, microgastria, and hypoplasia of the esophageal hiatus. However, we should at least reduce the stomach to the abdominal cavity as early as possible to increase thoracic cavity volume and allow good feeding. Increasing the volume of the thoracic cavity thus makes Glenn and Fontan circulations more stable. Duodenal obstruction secondary to vascular anomalies is also common, so the anatomy in the area near the duodenum should be evaluated pre- and intraoperatively.
LncVar: a database of genetic variation associated with long non-coding genes
Authors: Chen Xiaowei , Hao Yajing , Cui Ya , Fan Zhen , He Shunmin , Luo Jianjun , Chen Runsheng 
Published: September 2016

Abstract

Motivation
Long non-coding RNAs (lncRNAs) are essential in many molecular pathways, and are frequently associated with disease but the mechanisms of most lncRNAs have not yet been characterized. Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome, including lncRNA gene regions. As the number of studies on lncRNAs grows rapidly, it is necessary to evaluate the effects of genetic variations on lncRNAs.

Results
Here, we present LncVar, a database of genetic variation associated with long non-coding genes in six species. We collected lncRNAs from the NONCODE database, and evaluated their conservation. We systematically integrated transcription factor binding sites and m6A modification sites of lncRNAs and provided comprehensive effects of SNPs on transcription and modification of lncRNAs. We collected putatively translated open reading frames (ORFs) in lncRNAs, and identified both synonymous and non-synonymous SNPs in ORFs. We also collected expression quantitative trait loci of lncRNAs from the literature. Furthermore, we identified lncRNAs in CNV regions as prognostic biomarker candidates of cancers and predicted lncRNA gene fusion events from RNA-seq data from cell lines. The LncVar database can be used as a resource to evaluate the effects of the variations on the biological function of lncRNAs.

Availability and Implementation
LncVar is available at http://bioinfo.ibp.ac.cn/LncVar.

Supplementary information
Supplementary materials are available at Bioinformatics online.
PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
Authors: Nascimento Marta , Sousa Adriano , Ramirez Mário , Francisco Alexandre P , Carriço João A , Vaz Cátia 
Published: September 2016

Abstract

Summary
High Throughput Sequencing provides a cost effective means of generating high resolution data for hundreds or even thousands of strains, and is rapidly superseding methodologies based on a few genomic loci. The wealth of genomic data deposited on public databases such as Sequence Read Archive/European Nucleotide Archive provides a powerful resource for evolutionary analysis and epidemiological surveillance. However, many of the analysis tools currently available do not scale well to these large datasets, nor provide the means to fully integrate ancillary data. Here we present PHYLOViZ 2.0, an extension of PHYLOViZ tool, a platform independent Java tool that allows phylogenetic inference and data visualization for large datasets of sequence based typing methods, including Single Nucleotide Polymorphism (SNP) and whole genome/core genome Multilocus Sequence Typing (wg/cgMLST) analysis. PHYLOViZ 2.0 incorporates new data analysis algorithms and new visualization modules, as well as the capability of saving projects for subsequent work or for dissemination of results.

Availability and Implementation
http://www.phyloviz.net/ (licensed under GPLv3).

Supplementary information
Supplementary data are available at Bioinformatics online.
TRI_tool: a web-tool for prediction of protein–protein interactions in human transcriptional regulation
Authors: Perovic Vladimir , Sumonja Neven , Gemovic Branislava , Toska Eneda , Roberts Stefan G , Veljkovic Nevena 
Published: September 2016

Abstract

Summary
The TRI_tool, a sequence-based web tool for prediction of protein interactions in the human transcriptional regulation, is intended for biomedical investigators who work on understanding the regulation of gene expression. It has an improved predictive performance due to the training on updated, human specific, experimentally validated datasets. The TRI_tool is designed to test up to 100 potential interactions with no time delay and to report both probabilities and binarized predictions.

Availability and Implementation
http://www.vin.bg.ac.rs/180/tools/tfpred.php.

Supplementary information
Supplementary data are available at Bioinformatics online.
A radiation-hydrodynamics model of accretion columns for ultra-luminous X-ray pulsars
Authors: Kawashima Tomohisa , Mineshige Shin , Ohsuga Ken , Ogawa Takumi 
Published: September 2016

Abstract
Prompted by the recent discovery of pulsed emission from an ultra-luminous X-ray source, M 82 X-2 (“ULX-pulsar”), we perform a two-dimensional radiation-hydrodynamics simulation of a supercritical accretion flow onto a neutron star through a narrow accretion column. We set an accretion column with a cone shape filled with tenuous gas with the density of 10−4 g cm−3 above a neutron star and solve the two-dimensional gas motion and radiative transfer within the column. The side boundaries are set such that radiation can freely escape, but gas cannot. Since the initial gas layer is not in a hydrostatic balance, the column gas falls onto the neutron-star surface, and thereby a shock is generated. As a result, the accretion column is composed of two regions: an upper, nearly free-fall region and a lower settling region, as noted by Basko and Sunyaev (1976, MNRAS, 175, 395). The average accretion rate is very high; ${\skew{5}\dot{M}}\sim 10^{2{--}3} L_{\rm E}/c^{2}$ (with LE being the Eddington luminosity), and so radiation energy dominates over gas internal energy entirely within the column. Despite the high accretion rate, the radiation flux in the laboratory frame is kept barely below LE/(4πr2) at a distance r in the settling region so that matter can slowly accrete. This adjustment is made possible, since a large amount of photons produced via dissipation of kinetic energy of matter can escape through the side boundaries. The total luminosity can greatly exceed LE by several orders of magnitude, whereas the apparent luminosity observed from the top of the column is much less. Due to such highly anisotropic radiation fields, the observed flux should exhibit periodic variations with the rotation period, provided that the rotation and magnetic axes are misaligned.
Auditory Cortex Characteristics in Schizophrenia: Associations With Auditory Hallucinations
Authors: Mørch-Johnsen Lynn , Nesvåg Ragnar , Jørgensen Kjetil N. , Lange Elisabeth H. , Hartberg Cecilie B. , Haukvik Unn K. , Kompus Kristiina , Westerhausen René , Osnes Kåre , Andreassen Ole A. , Melle Ingrid , Hugdahl Kenneth , Agartz Ingrid 
Published: September 2016

Abstract

Background
Neuroimaging studies have demonstrated associations between smaller auditory cortex volume and auditory hallucinations (AH) in schizophrenia. Reduced cortical volume can result from a reduction of either cortical thickness or cortical surface area, which may reflect different neuropathology. We investigate for the first time how thickness and surface area of the auditory cortex relate to AH in a large sample of schizophrenia spectrum patients.

Methods
Schizophrenia spectrum (n = 194) patients underwent magnetic resonance imaging. Mean cortical thickness and surface area in auditory cortex regions (Heschl’s gyrus [HG], planum temporale [PT], and superior temporal gyrus [STG]) were compared between patients with (AH+, n = 145) and without (AH−, n = 49) a lifetime history of AH and 279 healthy controls.

Results
AH+ patients showed significantly thinner cortex in the left HG compared to AH− patients (d = 0.43, P = .0096). There were no significant differences between AH+ and AH− patients in cortical thickness in the PT or STG, or in auditory cortex surface area in any of the regions investigated. Group differences in cortical thickness in the left HG was not affected by duration of illness or current antipsychotic medication.

Conclusions
AH in schizophrenia patients were related to thinner cortex, but not smaller surface area of the left HG, a region which includes the primary auditory cortex. The results support that structural abnormalities of the auditory cortex underlie AH in schizophrenia.