bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Influence of OLR1 and PCSK9 Gene Polymorphisms on Ischemic Stroke: Evidence from a Meta-Analysis
Authors: Au Anthony , Griffiths Lyn R. , Cheng Kian-Kai , Wee Kooi Cheah , Irene Looi , Keat Wei Loo 
Published: December 2015

AbstractBoth OLR1 and PCSK9 genes are associated with atherosclerosis, cardiovascular disease and ischemic stroke. The overall prevalence of PCSK9 rs505151 and OLR1 rs11053646 variants in ischemic stroke were 0.005 and 0.116, respectively. However, to date, association between these polymorphisms and ischemic stroke remains inconclusive. Therefore, this first meta-analysis was carried out to clarify the presumed influence of these polymorphisms on ischemic stroke. All eligible case-control and cohort studies that met the search terms were retrieved in multiple databases. Demographic and genotyping data were extracted from each study and the meta-analysis was performed using RevMan 5.3 and Metafor R 3.2.1. The pooled odd ratios (ORs) and 95% confidence intervals (CIs) were calculated using both fixed- and random-effect models. Seven case-control studies encompassing 1897 cases and 2119 controls were critically evaluated. Pooled results from the genetic models indicated that OLR1 rs11053646 dominant (OR = 1.33, 95%  CI:1.11–1.58) and co-dominant models (OR = 1.24, 95%  CI:1.02–1.51) were significantly associated with ischemic stroke. For the PCSK9 rs505151 polymorphism, the OR of co-dominant model (OR = 1.36, 95%  CI:1.01–1.58) was found to be higher among ischemic stroke patients. In conclusion, the current meta-analysis highlighted that variant allele of OLR1 rs11053646 G > C and PCSK9 rs505151 A > G may contribute to the susceptibility risk of ischemic stroke.
Heterogeneity in the spread and control of infectious disease: consequences for the elimination of canine rabies
Authors: Ferguson Elaine A. , Hampson Katie , Cleaveland Sarah , Consunji Ramona , Deray Raffy , Friar John , Haydon Daniel T. , Jimenez Joji , Pancipane Marlon , Townsend Sunny E. 
Published: December 2015

AbstractUnderstanding the factors influencing vaccination campaign effectiveness is vital in designing efficient disease elimination programmes. We investigated the importance of spatial heterogeneity in vaccination coverage and human-mediated dog movements for the elimination of endemic canine rabies by mass dog vaccination in Region VI of the Philippines (Western Visayas). Household survey data was used to parameterise a spatially-explicit rabies transmission model with realistic dog movement and vaccination coverage scenarios, assuming a basic reproduction number for rabies drawn from the literature. This showed that heterogeneous vaccination reduces elimination prospects relative to homogeneous vaccination at the same overall level. Had the three vaccination campaigns completed in Region VI in 2010–2012 been homogeneous, they would have eliminated rabies with high probability. However, given the observed heterogeneity, three further campaigns may be required to achieve elimination with probability 0.95. We recommend that heterogeneity be reduced in future campaigns through targeted efforts in low coverage areas, even at the expense of reduced coverage in previously high coverage areas. Reported human-mediated dog movements did not reduce elimination probability, so expending limited resources on restricting dog movements is unnecessary in this endemic setting. Enhanced surveillance will be necessary post-elimination, however, given the reintroduction risk from long-distance dog movements.
Acid-sensing ion channel (ASIC) 4 predominantly localizes to an early endosome-related organelle upon heterologous expression
Authors: Schwartz Verena , Friedrich Katharina , Polleichtner Georg , Gründer Stefan 
Published: December 2015

AbstractAcid-sensing ion channels (ASICs) are voltage-independent proton-gated amiloride sensitive sodium channels, belonging to the DEG/ENaC gene family. Six different ASICs have been identified (ASIC1a, ASIC1b, ASIC2a, ASIC2b, ASIC3, ASIC4) that are activated by a drop in extracellular pH, either as homo- or heteromers. An exception is ASIC4, which is not activated by protons as a homomer and which does not contribute to functional heteromeric ASICs. Insensitivity of ASIC4 to protons and its comparatively low sequence identity to other ASICs (45%) raises the question whether ASIC4 may have different functions than other ASICs. In this study, we therefore investigated the subcellular localization of ASIC4 in heterologous cell lines, which revealed a surprising accumulation of the channel in early endosome-related vacuoles. Moreover, we identified an unique amino-terminal motif as important for forward-trafficking from the ER/Golgi to the early endosome-related compartment. Collectively, our results show that heterologously expressed ASIC4 predominantly resides in an intracellular endosomal compartment.
Annexin A1 Deficiency does not Affect Myofiber Repair but Delays Regeneration of Injured Muscles
Authors: Leikina Evgenia , Defour Aurelia , Melikov Kamran , Van der Meulen Jack H. , Nagaraju Kanneboyina , Bhuvanendran Shivaprasad , Gebert Claudia , Pfeifer Karl , Chernomordik Leonid V. , Jaiswal Jyoti K. 
Published: December 2015

AbstractRepair and regeneration of the injured skeletal myofiber involves fusion of intracellular vesicles with sarcolemma and fusion of the muscle progenitor cells respectively. In vitro experiments have identified involvement of Annexin A1 (Anx A1) in both these fusion processes. To determine if Anx A1 contributes to these processes during muscle repair in vivo, we have assessed muscle growth and repair in Anx A1-deficient mouse (AnxA1−/−). We found that the lack of Anx A1 does not affect the muscle size and repair of myofibers following focal sarcolemmal injury and lengthening contraction injury. However, the lack of Anx A1 delayed muscle regeneration after notexin-induced injury. This delay in muscle regeneration was not caused by a slowdown in proliferation and differentiation of satellite cells. Instead, lack of Anx A1 lowered the proportion of differentiating myoblasts that managed to fuse with the injured myofibers by days 5 and 7 after notexin injury as compared to the wild type (w.t.) mice. Despite this early slowdown in fusion of Anx A1−/− myoblasts, regeneration caught up at later times post injury. These results establish in vivo role of Anx A1 in cell fusion required for myofiber regeneration and not in intracellular vesicle fusion needed for repair of myofiber sarcolemma.
Population genetic analysis reveals cryptic sex in the phytopathogenic fungus Alternaria alternata
Authors: Meng Jing-Wen , Zhu Wen , He Meng-Han , Wu E-Jiao , Duan Guo-Hua , Xie Ye-Kun , Jin Yu-Jia , Yang Li-Na , Shang Li-Ping , Zhan Jiasui 
Published: December 2015

AbstractReproductive mode can impact population genetic dynamics and evolutionary landscape of plant pathogens as well as on disease epidemiology and management. In this study, we monitored the spatial dynamics and mating type idiomorphs in ~700 Alternaria alternata isolates sampled from the main potato production areas in China to infer the mating system of potato early blight. Consistent with the expectation of asexual species, identical genotypes were recovered from different locations separated by hundreds of kilometers of geographic distance and spanned across many years. However, high genotype diversity, equal MAT1-1 and MAT1-2 frequencies within and among populations, no genetic differentiation and phylogenetic association between two mating types, combined with random association amongst neutral markers in some field populations, suggested that sexual reproduction may also play an important role in the epidemics and evolution of the pathogen in at least half of the populations assayed despite the fact that no teleomorphs have been observed yet naturally or artificially. Our results indicated that A. alternata may adopt an epidemic mode of reproduction by combining many cycles of asexual propagation with fewer cycles of sexual reproduction, facilitating its adaptation to changing environments and making the disease management on potato fields even more difficult.
Brain plasticity and cognitive functions after ethanol consumption in C57BL/6J mice
Authors: Stragier E , Martin V , Davenas E , Poilbout C , Mongeau R , Corradetti R , Lanfumey L 
Published: December 2015

AbstractAcute or chronic administrations of high doses of ethanol in mice are known to produce severe cognitive deficits linked to hippocampal damage. However, we recently reported that chronic and moderate ethanol intake in C57BL/6J mice induced chromatin remodeling within the Bdnf promoters, leading to both enhanced brain-derived neurotrophic factor (BDNF) expression and hippocampal neurogenesis under free-choice protocol. We performed here a series of cellular and behavioral studies to analyze the consequences of these modifications. We showed that a 3-week chronic free-choice ethanol consumption in C57BL/6J mice led to a decrease in DNA methylation of the Bdnf gene within the CA1 and CA3 subfields of the hippocampus, and upregulated hippocampal BDNF signaling pathways mediated by ERK, AKT and CREB. However, this activation did not affect long-term potentiation in the CA1. Conversely, ethanol intake impaired learning and memory capacities analyzed in the contextual fear conditioning test and the novel object recognition task. In addition, ethanol increased behavioral perseveration in the Barnes maze test but did not alter the mouse overall spatial capacities. These data suggested that in conditions of chronic and moderate ethanol intake, the chromatin remodeling leading to BDNF signaling upregulation is probably an adaptive process, engaged via epigenetic regulations, to counteract the cognitive deficits induced by ethanol.
Nucleus accumbens deep brain stimulation in a rat model of binge eating
Authors: Doucette W T , Khokhar J Y , Green A I 
Published: December 2015

AbstractBinge eating (BE) is a difficult-to-treat behavior with high relapse rates, thus complicating several disorders including obesity. In this study, we tested the effects of high-frequency deep brain stimulation (DBS) in a rodent model of BE. We hypothesized that BE rats receiving high-frequency DBS in the nucleus accumbens (NAc) core would have reduced binge sizes compared with sham stimulation in both a ‘chronic BE’ model as well as in a ‘relapse to chronic BE’ model. Male Sprague–Dawley rats (N=18) were implanted with stimulating electrodes in bilateral NAc core, and they received either active stimulation (N=12) or sham stimulation (N=6) for the initial chronic BE experiments. After testing in the chronic BE state, rats did not engage in binge sessions for 1 month, and then resumed binge sessions (relapse to chronic BE) with active or sham stimulation (N=5–7 per group). A significant effect of intervention group was observed on binge size in the chronic BE state, but no significant difference between intervention groups was observed in the relapse to chronic BE experiments. This research, making use of both a chronic BE model as well as a relapse to chronic BE model, provides data supporting the hypothesis that DBS of the NAc core can decrease BE. Further research will be needed to learn how to increase the effect size and decrease deep brain stimulation-treatment outcome variability across the continuum of BE behavior.
Changing recruitment capacity in global fish stocks
Authors: Britten Gregory L. , Dowd Michael , Worm Boris 
Published: December 2015

Significance
Marine fish stocks play an important role in marine ecosystems and provide a source of protein for billions of people worldwide. Recent environmental changes have affected the distribution of many stocks, but it is yet unclear whether their productivity is affected as well. We show that recruitment capacity (the ability of stocks to produce surviving offspring) has been significantly altered by both environmental changes and biological changes brought about by overfishing. In total, these effects have reduced recruitment capacity by 3% of the historical maximum per decade, on average. This paper helps us to understand and track previously unrecognized changes in fish stock productivity during the early stages of their life cycle.
Target selection by natural and redesigned PUF proteins
Authors: Porter Douglas F. , Koh Yvonne Y. , VanVeller Brett , Raines Ronald T. , Wickens Marvin 
Published: December 2015

Significance
Pumilio/fem-3 mRNA binding factor (PUF) proteins have become a leading scaffold in designing proteins to bind and control RNAs at will. We analyze the effects of that reengineering across the transcriptome in vivo for the first time to our knowledge. We show that yeast Puf2p, a noncanonical PUF protein, binds more than 1,000 mRNA targets. Puf2p binds multiple UAAU elements, unlike canonical PUF proteins. We design a modified Puf2p to bind UAAG rather than UAAU, which allows us to align the protein with the binding site. In vivo, the redesigned protein binds UAAG sites. Its altered specificity redistributes the protein away from 3′UTRs, such that the protein tracks with its sites, binds throughout the mRNA and represses a novel RNA network.
Evolution of stickleback in 50 years on earthquake-uplifted islands
Authors: Lescak Emily A. , Bassham Susan L. , Catchen Julian , Gelmond Ofer , Sherbick Mary L. , von Hippel Frank A. , Cresko William A. 
Published: December 2015

SignificanceOn several Alaskan islands, phenotypically variable threespine stickleback fish now live in ponds that were formed during uplift caused by the 1964 Great Alaska Earthquake. We analyzed phenotypic and genome-wide genetic divergence of resident freshwater and oceanic threespine stickleback populations from three islands. These data support the hypothesis that the freshwater populations evolved repeatedly from their oceanic ancestors in the past half-century, and have differentiated to nearly the same extent as populations that were founded thousands of years ago. This work raises the possibility that much of the evolution that occurs when oceanic stickleback invade fresh water takes place in fewer than 50 generations after colonization, rather than gradually over thousands of years.
Human RNase L tunes gene expression by selectively destabilizing the microRNA-regulated transcriptome
Authors: Rath Sneha , Donovan Jesse , Whitney Gena , Chitrakar Alisha , Wang Wei , Korennykh Alexei 
Published: December 2015

Significance
The mammalian innate immune system recognizes double-stranded RNA (dsRNA) as a signature of infections and cell damage. Cells exposed to dsRNA release interferons to activate protective programs in surrounding tissues. One of these protective programs triggers regulated decay of intracellular RNA by the pseudokinase/endoribonuclease RNase L. Here we map the pathway of this RNA decay transcriptome-wide and identify groups of selectively destabilized human messenger RNAs. We show that RNA decay by RNase L has an important role in homeostasis and serves as a suppressor of cell adhesion. Our work defines the targets of RNase L and clarifies the role of the dsRNA-activated messenger RNA decay in the interferon response.
Dogs lap using acceleration-driven open pumping
Authors: Gart Sean , Socha John J. , Vlachos Pavlos P. , Jung Sunghwan 
Published: December 2015

Significance
Cats and dogs are assumed to drink similarly, but little is known about the actual physical mechanisms that dogs use to transport fluids when lapping. We observed the drinking behavior of a wide range of dogs across breeds and body size, and used physical experiments to mimic the motion of a dog’s tongue as it exits the water. Dogs accelerate the tongue upward more quickly than do cats, and then time their bite to coincide with the pinch-off of the column. The everyday experience of dogs as messy drinkers results from the backward curl of the tongue, which increases the size of the water column and thus enables dogs to drink more per lap than with a straight tongue.
High-energy resolution X-ray absorption and emission spectroscopy reveals insight into unique selectivity of La-based nanoparticles for CO2
Authors: Hirsch Ofer , Kvashnina Kristina O. , Luo Li , Süess Martin J. , Glatzel Pieter , Koziej Dorota 
Published: December 2015

SignificanceCO2has become a challenge for our society and we have to develop new materials for its photo-/electrocatalysis, chemoresistive sensing, and storage. Particularly, for the variety of electrochemical applications the selective interaction of CO2and charge transfer with solids is in the foreground, but their origins are poorly understood. Our story will undoubtedly showcase how to access the key information, which is relevant for electrochemical application from in situ X-ray absorption spectroscopy/X-ray emission spectroscopy studies.
Specific induction of endogenous viral restriction factors using CRISPR/Cas-derived transcriptional activators
Authors: Bogerd Hal P. , Kornepati Anand V. R. , Marshall Joy B. , Kennedy Edward M. , Cullen Bryan R. 
Published: December 2015

Significance
Cells encode several effective antiviral proteins, yet these are sometimes not expressed in infected cells. Using a synthetic transcriptional activator based on the bacterial RNA-guided DNA binding protein Cas9, we demonstrate the efficient induction of two antiviral effectors, APOBEC3G (A3G) and APOBEC3B (A3B), in human cells that normally express neither protein. A3G is susceptible to degradation by the HIV-1 Vif protein, whereas A3B is resistant to Vif. As a result, only the induced A3B inhibited wild-type HIV-1 infectivity. However, both induced factors blocked the replication of a Vif-deficient HIV-1 mutant. These data demonstrate that Cas9-derived transcription factors can effectively induce human genes that regulate virus replication, thus setting the scene for their use in genomic screens to identify such factors.
Negative membrane curvature catalyzes nucleation of endosomal sorting complex required for transport (ESCRT)-III assembly
Authors: Lee Il-Hyung , Kai Hiroyuki , Carlson Lars-Anders , Groves Jay T. , Hurley James H. 
Published: December 2015

Significance
The endosomal sorting complex required for transport (ESCRT) proteins remodel and sever membranes in a wide range of biology, including HIV budding. Electron microscopy has shown that ESCRT-III is often found in contact with concave (negatively curved) membrane surfaces. It has not been possible until now to determine whether the ESCRTs have an inherent preference for binding to concave membrane because it is difficult to make nanoscale concave membranes. Here we have made such membranes on the dimensions of an HIV budding site. We show that ESCRT-III assembly begins (nucleates) much faster on concave membranes, which explains why this complex is recruited in a rapid burst late in HIV budding.
Networks of military alliances, wars, and international trade
Authors: Jackson Matthew O. , Nei Stephen 
Published: December 2015

Significance
The incidence of interstate wars has dropped dramatically over time: The number of wars per pair of countries per year from 1950 to 2000 was roughly a 10th as high as it was from 1820 to 1949. This significant decrease in the frequency of wars correlates with a substantial increase in the number of military alliances per country and the stability of those alliances. We show that one possible explanation of this is an accompanying expansion of international trade. Increased trade decreases countries’ incentives to attack each other and increases their incentives to defend each other, leading to a stable and peaceful network of military and trade alliances that is consistent with observed data.
Transnational Public Attention in European Club Football: Current trends and driving forces
Authors: Mutz Michael 
Published: December 2015

ABSTRACT
Professional football is a highly globalized area. The paper analyses the impact of globalization on football audiences in European countries. It is argued that in the course of globalization, people are not only thrown into a transnational lifestyle, but may also develop a growing interest in what is going on outside their domestic territory. With regard to football, it is hypothesized that audiences may direct more and more attention to high-class football leagues and clubs abroad. This presumed shift of attention is empirically investigated with a new indicator: search engine queries. It is argued that queries addressing football clubs in foreign countries are expressions of transnational attention. These transnational queries are systematically analysed over a period of seven seasons (2005/2006–2011/2012). Results indicate that public attention to foreign football clubs has indeed increased over time, particularly in those countries with weaker domestic football leagues. Furthermore, the fluctuation of attention to these clubs can be explained systematically: attention increases with (a) the success of a club in European and national competitions, (b) the success of domestic players in an expatriate club and (c) the number of matches against domestic clubs in European club competitions. Although transnational attention is generally on the rise, its change over time still seems to depend largely on national identification.
Flavobacteria Isolated from the Milt of Feral Chinook Salmon of the Great Lakes
Authors: Loch T P , Faisal M 
Published: December 2015

Abstract
Fish diseases caused by multiple genera within the family Flavobacteriaceae (Phylum Bacteroidetes) are a major impediment to farmed teleosts. At least one fish-pathogenic flavobacterial species (e.g., Flavobacterium psychrophilum) is transmitted from parents to progeny via infected sexual products, but the majority of research has focused on the role that ovarian fluid and eggs play in bacterial transmission. However, a handful of studies have revealed that milt can also harbor F. psychrophilum. Herein, we report on the isolation and molecular identification of multiple Flavobacterium and Chryseobacterium spp. from the milt of feral Great Lakes Chinook Salmon Oncorhynchus tshawytscha. Some of the milt-associated flavobacteria were identified as well-known fish pathogens (e.g., F. columnare, etiological agent of columnaris disease), whereas others were most similar to emerging fish pathogens (e.g., C. piscium) or were distinct from all our described Flavobacterium and Chryseobacterium spp., according to partial 16S rRNA gene sequencing and phylogenetic analyses. Although systemic F. psychrophilum infections were detected in the kidneys of 35% of the 120 sampled male Chinook Salmon, the bacterium was never detected in the milt. The findings of this study highlight the role that milt can play in the transmission of a diversity of flavobacterial species.
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding
Authors: Chiu Tsu-Pei , Comoglio Federico , Zhou Tianyin , Yang Lin , Paro Renato , Rohs Remo 
Published: December 2015

Abstract
Summary: DNAshapeR predicts DNA shape features in an ultra-fast, high-throughput manner from genomic sequencing data. The package takes either nucleotide sequence or genomic coordinates as input and generates various graphical representations for visualization and further analysis. DNAshapeR further encodes DNA sequence and shape features as user-defined combinations of k-mer and DNA shape features. The resulting feature matrices can be readily used as input of various machine learning software packages for further modeling studies.
Availability and implementation: The DNAshapeR software package was implemented in the statistical programming language R and is freely available through the Bioconductor project at https://www.bioconductor.org/packages/devel/bioc/html/DNAshapeR.html and at the GitHub developer site, http://tsupeichiu.github.io/DNAshapeR/.
Contact: rohs@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.