bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diabetes, cardiac disorders and asthma as risk factors for severe organ involvement among adult dengue patients: A matched case-control study
Authors: Pang Junxiong , Hsu Jung Pu , Yeo Tsin Wen , Leo Yee Sin , Lye David C. 
Published: January 2017

AbstractProgression to severe organ involvement due to dengue infection has been associated with severe dengue disease, intensive care treatment, and mortality. However, there is a lack of understanding of the impact of pre-existing comorbidities and other risk factors of severe organ involvement among dengue adults. The aim of this retrospective case-control study is to characterize and identify risk factors that predispose dengue adults at risk of progression with severe organ involvement. This study involved 174 dengue patients who had progressed with severe organ involvement and 865 dengue patients without severe organ involvement, matched by the year of presentation of the cases, who were admitted to Tan Tock Seng Hospital between year 2005 and 2008. Age group of 60 years or older, diabetes, cardiac disorders, asthma, and having two or more pre-existing comorbidities were independent risk factors of severe organ involvement. Abdominal pain, clinical fluid accumulation, and hematocrit rise and rapid platelet count drop at presentation were significantly associated with severe organ involvement. These risk factors, when validated in a larger study, will be useful for triage by clinicians for prompt monitoring and clinical management at first presentation, to minimize the risk of severe organ involvement and hence, disease severity.
Simplifying multidimensional fermentation dataset analysis and visualization: One step closer to capturing high-quality mutant strains
Authors: Zhou Xiang , Xu Dan , Jiang Ting-Ting 
Published: January 2017

AbstractIn this study, we analyzed mutants of Clostridium acetobutylicum, an organism used in a broad range of industrial processes related to biofuel production, to facilitate future studies of bioreactor and bioprocess design and scale-up, which are very important research projects for industrial microbiology applications. To accomplish this, we generated 329 mutant strains and applied principal component analysis (PCA) to fermentation data gathered from these strains to identify a core set of independent features for comparison. By doing so, we were able to explain the differences in the mutant strains’ fermentation expression states and simplify the analysis and visualization of the multidimensional datasets related to the strains. Our study has produced a high-efficiency PCA application based on a data analytics tool that is designed to visualize screening results and to support several hundred sets of data on fermentation interactions to assist researchers in more precisely screening and capturing high-quality mutant strains. More importantly, although this study focused on the use of PCA in microbial fermentation engineering, its results are broadly applicable.
PHF14: an innate inhibitor against the progression of renal fibrosis following folic acid-induced kidney injury
Authors: Yang Bo , Chen Sixiu , Wu Ming , Zhang Lin , Ruan Mengna , Chen Xujiao , Chen Zhengjun , Mei Changlin , Mao Zhiguo 
Published: January 2017

AbstractPHF14 is a newly identified regulator of mesenchyme growth in embryonic tissues. Previous studies have shown that phf14-null mutants die just after birth due to interstitial tissue hyperplasia in major organs, including the kidneys. The aim of this study was to investigate PHF14 function in renal fibrosis. By studying the chronic kidney injury mouse model, we found that PHF14 was upregulated in fibrotic kidneys after renal insults induced by folic acid administration. Compared with wild-type mice, PHF14-null mice showed more severe renal fibrosis after pro-fibrotic stimuli. Moreover, PHF14 in rat renal fibroblasts was upregulated by transforming growth factor-β (TGF-β) stimulation; while this upregulation was inhibited when smad3 phosphorylation was blocked. A chromatin immunoprecipitation (ChIP) assay further indicated that phospho-smad3 (p-smad3) acted as a transcription factor to enhance PHF14 expression. A lack of PHF14 expression enhanced collagen I and α-smooth muscle actin (α-SMA) synthesis induced by TGF-β in vitro. PHF14 was involved in inhibition of platelet-derived growth factor (PDGF) signaling overactivation by selectively repressing PDGF receptor-α (PDGFR-α) transcription. In summary, PHF14 expression was upregulated in fibrotic models in vivo and in vitro, and the TGF-β/smad3/PHF14 pathway acted as a self-limiting mechanism in the TGF-β-dominated renal pro-fibrotic process by suppressing PDGFR-α expression.
Increased Uterine NK cell numbers and perforin expression during the implantation phase in IVF Cycles with GnRH Antagonist Protocol
Authors: Xu Bufang , Wang Jingwen , Xia Lan , Zhang Dan , Wu Xian , Zhang Aijun 
Published: January 2017

AbstractGnRH antagonist negatively affects endometrial receptivity inin vitrofertilization (IVF) cycles, however, its underlying mechanism remains unclear. To explore its target molecules, we studied endometria in the window phase of fixed GnRH antagonist, low-dose flexible GnRH antagonist, GnRH agonist long protocol, and untreated control groups. There were 384 differentially expressed genes (DEGs) in the fixed antagonist group with greater than twofold expression change compared with the control group and 197 DEGs between the fixed antagonist and agonist groups, the majority of which were associated with the natural killer (NK) cell-mediated cytotoxicity pathway. We then analysed the PRF1 and FASLG protein levels. The perforin level were significantly higher in both the antagonist groups than in other two groups, and was higher in the fixed antagonist group. Similarly, the uNK cell numbers were higher in the antagonist groups, and the highest uNK cell number occurred in the fixed group (p < 0.05). No significant differences existed in the Fas ligand levels and apoptosis rates among the three treatment groups, but were higher in the treatment groups than the control group. Together, these data indicate that GnRH antagonist may increase the uNK cell numbers and perforin expression, and this effect may be dose-dependent.
Batch effects and the effective design of single-cell gene expression studies
Authors: Tung Po-Yuan , Blischak John D. , Hsiao Chiaowen Joyce , Knowles David A. , Burnett Jonathan E. , Pritchard Jonathan K. , Gilad Yoav 
Published: January 2017

AbstractSingle-cell RNA sequencing (scRNA-seq) can be used to characterize variation in gene expression levels at high resolution. However, the sources of experimental noise in scRNA-seq are not yet well understood. We investigated the technical variation associated with sample processing using the single-cell Fluidigm C1 platform. To do so, we processed three C1 replicates from three human induced pluripotent stem cell (iPSC) lines. We added unique molecular identifiers (UMIs) to all samples, to account for amplification bias. We found that the major source of variation in the gene expression data was driven by genotype, but we also observed substantial variation between the technical replicates. We observed that the conversion of reads to molecules using the UMIs was impacted by both biological and technical variation, indicating that UMI counts are not an unbiased estimator of gene expression levels. Based on our results, we suggest a framework for effective scRNA-seq studies.
Social harassment induces anxiety-like behaviour in crayfish
Authors: Bacqué-Cazenave Julien , Cattaert Daniel , Delbecque Jean-Paul , Fossat Pascal 
Published: January 2017

AbstractSocial interactions leading to dominance hierarchies often elicit psychological disorders in mammals including harassment and anxiety. Here, we demonstrate that this sequence also occurs in an invertebrate, the crayfish Procambarus clarkii. When placed in the restricted space of an aquarium, crayfish dyads generally fight until one of the opponents suddenly escapes, thereafter clearly expressing a submissive behaviour. Nevertheless, the winner frequently keeps on displaying excessive aggressive acts, having deleterious consequences in losers and interpreted as harassment behaviour. We indeed observed that, contrary to winners, losers expressed anxiety-like behaviour (ALB) in correlation with the stress intensity they suffered during the harassment period mainly. Injections of an anxiolytic abolished ALB, confirming its homology with anxiety. A serotonin (5-HT) antagonist had the same effect, suggesting a role for 5-HT, whose brain concentrations increased much more in losers than in winners. Our findings suggest that the bases of harassment and of its anxiogenic consequences have emerged very early during evolution, and emphasize crayfish as an unexpected but potentially fruitful model for the study of these social disorders.
Chrna7 deficient mice manifest no consistent neuropsychiatric and behavioral phenotypes
Authors: Yin Jiani , Chen Wu , Yang Hongxing , Xue Mingshan , Schaaf Christian P. 
Published: January 2017

AbstractThe alpha7 nicotinic acetylcholine receptor, encoded by theCHRNA7gene, has been implicated in various psychiatric and behavioral disorders, including schizophrenia, bipolar disorder, epilepsy, autism, Alzheimer’s disease, and Parkinson’s disease, and is considered a potential target for therapeutic intervention. 15q13.3 microdeletion syndrome is a rare genetic disorder, caused by submicroscopic deletions on chromosome 15q.CHRNA7is the only gene in this locus that has been deleted entirely in cases involving the smallest microdeletions. Affected individuals manifest variable neurological and behavioral phenotypes, which commonly include developmental delay/intellectual disability, epilepsy, and autism spectrum disorder. Subsets of patients have short attention spans, aggressive behaviors, mood disorders, or schizophrenia. Previous behavioral studies suggested thatChrna7deficient mice had attention deficits, but were normal in baseline behavioral responses, learning, memory, and sensorimotor gating. Given a growing interest inCHRNA7-related diseases and a better appreciation of its associated human phenotypes, an in-depth behavioral characterization of theChrna7deficient mouse model appeared prudent. This study was designed to investigate whetherChrna7deficient mice manifest phenotypes related to those seen in human individuals, using an array of 12 behavioral assessments and electroencephalogram (EEG) recordings on freely-moving mice. Examined phenotypes included social interaction, compulsive behaviors, aggression, hyperactivity, anxiety, depression, and somatosensory gating. Our data suggests that mouse behavior and EEG recordings are not sensitive to decreasedChrna7copy number.
Bromodomain protein Brd3 promotes Ifnb1 transcription via enhancing IRF3/p300 complex formation and recruitment to Ifnb1 promoter in macrophages
Authors: Ren Wenhui , Wang Chunmei , Wang Qinlan , Zhao Dezhi , Zhao Kai , Sun Donghao , Liu Xingguang , Han Chaofeng , Hou Jin , Li Xia , Zhang Qian , Cao Xuetao , Li Nan 
Published: January 2017

AbstractAs members of bromodomain and extra-terminal motif protein family, bromodomain-containing proteins regulate a wide range of biological processes including protein scaffolding, mitosis, cell cycle progression and transcriptional regulation. The function of these bromodomain proteins (Brds) in innate immune response has been reported but the role of Brd3 remains unclear. Here we find that virus infection significantly downregulate Brd3 expression in macrophages and Brd3 knockout inhibits virus-triggered IFN-β production. Brd3 interacts with both IRF3 and p300, increases p300-mediated acetylation of IRF3, and enhances the association of IRF3 with p300 upon virus infection. Importantly, Brd3 promotes the recruitment of IRF3/p300 complex to the promoter of Ifnb1, and increases the acetylation of histone3/histone4 within the Ifnb1 promoter, leading to the enhancement of type I interferon production. Therefore, our work indicated that Brd3 may act as a coactivator in IRF3/p300 transcriptional activation of Ifnb1 and provided new epigenetic mechanistic insight into the efficient activation of the innate immune response.
TFP5 peptide, derived from CDK5-activating cofactor p35, provides neuroprotection in early-stage of adult ischemic stroke
Authors: Ji Ya-Bin , Zhuang Pei-Pei , Ji Zhong , Wu Yong-Ming , Gu Yong , Gao Xiao-Ya , Pan Su-Yue , Hu Ya-Fang 
Published: January 2017

AbstractCyclin-dependent kinase 5 (CDK5) is a multifaceted protein shown to play important roles in the central nervous system. Abundant evidence indicates that CDK5 hyperactivities associated with neuronal apoptosis and death following ischemic stroke. CDK5 activity increases when its cofactor p35 cleaves into p25 during ischemia. Theoretically, inhibition of CDK5/p25 activity or reduction of p25 would be neuroprotective. TFP5, a modified 24-aa peptide (Lys254-Ala277) derived from p35, was found to effectively inhibit CDK5 hyperactivity and improve the outcomes of Alzheimer’s disease and Parkinson’s disease in vivo. Here, we showed that intraperitoneal injection of TFP5 significantly decreased the size of ischemia in early-stage of adult ischemic stroke rats. Relative to controls, rats treated with TFP5 displayed reduced excitotoxicity, neuroinflammation, apoptosis, astrocytes damage, and blood-brain barrier disruption. Our findings suggested that TFP5 might serve as a potential therapeutic candidate for acute adult ischemic stroke.
The effects of Lactobacillus plantarum on small intestinal barrier function and mucosal gene transcription; a randomized double-blind placebo controlled trial
Authors: Mujagic Zlatan , de Vos Paul , Boekschoten Mark V. , Govers Coen , Pieters Harm-Jan H. M. , de Wit Nicole J. W. , Bron Peter A. , Masclee Ad A. M. , Troost Freddy J. 
Published: January 2017

AbstractThe aim of this study was to investigate the effects of three Lactobacillus plantarum strains on in-vivo small intestinal barrier function and gut mucosal gene transcription in human subjects. The strains were selected for their differential effects on TLR signalling and tight junction protein rearrangement, which may lead to beneficial effects in a stressed human gut mucosa. Ten healthy volunteers participated in four different intervention periods: 7-day oral intake of either L. plantarum WCFS1, CIP104448, TIFN101 or placebo, proceeded by a 4 weeks wash-out period. Lactulose-rhamnose ratio (an indicator of small intestinal permeability) increased after intake of indomethacin, which was given as an artificial stressor of the gut mucosal barrier (mean ratio 0.06 ± 0.04 to 0.10 ± 0.06, p = 0.001), but was not significantly affected by the bacterial interventions. However, analysis in small intestinal biopsies, obtained by gastroduodenoscopy, demonstrated that particularly L. plantarum TIFN101 modulated gene transcription pathways related to cell-cell adhesion with high turnover of genes involved in tight- and adhesion junction protein synthesis and degradation (e.g. actinin alpha-4, metalloproteinase-2). These effects were less pronounced for L. plantarum WCFS1 and CIP104448. In conclusion, L. plantarum TIFN101 induced the most pronounced probiotic properties with specific gene transcriptional effects on repair processes in the compromised intestine of healthy subjects.
Methylomic profiling of cortex samples from completed suicide cases implicates a role for PSORS1C3 in major depression and suicide
Authors: Murphy T M , Crawford B , Dempster E L , Hannon E , Burrage J , Turecki G , Kaminsky Z , Mill J 
Published: January 2017

AbstractMajor depressive disorder (MDD) represents a major social and economic health issue and constitutes a major risk factor for suicide. The molecular pathology of suicidal depression remains poorly understood, although it has been hypothesised that regulatory genomic processes are involved in the pathology of both MDD and suicidality. In this study, genome-wide patterns of DNA methylation were assessed in depressed suicide completers (n=20) and compared with non-psychiatric, sudden-death controls (n=20) using tissue from two cortical brain regions (Brodmann Area 11 (BA11) and Brodmann Area 25 (BA25)). Analyses focused on identifying differentially methylated regions (DMRs) associated with suicidal depression and epigenetic variation were explored in the context of polygenic risk scores for major depression and suicide. Weighted gene co-methylation network analysis was used to identify modules of co-methylated loci associated with depressed suicide completers and polygenic burden for MDD and suicide attempt. We identified a DMR upstream of the PSORS1C3 gene, subsequently validated using bisulfite pyrosequencing and replicated in a second set of suicide samples, which is characterised by significant hypomethylation in both cortical brain regions in MDD suicide cases. We also identified discrete modules of co-methylated loci associated with polygenic risk burden for suicide attempt, but not major depression. Suicide-associated co-methylation modules were enriched among gene networks implicating biological processes relevant to depression and suicidality, including nervous system development and mitochondria function. Our data suggest that there are coordinated changes in DNA methylation associated with suicide that may offer novel insights into the molecular pathology associated with depressed suicide completers.
Accuracy and computational efficiency of genomic selection with high-density SNP and whole-genome sequence data.
Authors: Wang TingTing Wang TingTing , Chen YiPing [Chen Y. P. P. ] , Hayes B. 
Published: January 2017

Abstract
The prediction of complex or quantitative traits from single nucleotide polymorphism (SNP) genotypes has transformed livestock and plant breeding, and is also playing an increasingly important role in prediction of human disease. Genomic predictions are made using a prediction equation derived from regressing the phenotypes of the individuals in a reference population on all available SNP simultaneously. Genomic selection is then selection of animals or plants for breeding based on these genomic predictions. As the rate of genetic gain that can be achieved with genomic selection is proportional to the accuracy of the genomic predictions, a key focus is now to increase the accuracy of genomic predictions. This can be achieved by increasing the size of the reference set, using denser markers, and using appropriate genomic prediction models. A wide range of genomic prediction models have been proposed, some of which use marker selection and either linear or non-linear Bayesian models for regression. The non-linear Bayesian models give higher accuracy of genomic prediction for some traits, particularly as marker density increases, but at the cost of high computational burden. Strategies to improve computational efficiency of the non-linear Bayesian methods are becoming more important, as the ultimate marker density is whole-genome sequence, and this is increasingly affordable in many species. In this paper, we review the performance of alternative models for genomic prediction. Strategies that have been proposed to improve the computational efficiency of implementing these models are evaluated. Finally, we outline what is required to enable genomic prediction from whole-genome sequence data.
A Refined Electrofishing Technique for Collecting Silver Carp: Implications for Management
Authors: Bouska Wesley W. , Glover David C. , Bouska Kristen L. , Garvey James E. 
Published: January 2017

Abstract
Detecting nuisance species at low abundance or in newly established areas is critical to developing pest management strategies. Due to their sensitivity to disturbance and erratic jumping behavior, Silver Carp Hypophthalmichthys molitrix can be difficult to collect with traditional sampling methods. We compared catch per unit effort (CPUE) of all species from a Long Term Resource Monitoring (LTRM) electrofishing protocol to an experimental electrofishing technique designed to minimize Silver Carp evasion through tactical boat maneuvering and selective application of power. Differences in CPUE between electrofishing methods were detected for 2 of 41 species collected across 2 years of sampling at 20 sites along the Illinois River. The mean catch rate of Silver Carp using the experimental technique was 2.2 times the mean catch rate of the LTRM electrofishing technique; the increased capture efficiency at low relative abundance emphasizes the utility of this method for early detection. The experimental electrofishing also collected slightly larger Silver Carp (mean: 510.7 mm TL versus 495.2 mm TL), and nearly four times as many Silver Carp independently jumped into the boat during experimental transects. Novel sampling approaches, such as the experimental electrofishing technique used in this study, should be considered to increase probability of detection for aquatic nuisance species.
Received June 9, 2016; accepted September 19, 2016 Published online January 3, 2017
Contact Selectivity for Four Fish Species Sampled with North American Standard Gill Nets
Authors: Smith Bradley J. , Blackwell Brian G. , Wuellner Melissa R. , Graeb Brian D. S. , Willis David W. 
Published: January 2017

Abstract
The American Fisheries Society (AFS) has recommended standard gears and methods for collecting North American freshwater fish data, but selectivity of these gears, including gill nets, is poorly described for most species. We calculated contact selectivity for species commonly collected with AFS standard gill nets in lakes and reservoirs of North America, including Black Bullhead Ameiurus melas, Channel Catfish Ictalurus punctatus, Walleye Sander vitreus, and Yellow Perch Perca flavescens. The normal selectivity curve provided the best fit to empirical catch data for all species. Inclusion of a tangle factor improved model fit for Black Bullhead, Channel Catfish, and Walleye, indicating that tangling is an important means of capture for these species. Channel Catfish were more susceptible to tangling than the closely related Black Bullhead, likely because larger Channel Catfish are more vulnerable to tangling by spines in the smallest meshes, whereas Black Bullhead in the same meshes were wedged. Failure to include a tangle factor for Channel Catfish and Walleye would have underestimated peak length of captured fish by 80 and 40 mm, respectively. Tangling was not an important factor in Yellow Perch capture. Total selectivity curves for each species captured with the AFS standard gill net were calculated, and relative selectivity values are provided as correction factors for size-selectivity bias. Our correction factors and modeled selectivity curves for Channel Catfish, Walleye, and Yellow Perch corroborate previous studies that modeled selectivity of the AFS standard gill net for Channel Catfish, Walleye, and Yellow Perch, but our study provided novel information on Black Bullhead. Improved selectivity information for the AFS standard gill net may help to promote further voluntary adoption of AFS standard gears and methods.
Received July 15, 2016; accepted October 24, 2016 Published online January 3, 2017