bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic differential susceptibility in literacy-delayed children: A randomized controlled trial on emergent literacy in kindergarten
Authors: Plak Rachel D. , Kegel Cornelia A. T. , Bus Adriana G. 
Published: February 2015

AbstractIn this randomized controlled trial, 508 5-year-old kindergarten children participated, of whom 257 were delayed in literacy skills because they belonged to the lowest quartile of a national standard literacy test. We tested the hypothesis that some children are more susceptible to school-entry educational interventions than their peers due to their genetic makeup, and thus whether the dopamine receptor D4 gene moderated intervention effects. Children were randomly assigned to a control condition or one of two interventions involving computer programs tailored to the literacy needs of delayed pupils: Living Letters for alphabetic knowledge and Living Books for text comprehension. Effects of Living Books met the criteria of differential susceptibility. For carriers of the dopamine receptor D4 gene seven-repeat allele (about one-third of the delayed group), the Living Books program was an important addition to the common core curriculum in kindergarten (effect size d = 0.56), whereas the program did not affect the other children (d = –0.09). The same seven-repeat carriers benefited more from Living Letters than did the noncarriers, as reflected in effect sizes of 0.63 and 0.34, respectively, although such differences did not fulfill the statistical criteria for differential susceptibility. The implications of differential susceptibility for education and regarding the crucial question “what works for whom?” are discussed.
Annexin A2 as a target endothelial cell membrane autoantigen in Behçet's disease
Authors: Chen Peng , Yan Hai , Tian Yaping , Xun Yiping , Shi Lili , Bao Ran , Zhang Huai , Chen Guangyu , Yang Chunhe , Sun Shutao , Wang Yajie , Liu Li , Zhou Yabin , Zhang Chunyan , Wang Xiaoxu , Wen Yongqiang , Bian Yongzhong , Du Hongwu 
Published: February 2015

AbstractCell membrane proteins are believed to play a critical role in the pathogenesis of autoimmune diseases. However, few membrane autoantigens have been linked with Behçet's disease. Here, a cell-chip was performed to identify autoantibody target cells and the suspected autoantigens were detected using immunoblotting. The amino acid sequences of the detected proteins were determined using LC-MALDI-TOF/TOF. Putative proteins were recombinantly expressed and purified and a corresponding ELISA was developed and clinically validated using real clinical samples. It was found that a 36-kDa membrane protein - annexin A2 - was detected in approximately one-third of the patients' blood circulation. The immunohistochemistry results showed that annexin A2 was highly expressed in vascular endothelial cells. Moreover, vascular involvement was significantly higher in the anti-annexin A2 antibody-positive group versus the anti-annexin A2 antibody-negative group among all the clinical samples analyzed, indicating that annexin A2 is a novel endothelial cell membrane antigen involved in Behçet's disease.
Multiple invasions of an infectious retrovirus in cat genomes
Authors: Shimode Sayumi , Nakagawa So , Miyazawa Takayuki 
Published: February 2015

AbstractEndogenous retroviruses (ERVs) are remnants of ancient retroviral infections of host germ-line cells. While most ERVs are defective, some are active and express viral proteins. The RD-114 virus is a replication-competent feline ERV and several feline cell lines produce infectious RD-114 viral particles. All domestic cats are considered to have an ERV locus encoding a replication-competent RD-114 virus in their genomes; however, the locus has not been identified. In this study, we investigated RD-114 virus-related proviral loci in genomes of domestic cats and found that none were capable of producing infectious viruses. We also found that all domestic cats have an RD-114 virus-related sequence on chromosome C2, termed RDRS C2a, but populations of the other RDRSs are different depending on the regions where cats live or breed. Our results indicate that RDRS C2a, the oldest RD-114-related provirus, entered the host genome before an ancestor of domestic cats started diverging and the other new RDRSs might have integrated into migrating cats in Europe. We also show that infectious RD-114 virus can be resurrected by the recombination between two non-infectious RDRSs. From these data, we conclude that cats do not harbor infectious RD-114 viral loci in their genomes and RD-114-related viruses invaded cat genomes multiple times.
Integrative analysis of differentially expressed microRNAs of pulmonary alveolar macrophages from piglets during H1N1 swine influenza A virus infection
Authors: Jiang Pengfei , Zhou Na , Chen Xinyu , Zhao Xing , Li Dengyun , Wang Fen , Bi Lijun , Zhang Deli 
Published: February 2015

AbstractH1N1 swine influenza A virus (H1N1 SwIV) is one key subtype of influenza viruses with pandemic potential. MicroRNAs (miRNAs) are endogenous small RNA molecules that regulate gene expression. MiRNAs relevant with H1N1 SwIV have rarely been reported. To understand the biological functions of miRNAs during H1N1 SwIV infection, this study profiled differentially expressed (DE) miRNAs in pulmonary alveolar macrophages from piglets during the H1N1 SwIV infection using a deep sequencing approach, which was validated by quantitative real-time PCR. Compared to control group, 70 and 16 DE miRNAs were respectively identified on post-infection day (PID) 4 and PID 7. 56 DE miRNAs were identified between PID 4 and PID 7. Our results suggest that most host miRNAs are down-regulated to defend the H1N1 SwIV infection during the acute phase of swine influenza whereas their expression levels gradually return to normal during the recovery phase to avoid the occurrence of too severe porcine lung damage. In addition, targets of DE miRNAs were also obtained, for which bioinformatics analyses were performed. Our results would be useful for investigating the functions and regulatory mechanisms of miRNAs in human influenza because pig serves as an excellent animal model to study the pathogenesis of human influenza.
Disentangling the relative effects of bushmeat availability on human nutrition in central Africa
Authors: Fa Julia E. , Olivero Jesús , Real Raimundo , Farfán Miguel A. , Márquez Ana L. , Vargas J. Mario , Ziegler Stefan , Wegmann Martin , Brown David , Margetts Barrie , Nasi Robert 
Published: February 2015

AbstractWe studied links between human malnutrition and wild meat availability within the Rainforest Biotic Zone in central Africa. We distinguished two distinct hunted mammalian diversity distributions, one in the rainforest areas (Deep Rainforest Diversity, DRD) containing taxa of lower hunting sustainability, the other in the northern rainforest-savanna mosaic, with species of greater hunting potential (Marginal Rainforest Diversity, MRD). Wild meat availability, assessed by standing crop mammalian biomass, was greater in MRD than in DRD areas. Predicted bushmeat extraction was also higher in MRD areas. Despite this, stunting of children, a measure of human malnutrition, was greater in MRD areas. Structural equation modeling identified that, in MRD areas, mammal diversity fell away from urban areas, but proximity to these positively influenced higher stunting incidence. In DRD areas, remoteness and distance from dense human settlements and infrastructures explained lower stunting levels. Moreover, stunting was higher away from protected areas. Our results suggest that in MRD areas, forest wildlife rational use for better human nutrition is possible. By contrast, the relatively low human populations in DRD areas currently offer abundant opportunities for the continued protection of more vulnerable mammals and allow dietary needs of local populations to be met.
The Endoparasitoid, Cotesia vestalis, Regulates Host Physiology by Reprogramming the Neuropeptide Transcriptional Network
Authors: Shi Min , Dong Shuai , Li Ming-tian , Yang Yan-yan , Stanley David , Chen Xue-xin 
Published: February 2015

AbstractEndoparasitoids develop inside another insect by regulating host immunity and development via maternal factors injected into hosts during oviposition. Prior results have provided insights into parasitism-induced immunosuppression, including the neuropeptide accumulation in parasitized insects. Nonetheless, our understanding of neuropeptide influence on host development and behavior is not yet complete. We posed the hypothesis that parasitization alters expression of genes encoding pro-neuropeptides and used larvae of Plutella xylostella and its endoparasitoid, Cotesia vestalis to test our hypothesis. We prepared transcriptomes from the larval P. xylostella brain-CC-CA complex and identified transcripts encoding 19 neuropeptides. All corresponding cDNAs were confirmed by RACE. Our results demonstrate that parasitism significantly down-regulated, or delayed, expression of genes encoding pro-neuropeptides within 48 h post-parasitization. Changing expression of these genes may account for the previously reported decreased feeding behavior, reduced growth rates and aborted development in the host larvae. In effect, parasitization may operate at the molecular level within the CNS to create global changes in larval host biology. The significance of our finding is that, in addition to the known effects on immunity, parasitoids influence host pro-neuropeptide gene transcription. This finding reveals a new mechanism operating in host-parasitoid relationships to the advantage of the parasitoid.
A concurrent excitation and inhibition of dopaminergic subpopulations in response to nicotine
Authors: Eddine Raphaël , Valverde Sebastien , Tolu Stefania , Dautan Daniel , Hay Audrey , Morel Carole , Cui Yihui , Lambolez Bertrand , Venance Laurent , Marti Fabio , Faure Philippe 
Published: February 2015

AbstractMidbrain dopamine (DA) neurons are key players in motivation and reward processing. Increased DA release is thought to be central in the initiation of drug addiction. Whereas dopamine neurons are generally considered to be activated by drugs such as nicotine, we report here that nicotine not only induces excitation of ventral tegmental area (VTA) DA cells but also induces inhibition of a subset of VTA DA neurons that are anatomically segregated in the medial part of the VTA. These opposite responses do not correlate with the inhibition and excitation induced by noxious stimuli. We show that this inhibition requires D2 receptor (D2-R) activation, suggesting that a dopaminergic release is involved in the mechanism. Our findings suggest a principle of concurrent excitation and inhibition of VTA DA cells in response to nicotine. It promotes unexplored roles for DA release in addiction contrasting with the classical views of reinforcement and motivation and give rise to a new interpretation of the mode of operation of the reward system.
Molecular evolution of the VP1, VP2 and VP3 genes in human rhinovirus species C
Authors: Kuroda Makoto , Niwa Shoichi , Sekizuka Tsuyoshi , Tsukagoshi Hiroyuki , Yokoyama Masaru , Ryo Akihide , Sato Hironori , Kiyota Naoko , Noda Masahiro , Kozawa Kunihisa , Shirabe Komei , Kusaka Takashi , Shimojo Naoki , Hasegawa Shunji , Sugai Kazuko , Obuchi Masatsugu , Tashiro Masato , Oishi Kazunori , Ishii Haruyuki , Kimura Hirokazu 
Published: February 2015

AbstractHuman rhinovirus species C (HRV-C) was recently discovered and this virus has been associated with various acute respiratory illnesses (ARI). However, the molecular evolution of the major antigens of this virus, including VP1, VP2 and VP3, is unknown. Thus, we performed complete VP1, VP2, and VP3 gene analyses of 139 clinical HRV-C strains using RT-PCR with newly designed primer sets and next-generation sequencing. We assessed the time-scale evolution and evolutionary rate of these genes using the Bayesian Markov chain Monte Carlo method. In addition, we calculated the pairwise distance and confirmed the positive/negative selection sites in these genes. The phylogenetic trees showed that the HRV-C strains analyzed using these genes could be dated back approximately 400 to 900 years and these strains exhibited high evolutionary rates (1.35 to 3.74 × 10−3 substitutions/site/year). Many genotypes (>40) were confirmed in the phylogenetic trees. Furthermore, no positively selected site was found in the VP1, VP2 and VP3 protein. Molecular modeling analysis combined with variation analysis suggested that the exterior surfaces of the VP1, VP2 and VP3 proteins are rich in loops and are highly variable. These results suggested that HRV-C may have an old history and unique antigenicity as an agent of various ARI.
Left Ventricular Systolic Dysfunction in Asymptomatic Black Hypertensive Subjects
Authors: Ojji Dike , Atherton John , Sliwa Karen , Alfa Jacob , Ngabea Murtala , Opie Lionel 
Published: January 2015

BACKGROUND
Hypertension has been established as one of the commonest causes of heart failure especially in sub-Saharan Africa. We have previously observed a high prevalence of left ventricular (LV) systolic dysfunction in hypertensive heart failure patients in Nigeria despite a low prevalence of ischemic heart disease. The present study was, therefore, undertaken to assess the prevalence of asymptomatic LV systolic dysfunction in hypertensive black African subjects with no history of heart failure.

METHODS
One thousand nine hundred forty-seven hypertensive subjects without heart failure presenting to the Cardiology Unit, Department of Medicine, University of Abuja Teaching Hospital, Nigeria, from April 2006 to August 2013 had clinical and echocardiographic evaluation.

RESULTS
Nine hundred fifty-three (48.9%) were males and 994 (51.1%) were females. One thousand eight hundred seventeen (93.3%) had normal LV systolic function (LV ejection fraction (LVEF) ≥ 54%), 68 (3.5%) had mild LV systolic dysfunction (LVEF 45–54%), 43 (2.3%) had moderate LV systolic dysfunction (LVEF 30–44%), and 16 (0.9%) had severe LV systolic dysfunction (LVEF &lt; 30%). Male subjects had worse LV systolic function compared to women (mean LVEF 73.2% vs. 75.6%, P value &lt; 0.0001) and diabetic subjects had worse LV systolic function compared to nondiabetic subjects (LVEF 72.3% vs. 75.7%, P = 0.02). In multivariate regression analysis, lower LVEF as a continuous variable was associated with older age, male sex, diabetes mellitus, LV mass indexed for body surface area, diastolic blood pressure, posterior wall thickness in diastole, left atrial diameter, and LV internal diameter in diastole.

CONCLUSIONS
In a cohort of asymptomatic Black hypertensive subjects, 6.7% had LV systolic dysfunction, which was associated with male gender, diabetes mellitus, and larger LV mass.
Variant Near FGF5 Has Stronger Effects on Blood Pressure in Chinese With a Higher Body Mass Index
Authors: Li Jin , Shi Jinxiu , Huang Wei , Sun Jielin , Wu Ying , Duan Qing , Luo Jingchun , Lange Leslie A. , Gordon-Larsen Penny , Zheng S. Lilly , Yuan Wentao , Wang Ying , Popkin Barry M. , Mo Zengnan , Xu Jianfeng , Du Shufa , Mohlke Karen L. , Lange Ethan M. 
Published: January 2015

BACKGROUND
The objective of this study was to investigate the genetic association of 4 candidate variants with blood pressure and test the modifying effects of environmental factors including age, sex, and body mass index (BMI).

METHODS
We used a linear mixed-effects model to test for variant main effects and variant interactions with age, sex, and BMI on systolic (SBP) and diastolic (DBP) blood pressure in 7,319 Chinese adults from the China Health and Nutrition Survey (CHNS). We attempted to replicate our significant interaction findings in 1,996 Chinese men from the Fangchenggang Area Male Health and Examination Survey (FAMHES).

RESULTS
Two variants (rs11105378 near ATP2B1 and rs1458038 near FGF5) were significantly associated (P &lt; 0.00625 = 0.05/8) with both SBP and DBP in CHNS. Variant rs1378942 near CSK was nominally associated with SBP (P = 0.01). The signal at rs1458038 exhibited a genotype-by-BMI interaction affecting blood pressure (Pinteraction = 0.0018 for SBP; Pinteraction = 0.049 for DBP), with the strongest variant effects in those with the highest BMI. In FAMHES, rs1458038 also showed stronger effects on SBP and DBP among men with the highest BMI.

CONCLUSIONS
Our findings suggest high BMI increases the effect of the blood pressure-increasing allele at rs1458038 near FGF5, further highlighting the importance of obesity prevention in reducing hypertension risk.
Prevalence of Prehypertension in Mexico and Its Association With Hypomagnesemia
Authors: Rodríguez-Ramírez Mariana , Simental-Mendía Luis E. , González-Ortiz Manuel , Martínez-Abundis Esperanza , Madero Agustín , Brito-Zurita Olga , Pérez-Fuentes Ricardo , Revilla-Monsalve Cristina , Islas-Andrade Sergio , Rodríguez-Morán Martha , Guerrero-Romero Fernando 
Published: January 2015

BACKGROUND
Prehypertension (preHTN) increases the risk of developing hypertension. The objectives of this study were to estimate the prevalence of preHTN in the Mexican adult population and evaluate the association between hypomagnesemia and preHTN.

METHODS
This study was a 2-phase, population-based study. In the first phase, 4,272 Mexican adults (aged 20–65 years) were enrolled to determine the prevalence of preHTN. In the second phase, a cross-sectional analysis was performed to evaluate the association between hypomagnesemia and preHTN. The exclusion criteria were chronic diarrhea, malignancy, hepatic and renal diseases, chronic inflammatory disease, and the intake of magnesium supplements. PreHTN was defined as a systolic blood pressure (BP) of 120–139mm Hg and/or diastolic BP of 80–89mm Hg, and hypomagnesemia was defined as a serum magnesium concentration &lt;1.8mg/dl.

RESULTS
The prevalence of preHTN was 37.5% (95% confidence interval (CI): 36.0–39.0): 46.7% were men (95% CI: 44.1–49.4) and 33.2% (95% CI: 31.5–5.0) were women. The serum magnesium data were available for 921 participants. Hypomagnesemia was identified in 276 (30.0%; 95% CI: 27.1–33.0) subjects; of them, 176 (63.8%; 95% CI: 58.3–69.6) had preHTN. Individuals with preHTN exhibited lower magnesium levels than individuals without preHTN (1.78±0.36 vs. 1.95±0.37, P &lt; 0.0005). A multiple logistic regression analysis (adjusted for age, sex, smoking, body mass index, waist circumference, fasting glucose, total cholesterol, high-density lipoprotein cholesterol, and triglycerides levels) indicated a significant association between hypomagnesemia and preHTN (odds ratio = 1.78; 95% CI: 1.5–4.0, P &lt; 0.0005).

CONCLUSIONS
The prevalence of preHTN in the Mexican population is 37.5%, and hypomagnesemia is strongly associated with preHTN.
Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data
Authors: Tobalina Luis , Bargiela Rafael , Pey Jon , Herbst Florian-Alexander , Lores Iván , Rojo David , Barbas Coral , Peláez Ana I. , Sánchez Jesús , von Bergen Martin , Seifert Jana , Ferrer Manuel , Planes Francisco J. 
Published: January 2015

AbstractMotivation: With the advent of meta-‘omics’ data, the use of metabolic networks for the functional analysis of microbial communities became possible. However, while network-based methods are widely developed for single organisms, their application to bacterial communities is currently limited.Results: Herein, we provide a novel, context-specific reconstruction procedure based on metaproteomic and taxonomic data. Without previous knowledge of a high-quality, genome-scale metabolic networks for each different member in a bacterial community, we propose a meta-network approach, where the expression levels and taxonomic assignments of proteins are used as the most relevant clues for inferring an active set of reactions. Our approach was applied to draft the context-specific metabolic networks of two different naphthalene-enriched communities derived from an anthropogenically influenced, polyaromatic hydrocarbon contaminated soil, with (CN2) or without (CN1) bio-stimulation. We were able to capture the overall functional differences between the two conditions at the metabolic level and predict an important activity for the fluorobenzoate degradation pathway in CN1 and for geraniol metabolism in CN2. Experimental validation was conducted, and good agreement with our computational predictions was observed. We also hypothesize different pathway organizations at the organismal level, which is relevant to disentangle the role of each member in the communities. The approach presented here can be easily transferred to the analysis of genomic, transcriptomic and metabolomic data.Contact: fplanes@ceit.es or mferrer@icp.csic.esSupplementary information: Supplementary data are available at Bioinformatics online.
Prediction of potential disease-associated microRNAs based on random walk
Authors: Xuan Ping , Han Ke , Guo Yahong , Li Jin , Li Xia , Zhong Yingli , Zhang Zhaogong , Ding Jian 
Published: January 2015

Abstract
Motivation: Identifying microRNAs associated with diseases (disease miRNAs) is helpful for exploring the pathogenesis of diseases. Because miRNAs fulfill function via the regulation of their target genes and because the current number of experimentally validated targets is insufficient, some existing methods have inferred potential disease miRNAs based on the predicted targets. It is difficult for these methods to achieve excellent performance due to the high false-positive and false-negative rates for the target prediction results. Alternatively, several methods have constructed a network composed of miRNAs based on their associated diseases and have exploited the information within the network to predict the disease miRNAs. However, these methods have failed to take into account the prior information regarding the network nodes and the respective local topological structures of the different categories of nodes. Therefore, it is essential to develop a method that exploits the more useful information to predict reliable disease miRNA candidates.
Results: miRNAs with similar functions are normally associated with similar diseases and vice versa. Therefore, the functional similarity between a pair of miRNAs is calculated based on their associated diseases to construct a miRNA network. We present a new prediction method based on random walk on the network. For the diseases with some known related miRNAs, the network nodes are divided into labeled nodes and unlabeled nodes, and the transition matrices are established for the two categories of nodes. Furthermore, different categories of nodes have different transition weights. In this way, the prior information of nodes can be completely exploited. Simultaneously, the various ranges of topologies around the different categories of nodes are integrated. In addition, how far the walker can go away from the labeled nodes is controlled by restarting the walking. This is helpful for relieving the negative effect of noisy data. For the diseases without any known related miRNAs, we extend the walking on a miRNA-disease bilayer network. During the prediction process, the similarity between diseases, the similarity between miRNAs, the known miRNA-disease associations and the topology information of the bilayer network are exploited. Moreover, the importance of information from different layers of network is considered. Our method achieves superior performance for 18 human diseases with AUC values ranging from 0.786 to 0.945. Moreover, case studies on breast neoplasms, lung neoplasms, prostatic neoplasms and 32 diseases further confirm the ability of our method to discover potential disease miRNAs.
Availability and implementation: A web service for the prediction and analysis of disease miRNAs is available at http://bioinfolab.stx.hk/midp/ .
Contact: guoyahong_hlju@163.com or lixia@hrbmu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.