bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA
Authors: Chen Xing 
Published: August 2015

AbstractAccumulating experimental studies have indicated that lncRNAs play important roles in various critical biological process and their alterations and dysregulations have been associated with many important complex diseases. Developing effective computational models to predict potential disease-lncRNA association could benefit not only the understanding of disease mechanism at lncRNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis and prevention. However, known experimentally confirmed disease-lncRNA associations are still very limited. In this study, a novel model of HyperGeometric distribution for LncRNA-Disease Association inference (HGLDA) was developed to predict lncRNA-disease associations by integrating miRNA-disease associations and lncRNA-miRNA interactions. Although HGLDA didn’t rely on any known disease-lncRNA associations, it still obtained an AUC of 0.7621 in the leave-one-out cross validation. Furthermore, 19 predicted associations for breast cancer, lung cancer and colorectal cancer were verified by biological experimental studies. Furthermore, the model of LncRNA Functional Similarity Calculation based on the information of MiRNA (LFSCM) was developed to calculate lncRNA functional similarity on a large scale by integrating disease semantic similarity, miRNA-disease associations and miRNA-lncRNA interactions. It is anticipated that HGLDA and LFSCM could be effective biological tools for biomedical research.
Association of p21 3′ UTR gene polymorphism with cancer risk: Evidence from a meta-analysis
Authors: Li Jie , Li Zhenzhen , Kan Quancheng , Sun Suke , Li Yidong , Wang Suyun 
Published: August 2015

AbstractNumerous studies have investigated the risk of cancer associated with the polymorphism of p21 3′ UTR (rs1059234 C > T), but results have been inconsistent. We performed this meta-analysis to drive a more precise estimation of the association between this polymorphism and risk of cancer. A comprehensive search was conducted to identify all case-control studies of the rs1059234 C > T polymorphism of p21 3′ UTR and cancer susceptibility. A total of eleven eligible studies, including 3,099 cases and 4,354 controls, relating to the rs1059234 polymorphism of p21 3′ UTR to the risk of cancer were identified. Multivariate and univariate methods revealed no association between this polymorphism and cancer risk. However, subgroup analysis by cancer type suggested that rs1059234 C > T polymorphism was associated with increased risk of squamous cell carcinoma of the head and neck (SCCHN) (dominant model CT + TT vs. CC: OR = 1.51, 95% CI = 1.17–1.94). No significant association was found in other subgroup analyses. This meta-analysis suggested that rs1059234 polymorphism of p21 3′ UTR may be associated with increased SCCHN risk. And larger scale primary studies are required to further evaluate the interaction of p21 3′ UTR rs1059234 polymorphism and cancer risk in specific populations.
Moyamoya disease susceptibility gene RNF213 links inflammatory and angiogenic signals in endothelial cells
Authors: Ohkubo Kazuhiro , Sakai Yasunari , Inoue Hirosuke , Akamine Satoshi , Ishizaki Yoshito , Matsushita Yuki , Sanefuji Masafumi , Torisu Hiroyuki , Ihara Kenji , Sardiello Marco , Hara Toshiro 
Published: August 2015

AbstractMoyamoya disease (MMD) is a cerebrovascular disorder characterized by occlusive lesions of the circle of Willis. To date, both environmental and genetic factors have been implicated for pathogenesis of MMD. Allelic variations in RNF213 are known to confer the risk of MMD; however, functional roles of RNF213 remain to be largely elusive. We herein report that pro-inflammatory cytokines, IFNG and TNFA, synergistically activated transcription of RNF213 both in vitro and in vivo. Using various chemical inhibitors, we found that AKT and PKR pathways contributed to the transcriptional activation of RNF213. Transcriptome-wide analysis and subsequent validation with quantitative PCR supported that endogenous expression of cell cycle-promoting genes were significantly decreased with knockdown of RNF213 in cultured endothelial cells. Consistently, these cells showed less proliferative and less angiogenic profiles. Chemical inhibitors for AKT (LY294002) and PKR (C16) disrupted their angiogenic potentials, suggesting that RNF213 and its upstream pathways cooperatively organize the process of angiogenesis. Furthermore, RNF213 down-regulated expressions of matrix metalloproteases in endothelial cells, but not in fibroblasts or other cell types. Altogether, our data illustrate that RNF213 plays unique roles in endothelial cells for proper gene expressions in response to inflammatory signals from environments.
Duration of dual antiplatelet therapy after drug-eluting stent implantation: Meta-analysis of large randomised controlled trials
Authors: Tsoi Man-Fung , Cheung Ching-Lung , Cheung Tommy Tsang , Wong Ian Chi-Kei , Kumana Cyrus Rustam , Tse Hung-Fat , Cheung Bernard Man-Yung 
Published: August 2015

AbstractPatients receive dual antiplatelet therapy (DAPT) for 6–12 months after drug-eluting stents (DES) implantation. The efficacy and safety of prolonged DAPT has been questioned. Therefore, we performed a meta-analysis on randomised trials comparing different DAPT durations. Literature was searched on trials comparing different DAPT durations. For inclusion, reports must report frequency of cardiovascular and bleeding events. Ten trials were included. Compared to 12 months, DAPT beyond 12 months was associated with fewer myocardial infarctions (OR 0.58 95%CI: 0.40–0.84) and stent thrombosis (OR 0.35 95%CI: 0.20–0.62), but more major bleeds (OR 1.60 95%CI: 1.22–2.11) and all-cause (OR 1.30 95%CI: 1.02–1.66) mortality. There was no significant alteration in risk of stroke (OR 0.93 95%CI: 0.66–1.31) or cardiac (OR 1.12 95%CI: 0.73–1.71) mortality. Compared to less than 12 months DAPT, 12 months DAPT did not reduce risk of myocardial infarction, stent thrombosis, strokes, cardiac or all-cause mortality, but increased the risk of major bleeds (OR 1.60 95%CI: 1.22–2.11). DAPT beyond 12 months reduce risk of myocardial infarction and stent thrombosis, but there is substantial increase in major bleeding risk and all-cause mortality which need to be addressed. DAPT beyond 12 months does not appear to alter the risk of stroke.
The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes
Authors: Fugmann Marina , Breier Michaela , Rottenkolber Marietta , Banning Friederike , Ferrari Uta , Sacco Vanessa , Grallert Harald , Parhofer Klaus G. , Seissler Jochen , Clavel Thomas , Lechner Andreas 
Published: August 2015

AbstractThe gut microbiota has been linked to metabolic diseases. However, information on the microbiome of young adults at risk for type 2 diabetes (T2D) is lacking. The aim of this cross-sectional analysis was to investigate whether insulin resistant women with previous gestational diabetes (pGDM), a high risk group for T2D, differ in their stool microbiota from women after a normoglycemic pregnancy (controls). Bacterial communities were analyzed by high-throughput 16S rRNA gene sequencing using fecal samples from 42 pGDM and 35 control subjects 3–16 months after delivery. Clinical characterization included a 5-point OGTT, anthropometrics, clinical chemistry markers and a food frequency questionnaire. Women with a Prevotellaceae-dominated intestinal microbiome were overrepresented in the pGDM group (p < 0.0001). Additionally, the relative abundance of the phylum Firmicutes was significantly lower in women pGDM (median 48.5 vs. 56.8%; p = 0.013). Taxa richness (alpha diversity) was similar between the two groups and with correction for multiple testing we observed no significant differences on lower taxonomic levels. These results suggest that distinctive features of the intestinal microbiota are already present in young adults at risk for T2D and that further investigations of a potential pathophysiological role of gut bacteria in early T2D development are warranted.
Chronic fetal exposure to caffeine altered resistance vessel functions via RyRs-BKCa down-regulation in rat offspring
Authors: Li Na , Li Yongmei , Gao Qinqin , Li Dawei , Tang Jiaqi , Sun Miao , Zhang Pengjie , Liu Bailin , Mao Caiping , Xu Zhice 
Published: August 2015

AbstractCaffeine modifies vascular/cardiac contractility. Embryonic exposure to caffeine altered cardiac functions in offspring. This study determined chronic influence of prenatal caffeine on vessel functions in offspring. Pregnant Sprague-Dawley rats (5-month-old) were exposed to high dose of caffeine, their offspring (5-month-old) were tested for vascular functions in mesenteric arteries (MA) and ion channel activities in smooth muscle cells. Prenatal exposure to caffeine increased pressor responses and vasoconstrictions to phenylephrine, accompanied by enhanced membrane depolarization. Large conductance Ca2+-activated K+ (BKCa) channels in buffering phenylephrine-induced vasoconstrictions was decreased, whole cell BKCa currents and spontaneous transient outward currents (STOCs) were decreased. Single channel recordings revealed reduced voltage/Ca2+ sensitivity of BKCa channels. BKCa α-subunit expression was unchanged, BKCa β1-subunit and sensitivity of BKCa to tamoxifen were reduced in the caffeine offspring as altered biophysical properties of BKCa in the MA. Simultaneous [Ca2+]i fluorescence and vasoconstriction testing showed reduced Ca2+, leading to diminished BKCa activation via ryanodine receptor Ca2+ release channels (RyRs), causing enhanced vascular tone. Reduced RyR1 was greater than that of RyR3. The results suggest that the altered STOCs activity in the caffeine offspring could attribute to down-regulation of RyRs-BKCa, providing new information for further understanding increased risks of hypertension in developmental origins.
Nano-encapsulated PCM via Pickering Emulsification
Authors: Wang Xuezhen , Zhang Lecheng , Yu Yi-Hsien , Jia Lisi , Sam Mannan M. , Chen Ying , Cheng Zhengdong 
Published: August 2015

AbstractWe designed a two-step Pickering emulsification procedure to create nano-encapsulated phase changing materials (NEPCMs) using a method whose simplicity and low energy consumption suggest promise for scale-up and mass production. Surface-modified amphiphilic zirconium phosphate (ZrP) platelets were fabricated as the Pickering emulsifiers, nonadecane was chosen as the core phase change material (PCM) and polystyrene, the shell material. The resultant capsules were submicron in size with remarkable uniformity in size distribution, which has rarely been reported. Differential scanning calorimetry (DSC) characterization showed that the capsulation efficiency of NEPCMs and they were found to be thermal stable, as characterized by the DSC data for the sample after 200 thermal cycles. NEPCMs exhibit superior mechanical stability and mobility when compared with the well-developed micro-encapsulated phase change materials (MEPCMs). NEPCMs find useful applications in thermal management, including micro-channel coolants; solar energy storage media; building temperature regulators; and thermal transfer fabrics.
Fish Community Distributions and Movements in Two Tributaries of the San Juan River, USA
Authors: Cathcart C. Nathan , Gido Keith B. , McKinstry Mark C. 
Published: August 2015

AbstractRecognizing how stream fish communities—and their habitats—differ across space and time relative to their position in stream networks (i.e., main‐stem versus tributary habitats) is increasingly important for the conservation of imperiled native fish communities in altered river networks such as those in the Colorado River basin. We studied the patterns (community composition) and processes (movements) that shape species occurrences and distributions in two tributaries of the San Juan River, Utah and New Mexico, between 2012 and 2014. Our results show that distance from the San Juan River was a strong driver of tributary fish community structure, whether through declines in species richness (Chaco Wash) or species turnover (McElmo Creek), and that these patterns coincided with habitat gradients (i.e., depth, substrate, and width). Occurrences of passive integrated transponder (PIT)–tagged fish at a stationary antenna in McElmo Creek just upstream of its confluence with the San Juan River varied by species but generally were associated with spring spawning migrations (Flannelmouth Sucker Catostomus latipinnis, Razorback Sucker Xyrauchen texanus), exploratory movements (Colorado Pikeminnow Ptychocheilus lucius), and monsoon flooding (Channel Catfish Ictalurus punctatus, Razorback Sucker). Occurrences of PIT‐tagged fish in Chaco Wash were dominated by endangered Razorback Suckers and Colorado Pikeminnows, suggesting that this habitat supplies useful habitat, forage, or both. Given the common occurrences of native fishes in these tributaries, incorporating these habitats into basinwide management actions seems necessary to fully understand the spatiotemporal dynamics of native and nonnative fish communities.
Low Variation in a Y‐Chromosomal Growth Hormone Pseudogene Relative to its Functional Autosomal Progenitor Gene in Chinook Salmon
Authors: Muttray Annette F. , Sakhrani Dionne , Withler Ruth E. , Devlin Robert H. 
Published: August 2015

AbstractMost fish species do not have single‐chromosome‐based sex determination or display cytologically distinguishable sex chromosomes. The selective forces acting on homologous sequences in diploid autosomal versus haploid sex‐chromosomal regions are expected to be distinct and thus to differentially influence genetic variation. In Chinook Salmon Oncorhynchus tshawytscha, the Y chromosome possesses a growth hormone pseudogene (ghp) that is linked to the sex‐determination locus and is derived from the functional autosomal growth hormone 2 gene (gh2). Thus, examining these two paralogues provides a model with which to study the forces affecting the persistence of genetic variation between sex‐linked and autosomal loci among individuals in Chinook Salmon populations. We characterized single‐nucleotide polymorphisms in a 1.6‐kb contiguous homologous region in gh2 and ghp in 315 individuals from 19 Chinook Salmon populations ranging from Russia to Alaska, British Columbia, and California. The ghp sequence was highly similar among individuals and populations, with variant haplotypes being detected in only 5.4% of individuals and restricted to just two populations. In contrast, gh2 variants from the most common haplotype were found in 46.7% of individuals. We detected more sites of variation in ghp (nine positions, five haplotypes) than in gh2 (three positions, five haplotypes), but these were restricted to just four genotypes for ghp, compared with nine for gh2. Selection may have caused a single Y chromosome to become fixed among most populations in this species, while the variation at the gh2 locus is maintained under diploid autosomal conditions. Since the ghp locus variants are not likely to be directly associated with strong functions, other linked Y‐chromosomal loci may have important functions that, when selected, cause Y chromosomes to either be damaged and rapidly eliminated or to have enhanced fitness and sweep through the species. Whether such loci include the sex‐determination locus itself or other functional loci is not yet known.
Multiscale Environmental Influences on Fish Assemblage Structure of South Atlantic Coastal Plain Streams
Authors: Marion Cathy A. , Scott Mark C. , Kubach Kevin M. 
Published: August 2015

AbstractSouth Atlantic coastal plain streams are unique and understudied freshwater environments that provide crucial habitats for a wide range of aquatic taxa. We investigated patterns in fish assemblages across South Carolina's coastal plain, and developed statistical models to identify the dominant multiscale abiotic environmental factors that influence assemblage structure. Cluster and indicator species analyses of fish assemblage data collected at 208 wadeable streams indicated the presence of four predominant species associations that commonly occur in the South Atlantic coastal plain, which we termed the (1) fluvial, (2) Eastern Mudminnow, (3) centrarchid, and (4) nonfluvial assemblages. A random forest analysis indicated that geographic gradients and instream habitat variables associated with velocity, channel form, stream size, depth, and large wood generally played a greater role in distinguishing fish assemblages than catchment land cover. A follow‐up principal component analysis showed that these instream habitat variables showed weak relationships with current anthropogenic land‐cover conditions. We suggest several possible explanations for our findings, including (1) a sustained dynamic equilibrium among catchment, riparian, and instream conditions over time may encourage assemblage partitioning among differential instream habitats, (2) past landscape conditions may have a greater influence on current instream habitat conditions and fish assemblage structure than current landscape conditions, (3) weak relationships between catchment land cover and instream habitats may be common in low‐elevation regions, and (4) seasonal variation in hydrologic patterns may dominantly influence instream habitat conditions and fish assemblage structure. Our study adds essential information towards a better understanding of how South Atlantic coastal plain fish assemblages respond to environmental factors across multiple spatial scales. Such knowledge will help improve management and conservation strategies, as well as assist in the development of appropriate indicators for standardized evaluations of ecological integrity.
Using Salmon Survey and Commercial Fishery Data to Index Nearshore Rearing Conditions and Recruitment of Alaskan Sablefish
Authors: Yasumiishi Ellen M. , Shotwell S. Kalei , Hanselman Dana H. , Orsi Joseph A. , Fergusson Emily A. 
Published: August 2015

Abstract
We examined physical and biological indices from Pacific salmon Oncorhynchus spp. surveys and commercial fisheries to index nearshore rearing habitats used by age-0 and age-1 Sablefish Anoplopoma fimbria in the eastern Gulf of Alaska and as indicators for their recruitment to age2 during the period 2001–2013. The best-fitting general linear model used to estimate age-2 Sablefish recruitment included chlorophyll-a concentration during late August and an index of juvenile Pink Salmon O. gorbuscha abundance during the age-0 stage of Sablefish. The model and biophysical indices from 2012 and 2013 produced a forecast of 23 million age-2 Sablefish for 2014 and a forecast of 8 million Sablefish for 2015. This study highlights the opportunity to use proxies for direct ambient physical and biological observations of rearing habitats in estimating groundfish recruitment to older ages.
Received November 6, 2014; accepted April 10, 2015
Cookiecutter: a tool for kmer-based read filtering and extraction
Authors: Starostina Ekaterina , Tamazian Gaik , Dobrynin Pavel , O’Brien Stephen , Komissarov Aleksey 
Published: August 2015

MotivationKmer-based analysis is a powerful method used in read error correction and implemented in various genome assembly tools. A number of read processing routines include extracting or removing sequence reads from the results of high-throughput sequencing experiments prior to further analysis. Here we present a new approach to sorting or filtering of raw reads based on a provided list of kmers.ResultsWe developed Cookiecutter — a computational tool for rapid read extraction or removing according to a provided list of k-mers generated from a FASTA file. Cookiecutter is based on the implementation of the Aho-Corasik algorithm and is useful in routine processing of high-throughput sequencing datasets. Cookiecutter can be used for both removing undesirable reads and read extraction from a user-defined region of interest.AvailabilityThe open-source implementation with user instructions can be obtained from GitHub:https://github.com/ad3002/Cookiecutter.
The atomic scale structure of graphene powder studied by neutron and X-ray diffraction
Authors: Woznica Natalia , Hawelek Lukasz , Fischer Henry E. , Bobrinetskiy Ivan , Burian Andrzej 
Published: August 2015

The structure of graphene obtained by chemical exfoliation of graphiteviathe oxidation/reduction procedure has been determined using wide-angle scattering of neutrons and X-rays combined with computer simulations based on classical molecular dynamics (MD). A comparison of results obtained from wide-angle neutron scattering (WANS) with the D4 neutron diffractometer dedicated for liquids and amorphous materials (Institute Laue–Langevin in Grenoble) and from wide-angle X-ray scattering (WAXS) with the laboratory Rigaku-Denki D/MAX RAPID II diffractometer has shown that both techniques provide data of a good quality that can be used to derive precise and valuable structural information about graphene. To obtain detailed structural information, the paracrystal formalism has been used along with MD simulations. The MD simulations were performed at 300 K with second-generation reactive empirical bond order potential for atoms lying in the same layer and the Lennard–Jones potential for interlayer interactions. The proposed models consist of three-layered systems, 36 Å in diameter, in which mono-vacancy, di-vacancy and Stone–Thrower–Wales types of defects are introduced. The reported results show that the WANS and WAXS methods together with the MD simulations contribute to a detailed description of the graphene materials, including the presence of topological defects, which is important as their structure at the atomic scale dramatically affects their electrical and mechanical properties.
Synthesis and investigation of the properties of tungstate-based anticorrosion pigments in coatings
Authors: Kalendova Andrea , Hájková Tereza 
Published: August 2015

Purpose
– This paper aims to synthesize anticorrosion pigments containing tungsten for paints intended for corrosion protection of metals.

Design/methodology/approach
– The anticorrosion pigments were prepared by high-temperature, solid-state synthesis from the respective oxides, carbonates and calcium metasilicate. Stoichiometric tungstates and core-shell tungstates with a nonisometric particle shape containing Ca, Sr, Zn, Mg and Fe were synthesized. The pigments were examined by X-ray diffraction analysis and by scanning electron microscopy. Paints based on an epoxy resin and containing the substances at a pigment volume concentration (PVC) = 10 volume per cent were prepared. The paints were subjected to physico-mechanical tests and to tests in corrosion atmospheres. The corrosion test results were compared to those of the paint with a commercial pigment, which is used in many industrial applications.

Findings
– The tungstate structure of each pigment was elucidated. The core-shell tungstates exhibit a nonisometric particle shape. The pigments prepared were found to impart a very good anticorrosion efficiency to the paints. A high efficiency was demonstrated for the stoichiometric tungstates containing Fe and Zn and for core-shell tungstates containing Mg and Zn.

Practical implications
– The pigments can be used with advantage for the formulation of paints intended for corrosion protection of metals. The pigments also improve the paints’ physical properties.

Originality/value
– The use of the pigments in anticorrosion paints for the protection of metals is new. The benefits include the use and the procedure of synthesis of anticorrosion pigments which are free from heavy metals and are acceptable from the environmental protection point of view. Moreover, the core-shell tungstates, whose high efficiency is comparable to that of the stoichiometric tungstates, have lower tungsten content.