bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Experimental Investigation of the Risk of Triggering Geological Disasters by Injection under Shear Stress
Authors: Liu Yixin , Xu Jiang , Peng Shoujian 
Published: December 2016

AbstractFluid injection has been applied in many fields, such as hazardous waste deep well injection, forced circulation in geothermal fields, hydraulic fracturing, and CO2 geological storage. However, current research mainly focuses on geological data statistics and the dominating effects of pore pressure. There are only a few laboratory-conditioned studies on the role of drilling boreholes and the effect of injection pressure on the borehole wall. Through experimental phenomenology, this study examines the risk of triggering geological disasters by fluid injection under shear stress. We developed a new direct shear test apparatus, coupled Hydro-Mechanical (HM), to investigate mechanical property variations when an intact rock experienced step drilling borehole, fluid injection, and fluid pressure acting on the borehole and fracture wall. We tested the peak shear stress of sandstone under different experimental conditions, which showed that drilling borehole, water injection, and increased pore pressure led to the decrease in peak shear stress. Furthermore, as pore pressure increased, peak shear stress dispersion increased due to crack propagation irregularity. Because the peak shear stress changed during the fluid injection steps, we suggest that the risk of triggering geological disaster with injection under shear stress, pore, borehole, and fluid pressure should be considered.
Acfs: accurate circRNA identification and quantification from RNA-Seq data
Authors: You Xintian , Conrad Tim OF 
Published: December 2016

AbstractCircular RNAs (circRNAs) are a group of single-stranded RNAs in closed circular form. They are splicing-generated, widely expressed in various tissues and have functional implications in development and diseases. To facilitate genome-wide characterization of circRNAs using RNA-Seq data, we present a freely available software package named acfs. Acfs allows de novo, accurate and fast identification and abundance quantification of circRNAs from single- and paired-ended RNA-Seq data. On simulated datasets, acfs achieved the highest F1 accuracy and lowest false discovery rate among current state-of-the-art tools. On real-world datasets, acfs efficiently identified more bona fide circRNAs. Furthermore, we demonstrated the power of circRNA analysis on two leukemia datasets. We identified a set of circRNAs that are differentially expressed between AML and APL samples, which might shed light on the potential molecular classification of complex diseases using circRNA profiles. Moreover, chromosomal translocation, as manifested in numerous diseases, could produce not only fusion transcripts but also fusion circRNAs of clinical relevance. Featured with high accuracy, low FDR and the ability to identify fusion circRNAs, we believe that acfs is well suited for a wide spectrum of applications in characterizing the landscape of circRNAs from non-model organisms to cancer biology.
Age-Related Progressions in Story Structure in Young Children's Narratives
Authors: Khan Kiren S. , Gugiu Mihaiela R. , Justice Laura M. , Bowles Ryan P. , Skibbe Lori E. , Piasta Shayne B. 
Published: December 2016

Purpose
Prior theoretical and empirical work has referenced several broad stages of narrative development, particularly in terms of young children's understanding of story structure. However, there is considerable variation in how story structure has been defined and assessed across these studies. The aims of the present study were threefold: (a) to test the unidimensionality of items designed to assess story-structure knowledge, (b) to examine story-structure item difficulty levels, and (c) to examine age-related progressions on individual story-structure components across 3-, 4-, 5-, and 6-year-olds.

Method

Participants included 386 children (
M
= 4.8 years,
SD
= 11.67 months) from the Narrative Assessment Protocol study (
http://www.narrativeassessment.com/
), which was designed to revise a new narrative assessment tool for children between the ages of 3 and 6 years.

Results
Factor analysis indicated that 16 of 21 items reflecting story-structure knowledge constituted a unidimensional construct. Individual story-structure item analyses further revealed that establishing subgoals and tracking the overall goals in the stories were particularly challenging for 3- and 4-year-olds.

Conclusion
These findings hold implications for refinement of theoretical models of story-structure emergence in early childhood.
Electrotonic coupling of excitable and nonexcitable cells in the heart revealed by optogenetics
Authors: Quinn T. Alexander , Camelliti Patrizia , Rog-Zielinska Eva A. , Siedlecka Urszula , Poggioli Tommaso , O'Toole Eileen T. , Knöpfel Thomas , Kohl Peter 
Published: December 2016

Significance
Heart pumping is triggered and coordinated by action potentials (APs) originating in and spreading among electrically excitable heart muscle cells (myocytes) via electrotonic coupling. Cardiac nonmyocytes are thought not to participate in AP conduction in situ, although heterocellular electrotonic coupling is common in cell culture. We used optogenetic tools involving cell-specific expression of a voltage-reporting fluorescent protein to monitor electrical activity in myocytes or nonmyocytes of mouse hearts. We confirm the suitability of this technique for measuring cell type-specific voltage signals and show that, when expressed in nonmyocytes, myocyte AP-like signals can be recorded in cryoinjured scar border tissue. This direct evidence of heterocellular electrotonic coupling in the whole heart necessitates a review of current concepts on cardiac electrical connectivity.
Direct evidence of interaction-induced Dirac cones in a monolayer silicene/Ag(111) system
Authors: Feng Ya , Liu Defa , Feng Baojie , Liu Xu , Zhao Lin , Xie Zhuojin , Liu Yan , Liang Aiji , Hu Cheng , Hu Yong , He Shaolong , Liu Guodong , Zhang Jun , Chen Chuangtian , Xu Zuyan , Chen Lan , Wu Kehui , Liu Yu-Tzu , Lin Hsin , Huang Zhi-Quan , Hsu Chia-Hsiu , Chuang Feng-Chuan , Bansil Arun , Zhou X. J. 
Published: December 2016

Significance
Silicene is a one-atom-thick 2D crystal of silicon. The low-energy Dirac cone states in silicene lie at the heart of all novel quantum phenomena and potential applications. However, so far, the evidence of Dirac cones in silicene is highly controversial. We report a direct observation of Dirac cones in monolayer silicene grown on a Ag(111) substrate. We further show that this unusual Dirac cone structure originates from the interaction of silicene with the Ag(111) substrate, establishing the case of a unique type of Dirac fermion generated through the interaction of two different constituents. The observation of Dirac cones in silicene(3 × 3)/Ag(111) opens a unique materials platform for investigating unusual quantum phenomena and for applications based on 2D silicon systems.
Unexpected central role of the androgen receptor in the spontaneous regeneration of myelin
Authors: Bielecki Bartosz , Mattern Claudia , Ghoumari Abdel M. , Javaid Sumaira , Smietanka Kaja , Abi Ghanem Charly , Mhaouty-Kodja Sakina , Ghandour M. Said , Baulieu Etienne-Emile , Franklin Robin J. M. , Schumacher Michael , Traiffort Elisabeth 
Published: December 2016

Significance
Myelin allows the rapid conduction of electrical signals and provides axons with metabolic support. It appeared relatively late in evolution in hinge-jawed vertebrates and concomitantly with the emergence of the androgen receptor (AR), hinting at a specific role for androgens in myelination. Here, we show that after demyelination of the central nervous system (CNS), the male gonad, testosterone, and AR favor astrocyte recruitment and myelin regeneration by oligodendrocytes. In their absence, astrocytes remain sparse and peripheral-type remyelination, classically associated with Schwann cells, is predominantly detected. These findings reveal a novel role of androgen signaling in CNS myelin formation and glial cell communication, with possible implications for demyelinating, psychiatric, and age-related disorders.
Simultaneous dimension reduction and adjustment for confounding variation
Authors: Lin Zhixiang , Yang Can , Zhu Ying , Duchi John , Fu Yao , Wang Yong , Jiang Bai , Zamanighomi Mahdi , Xu Xuming , Li Mingfeng , Sestan Nenad , Zhao Hongyu , Wong Wing Hung 
Published: December 2016

Significance
With the advancement in high-throughput technologies, analyzing high-dimensional data has become a common task. Dimension reduction methods have been applied to visualize and identify dominant patterns in high-dimensional data. Confounding factors, commonly observed in high-throughput biological experiments, can affect the performance of these methods, and other downstream analysis. Here, we develop a method by coupling dimension reduction with the adjustment for confounder effects. Our method is able to capture the underlying patterns, as demonstrated by a human brain exon array dataset, a model organism ENCODE RNA sequencing dataset, and simulations.
Growth hormone-releasing hormone receptor antagonists inhibit human gastric cancer through downregulation of PAK1–STAT3/NF-κB signaling
Authors: Gan Jinfeng , Ke Xiurong , Jiang Jiali , Dong Hongmei , Yao Zhimeng , Lin Yusheng , Lin Wan , Wu Xiao , Yan Shumei , Zhuang Yixuan , Chu Wai Kit , Cai Renzhi , Zhang Xianyang , Cheung Herman S. , Block Norman L. , Pang Chi Pui , Schally Andrew V. , Zhang Hao 
Published: December 2016

Significance
Gastric cancer (GC) is a leading and lethal malignancy in the world. Unfortunately, therapeutics targeting GC lag behind those of many other cancers, and the effective treatment options are limited. Here we report that increased expression of growth hormone-releasing hormone receptor (GHRH-R) in tumor specimens is significantly associated with tumorigenic progression and poor clinical outcome of GC patients. MIA-602, a highly potent GHRH-R antagonist, effectively inhibits GC growth in vitro and in vivo. The anti-neoplastic effects were mediated by blockage of the p21-activated kinase 1 (PAK1)–signal transducer and activator of transcription 3 (STAT3)/nuclear factor-κB (NF-κB) axis. Thus, GHRH-R presents a molecular marker and therapeutic target of GC, and MIA-602 demonstrates excellent therapeutic potential against human GC.
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
Authors: McCarthy Davis J , Campbell Kieran R , Lun Aaron T L , Wills Quin F 
Published: December 2016

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene expression at the level of individual cells. However, preparing raw sequence data for further analysis is not a straightforward process. Biases, artifacts and other sources of unwanted variation are present in the data, requiring substantial time and effort to be spent on pre-processing, quality control (QC) and normalization.

Results
We have developed the R/Bioconductor package scater to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. The package provides a convenient, flexible workflow to process raw sequencing reads into a high-quality expression dataset ready for downstream analysis. scater provides a rich suite of plotting tools for single-cell data and a flexible data structure that is compatible with existing tools and can be used as infrastructure for future software development.

Availability and Implementation
The open-source code, along with installation instructions, vignettes and case studies, is available through Bioconductor at http://bioconductor.org/packages/scater.

Supplementary information
Supplementary data are available at Bioinformatics online.
RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening
Authors: Wang Ling , Pang Xiaoqian , Li Yecheng , Zhang Ziying , Tan Wen 
Published: December 2016

Abstract

Summary
Evaluation of the capacity for separating actives from challenging decoys is a crucial metric of performance related to molecular docking or a virtual screening workflow. The Directory of Useful Decoys (DUD) and its enhanced version (DUD-E) provide a benchmark for molecular docking, although they only contain a limited set of decoys for limited targets. DecoyFinder was released to compensate the limitations of DUD or DUD-E for building target-specific decoy sets. However, desirable query template design, generation of multiple decoy sets of similar quality, and computational speed remain bottlenecks, particularly when the numbers of queried actives and retrieved decoys increases to hundreds or more. Here, we developed a program suite called RApid DEcoy Retriever (RADER) to facilitate the decoy-based assessment of virtual screening. This program adopts a novel database-management regime that supports rapid and large-scale retrieval of decoys, enables high portability of databases, and provides multifaceted options for designing initial query templates from a large number of active ligands and generating subtle decoy sets. RADER provides two operational modes: as a command-line tool and on a web server. Validation of the performance and efficiency of RADER was also conducted and is described.

Availability and Implementation
RADER web server and a local version are freely available at http://rcidm.org/rader/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Structural insight to mutation effects uncover a common allosteric site in class C GPCRs
Authors: Harpsøe Kasper , Boesgaard Michael W , Munk Christian , Bräuner-Osborne Hans , Gloriam David E 
Published: December 2016

Abstract

Motivation
Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry. Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics.

Results
We uncover one common site for both positive and negative modulators with different amino acid layouts that can be utilized to obtain selectivity. Additionally, we show a large potential for structure-based modulator design, especially for four orphan receptors with high similarity to the crystal structures.

Availability and Implementation
All collated mutagenesis data is available in the GPCRdb mutation browser at http://gpcrdb.org/mutations/ and can be analyzed online or downloaded in excel format.

Supplementary information
Supplementary data are available at Bioinformatics online.
Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data
Authors: Shringarpure Suyash S , Mathias Rasika A , Hernandez Ryan D , O’Connor Timothy D , Szpiech Zachary A , Torres Raul , De La Vega Francisco M , Bustamante Carlos D , Barnes Kathleen C , Taub Margaret A ,   CAAPA Consortium
Published: December 2016

Abstract

Motivation
Variant calling from next-generation sequencing (NGS) data is susceptible to false positive calls due to sequencing, mapping and other errors. To better distinguish true from false positive calls, we present a method that uses genotype array data from the sequenced samples, rather than public data such as HapMap or dbSNP, to train an accurate classifier using Random Forests. We demonstrate our method on a set of variant calls obtained from 642 African-ancestry genomes from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), sequenced to high depth (30X).

Results
We have applied our classifier to compare call sets generated with different calling methods, including both single-sample and multi-sample callers. At a False Positive Rate of 5%, our method determines true positive rates of 97.5%, 95% and 99% on variant calls obtained using Illuminas single-sample caller CASAVA, Real Time Genomics multisample variant caller, and the GATK UnifiedGenotyper, respectively. Since NGS sequencing data may be accompanied by genotype data for the same samples, either collected concurrent to sequencing or from a previous study, our method can be trained on each dataset to provide a more accurate computational validation of site calls compared to generic methods. Moreover, our method allows for adjustment based on allele frequency (e.g. a different set of criteria to determine quality for rare versus common variants) and thereby provides insight into sequencing characteristics that indicate call quality for variants of different frequencies.

Availability and Implementation
Code is available on Github at: https://github.com/suyashss/variant_validation

Supplementary information
Supplementary data are available at Bioinformatics online.
SVScore: an impact prediction tool for structural variation
Authors: Ganel Liron , Abel Haley J ,   FinMetSeq Consortium, Hall Ira M 
Published: December 2016

Abstract

Summary
Here we present SVScore, a tool for in silico structural variation (SV) impact prediction. SVScore aggregates per-base single nucleotide polymorphism (SNP) pathogenicity scores across relevant genomic intervals for each SV in a manner that considers variant type, gene features and positional uncertainty. We show that the allele frequency spectrum of high-scoring SVs is strongly skewed toward lower frequencies, suggesting that they are under purifying selection, and that SVScore identifies deleterious variants more effectively than alternative methods. Notably, our results also suggest that duplications are under surprisingly strong selection relative to deletions, and that there are a similar number of strongly pathogenic SVs and SNPs in the human population.

Availability and Implementation
SVScore is implemented in Perl and available freely at {{http://www.github.com/lganel/SVScore}} for use under the MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Cluster-Randomized Trial to Assess the Efficacy of Targeting Trachoma Treatment to Children
Authors: Amza Abdou , Kadri Boubacar , Nassirou Beido , Cotter Sun Y. , Stoller Nicole E. , Zhou Zhaoxia , Bailey Robin L. , Mabey David C. , Porco Travis C. , Keenan Jeremy D. , Gaynor Bruce D. , West Sheila K. , Lietman Thomas M. 
Published: December 2016

Abstract

Background.
The World Health Organization recommends annual treatment of entire trachoma-endemic communities, although children typically have a higher load, longer duration, and greater likelihood of infection.

Methods.
Forty-eight communities in Matameye, Niger, were randomized to annual oral azithromycin treatment of the entire community or biannual treatment of children aged 0–12 years only. Both children and adults were monitored for ocular chlamydial infection by polymerase chain reaction.

Results.
The prevalence of childhood infection was reduced in the annually treated arm from 21.2% (95% confidence interval [CI], 15.2%–28.0%) at baseline to 5.8% (95% CI, 3.2%–9.0%) at 36 months (P &lt; .001) and in the biannual arm from 20.2% (95% CI, 15.5%–25.3%) to 3.8% (95% CI, 2.2%–6.0%; P &lt; .001). Adult infection in the annual arm was reduced from 1.7% (95% CI, .9%–2.7%) to 0.3% (95% CI, .0%–.7%) and in the biannual arm from 1.2% (95% CI, .5%–2.2%) to 0.0% (95% CI, .0%–.7%; P = .005). The effect of biannual treatment of children compared with annual treatment of the entire community in both children (95% CI, –.04% to .02%) and adults (95% CI, .9%–2.7%) excluded the prespecified noninferiority threshold of 6% (P = .003 and P &lt; .001, respectively).

Conclusions.
Periodic distribution of antibiotics to children in trachoma-endemic communities reduces chlamydial infection in both children and untreated adults, suggesting a form of herd protection. Biannual treatment of children was comparable to (specifically, noninferior to) annual treatment of the entire community, and may offer lower antibiotic use and other logistical advantages.

Clinical Trials Registration.
NCT00792922.
Increased Sexually Transmitted Disease Testing Among Sexually Active Persons Receiving Medical Care for Human Immunodeficiency Virus Infection in the United States, 2009–2013
Authors: Mattson Christine L. , Bradley Heather , Beer Linda , Johnson Christopher , Pearson William S. , Shouse R. Luke ,   for the Medical Monitoring Project
Published: December 2016

Abstract

Background.
Current guidelines recommend that all sexually active human immunodeficiency virus (HIV)–infected persons be tested at least annually for syphilis, chlamydia, and gonorrhea. We examined temporal trends in syphilis, chlamydia, and gonorrhea testing among sexually active HIV-infected adults receiving medical care in the United States during 2009–2013.

Methods.
Using medical record data from the Medical Monitoring Project, a population-based HIV surveillance system, we assessed the proportion of adults receiving HIV medical care who were tested for syphilis, chlamydia, and gonorrhea in the past 12 months by year and stratified by sex and sexual behavior, age, and race/ethnicity.

Results.
During 2009–2013, the proportion of sexually active HIV-infected adults receiving medical care who were tested in the past year for all 3 examined sexually transmitted diseases (STDs) increased from 20% to 36% (PTREND &lt; .01). Overall testing for syphilis increased from 55% to 65% (PTREND &lt; .01), and significant increases were noted for the following subgroups: men who have sex with men (58% to 69%), non-Hispanic whites (48% to 64%), and all age groups with the exception of persons aged 18–29 year. Overall testing for chlamydia and gonorrhea increased from 22% to 42% (PTREND &lt; .01), and significant increases were noted for most subgroups.

Conclusions.
STD testing significantly increased among sexually active HIV-infected adults receiving medical care; however, the majority of persons were not tested for all 3 STDs in 2013. While increased testing indicates progress, testing remained far below recommended guidelines. Our findings suggest enhanced efforts may be warranted to screen all sexually active HIV-infected adults for syphilis, chlamydia, and gonorrhea.
A search for host galaxies of potentially extragalactic rotating radio transients
Authors: Rane A. , Loeb A. 
Published: December 2016

Abstract
We report on a search for host galaxies of a subset of rotating radio transients (RRATs) that possess a dispersion measure (DM) near or above the maximum Galactic value in their direction. These RRATs could have an extragalactic origin and therefore be fast radio bursts (FRBs). The sizes of related galaxies on the sky at such short distances are comparable to the beam size of a single-dish telescope (for example, the 7.0 arcmin radius of the Parkes beam). Hence, the association, if found, could be more definitive as compared to finding host galaxies for more distant FRBs. We did not find any host galaxy associated with six RRATs near the maximum Galactic DM. This result is consistent with the fact that the probability of finding an FRB host galaxy within this volume is also very small, therefore indicating a Galactic origin. We propose that future follow-up observations of such RRATs be carried out in searching for local host galaxies as well as the sources of FRBs.