bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method
Authors: Zhang Aidi , Huang Rong , Chen Liangming , Xiong Lv , He Libo , Li Yongming , Liao Lanjie , Zhu Zuoyan , Wang Yaping 
Published: August 2017

AbstractThe molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method. In total, we identified five Y-linked scaffolds (totaling 347 Kb) and six Y-specific sequences that could be used as sex-specific markers, demonstrating the suitability of NGS-based re-sequencing of pooled DNAs for the identification of sex markers in fish. Moreover, 14 putative Y-linked genes were described for the first time. All the genes, except for un-y1, un-y2, and ubq-y, showed high similarity to their female homologs. RT-PCR revealed that ubq-y was only expressed in the male hypothalamus and pituitary. These findings provided an abundant resource for the Y chromosome of grass carp, and may help elucidate sex chromosome evolution in cyprinid fish.
Alteration of sheep coat color pattern by disruption of ASIP gene via CRISPR Cas9
Authors: Zhang Xuemei , Li Wenrong , Liu Chenxi , Peng Xinrong , Lin Jiapeng , He Sangang , Li Xuejiao , Han Bing , Zhang Ning , Wu Yangsheng , Chen Lei , Wang Liqin , MaYila  , Huang Juncheng , Liu Mingjun 
Published: August 2017

AbstractCoat color is an important characteristic and economic trait in domestic sheep. Aiming at alteration of Chinese merino sheep coat color by genome manipulation, we disrupted sheep agouti signaling protein gene by CRISPR/Cas9. A total of seven indels were identified in 5 of 6 born lambs. Each targeted lamb happened at least two kinds of modifications, and targeted lambs with multiple modifications displayed variety of coat color patterns. Three lambs with 4 bp deletion showed badgerface with black body coat color in two lambs, and brown coat color with light ventral pigmentation in another one. The black-white spotted color was observed in two lambs with 2 bp deletion. Further analysis unraveled that modifications happened in one or more than two copies of ASIP gene, and moreover, the additional spontaneous mutations of D9 and/or D5 preceding the targeting modification could also involve the formation of coat color patterns. Taken together, the entanglement of ASIP modifications by CRISPR/Cas9, spontaneous D9/D5 mutations, and ASIP gene duplications contributed to the variety of coat color patterns in targeted lambs.
Identification of ciguatoxins in a shark involved in a fatal food poisoning in the Indian Ocean
Authors: Diogène Jorge , Reverté Laia , Rambla-Alegre Maria , del Río Vanessa , de la Iglesia Pablo , Campàs Mònica , Palacios Oscar , Flores Cintia , Caixach Josep , Ralijaona Christian , Razanajatovo Iony , Pirog Agathe , Magalon Hélène , Arnich Nathalie , Turquet Jean 
Published: August 2017

AbstractSevere food poisoning events after the consumption of sharks have been reported since the 1940s; however, there has been no clear understanding of their cause. Herein, we report for the first time the presence of ciguatoxins (CTXs) in sharks. The identification by mass spectrometry of CTXs, including two new analogues, in a bull shark (Carcharhinus leucas) that was consumed by humans, causing the poisoning and death of 11 people in Madagascar in 2013 is described. Typical neurotoxic ciguatera symptoms were recorded in patients, and toxicological assays on extracts of the shark demonstrated CTX-like activity. These results confirm this episode as a ciguatera poisoning event and expand the range of pelagic fish species that are involved in ciguatera in the Indian Ocean. Additionally, gambieric acid D, a molecule originally described in CTX-producing microalgae, was identified for the first time in fish. This finding can contribute to a better understanding of trophic relations within food webs. The present work confirms that consumption of sharks from the Indian Ocean should be considered a ciguatera risk, and actions should be taken to evaluate its magnitude and risk in order to manage shark fisheries.
Biogenesis of Pro-senescent Microparticles by Endothelial Colony Forming Cells from Premature Neonates is driven by SIRT1-Dependent Epigenetic Regulation of MKK6
Authors: Simoncini Stéphanie , Chateau Anne-Line , Robert Stéphane , Todorova Dilyana , Yzydorzick Catherine , Lacroix Romaric , Ligi Isabelle , Louis Laurence , Bachelier Richard , Simeoni Umberto , Magdinier Frédérique , Dignat-George Françoise , Sabatier Florence 
Published: August 2017

AbstractSenescent cells may exert detrimental effect on microenvironment through the secretion of soluble factors and the release of extracellular vesicles, such as microparticles, key actors in ageing and cardiovascular diseases. We previously reported that sirtuin-1 (SIRT1) deficiency drives accelerated senescence and dysfunction of endothelial colony-forming cells (ECFC) in PT neonates. Because preterm birth (PT) increases the risk for cardiovascular diseases during neonatal period as well as at adulthood, we hypothesized that SIRT1 deficiency could control the biogenesis of microparticles as part of a senescence–associated secretory phenotype (SASP) of PT-ECFC and investigated the related molecular mechanisms. Compared to control ECFC, PT-ECFC displayed a SASP associated with increased release of endothelial microparticles (EMP), mediating a paracrine induction of senescence in naïve endothelial cells. SIRT1 level inversely correlated with EMP release and drives PT-ECFC vesiculation. Global transcriptomic analysis revealed changes in stress response pathways, specifically the MAPK pathway. We delineate a new epigenetic mechanism by which SIRT1 deficiency regulates MKK6/p38MAPK/Hsp27 pathway to promote EMP biogenesis in senescent ECFC. These findings deepen our understanding of the role of ECFC senescence in the disruption of endothelial homeostasis and provide potential new targets towards the control of cardiovascular risk in individuals born preterm.
A complex network analysis of ethnic conflicts and human rights violations
Authors: Sharma Kiran , Sehgal Gunjan , Gupta Bindu , Sharma Geetika , Chatterjee Arnab , Chakraborti Anirban , Shroff Gautam 
Published: August 2017

AbstractNews reports in media contain records of a wide range of socio-economic and political events in time. Using a publicly available, large digital database of news records, and aggregating them over time, we study the network of ethnic conflicts and human rights violations. Complex network analyses of the events and the involved actors provide important insights on the engaging actors, groups, establishments and sometimes nations, pointing at their long range effect over space and time. We find power law decays in distributions of actor mentions, co-actor mentions and degrees and dominance of influential actors and groups. Most influential actors or groups form a giant connected component which grows in time, and is expected to encompass all actors globally in the long run. We demonstrate how targeted removal of actors may help stop spreading unruly events. We study the cause-effect relation between types of events, and our quantitative analysis confirm that ethnic conflicts lead to human rights violations, while it does not support the converse.
(Central) Auditory Processing Disorder Grand Rounds: Multiple Cases, Multiple Causes, Multiple Outcomes
Authors: Richburg Cynthia McCormick , Atcherson Samuel R. , Findlen Ursula M. , Wakefield Sarah , Benafield Natalie J. 
Published: August 2017

PurposeThe purpose of this article was to provide multiple examples of how (central) auditory processing disorder ([C]APD) is being evaluated and treated at various audiology clinics throughout the United States.MethodThe authors present 5 cases highlighting the diagnosis and treatment of (C)APD in children and adults. Similarities and differences between these cases have been showcased through detailed histories, evaluation protocol, and treatment options. When possible, the rationale for evaluation procedures and intervention processes were described and compared with guidelines and findings within the literature.Results and ConclusionsThese cases illustrate the varied processes and clinical protocols by which children and adults are evaluated, diagnosed, counseled, and treated for (C)APD. In addition, similarities and differences between the referral source, evaluation team, developmental history, comorbidities, test battery, recommendations, and remediations were described. The multiple clinic sites, diversity of clinical philosophies, variety of test measures, and diversity of patient populations make these cases ideal for showcasing the assortment of methodologies used with patients who present with histories and characteristics consistent with (C)APD.
Visuospatial and Verbal Short-Term Memory Correlates of Vocabulary Ability in Preschool Children
Authors: Stokes Stephanie F. , Klee Thomas , Kornisch Myriam , Furlong Lisa 
Published: August 2017

BackgroundRecent studies indicate that school-age children's patterns of performance on measures of verbal and visuospatial short-term memory (STM) and working memory (WM) differ across types of neurodevelopmental disorders. Because these disorders are often characterized by early language delay, administering STM and WM tests to toddlers could improve prediction of neurodevelopmental outcomes. Toddler-appropriate verbal, but not visuospatial, STM and WM tasks are available. A toddler-appropriate visuospatial STM test is introduced.MethodTests of verbal STM, visuospatial STM, expressive vocabulary, and receptive vocabulary were administered to 92 English-speaking children aged 2–5 years.ResultsMean test scores did not differ for boys and girls. Visuospatial and verbal STM scores were not significantly correlated when age was partialed out. Age, visuospatial STM scores, and verbal STM scores accounted for unique variance in expressive (51%, 3%, and 4%, respectively) and receptive vocabulary scores (53%, 5%, and 2%, respectively) in multiple regression analyses.ConclusionReplication studies, a fuller test battery comprising visuospatial and verbal STM and WM tests, and a general intelligence test are required before exploring the usefulness of these STM tests for predicting longitudinal outcomes. The lack of an association between the STM tests suggests that the instruments have face validity and test independent STM skills.
Synthesis of α-Amino Esters via α-Nitro or α-Oxime Esters: A Review
Authors: Janin Yves , Hervin Vincent , Coutant Eloi , Gagnot Glwadys 
Published: August 2017

This review is an in-depth survey of the reported synthetic approaches for the preparation of racemic α-amino esters via the reduction of α-nitro or α-oxime ester intermediates. Accordingly, it describes the many pathways that have been designed to prepare such intermediates­. This includes synthesis starting with α-nitroacetates, dialkyl malonates, acetoacetates, diethyl oxalates as well as [2+3] or [2+4] cycloadditions using, respectively, alkyl carbonocyanidate N-oxides or alkyl 2-nitrosoacrylates. This review also contains the description of a myriad of side reactions which can occur when working with α-nitro esters­.1	Introduction2	α-Amino Esters from α-Nitroacetates via Condensation Reactions3	α-Amino Esters via C-Alkylation or C-Arylation of α-Nitroacetates4	α-Amino Esters from α-Nitroacetates Using Other Reactions5	Synthesis of α-Amino Esters via α-Oxime Esters6	Synthesis of α-Amino Esters via [2+3] Cycloadditions7	Synthesis of α-Amino Esters via [2+4] Cycloadditions8	On the Reduction of α-Oxime Esters9	Conclusion
British popular newspaper traditions
Authors: Conboy Martin 
Published: August 2017

Abstract
This article traces continuities within the development of British popular newspaper traditions from the Sunday weekly publications of the early and mid-nineteenth century, through the rise of the mass daily press and culminating in the launch of the first British newspaper that could be accurately termed “tabloid” in both format and style: the Daily Mirror. It is claimed that an explicit appeal in these newspapers to readers who see themselves as outside a privileged elite and a corresponding critical approach to elites, both political and social, has always formed part of this commercially successful manifestation of popular culture.
The Poor Man’s Guardian
Authors: Claridge Claudia 
Published: August 2017

Abstract
Radical papers like The Poor Man’s Guardian had an important role in bringing about class consciousness in nineteenth-century Britain. The newspaper linguistically constructs three groups involved in the class struggle in an extended us vs. them deictic constellation, namely the rich and powerful “capitalists” vs. the working class and the radical journalists. Strategies of delegitimisation, such as third-person forms, derogatory epithets, scare quotes, are used for the rich. The other side is split into we-the journalists and we/you-working class readers. The latter are presented positively in contrast to the rich, but also as ignorant, immature, and in need of education by the journalists. The strongly pathos-oriented rhetorical style of the paper underlines the didactic aim of the paper.
The public identity of Jack the Ripper in late nineteenth-century British newspapers
Authors: Nevala Minna 
Published: August 2017

Abstract
The article studies evaluative language in 200 newspaper articles from the latter half of 1888, focusing on the five canonical Ripper murders. The aim is to study terms used to refer to the Ripper and his murders on the basis of the parameters of intensity, solidarity, and objectivity. This pilot study discusses how in the newspapers the public identity of Jack the Ripper was ultimately developed from a plain perpetrator into a murderous maniac capable of monstrous deeds. The findings indicate that an increase in intensity seems to be linked to a decrease in both solidarity and objectivity. Thus, negative evaluation was increasingly used and person reference to the Ripper changed towards extreme negativity over a relatively short period of time.
Movement concepts approach in studies on flamenco dancing: A systematic review
Authors: Forczek Wanda , Baena‐Chicón Irene , Vargas‐Macías Alfonso 
Published: August 2017

AbstractBackground: Flamenco is a highly emotional and demanding dance form. It is important to understand how the dancer's body works in order to improve fitness levels and reduce injuries. Thus, our investigation reviewed studies on kinesiological aspects of flamenco over recent years. Methods: The review was restricted to experimental studies. Literature searches were conducted using the following databases: PubMed, Scopus, and Ebsco: SPORTDiscus with Full Text, Medline, Health Source: Nursing/Academic Edition, Health Source – Consumer Edition. After limiting the search, 180 potential articles remained for analysis. Results: A total of 27 papers on different aspects of flamenco dance were finally selected: biomechanics (14), podiatry (6), injury incidence (3), anthropometry (2), and physiology (2). These studies have applied well‐established methods from sports studies. However, we noted a number of potential limitations when applied to flamenco. Conclusions: The evidence from this review shows that flamenco dancing demands high levels of effort. Further research is required to understand how the dancer's body works in order to improve fitness levels and reduce injuries. Most of the results presented here are consistent among studies. However, there is a great scarcity of research addressing flamenco movement in a more comprehensive perspective.
Associations of Residential Socioeconomic, Food, and Built Environments With Glycemic Control in Persons With Diabetes in New York City From 2007–2013
Authors: Tabaei Bahman P , Rundle Andrew G , Wu Winfred Y , Horowitz Carol R , Mayer Victoria , Sheehan Daniel M , Chamany Shadi 
Published: August 2017

Abstract
In the present study, we examined the longitudinal associations between residential environmental factors and glycemic control in 182,756 adults with diabetes in New York City from 2007 to 2013. Glycemic control was defined as a hemoglobin A1c (HbA1c) level less than 7%. We constructed residential-level measures and performed principle component analysis to formulate a residential composite score. On the basis of this score, we divided residential areas into quintiles, with the lowest and highest quintiles reflecting the least and most advantaged residential environments, respectively. Several residential-level environmental characteristics, including more advantaged socioeconomic conditions, greater ratio of healthy food outlets to unhealthy food outlets, and residential walkability were associated with increased glycemic control. Individuals who lived continuously in the most advantaged residential areas took less time to achieve glycemic control compared with the individuals who lived continuously in the least advantaged residential areas (9.9 vs. 11.5 months). Moving from less advantaged residential areas to more advantaged residential areas was related to improved diabetes control (decrease in HbA1c = 0.40%, 95% confidence interval: 0.22, 0.55), whereas moving from more advantaged residential areas to less advantaged residential areas was related to worsening diabetes control (increase in HbA1c = 0.33%, 95% confidence interval: 0.24, 0.44). These results show that residential areas with greater resources to support healthy food and residential walkability are associated with improved glycemic control in persons with diabetes.
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development
Authors: Kaczor-Urbanowicz Karolina Elżbieta , Kim Yong , Li Feng , Galeev Timur , Kitchen Rob R , Gerstein Mark , Koyano Kikuye , Jeong Sung-Hee , Wang Xiaoyan , Elashoff David , Kang So Young , Kim Su Mi , Kim Kyoung , Kim Sung , Chia David , Xiao Xinshu , Rozowsky Joel , Wong David T W 
Published: August 2017

Abstract

Motivation
Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva‘s diagnostic potential. Thus, it motivated us to perform this study.

Results
We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva.

Availability and implementation
Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin.
psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes
Authors: Gutiérrez-Sacristán Alba , Hernández-Ferrer Carles , González Juan R , Furlong Laura I 
Published: August 2017

Abstract

Motivation
Psychiatric disorders have a great impact on morbidity and mortality. Genotype–phenotype resources for psychiatric diseases are key to enable the translation of research findings to a better care of patients. PsyGeNET is a knowledge resource on psychiatric diseases and their genes, developed by text mining and curated by domain experts.

Results
We present psygenet2r, an R package that contains a variety of functions for leveraging PsyGeNET database and facilitating its analysis and interpretation. The package offers different types of queries to the database along with variety of analysis and visualization tools, including the study of the anatomical structures in which the genes are expressed and gaining insight of gene‘s molecular function. Psygenet2r is especially suited for network medicine analysis of psychiatric disorders.

Availability and implementation
The package is implemented in R and is available under MIT license from Bioconductor (http://bioconductor.org/packages/release/bioc/html/psygenet2r.html).

Supplementary information
Supplementary data are available at Bioinformatics online.
Order and Disorder in the Extracellular Matrix
Authors: van der Horst Astrid , Wuite Gijs J. L. 
Published: August 2017

Abstract
This article examines order and disorder in the extracellular matrix (ECM). The mechanical and structural properties of the tissues in the human body are largely determined by the ECM, the fibrillar network of proteins surrounding the cells. The main component of the ECM is collagen, which self-assembles in vivo into fibrils and fibers that supply rigidity and tensile strength to the ECM. The protein is often found together with elastin, another self-assembling ECM scleroprotein, whose properties of elasticity, extensibility, and elastic recoil supplement the mechanical properties of collagen. This article first provides an overview of protein synthesis and structure, with particular emphasis on tropocollagen, tropoelastin, and recombinantly-made polypeptides. It then considers the hierarchical supramolecular organization of the ECM, collagen and elastin before concluding with an assessment of structure-function relations at the matrix level.
Biological Fluid Interfaces and Membranes
Authors: Brown Aidan T. , Cicuta Pietro 
Published: August 2017

Abstract
This article examines the properties of biological fluid interfaces and membranes, with particular emphasis on monolayers and bilayers. There are several examples of interfaces between biological fluids; the most relevant to human physiology are probably the liquid/air interfaces in the lungs and on the surface of the eyes. Both of these feature films with remarkable properties of compressibility and self-healing. After providing an overview of the constituent molecules of biological interfaces, this article reviews the current knowledge on surface films and membranes, giving context for their role in biology, but paying special attention to the basic physical ideas that underpin fundamental studies of in-vitro model systems. It also considers isolated membranes, characterized by tension, elasticity and viscous damping, as well as closed vesicles and cells where the membrane separates the cytoskeleton from the extracellular matrix.