bluuebunny/crossref_metadata_2025_split huggingface dataset:
VariantQC: a visual quality control report for variant evaluation
Authors: Yan Melissa Y , Ferguson Betsy , Bimber Benjamin N 
Published: July 2019

Abstract

Summary
Large scale genomic studies produce millions of sequence variants, generating datasets far too massive for manual inspection. To ensure variant and genotype data are consistent and accurate, it is necessary to evaluate variants prior to downstream analysis using quality control (QC) reports. Variant call format (VCF) files are the standard format for representing variant data; however, generating summary statistics from these files is not always straightforward. While tools to summarize variant data exist, they generally produce simple text file tables, which still require additional processing and interpretation. VariantQC fills this gap as a user friendly, interactive visual QC report that generates and concisely summarizes statistics from VCF files. The report aggregates and summarizes variants by dataset, chromosome, sample and filter type. The VariantQC report is useful for high-level dataset summary, quality control and helps flag outliers. Furthermore, VariantQC operates on VCF files, so it can be easily integrated into many existing variant pipelines.

Availability and implementation
DISCVRSeq's VariantQC tool is freely available as a Java program, with the compiled JAR and source code available from https://github.com/BimberLab/DISCVRSeq/. Documentation and example reports are available at https://bimberlab.github.io/DISCVRSeq/.
Advances in the phylogeny of the South American cool-season grass genus Chascolytrum (Poaceae, Pooideae): a new infrageneric classification
Authors: Da Silva Leonardo Nogueira , Essi Liliana , Iganci João Ricardo Vieira , Souza-Chies Tatiana Teixeira De 
Published: July 2019

Abstract
Chascolytrum, as currently circumscribed, includes 22–23 South American species that were previously included in nine different genera (Chascolytrum, Briza, Poidium, Calotheca, Microbriza, Gymnachne, Rhombolytrum, Lombardochloa and Erianthecium). Due to the remarkable morphological diversity, the relationships in Chascolytrum s.l. have remained poorly understood, and no infrageneric classification could be proposed based on the latest molecular phylogenetic studies. In this study, we combined molecular (GBSSI, trnL-trnL-trnF and rps16 intron) and morphological characters to investigate the phylogenetic relationships in Chascolytrum s.l. Based on this, morphologically diagnosable clades were recognized as eight sections (Calotheca, Chascolytrum, Hildaea, Lombardochloa, Microbriza, Obovatae, Poidium and Tricholemma), of which three are new and three are monospecific. We describe each section and discuss the new infrageneric classification in comparison with the previous infrageneric classification proposed for the group under the genus Briza. A taxonomic key and images for most of the species in each section are provided. Last, the use of single-copy nuclear genes and morphological data for future phylogenetic reconstructions encompassing Chascolytrum is highlighted.
Effect of vacuum-carbonization treatment of soft carbon anodes derived from coal-based mesophase pitch for lithium-ion batteries
Authors: Pan Guanghong , Liang Wenbin , Liang Peng , Chen Quanbin 
Published: July 2019

AbstractDevelopment of new power anode material with both high capacity and high-rate capability for lithium-ion batteries is highly desired. In this paper, a novel soft carbon anode for rechargeable lithium-ion batteries was developed using coal-based mesophase pitch. The structures of the materials were characterized by X-ray diffraction (XRD), Raman, N2 adsorption–desorption, Scanning Electron Microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). The electrochemical characteristics of the new anode material were investigated. It was found that the soft carbon anode from coal-based mesophase pitch carbonized under vacuum conditions can deliver higher energy density and higher rate capability compared to soft carbon carbonized under a nitrogen atmosphere. The enhanced electrochemical properties are attributed to smaller nanocrystallites, more porosity, defects and carbon species of the resulting anode material.
Vertical Fiscal Externalities and Federal Tax-Transfers under Variable Factor Supplies
Authors: Tsakiris Nikos , Hatzipanayotou Panos , Michael Michael S 
Published: July 2019

Abstract
Within a model of variable supply of capital due to international mobility and variable labor supply due to endogenous labor-leisure choice, we revisit the issues of vertical fiscal externalities, and of federal tax-transfers. Capital and labor taxes by federal and state governments finance the provision of federal and of state public consumption goods. When capital and labor are substitutes in production, we show that (i) the state’s optimal policy calls for capital and labor taxes, (ii) the vertical fiscal externality can be reversed from negative, implying inefficiently high noncooperative capital taxes, to positive, implying inefficiently low noncooperative capital taxes, and (iii) under centralized leadership the federal government replicates the second best optimum with a capital tax, and possibly, top-down transfers. (JEL codes: F18, F21, H21).
Influencer identification in dynamical complex systems
Authors: Pei Sen , Wang Jiannan , Morone Flaviano , Makse Hernán A 
Published: July 2019

AbstractThe integrity and functionality of many real-world complex systems hinge on a small set of pivotal nodes, or influencers. In different contexts, these influencers are defined as either structurally important nodes that maintain the connectivity of networks, or dynamically crucial units that can disproportionately impact certain dynamical processes. In practice, identification of the optimal set of influencers in a given system has profound implications in a variety of disciplines. In this review, we survey recent advances in the study of influencer identification developed from different perspectives, and present state-of-the-art solutions designed for different objectives. In particular, we first discuss the problem of finding the minimal number of nodes whose removal would breakdown the network (i.e. the optimal percolation or network dismantle problem), and then survey methods to locate the essential nodes that are capable of shaping global dynamics with either continuous (e.g. independent cascading models) or discontinuous phase transitions (e.g. threshold models). We conclude the review with a summary and an outlook.
Aortic valve replacement-induced changes in native T1 are related to prognosis in severe aortic stenosis: T1 mapping cardiac magnetic resonance imaging study
Authors: Hwang In-Chang , Kim Hyung-Kwan , Park Jun-Bean , Park Eun-Ah , Lee Whal , Lee Seung-Pyo , Kim Yong-Jin , Sohn Dae-Won , Oh Jae K 
Published: July 2019

Abstract

Aims
Native T1 times from T1 mapping cardiac magnetic resonance (CMR) are associated with myocardial fibrosis in aortic stenosis (AS). We investigated whether changing patterns in native T1 predict clinical outcomes after aortic valve replacement (AVR) in severe AS patients.

Methods and results
Forty-three patients with severe AS (65.9 ± 8.1 years; 24 men) who underwent T1 mapping CMR at baseline and 1 year after AVR were prospectively enrolled. Upper limit of native T1 from healthy volunteers was used to define normal myocardium and diffuse fibrosis (native T1 &lt; 1208.4 and ≥1208.4 ms, respectively). Participants were categorized into Group 1 (pre- and post-AVR normal myocardium; n = 11), Group 2 (pre-AVR diffuse fibrosis and post-AVR normal myocardium; n = 18), and Group 3 (post-AVR diffuse fibrosis; n = 14). Native T1 significantly decreased 1 year after AVR (pre-AVR, 1233.8 ± 49.7 ms; post-AVR, 1189.1 ± 58.4 ms; P &lt; 0.001), which was associated with left ventricular (LV) mass regression (△native T1 vs. △LV mass index, r = 0.454, P = 0.010) and systolic function improvement (△native T1 vs. △LV ejection fraction, r = −0.379, P = 0.012). Group 2 showed greater functional improvements, whereas these benefits were blunted in Group 3. Group 3 had significantly worse outcomes than Group 1 [hazard ratio (HR), 9.479, 95% confidence interval (CI) 1.176–76.409; P = 0.035] and Group 2 (HR 3.551, 95% CI 1.178–10.704; P = 0.024).

Conclusion
AVR-induced changes in native T1 values are associated with LV systolic functional changes as well as prognosis in severe AS. Post-AVR T1 mapping CMR can be used as an imaging biomarker.
Prolonged mental health sequelae among doctors and nurses involved in patient safety incidents with formal complaints and lawsuits
Authors: Zeeman Gerda , Schouten Loes , Seys Deborah , Coeckelberghs Ellen , Weijenborg Philomeen , Bruyneel Luk , Vanhaecht Kris 
Published: July 2019

Abstract
We evaluated the presence of prolonged mental health sequelae in the aftermath of a patient safety incident and the impact of a formal complaint or lawsuit on these mental health sequelae in 19 hospitals and 2635 nurses and doctors. Of 2635 respondents, 983 (37.3%) reported a complaint and 190 (7.2%) reported a lawsuit. In both doctors and nurses prolonged mental health sequelae reflecting a stressor-related disorder were highly prevalent, each well over 20% overall. They were consistently more prevalent in case of a formal complaint or lawsuit. Lawsuits showed 2-, 3- and 4-fold increases in prevalence of mental health sequelae.
Neighborhood Experiences of People Over Age 50: Factor Structure and Validity of a Scale
Authors: Gan Daniel Rong Yao , Fung John Chye , Cho Im Sik 
Published: July 2019

AbstractBackground and ObjectivesVarious aspects of the neighborhood environment have been shown to correlate with older adults’ health. Socio-ecological models of health posit that interventions in the living environment can influence population health. Yet, there are no scales to comprehensively measure older people’s experiences of their neighborhoods especially in dense urban contexts. This study analyzes the psychometric properties and factor structure of a holistic measure of Older People’s Neighborhood Experience (OpenX) to understand constituent factors of residential satisfaction and well-being in dense urban contexts.Research Design and MethodsParticipants were 1,011 community-dwelling older adults aged 50 and older in Singapore. Face-to-face interviews were conducted. Questions were drawn to measure physical and social aspects of the neighborhood as well as sociodemographic variables. Exploratory and confirmatory factor analyses were conducted to obtain a shorter version; content validity, internal consistency, and external validity were assessed.ResultsThe OpenX has a 4-dimensional structure, explaining 45.5% of the variance of neighborhood experience. They are communal affordance, embeddedness, environment pleasantness, and time outdoors. Good reliability and validity were found, including Cronbach’s alpha of 0.827. The correlation between neighborhood experience and objectively measured proximity to parks and fitness corners approached significance (p = .082).Discussion and ImplicationsThe 16-item OpenX demonstrated good psychometric properties. With reference to the transdisciplinary neighborhood health framework, it is useful for assessing older adults’ neighborhood environment, identifying neighborhoods for pilot population health interventions, and understanding how the neighborhood environment affects older adults’ health.
Developing the Person–Place Fit Measure for Older Adults: Broadening Place Domains
Authors: Weil Joyce 
Published: July 2019

AbstractBackground and ObjectivesLiterature calls for larger studies with empirically tested instruments about the meaning of place for older adults—studies that include a broader range of domains and neighborhood characteristics. Although rich narrative and qualitative data for small groups of older individuals exist, a measure with valid and reliable scores that includes the new, multiple domains about aging in place does not.Research Design and MethodsFindings are reported from a two-phase, nine-step, exploratory sequential mixed-methods process of measurement development for the Person-Place Fit Measure for Older Adults (PPFM-OA). In Phase I, a focus group (n = 8) and qualitative interviews (n = 77) with persons 65 and older were used to develop emerging domains of aging in place. Qualitative data about concepts and language informed the development of a quantitative item pool for the Mechanical Turk-distributed survey. Phase II included a Delphi process reducing the number of items in the PPFM-OA. Exploratory factor analysis (EFA) and reliability analysis further reduced the number of potential measure items.ResultsFive factors emerged from the EFA. They were primary or basic needs/necessities (α = .84), neighborhood changes and moving (α = .88), identity and place attachment (α = .86), community value (α = .89), and services and resources (α = .78).Discussion and ImplicationsThe development of a measure, such as the PPFM-OA, is crucial as more programs and services are created to address aging in place but uniform data for planning and evaluation are lacking. These initial quantitative analyses are informative for the next step, a larger-scale, quantitative evaluation.
Regulation of phagolysosomal activity by miR-204 critically influences structure and function of retinal pigment epithelium/retina
Authors: Zhang Congxiao , Miyagishima Kiyoharu J , Dong Lijin , Rising Aaron , Nimmagadda Malika , Liang Genqing , Sharma Ruchi , Dejene Roba , Wang Yuan , Abu-Asab Mones , Qian Haohua , Li Yichao , Kopera Megan , Maminishkis Arvydas , Martinez Jennifer , Miller Sheldon 
Published: July 2019

AbstractMicroRNA-204 (miR-204) is expressed in pulmonary, renal, mammary and eye tissue, and its reduction can result in multiple diseases including cancer. We first generated miR-204−/− mice to study the impact of miR-204 loss on retinal and retinal pigment epithelium (RPE) structure and function. The RPE is fundamentally important for maintaining the health and integrity of the retinal photoreceptors. miR-204−/− eyes evidenced areas of hyper-autofluorescence and defective photoreceptor digestion, along with increased microglia migration to the RPE. Migratory Iba1+ microglial cells were localized to the RPE apical surface where they participated in the phagocytosis of photoreceptor outer segments (POSs) and contributed to a persistent build-up of rhodopsin. These structural, molecular and cellular outcomes were accompanied by decreased light-evoked electrical responses from the retina and RPE. In parallel experiments, we suppressed miR-204 expression in primary cultures of human RPE using anti-miR-204. In vitro suppression of miR-204 in human RPE similarly showed abnormal POS clearance and altered expression of autophagy-related proteins and Rab22a, a regulator of endosome maturation. Together, these in vitro and in vivo experiments suggest that the normally high levels of miR-204 in RPE can mitigate disease onset by preventing generation of oxidative stress and inflammation originating from intracellular accumulation of undigested photoreactive POS lipids. More generally, these results implicate RPE miR-204-mediated regulation of autophagy and endolysosomal interaction as a critical determinant of normal RPE/retina structure and function.
Novel use of COMET parameters of sperm DNA damage may increase its utility to diagnose male infertility and predict live births following both IVF and ICSI
Authors: Nicopoullos James , Vicens-Morton Andrew , Lewis Sheena E M , Lee Kathryn , Larsen Peter , Ramsay Jonathan , Yap Tet , Minhas Suks 
Published: July 2019

AbstractSTUDY QUESTIONDo the Comet parameters of the proportions of sperm with low or high DNA damage improve the power of the test in the diagnosis of male infertility and/or prediction of IVF and ICSI live birth rates?SUMMARY ANSWERThe mean Comet score and the scores for proportions of sperm with high or low DNA damage were useful in diagnosing male infertility and provided additional discriminatory information for the prediction of both IVF and ICSI live births.WHAT IS KNOWN ALREADYSperm DNA damage impacts adversely on male fertility and IVF outcomes.STUDY DESIGN, SIZE, DURATIONA retrospective study was performed involving a total of 457 participants (381 patients and 76 fertile donors). Data was collected from a fertility clinic between 2015 and 2017.PARTICIPANTS/MATERIALS, SETTING, METHODSA total of 381 consecutive male partners of couples attending for ART and 76 fertile donors were included in the study. DNA fragmentation was measured by the alkaline Comet assay. Receiver operator characteristic curve analysis (area under the ROC curve (AUC)) was used to determine the value of average Comet score (ACS), low Comet score (LCS) and high Comet score (HCS) to diagnose male factor infertility. In total, 77 IVF and 226 ICSI cycles were included to determine thresholds for each parameter (AUC analysis) and to compare live birth rates (LBRs) following each ART.MAIN RESULTS AND THE ROLE OF CHANCEACS, HCS and LCS were predictive of male infertility (AUC > 0.9, P < 0.0001). IVF LBRs declined once DNA damage exceeded the threshold levels. HCS showed the sharpest decline. Following ICSI, the highest LBRs were in men whose DNA damage levels approached the fertile range. Trends differed in IVF. LBRs decreased as damage increased whereas in ICSI the LBRs decreased but then remained stable.LIMITATIONS, REASONS FOR CAUTIONSince this is the first study to show the impact of sperm DNA damage on ICSI live births, a prospective study should be performed (stratifying patients to IVF or ICSI based on these thresholds) to validate this study.WIDER IMPLICATIONS OF THE FINDINGSOur study presents novel information towards elucidating the genetic basis of male infertility and secondly on relevance of the extent of DNA damage as an impending factor in both IVF and ICSI success.STUDY FUNDING/COMPETING INTEREST(S)This study was supported by Examenlab Ltd, The Lister Clinic, Cryos International and Imperial College London NHS Trust. No external funding was obtained for this study. SL and KL are employees of Examenlab Ltd, a university spin-out company with a commercial interest in sperm DNA damage. No other author has a conflict of interest to declare.TRIAL REGISTRATION NUMBERNon-applicable.
Private Actors as Transnational Regulators: The Case of Freedom of Association
Authors: Menashe Maayan 
Published: July 2019

Abstract
This article examines whether content of international public norms is significantly altered when embedded in transnational private labour regulations (TPLR); and, if it is, whether these alterations enrich or weaken the effect of these norms. Through a case study of freedom of association as regulated in five major TPLR initiatives, this research pursues a textual analysis of TPLR generated norms, to evaluate their content and to assess the nature of any modifications of international labour law norms. The findings reveal that although TPLR instruments are generally perceived as merely implementing internationally accepted norms, they in fact have a substantial norm-generating role, actively shaping the content of the norms they apply. The evidence further indicates that private actors can contribute to the design of innovative norms. At the same time, it was found that corporations had in several instances exerted negative influences over freedom of association norms and that when additional actors participated in the regulatory process, this right was better fulfilled. In addition, although meaningful participation of public actors in private regulatory initiatives was found to effectively prevent the undermining of the right to freedom of association, global union federations were less successful in this regard.
Maintaining progress for the most beautiful chart in the world
Authors: Hay Simon I 
Published: July 2019

Abstract
The decline in child mortality over the past two decades has been described as the greatest story in global public health. Indeed, using modern tools and interventions, there has been remarkable progress, reducing deaths in children <5 y of age by nearly half from 2000 to 2017. However, as a consequence of persistent geographic inequalities, we fall short of the United Nations Sustainable Development Goal to end all preventable child deaths by 2030, with an estimated 44.6 million preventable deaths expected to occur by the target year. This article discusses how we might further improve the downward trend in child mortality over the next decade to end preventable child deaths.
Social Ties and the Strategy of Civil Resistance
Authors: Thurber Ches 
Published: July 2019

AbstractThis article examines the impact of social ties on a challenger's ability to initiate a civil resistance campaign. Recent waves of nonviolent uprisings, from the color revolutions of Eastern Europe to the Arab Spring, have sparked renewed scholarly interest in civil resistance as a strategy in conflict. However, most research has focused on the effectiveness and outcomes of civil resistance, with less attention paid to when, why, and how challengers to regime power come to embrace a strategy of nonviolent action in the first place. Drawing upon a longitudinal analysis of challenger organizations and coalitions in Nepal, this article illustrates how social ties inform challengers’ assessments of the viability of civil resistance and consequently shape their strategic behavior. The findings complicate state-centric approaches to contentious politics by showing how diverse actors within the same state face different sets of political opportunities and constraints. They also highlight the indeterminate effects of ideology, as variation in challengers’ social ties drive Gandhians to take up arms and Maoists to lay them down.
Method for Postmortem Quantification of Δ9-Tetrahydrocannabinol and Metabolites Using LC–MS–MS
Authors: Al-Asmari Ahmed I 
Published: July 2019

AbstractA specific, sensitive, fast and simple method for analysis of Δ9-tetrahydrocannabinol (THC), 11-hydroxy-Δ9-THC (THC-OH) and 11-nor-Δ9-THC-9-carboxylic acid (THC-COOH) in routine postmortem cases using LC–MS–MS was developed and validated. Prior to solid phase extraction, urine, stomach contents and bile were pretreated using alkaline hydrolysis, while blood and vitreous humor were pretreated with protein precipitation. The distribution of THC, THC-OH and THC-COOH were investigated in 31 postmortem cases that tested positive for cannabinoids. This revealed new information regarding the distribution of THC in stomach contents and vitreous humor. Alkaline hydrolysis was sufficient for the deglucuronidation of THC-COOH-glucuronide to its free form, THC-COOH, in urine, bile and stomach contents. However, the THC-OH concentration in bile reported in this study is considerably high compared to that of previous studies. In conclusion, including THC and its metabolites (THC-OH and THC-COOH) is crucial for any forensic toxicology detection method to most accurately determine the role of cannabinoids in deaths.
Language Loss and Illocutionary Silencing
Authors: Nowak Ethan 
Published: July 2019

AbstractThe twenty-first century will witness an unprecedented decline in the diversity of the world’s languages. While most philosophers will likely agree that this decline is lamentable, the question of what exactly is lost with a language has not been systematically explored in the philosophical literature. In this paper, I address this lacuna by arguing that language loss constitutes a problematic form of illocutionary silencing. When a language disappears, past and present speakers lose the ability to realize a range of speech acts that can only be realized in that language. With that ability, speakers lose something in which they have a fundamental interest: their standing as fully empowered members of a linguistic community.