bluuebunny/crossref_metadata_2025_split huggingface dataset:
DiNGO: standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis
Authors: Davidović Radoslav , Perovic Vladimir , Gemovic Branislava , Veljkovic Nevena 
Published: November 2019

Abstract

Summary
Although various tools for Gene Ontology (GO) term enrichment analysis are available, there is still room for improvement. Hence, we present DiNGO, a standalone application based on an open source code from BiNGO, a widely-used application to assess the overrepresentation of GO categories. Besides facilitating GO term enrichment analyses, DiNGO has been developed to allow for convenient Human Phenotype Ontology (HPO) term overrepresentation investigation. This is an important contribution considering the increasing interest in HPO in scientific research and its potential in clinical settings. DiNGO supports gene/protein identifier conversion and an automatic updating of GO and HPO annotation resources. Finally, DiNGO can rapidly process a large amount of data due to its multithread design.

Availability and implementation
DiNGO is implemented in the JAVA language, and its source code, example datasets and instructions are available on GitHub: https://github.com/radoslav180/DiNGO. A pre-compiled jar file is available at: https://www.vin.bg.ac.rs/180/tools/DiNGO.php.

Supplementary information
Supplementary data are available at Bioinformatics online.
Pathophysiology and diagnosis of coronary microvascular dysfunction in ST-elevation myocardial infarction
Authors: Konijnenberg Lara S F , Damman Peter , Duncker Dirk J , Kloner Robert A , Nijveldt Robin , van Geuns Robert-Jan M , Berry Colin , Riksen Niels P , Escaned Javier , van Royen Niels 
Published: November 2019

AbstractEarly mechanical reperfusion of the epicardial coronary artery by primary percutaneous coronary intervention (PCI) is the guideline-recommended treatment for ST-elevation myocardial infarction (STEMI). Successful restoration of epicardial coronary blood flow can be achieved in over 95% of PCI procedures. However, despite angiographically complete epicardial coronary artery patency, in about half of the patients perfusion to the distal coronary microvasculature is not fully restored, which is associated with increased morbidity and mortality. The exact pathophysiological mechanism of post-ischaemic coronary microvascular dysfunction (CMD) is still debated. Therefore, the current review discusses invasive and non-invasive techniques for the diagnosis and quantification of CMD in STEMI in the clinical setting as well as results from experimental in vitro and in vivo models focusing on ischaemic-, reperfusion-, and inflammatory damage to the coronary microvascular endothelial cells. Finally, we discuss future opportunities to prevent or treat CMD in STEMI patients.
Increasing Education-Based Disparities in Healthy Life Expectancy Among U.S. Non-Hispanic Whites, 2000–2010
Authors: Cantu Phillip A , Sheehan Connor M , Sasson Isaac , Hayward Mark D 
Published: November 2019

Abstract

Objectives
To examine changes in Healthy Life Expectancy (HLE) against the backdrop of rising mortality among less-educated white Americans during the first decade of the twenty-first century.

Methods
This study documented changes in HLE by education among U.S. non-Hispanic whites, using data from the U.S. Multiple Cause of Death public-use files, the Integrated Public Use Microdata Sample (IPUMS) of the 2000 Census and the 2010 American Community Survey, and the Health and Retirement Study (HRS). Changes in HLE were decomposed into contributions from: (i) change in age-specific mortality rates; and (ii) change in disability prevalence, measured via Activities of Daily Living (ADL) and Instrumental Activities of Daily Living (IADL).

Results
Between 2000 and 2010, HLE significantly decreased for white men and women with less than 12 years of schooling. In contrast, HLE increased among college-educated white men and women. Declines or stagnation in HLE among less-educated whites reflected increases in disability prevalence over the study period, whereas improvements among the college educated reflected decreases in both age-specific mortality rates and disability prevalence at older ages.

Discussion
Differences in HLE between education groups increased among non-Hispanic whites from 2000 to 2010. In fact, education-based differences in HLE were larger than differences in total life expectancy. Thus, the lives of less-educated whites were not only shorter, on average, compared with their college-educated counterparts, but they were also more burdened with disability.
Social Progress and Global Governance
Authors: Fleurbay Marc , Kanbur Ravi 
Published: November 2019

Abstract
Over the last four years, we have worked with a large, international, and multidisciplinary group of scholars and social scientists, in the preparation of the first report of the International Panel on Social Progress (IPSP) (Rethinking Society for the 21st Century, Cambridge University Press, 2018). The question this group set itself to answer was whether we can hope for better institutions and less social injustice in the world in the coming decades, given the ongoing trends.
Structural Constraints and Human Agency in Global Summitry and the Liberal Order
Authors: Alexandroff Alan S , Stein Arthur A 
Published: November 2019

AbstractConfusion surrounds how best to describe today the architecture of the liberal international order, its challenges, and prospects. The Liberal Order’s various and changing configurations its distributions of power, as well as the variety of major actors, portend consequences for the operation of the international system. Although structural approaches remain dominant in international relations analysis, it is evident that there is an interaction of structure, the distribution, and redistribution of power, and agency—the diplomatic actions, norms, and rules of international politics. Historical and existing institutions, ongoing debates, and political efforts all point to the role of agency in global governance. The ongoing search for order was the basis for the Peace of Westphalia, the Concert of Europe, the effort to construct collective security following World War I, the Western liberal order of the Cold War, and global governance constructions of the post-Cold War era. The continuing existence and direction of the liberal international order are proving difficult to determine. There are rising powers and growing geopolitical rivalry. There are many new nonstate actors affecting international politics. And, there is current U.S. policy that puts in question its collaborative role and its continuing leadership. The many architectures of global governance, even competing ones, underline that structure alone is not determinative. In addition, debates over what course to take imply that the force of circumstance does not make one and only choice possible and inevitable, and that the search for order is ongoing and omnipresent.
Colocalization of GWAS and eQTL signals at loci with multiple signals identifies additional candidate genes for body fat distribution
Authors: Wu Ying , Broadaway K Alaine , Raulerson Chelsea K , Scott Laura J , Pan Calvin , Ko Arthur , He Aiqing , Tilford Charles , Fuchsberger Christian , Locke Adam E , Stringham Heather M , Jackson Anne U , Narisu Narisu , Kuusisto Johanna , Pajukanta Päivi , Collins Francis S , Boehnke Michael , Laakso Markku , Lusis Aldons J , Civelek Mete , Mohlke Karen L 
Published: November 2019

Abstract
Integration of genome-wide association study (GWAS) signals with expression quantitative trait loci (eQTL) studies enables identification of candidate genes. However, evaluating whether nearby signals may share causal variants, termed colocalization, is affected by the presence of allelic heterogeneity, different variants at the same locus impacting the same phenotype. We previously identified eQTL in subcutaneous adipose tissue from 770 participants in the Metabolic Syndrome in Men (METSIM) study and detected 15 eQTL signals that colocalized with GWAS signals for waist–hip ratio adjusted for body mass index (WHRadjBMI) from the Genetic Investigation of Anthropometric Traits consortium. Here, we reevaluated evidence of colocalization using two approaches, conditional analysis and the Bayesian test COLOC, and show that providing COLOC with approximate conditional summary statistics at multi-signal GWAS loci can reconcile disagreements in colocalization classification between the two tests. Next, we performed conditional analysis on the METSIM subcutaneous adipose tissue data to identify conditionally distinct or secondary eQTL signals. We used the two approaches to test for colocalization with WHRadjBMI GWAS signals and evaluated the differences in colocalization classification between the two tests. Through these analyses, we identified four GWAS signals colocalized with secondary eQTL signals for FAM13A, SSR3, GRB14 and FMO1. Thus, at loci with multiple eQTL and/or GWAS signals, analyzing each signal independently enabled additional candidate genes to be identified.
G2019S-LRRK2 mutation enhances MPTP-linked Parkinsonism in mice
Authors: Arbez Nicolas , He XiaoFei , Huang Yong , Ren Mark , Liang Yideng , Nucifora Frederick C , Wang Xiaofang , Pei Zhong , Tessarolo Lino , Smith Wanli W , Ross Christopher A 
Published: November 2019

Abstract
Parkinson’s disease (PD) is a common neurodegenerative disease with a heterogeneous etiology that involves genetic and environmental factors or exogenous. Current LRRK2 PD animal models only partly reproduce the characteristics of the disease with very subtle dopaminergic neuron degeneration. We developed a new model of PD that combines a sub-toxic MPTP insult to the G2019S-LRRK2 mutation. Our newly generated mice, overexpressing mutant G2019S-LRRK2 protein in the brain, displayed a mild, age-dependent progressive motor impairment, but no reduction of lifespan. Cortical neurons from G2019S-LRRK2 mice showed an increased vulnerability to stress insults, compared with neurons overexpressing wild-type WT-LRRK2, or non-transgenic (nTg) neurons. The exposure of LRRK2 transgenic mice to a sub-toxic dose of MPTP resulted in severe motor impairment, selective loss of dopamine neurons and increased astrocyte activation, whereas nTg mice with MPTP exposure showed no deficits. Interestingly, mice overexpressing WT-LRRK2 showed a significant impairment that was milder than for the mutant G2019S-LRRK2 mice. L-DOPA treatments could partially improve the movement impairments but did not protect the dopamine neuron loss. In contrast, treatments with an LRRK2 kinase inhibitor significantly reduced the dopaminergic neuron degeneration in this interaction model. Our studies provide a novel LRRK2 gene-MPTP interaction PD mouse model, and a useful tool for future studies of PD pathogenesis and therapeutic intervention.
What about men? Towards a critical interrogation of sexual violence against men in global politics
Authors: Drumond Paula 
Published: November 2019

Abstract
In recent years, debates around sexual violence against men (SVAM) started to gain momentum in policy and research. Yet, the conceptualization and empirical identification of SVAM became a matter of political contestation, with incidents often being depicted through de-sexualized labels such as ‘inhumane acts’ and ‘cruel treatment’. The fluidity of sexual meanings surrounding these episodes highlights the intricate relationship between ‘sex’ and ‘violence’: Do we always already know what sexual violence is? What does the language of sexual violence obscure, flatten and trivialize? This contribution draws on Marysia Zalewski's interventions to interrogate concepts and framings commonly used to ‘read’ episodes of sexual violence against men. In particular, it follows Zalewski and Runyan's efforts to ‘unthink’ what we ‘know’ and how we ‘know’ sexual violence against men in global politics, while interrogating the relationship between sex and violence in particular performances of bodily violence. The analysis draws on extensive archival research conducted in the files of the International Criminal Tribunal for the former Yugoslavia and of the Peruvian Truth and Reconciliation Commission. Surveyed documents include records and proceedings, such as trial transcripts and statements of victims and witnesses involved in incidents of violence against men during the conflicts in former Yugoslavia and Peru.
Cost Burden of Crohn’s Disease and Ulcerative Colitis in the 10-Year Period Before Diagnosis—A Danish Register-Based Study From 2003–2015
Authors: Vadstrup Kasper , Alulis Sarah , Borsi Andras , Gustafsson Nina , Nielsen Agnete , Wennerström E Christina M , Jørgensen Tine Rikke , Qvist Niels , Munkholm Pia 
Published: November 2019

Abstract

Background
The diagnostic delay in inflammatory bowel disease (IBD) is well known, yet the costs associated with diagnoses before IBD diagnosis have not yet been reported. This study explored societal costs and disease diagnoses 10 years before Crohn’s disease (CD) and ulcerative colitis (UC) diagnosis in Denmark.

Methods
This national register study included patients diagnosed between 2003 and 2015 identified in the Danish National Patient Registry (NPR) and controls who were individually matched on age and sex from the general population. Societal costs included health care services, prescription medicine, home care services, and labor productivity loss. Prediagnostic hospital contact occurring before CD or UC diagnosis was identified using the NPR. Average annual costs per individual were calculated before the patient’s first CD or UC diagnosis. A 1-sample t test was then applied to determine significance in differences between cases and controls.

Results
Among CD (n = 9019) and UC patients (n = 20,913) the average societal costs were higher throughout the entire 10-year period before the diagnosis date compared with the general population. The difference increased over time and equaled €404 for CD patients and €516 for UC patients 10 years before diagnosis and €3377 and €2960, respectively, in the year before diagnosis. Crohn’s disease and UC patients had significantly more diagnoses before their CD and UC diagnosis compared with the general population.

Conclusions
Compared with the general population, the societal costs and number of additional diagnoses among CD and UC patients were substantially higher in the 10-year period before diagnosis.
Associations of exposure to green space with problem behaviours in preschool-aged children
Authors: Liao Jiaqiang , Yang Shaoping , Xia Wei , Peng Anna , Zhao Jinzhu , Li Yuanyuan , Zhang Yimin , Qian Zhengmin , Vaughn Michael G , Schootman Mario , Zhang Bin , Xu Shunqing 
Published: November 2019

AbstractBackgroundLimited evidence is available regarding the association of green-space exposure with childhood behavioural development. This study aimed to investigate the associations of exposure to green space with multiple syndromes of behavioural development in preschool children.MethodsThis cross-sectional study was conducted in Wuhan, China from April 2016 to June 2018. We recruited a sample of 6039 children aged 5–6 years from 17 kindergartens located in five urban districts of the city. We measured the greenness using average Normalized Difference Vegetation Index (NDVI) within a circular buffer area of 100 metres surrounding the central point of residences and kindergartens. We calculated the residence–kindergarten-weighted greenness by assuming that children spent 16 hours per day at home and 8 hours at kindergarten. The problem behaviours of children were evaluated at kindergarten using the Childhood Behavioral Checklist (CBCL) and standardized into problem behavioural T scores. Linear mixed-effect models and linear-regression models were used to estimate the associations.ResultsWe observed decreases in problem behaviours associated with kindergarten and residence–kindergarten-weighted surrounding greenness in preschool children. For example, a one-interquartile range increase in kindergarten and residence–kindergarten-weighted NDVI was associated with decreased T scores for total behaviour by −0.61 [95% confidence interval (CI): −1.09, −0.13) and −0.49 (95% CI −0.85, −0.12), anxiety and depression by −0.65 (95% CI: −1.13, −0.17) and −0.46 (95% CI: −0.82, −0.10), aggressive behaviour by −0.53 (95% CI: −1.01, −0.05) and −0.38 (95% CI: −0.75, −0.02) and hyperactivity and attention deficit by −0.54 (95% CI: −1.01, −0.07) and −0.48 (95% CI: −0.83, −0.12), respectively. Stratified analyses indicated that the associations of green-space exposure with problem behaviours were stronger in boys than in girls.ConclusionsChildren attending kindergartens with higher levels of surrounding green space exhibited better behavioural development. The mechanisms underlying these associations should be explored further.
Categorical Primitive Forms and Gromov–Witten Invariants of An Singularities
Authors: Căldăraru Andrei , Li Si , Tu Junwu 
Published: November 2019

Abstract
We introduce a categorical analogue of Saito’s notion of primitive forms. For the category $\textsf{MF}(\frac{1}{n+1}x^{n+1})$ of matrix factorizations of $\frac{1}{n+1}x^{n+1}$, we prove that there exists a unique, up to non-zero constant, categorical primitive form. The corresponding genus zero categorical Gromov–Witten invariants of $\textsf{MF}(\frac{1}{n+1}x^{n+1})$ are shown to match with the invariants defined through unfolding of singularities of $\frac{1}{n+1}x^{n+1}$.
Stacky Hamiltonian Actions and Symplectic Reduction
Authors: Hoffman Benjamin , Sjamaar Reyer 
Published: November 2019

Abstract
We introduce the notion of a Hamiltonian action of an étale Lie group stack on an étale symplectic stack and establish versions of the Kirwan convexity theorem, the Meyer–Marsden–Weinstein symplectic reduction theorem, and the Duistermaat–Heckman theorem in this context.
RETRACTED: Sorry by Size: How the Number of Apologizers Affects Apology Effectiveness
Authors: Ran Yaxuan , Maglio Sam J 
Published: November 2019

Abstract
Company apologies require apologizers, which can take the form of one person or multiple people. Does the number of apologizers influence how consumers interpret and respond to that apology? The current research suggests that a single apologizer proves more effective than multiple apologizers because consumers tend to have a stronger empathic response towards one person than towards multiple people. Across one archival study and four experiments, a single apologizer (relative to multiple apologizers) garners higher stock returns (study 1), elicits a higher rate of behavior indicative of acceptance of the apology (study 2), and more readily facilitates consumer forgiveness of the company, perceived company integrity, and satisfaction with the apology (studies 3-5). This effect is mediated by empathy for the apologizer (studies 4 and 5), and the benefit for a single apologizer dissipates when consumers perceive multiple apologizers as entitative, united members (study 5). Contributions and implications are discussed.
Domestic Cats (Felis catus) and European Nature Conservation Law—Applying the EU Birds and Habitats Directives to a Significant but Neglected Threat to Wildlife
Authors: Trouwborst Arie , Somsen Han 
Published: November 2019

Abstract
Free-ranging domestic cats (Felis catus) impact biodiversity through predation, disturbance, competition, disease and hybridisation. Scientific knowledge regarding these impacts has recently increased. This article interprets the European Union (EU) Birds and Habitats Directives (Nature Directives) in light of this knowledge. The outcome indicates that various obligations in the Directives, particularly concerning Natura 2000 sites and the generic protection of birds and other species, have significant implications for the management of free-ranging domestic cats. Regarding (unowned) stray and feral cats, these must be removed or controlled when they pose a threat to protected species and/or sites. Regarding (owned) pet and farm cats, the Nature Directives require EU Member States to ensure that letting cats roam free outdoors is forbidden and effectively prevented. Current practice across the EU does not yet conform to these requirements. Whereas the article identifies and assesses various factors that may explain this compliance gap, legally valid justifications appear absent.
Mark my words: experts’ choice of marking methods used in capture-mark-recapture studies of small mammals
Authors: Jung Thomas S , Boonstra Rudy , Krebs Charles J 
Published: November 2019

Abstract
Crucial to the success of studies based on capture-mark-recapture (CMR) designs is the retention (permanency) and recognition (readability) of marks to identify individuals. Several marking methods for small mammals (&lt; 60 g) are available, but their efficacy and use is not well known. We implemented a targeted survey of experts to gather their experiences and opinions regarding marking small mammals. Respondents (n = 114) stated their beliefs, perceptions, and current and future use, of marking methods, as well as factors influencing their choices, based on Likert and rank order scale questions. We compared responses based on where researchers’ studies occurred, their level of experience, and their subfield of mammalogy. Most respondents (73%) had &gt; 5 years experience marking small mammals, with 60% each marking &gt; 1,000 individuals. Respondents believed that ear-tagging was most preferable in terms of efficiency, impact to affected animals (survival, pain), and personal ethics, whereas passive integrated transponder (PIT)-tagging was the most preferable with regard to retention and recognition, and toe-clipping with respect to cost. Most respondents plan to use ear-tagging (78%) or PIT-tagging (70%) in the future. PIT- and genetic-tagging are expected to increase, and toe-clipping to decline, in the future. The factors influencing which marking method respondents used were ranked—in order of decreasing preference—as impact, retention, recognition, cost, efficiency, and ethics. There were few differences in the mean response or consensus among respondents, regardless of their experience, location, or subfield. Most respondents (66%) agreed that additional studies on the performance and impact of various marking methods are needed to assess their costs and benefits for CMR-based studies. Ultimately, choice of marking method will depend on the species, research question, available resources, and local legislation and permitting. Our study, however, illustrates that collective insights by experienced mammalogists may aid individual researchers in deciding on study designs and protocols, particularly early career scientists.