bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of simulated warming on the functional traits of Leymus chinensis plant in Songnen grassland
Authors: Guo Rui , Zhou Ji , Zhong Xiuli , Gu Fengxue , Liu Qi , Li Haoru
Published: November 2019

Leymus chinensis grassland in Northeast China provides a natural laboratory for the investigation of climate change. The response of L. chinensis to experimental warming can provide insight into its regeneration behaviour and the likely composition of future communities under warmer climate. We used MSR-2420 infrared radiators to elevate temperature and examined soil organic carbon and nitrogen and soil total phosphorus and determined the growth and physiology of L. chinensis in response to manipulations of ambient condition and warming. Results showed that compared with the control, L. chinensis subjected to warming treatment showed increased soil organic carbon and soil total nitrogen, but no significant difference was observed in soil total phosphorus. Climate warming increased shoot biomass, ecosystem respiration, and ecosystem water-use efficiency and reduced net ecosystem CO2 exchange and evapotranspiration. This result implies that warming could rapidly alter carbon fluxes. The effect of warming treatment significantly increased the contents of glucose and fructose and significantly inhibited sucrose synthesis. However, the TCA cycle was enhanced when citric and malic acid contents further accumulated. The results implied that L. chinensis probably enhanced its warming adaption mechanism mainly through increasing glycolysis consumption when it was exposed to elevated temperature. These results provide an understanding of the fundamental evidence explaining the primary metabolism of L. chinensis in response to warming and suggest the future impact of the terrestrial carbon-cycle feedback on global climate change.
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

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

Early 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

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

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

Confusion 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

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

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

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

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

Background

Limited 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.

Methods

This 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.

Results

We 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.

Conclusions

Children 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

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

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

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

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

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 (< 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 > 5 years experience marking small mammals, with 60% each marking > 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.
Target and Nontarget Toxicity of Cassia fistula Fruit Extract Against Culex pipiens (Diptera: Culicidae), Lung Cells (BEAS-2B) and Zebrafish (Danio rerio) Embryos
Authors: Abutaha Nael , Al-Mekhlafi Fahd A , Farooq Muhammad
Published: November 2019

Mosquitoes transmit serious diseases, which threaten humans and severely affect livestock. The half-lethal concentration (LC50) was calculated by log probit analysis. The LC50 and LC90 values of larvicidal activity of Cassia fistula Linn. hexane-methanol soluble fraction (HMSF) after 24 h of exposure were 21.04 and 34.68 µg/ml, respectively. The LC50 values after 24 h of exposure were 84.09 µg/ml and 108.08 µg/ml for chloroform–methanol soluble fraction (CMSF) and ethyl acetate-methanol soluble fraction (EMSF) respectively. The percent hatchability of eggs exposed to the hexane extract was 90 ± 5.0, 68.33 ± 7.6, 46.6 ± 11.5, 10 ± 0.0, and 0 ± 0.0% at 10, 20, 40, 60, and 80 ppm, respectively. The pupicidal activity of the hexane extract at 40 µg/ml was 0.0%. The LC50 value of adulticidal activity of the hexane extract was 12.8 mg/test tube. The biosafety of the hexane extract was assessed in nontarget organisms, i.e., zebrafish (Danio rerio) embryos and normal lung cells (BEAS-2B). The hexane extract of C. fistula was well tolerated by zebrafish embryos, and no mortality or toxicity was found in the embryos exposed to the highest tested concentration of 300 µg/ml. Similarly, all the concentrations tested against the normal lung cells (BEAS-2B) showed more than 95% survival. The gas chromatography–mass spectroscopy analysis identified 12 compounds, and 2-methyl hexanoic acid and 2-methyl butanoic acid were the major compounds identified in the hexane extract. The larvicidal activity of C. fistula extracts will help in the development of natural substitutes for vector management of mosquito populations.
Urban Landscape Features Influence the Movement and Distribution of the Australian Container-Inhabiting Mosquito Vectors Aedes aegypti (Diptera: Culicidae) and Aedes notoscriptus (Diptera: Culicidae)
Authors: Trewin Brendan J , Pagendam Daniel E , Zalucki Myron P , Darbro Jonathan M , Devine Gregor J , Jansen Cassie C , Schellhorn Nancy A
Published: November 2019

Urban landscape features play an important role in the distribution and population spread of mosquito vectors. Furthermore, current insecticide and novel rear-and-release strategies for urban mosquito management rarely consider the spatial structure of the landscape when applying control practices. Here, we undertake a mark-recapture experiment to examine how urban features influence the movement and distribution of Australian container-inhabiting Aedes vectors. We pay attention to the role of semipermanent water storage containers, called rainwater tanks, and the influence of movement barriers, such as roads, on the spread and distribution of vector populations. Results suggest that Aedes aegypti (Linnaeus) (Diptera: Culicidae) were more likely to be captured around rainwater tanks, and that released males travel throughout residential blocks but do not cross roads. Conversely, female Aedes notoscriptus (Skuse) (Diptera: Culicidae) movement was uninhibited by roads and rainwater tanks did not influence female distribution or oviposition behavior. Using an isotropic Gaussian kernel framework, we show that vector movement is likely to be greater when applying a temporal effect, than when estimated by traditional methods. We conclude that a greater understanding on the role of urban features on vector movement will be important in the new age of rear-and-release mosquito control strategies, particularly those where estimations of movement are important for ensuring efficacy of application.
Detection of Leishmania DNA in Sand Flies (Diptera: Psychodidae) From a Cutaneous Leishmaniasis Outbreak Area in Northeastern Brazil
Authors: Da Silva Yury Yzabella , Sales Kamila Gaudêncio Da Silva , Miranda Débora Elienai De Oliveira , Figueredo Luciana Aguiar , Brandão-Filho Sinval P , Dantas-Torres Filipe
Published: November 2019

Cutaneous leishmaniasis (CL) by Leishmania braziliensis Vianna (Kinetoplastida: Trypanosomatidae) is a widespread disease in the western hemisphere and Brazil is the country reporting the majority of the human cases each year. Several phlebotomine sand flies have been regarded as putative or proven vectors of L. braziliensis and multiple vectors may be involved in the transmission of this parasite in the same endemic foci. In this study, we tested a subset of female phlebotomine sand flies collected in the frame of a previous study conducted in a military training camp, where outbreaks of CL by L. braziliensis have sporadically been reported. In total, 1,807 female phlebotomine sand flies were tested (individually or in pools) by real-time PCR and a minimum infection rate of 0.9% (95% CI: 0.6–1.5%) was detected. Positive females belonged to the species Psychodopygus complexus (Mangabeira) or Psychodopygus wellcomei Fraiha, Shaw & Lainson (females of these species are morphologically indistinguishable), Trichopygomyia longispina (Mangabeira), and Sciopemyia sordellii (Shannon & Del Ponte) (Diptera: Psychodidae). By restriction enzyme analysis, 13 samples (nine of Ty. longispina, two of Ps. complexus/wellcomei, and two of Sc. sordellii) presented a HaeIII restriction profile identical to L. braziliensis. The results of this study reinforce the notion that multiple vectors may be involved in the transmission of L. braziliensis in a single focus, ultimately making the epidemiological picture more complex than currently recognized.
Oxidation resistance 1 prevents genome instability through maintenance of G2/M arrest in gamma-ray-irradiated cells
Authors: Matsui Ako , Kobayashi Junya , Kanno Shin-ichiro , Hashiguchi Kazunari , Miyaji Masahiro , Yoshikawa Yukihiro , Yasui Akira , Zhang-Akiyama Qiu-Mei
Published: November 2019

Human oxidation resistance 1 (OXR1) was identified as a protein that decreases genomic mutations in Escherichia coli caused by oxidative DNA damage. However, the mechanism by which OXR1 defends against genome instability has not been elucidated. To clarify how OXR1 maintains genome stability, the effects of OXR1-depletion on genome stability were investigated in OXR1-depleted HeLa cells using gamma-rays (γ-rays). The OXR1-depleted cells had higher levels of superoxide and micronucleus (MN) formation than control cells after irradiation. OXR1-overexpression alleviated the increases in reactive oxygen species (ROS) level and MN formation after irradiation. The increased MN formation in irradiated OXR1-depleted cells was partially attenuated by the ROS inhibitor N-acetyl-L-cysteine, suggesting that OXR1-depeletion increases ROS-dependent genome instability. We also found that OXR1-depletion shortened the duration of γ-ray-induced G2/M arrest. In the presence of the cell cycle checkpoint inhibitor caffeine, the level of MN formed after irradiation was similar between control and OXR1-depleted cells, demonstrating that OXR1-depletion accelerates MN formation through abrogation of G2/M arrest. In OXR1-depleted cells, the level of cyclin D1 protein expression was increased. Here we report that OXR1 prevents genome instability by cell cycle regulation as well as oxidative stress defense.
Risk factors for acquisition of multidrug-resistant Enterobacterales among international travellers: a synthesis of cumulative evidence
Authors: Furuya-Kanamori Luis , Stone Jennifer , Yakob Laith , Kirk Martyn , Collignon Peter , Mills Deborah J , Lau Colleen L
Published: November 2019

Background

Recent studies have shown that over 50% of people travelling to Southeast Asia return colonized with multidrug-resistant Enterobacterales (MRE) including carbapenemase-producing Enterobacterales. Importation of MRE by travellers and subsequent spread to family members, communities and healthcare facilities poses real risks that have not yet been adequately assessed. This systematic review and meta-analysis aims to quantify the risk factors and interventions for reducing the risk of MRE acquisition among international travellers.

Methods

A systematic search was conducted in PubMed, Web of Science and Scopus for analytical epidemiological studies containing data post-2000 that assessed the risk factors to acquire and/or interventions to reduce the risk of MRE acquisition in travellers. Two researchers independently screened all the studies and extracted the information, and disagreements were resolved through consensus. The proportions of MRE acquisition by the region of destination and the odds ratio (OR) for the different risk factors and/or interventions were pooled using the inverse variance heterogeneity model.

Results

A total of 20 studies (5253 travellers from high-income countries) were included in the meta-analysis. South Asia [58.7%; 95% confidence interval (CI), 44.5–72.5%] and Northern Africa (43.9%; 95% CI 37.6–50.3%) were the travel destinations with the highest proportion of MRE acquisition. Inflammatory bowel disease (OR 2.1; 95% CI 1.2–3.8), use of antibiotics (OR 2.4; 95% CI 1.9–3.0), traveller’s diarrhoea (OR 1.7; 95% CI 1.3–2.3) and contact with the healthcare system overseas (OR 1.5; 95% CI 1.1–2.2) were associated with MRE colonization. Vegetarians (OR 1.4; 95% CI 1.0–2.0) and backpackers (OR 1.5; 95% CI 1.2–1.8) were also at increased odds of MRE colonization. Few studies (n = 6) investigated preventive measures and found that consuming only bottled water/beverages, meticulous hand hygiene and probiotics had no protective effect on MRE colonization.

Conclusions

International travel is an important driver for MRE spread worldwide. Future research needs to identify effective interventions to reduce the risk of MRE acquisition as well as design strategies to reduce local transmission on return.
A lipid transfer protein variant with a mutant eight-cysteine motif causes photoperiod- and thermo-sensitive dwarfism in rice
Authors: Deng Wenjun , Li Riqing , Xu Yiwei , Mao Runyuan , Chen Shuifu , Chen Libin , Chen Letian , Liu Yao-Guang , Chen Yuanling
Published: November 2019

Plant height is an important trait for architecture patterning and crop yield improvement. Although the pathways involving gibberellins and brassinosteroids have been well studied, there are still many gaps in our knowledge of the networks that control plant height. In this study, we determined that a dominant photoperiod- and thermo-sensitive dwarf mutant is caused by the active role of a mutated gene Photoperiod-thermo-sensitive dwarfism 1 (Ptd1), the wild-type of which encodes a non-specific lipid transfer protein (nsLTP). Ptd1 plants showed severe dwarfism under long-day and low-temperature conditions, but grew almost normal under short-day and high-temperature conditions. These phenotypic variations were associated with Ptd1 mRNA levels and accumulation of the corresponding protein. Furthermore, we found that the growth inhibition in Ptd1 may result from the particular protein conformation of Ptd1 due to loss of two disulfide bonds in the eight-cysteine motif (8-CM) that is conserved among nsLTPs. These results contribute to our understanding of the novel function of disulfide bonds in the 8-CM, and provide a potential new strategy for regulation of cell development and plant height by modifying the amino acid residues involved in protein conformation patterning.
Spectrally resolved cosmic ray hydrodynamics – I. Spectral scheme
Authors: Girichidis Philipp , Pfrommer Christoph , Hanasz Michał , Naab Thorsten
Published: November 2019

Cosmic ray (CR) protons are an important component in many astrophysical systems. Processes like CR injection, cooling, adiabatic changes as well as active CR transport through the medium strongly modify the CR momentum distribution and have to be taken into account in hydrodynamical simulations. We present an efficient novel numerical scheme to accurately compute the evolution of the particle distribution function by solving the Fokker-Planck equation with a low number of spectral bins (10 − 20), which is required to include a full spectrum for every computational fluid element. The distribution function is represented by piecewise power laws and is not forced to be continuous, which enables an optimal representation of the spectrum. The Fokker-Planck equation is solved with a two-moment approach evolving the CR number and energy density. The low numerical diffusion of the scheme reduces the numerical errors by orders of magnitude in comparison to classical schemes with piecewise constant spectral representations. With this method not only the spectral evolution of CRs can be computed accurately in magnetohydrodynamic simulations but also their dynamical impact as well as CR ionisation. This allows for more accurate models for astrophysical plasmas, like the interstellar medium, and direct comparisons with observations.
First stars that could significantly perturb comet motion are finally found.
Authors: Wysoczańska Rita , Dybczyński Piotr A , Królikowska Małgorzata
Published: November 2019

Since 1950 when Oort published his paper on the structure of the cloud of comets it is believed that stars passing near this hypothetical cometary reservoir play an important role in the dynamical evolution of long period comets and injecting them into the observability region of the Solar System. The aim of this paper is to discuss two cases in which the data obtained from observations were used and stellar perturbations (of different intensity, strong case of C/2002 A3 LINEAR and weaker case of C/2013 F3 PANSTARRS) on cometary motion were detected. Using the best available data from the Gaia DR2 catalogue and some other sources we searched for close stellar passages near the Sun. Our study took into account that some of the stars are parts of multiple systems. Over 600 stars or systems that approached or will approach the Sun closer than 4.0 pc were found. Having the list of perturbers completed we studied their influence on a sample of 277 Oort spike comets that were observed since 1901 and discovered that two comets might have their orbits fundamentally changed due to a close stellar encounter. Our results show how much different the dynamical evolution of comets would have looked when their motion was considered only in the Galactic potential. Uncertainties both in stellar and cometary data were carefully taken into account. Our analysis indicates that the occurrence of stellar perturbations on cometary motions is very rare and the uncertainties of these effects are hard to estimate.
Probing hot gas around luminous red galaxies through the Sunyaev–Zel’dovich effect
Authors: Tanimura Hideki , Hinshaw Gary , McCarthy Ian G , Van Waerbeke Ludovic , Aghanim Nabila , Ma Yin-Zhe , Mead Alexander , Tröster Tilman , Hojjati Alireza , Moraes Bruno
Published: November 2019

We construct the mean thermal Sunyaev–Zel’dovich (tSZ) Comptonization y-profile around luminous red galaxies (LRGs) in the redshift range 0.16 < z < 0.47 from the Sloan Digital Sky Survey Data Release 7 using the Planck y-map. We detect a significant tSZ signal out to ∼30 arcmin, which is well beyond the 10 arcmin angular resolution of the y-map and well beyond the virial radii of the LRGs. We compare the measured profile with predictions from the cosmo-OWLS suite of cosmological hydrodynamical simulations. The best agreement is obtained for models that include efficient feedback from active galactic nuclei, over and above feedback associated with star formation. We also compare our results with predictions based on the halo model with a universal pressure profile giving the y-signal. The predicted profile is consistent with the data when using stacked weak lensing measurements to estimate the halo masses of the LRGs, but only if we account for the clustering of neighbouring haloes via a two-halo term.
Constraints on running of non-Gaussianity from large-scale structure probes
Authors: Dai Ji-Ping , Xia Jun-Qing
Published: November 2019

In this letter, we present constraints on the scale-dependent ‘local’-type primordial non-Gaussianity, which is described by non-Gaussianity’s spectral index nNG, from the NRAO VLA Sky Survey and the quasar catalogue of the Sloan Digital Sky Survey (SDSS) Data Release 6, together with the SDSS Data Release 12 photo-z sample. Here, we use the autocorrelation analyses of these three probes and their cross-correlation analyses with the cosmic microwave background (CMB) temperature map, and obtain the tight constraint on the spectral index: $n_{\rm NG}=0.2 ^{+0.7}_{-1.0}$ ($1\sigma$ C.L.), which shows the first competitive constraint on the running of non-Gaussianity from current large-scale structure clustering data. Furthermore, we also perform the forecast calculations and improve the limit of nNG using the future Euclid mission, and obtain the standard deviation at a 68 per cent confidence level: ΔnNG = 1.74 when considering the fiducial value fNL = 3, which provides the complementary constraining power to those from the CMB bispectrum information.
USP14 is a deubiquitinase for Ku70 and critical determinant of non-homologous end joining repair in autophagy and PTEN-deficient cells
Authors: Sharma Arishya , Alswillah Turkeya , Kapoor Isha , Debjani Pal , Willard Belinda , Summers Matthew K , Gong Zihua , Almasan Alexandru
Published: November 2019

Ionizing radiation (IR)-induced DNA double-strand breaks (DSBs) are predominantly repaired by non-homologous end joining (NHEJ). IR-induced DNA damage activates autophagy, an intracellular degradation process that delivers cytoplasmic components to the lysosome. We identified the deubiquitinase USP14 as a novel autophagy substrate and a regulator of IR-induced DNA damage response (DDR) signaling. Inhibition of autophagy increased levels and DSB recruitment of USP14. USP14 antagonized RNF168-dependent ubiquitin signaling and downstream 53BP1 chromatin recruitment. Here we show that autophagy-deficient cells are defective in NHEJ, as indicated by decreased IR-induced foci (IRIF) formation by pS2056-, pT2609-DNA-PKcs, pS1778-53BP1, RIF1 and a reporter assay activation. Moreover, chromatin recruitment of key NHEJ proteins, including, Ku70, Ku80, DNA-PKcs and XLF was diminished in autophagy-deficient cells. USP14 inhibition rescued the activity of NHEJ-DDR proteins in autophagy-deficient cells. Mass spectrometric analysis identified USP14 interaction with core NHEJ proteins, including Ku70, which was validated by co-immunoprecipitation. An in vitro assay revealed that USP14 targeted Ku70 for deubiquitination. AKT, which mediates Ser432-USP14 phosphorylation, was required for IRIF formation by USP14. Similar to USP14 block, AKT inhibition rescued the activity of NHEJ-DDR proteins in autophagy- and PTEN-deficient cells. These findings reveal a novel negative PTEN/Akt-dependent regulation of NHEJ by USP14.
DriverDBv3: a multi-omics database for cancer driver gene research
Authors: Liu Shu-Hsuan , Shen Pei-Chun , Chen Chen-Yang , Hsu An-Ni , Cho Yi-Chun , Lai Yo-Liang , Chen Fang-Hsin , Li Chia-Yang , Wang Shu-Chi , Chen Ming , Chung I-Fang , Cheng Wei-Chung
Published: November 2019

An integrative multi-omics database is needed urgently, because focusing only on analysis of one-dimensional data falls far short of providing an understanding of cancer. Previously, we presented DriverDB, a cancer driver gene database that applies published bioinformatics algorithms to identify driver genes/mutations. The updated DriverDBv3 database (http://ngs.ym.edu.tw/driverdb) is designed to interpret cancer omics’ sophisticated information with concise data visualization. To offer diverse insights into molecular dysregulation/dysfunction events, we incorporated computational tools to define CNV and methylation drivers. Further, four new features, CNV, Methylation, Survival, and miRNA, allow users to explore the relations from two perspectives in the ‘Cancer’ and ‘Gene’ sections. The ‘Survival’ panel offers not only significant survival genes, but gene pairs synergistic effects determine. A fresh function, ‘Survival Analysis’ in ‘Customized-analysis,’ allows users to investigate the co-occurring events in user-defined gene(s) by mutation status or by expression in a specific patient group. Moreover, we redesigned the web interface and provided interactive figures to interpret cancer omics’ sophisticated information, and also constructed a Summary panel in the ‘Cancer’ and ‘Gene’ sections to visualize the features on multi-omics levels concisely. DriverDBv3 seeks to improve the study of integrative cancer omics data by identifying driver genes and contributes to cancer biology.
Cytomegalovirus Retinitis Screening and Treatment in Human Immunodeficiency Virus Patients in Malawi: A Feasibility Study
Authors: Ocieczek Paulina , Barnacle James R , Gumulira Joe , Phiri Sam , Heller Tom , Grabska-Liberek Iwona
Published: November 2019

Background

Cytomegalovirus retinitis is a treatable cause of blindness in people with human immunodeficiency virus (HIV) typically with CD4 counts <50 cells/mm3. Diagnosis is with indirect fundoscopy, and treatment is with intravitreal ganciclovir injections or systemic therapy. However, diagnosis and treatment are not widely available in Malawi, which has an adult HIV prevalence estimated at 10.6%. This study aimed to establish the prevalence of cytomegalovirus retinitis among people with HIV in Malawi and the feasibility of screening.

Methods

Patients with CD4 counts <200 cells/mm3 were examined from 2 HIV clinics in Lilongwe and the main government hospital. Data were collected on antiretroviral therapy, ocular symptoms, and visual acuity. Fundoscopy was performed to investigate for features of cytomegalovirus retinitis. Retinal photographs were reviewed by an ophthalmologist. Patients diagnosed with cytomegalovirus retinitis were offered weekly ganciclovir injections, because systemic treatment was not available.

Results

Five of the 102 people with HIV screened had cytomegalovirus retinitis (4.9%). All affected patients had CD4 counts <50 cells/mm3 (mean, 15 cells/mm3; range, 3–22 cells/mm3). Visual acuity was unhelpful in identifying those with cytomegalovirus retinitis. Symptomatically, only blurred vision was useful. Two patients consented to treatment, 1 of which improved but relapsed after defaulting.

Conclusions

Cytomegalovirus retinitis screening based on CD4 count is essential to early recognition because visual acuity and symptoms are unreliable. Cytomegalovirus retinitis is a significant yet neglected public health issue in Malawi. Oral valganciclovir is essential to reduce blindness and mortality in those diagnosed but is not yet available. Further screening and advocacy are needed.
Sharia Law in Europe? Legacies of the Ottoman Empire and the European Convention on Human Rights
Authors: McGoldrick Dominic
Published: November 2019

In Western Thrace in Greece, a legacy of the Ottoman Empire survives in the form of religious law (Sharia). This article examines how international human rights law has approached the compatibility of such religious laws with modern human rights instruments and particularly with the European Convention on Human Rights (ECHR). It portrays the situation on Western Thrace within the wider historical, legal and social contexts of Muslims in Greece. It explains how the ‘Muslims in Western Thrace’ came to be identified as a particular legal minority, why Sharia continued to be applied to them and only to them, and examines their contemporary legal and human rights status. There follows an extensive critique of the judgment of the Grand Chamber of the European Court of Human Rights in Molla Sali v. Greece in December 2018. Although the narrow factual issue in the case concerned inheritance rights, the case raised general issues concerning the individual as the central subject of human rights law and the relationship between individual and minority rights protection. The article concludes by reflecting on the place of individual consent within a human rights framework and the systemic implications of the Molla Sali case with respect to the possible future of Sharia in the social and legal spaces of the ECHR.