bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping changes in the spatiotemporal distribution of lumpy skin disease virus
Authors: Machado G. , Korennoy F. , Alvarez J. , Picasso-Risso C. , Perez A. , VanderWaal K. 
Published: February 2019

SummaryLumpy skin disease virus (LSDV) is an infectious disease of cattle transmitted by arthropod vectors which results in substantial economic losses due to impact on production efficiency and profitability, and represents an emerging threat to international trade of livestock products and live animals. Since 2015, the disease has spread across many Eastern European countries as well as Russia and Kazakhstan. This rapid expansion highlights the emergent nature of the virus in more temperate regions than those in which LSDV traditionally occurred. The goal of this study was to assess the risk for further LSDV spread in Eurasia through a) analysis of environmental factors conducive for LSDV and b) estimate of the underlying LSDV risk using a fine spatiotemporally explicit Bayesian hierarchical model on LSDV outbreak occurrence information. We used ecological niche modeling to estimate the potential distribution of LSDV outbreaks for 2014-2016. This analysis resulted in a spatial representation of environmental limits where, if introduced, LSDV is expected to efficiently spread. The Bayesian space-time model incorporated both environmental factors and the changing spatiotemporal distribution of the disease to capture the dynamics of disease spread and predict areas in which there is an increased risk of LSDV occurrence. Variables related to the average temperature, precipitation, wind speed, as well as land cover and host densities were found to be important drivers explaining the observed distribution of LSDV in both modeling approaches. Areas of elevated LSDV risks were identified mainly in Russia, Turkey, Serbia, and Bulgaria. Results suggest that prevailing ecological conditions may be compatible with further spread of LSDV in Eurasia, though models should be continually updated to reflect the current epidemiologic conditions. The results presented here advance our understanding of the ecological requirements of LSDV in temperate regions and may help in the design and implementation of prevention and surveillance strategies in the region.
Dose-specific effectiveness of 7- and 13-valent pneumococcal conjugate vaccines against vaccine-serotype Streptococcus pneumoniae colonization: a matched, case-control study
Authors: Lewnard Joseph A. , Givon-Lavi Noga , Dagan Ron 
Published: February 2019

ABSTRACTBackgroundReduced-dose pneumococcal conjugate vaccine (PCV) schedules are under consideration in countries where children are currently recommended to receive three PCV doses. However, dose-specific PCV effectiveness against vaccine-serotype colonization is uncertain.MethodsFrom 2009-2016, we conducted surveillance of pneumococcal carriage in southern Israel, where PCV is administered at ages 2, 4, and 12 months (2+1 schedule). We obtained nasopharyngeal swabs and vaccination histories from 4245 children ages 0-59 months without symptoms of diseases that could be caused by pneumococci. In a case-control analysis, we measured protection against vaccine-serotype colonization as one minus the matched odds ratio for PCV doses received.ResultsAt ages 5-12 months, a second PCV7/13 dose increased protection against PCV7-serotype carriage from –23.6% (95%CI: –209.7-39.1%) to 27.1% (–69.2-64.5%), and a second PCV13 dose increased protection against carriage of all PCV13 serotypes from –54.8% (–404.3-39.1%) to 23.4% (– 128.5-67.1%). At ages 13-24 months, a third PCV7/13 dose increased protection against PCV7-serotype carriage from 32.4% (–8.4-58.0%) to 74.1% (58.4-84.6%), and a third PCV13 dose increased protection against carriage of all PCV13 serotypes from –50.0% (–194.0-42.7%) to 49.7% (15.8-83.3%). On average, each PCV13 dose conferred 37.7% (7.0-61.8%) greater protection against carriage of serotypes 1, 5, 6A, 7F, and 19A than carriage of serotype 3. PCV13-derived protection against carriage of serotypes 1, 5, 6A, 7F, and 19A was equivalent to PCV7/13-derived protection against carriage of PCV7 serotypes.ConclusionsIn a setting implementing a 2+1 PCV schedule, protection against vaccine-serotype colonization is sustained primarily by the third dose.
Upscaling the surveillance of tick-borne pathogens in the French Caribbean islands
Authors: Gondard Mathilde , Delannoy Sabine , Pinarello Valérie , Aprelon Rosalie , Devillers Elodie , Galon Clémence , Pradel Jennifer , Vayssier-Taussat Muriel , Albina Emmanuel , Moutailler Sara 
Published: February 2019

AbstractDespite the high burden of vector-borne disease in (sub)-tropical areas, few information are available regarding the diversity of tick and tick-borne pathogens circulating in the Caribbean. Management and control of vector-borne disease require actual epidemiological data to better assess and anticipate the risk of (re)-emergence of tick-borne diseases in the region. To simplify and reduce the costs of such large-scale surveys, we implemented a high-throughput microfluidic real-time PCR system suitable for the screening of the main bacterial and parasitic genera involved in tick-borne disease and potentially circulating in the area. We used the new screening tool to perform an exploratory epidemiological study on 132 specimens of Amblyomma variegatum and 446 of Rhipicephalus microplus collected in Guadeloupe and Martinique. Not only the system was able to detect the main pathogens of the area– Ehrlichia ruminantium, Rickettsia africae, Anaplasma marginale, Babesia bigemina, Babesia bovis– but the system also provided evidence of unsuspected microorganisms in Caribbean ticks, belonging to the Anaplasma, Ehrlichia, Borrelia and Leishmania genera. Our study demonstrated how high-throughput microfluidic real-time PCR technology can assist large-scale epidemiological studies, providing a rapid overview of tick-borne pathogen and microorganism diversity, and opening up new research perspectives for the epidemiology of tick-borne pathogens.
HIV infection and incidence of cardiovascular diseases: an analysis of a large healthcare database
Authors: Alonso Alvaro , Barnes A. Elise , Guest Jodie L. , Shah Amit , Shao Iris Yuefan , Marconi Vincent 
Published: February 2019

ABSTRACTBackgroundPersons living with HIV (PLWH) experience higher risk of cardiovascular diseases (CVD) such as myocardial infarction (MI) and heart failure (HF) compared to uninfected individuals. Risk of other CVDs in PLWH has received less attention.MethodsWe studied 19,798 PLWH and 59,302 age and sex-matched uninfected individuals identified from the MarketScan Commercial and Medicare databases in the period 2009-2015. Incidence of CVDs, including MI, HF, atrial fibrillation (AF), peripheral artery disease (PAD), stroke and any CVD-related hospitalization, were identified using validated algorithms. We used adjusted Cox models to estimate hazard ratios (HR) and 95% confidence interval (95%CI) of CVD endpoints and performed probabilistic bias analysis to control for unmeasured confounding by race.ResultsAfter a mean (median) follow-up of 20 (17) months, study patients experienced 154 MIs, 223 HF, 93 stroke, 397 AF, 98 PAD and 935 CVD hospitalizations. HR (95%CI) comparing PLWH to uninfected controls were 1.3 (0.9, 1.9) for MI, 3.2 (2.4, 4.2) for HF, 2.7 (1.7, 4.0) for stroke, 1.2 (1.0, 1.5) for AF, 1.1 (0.7, 1.7) for PAD, and 1.7 (1.5, 2.0) for any CVD-related hospitalization. Adjustment for unmeasured confounding led to similar associations [1.2 (0.8, 1.8) for MI, 2.8 (2.0, 3.8) for HF, 2.3 (1.5, 3.6) for stroke, 1.3 (1.0, 1.7) for AF, 0.9 (0.5, 1.4) for PAD, and 1.6 (1.3, 1.9) for CVD hospitalization].ConclusionUsing a large health insurance database, we showed that PLWH have an elevated risk of CVD, particularly HF and stroke. With the aging of the HIV population, developing interventions for cardiovascular health promotion and CVD prevention is imperative.
Subcortical Shape Alterations in Major Depressive Disorder: Findings from the ENIGMA Major Depressive Disorder Working Group
Authors: Ho Tiffany C. , Gutman Boris , Pozzi Elena , Grabe Hans J. , Hosten Norbert , Wittfeld Katharina , Völzke Henry , Baune Bernhard , Dannlowski Udo , Förster Katharina , Grotegerd Dominik , Redlich Ronny , Jansen Andreas , Kircher Tilo , Krug Axel , Meinert Susanne , Nenadic Igor , Opel Nils , Dinga Richard , Veltman Dick J. , Schnell Knut , Veer Ilya , Walter Henrik , Gotlib Ian H. , Sacchet Matthew D. , Aleman André , Groenewold Nynke A. , Stein Dan J. , Li Meng , Walter Martin , Jahanshad Neda , Thompson Paul M. , Sämann Philipp G. , Schmaal Lianne 
Published: February 2019

AbstractAlterations in regional subcortical brain volumes have been widely investigated as part of the efforts of an international consortium, ENIGMA, to determine reliable structural brain signatures for Major Depressive Disorder (MDD). Given that subcortical structures are comprised of distinct subfields, we sought to build significantly from prior work to precisely map localized MDD-related differences in subcortical regions using shape analysis. In this meta-analysis of subcortical shape from the ENIGMA-MDD working group, we compared 1,781 patients with MDD and 2,953 healthy controls (CTL) on individual measures of shape metrics (thickness and surface area) on the surface of seven bilateral subcortical structures: nucleus accumbens, amygdala, caudate, hippocampus, pallidum, putamen, and thalamus. Harmonized data processing and statistical analyses were conducted locally at each site, and findings were aggregated by meta-analysis. Relative to CTL, patients with MDD had lower surface area in the subiculum of the hippocampus, the basolateral amygdala, and the nucleus accumbens shell. Relative to CTL, patients with adolescent-onset MDD (≤ 21 years) had lower thickness and surface area of the subiculum of the hippocampus and the basolateral amygdala. Relative to first-episode MDD, recurrent MDD patients had lower thickness and surface area in the CA1 of the hippocampus and the basolateral amygdala. Our results suggest that previously reported MDD-associated volumetric differences may be localized to specific subfields of these structures that have been shown to be sensitive to the effects of stress, with important implications for mapping treatments to patients based on specific neural targets and key clinical features.
Global variability of the human IgG glycome
Authors: Štambuk Jerko , Nakić Natali , Vučković Frano , Pučić-Baković Maja , Razdorov Genadij , Trbojević-Akmačić Irena , Novokmet Mislav , Keser Toma , Vilaj Marija , Pavić Tamara , Gudelj Ivan , Šimurina Mirna , Song Manshu , Wang Hao , Salihović Marijana Peričić , Campbell Harry , Rudan Igor , Kolčić Ivana , Eller Leigh Anne , McKeigue Paul , Robb Merlin L. , Halfvarson Jonas , Kurtoglu Metin , Annese Vito , Škarić-Jurić Tatjana , Molokhia Mariam , Polašek Ozren , Hayward Caroline , Kibuuka Hannah , Thaqi Kujtim , Primorac Dragan , Gieger Christian , Nitayaphan Sorachai , Spector Tim , Wang Youxin , Tillin Therese , Chaturvedi Nish , Wilson James F. , Schanfield Moses , Filipenko Maxim , Wang Wei , Lauc Gordan 
Published: February 2019

AbstractImmunoglobulin G (IgG) is the most abundant serum antibody and is a key determinant of the humoral immune response. Its structural characteristics and effector functions are modulated through the attachment of various sugar moieties called glycans. IgG N-glycome patterns change with the age of individual and in different diseases. Variability of IgG glycosylation within a population is well studied and is affected by a combination of genetic and environmental factors. However, global inter-population differences in IgG glycosylation have never been properly addressed. Here we present population-specific N-glycosylation patterns of whole IgG, analysed in 5 different populations totalling 10,482 IgG glycomes, and of IgG’s fragment crystallisable region (Fc), analysed in 2,530 samples from 27 populations sampled across the world. We observed that country of residence associates with many N-glycan features and is a strong predictor of monogalactosylation variability. IgG galactosylation also strongly correlated with the development level of a country, defined by United Nations health and socioeconomic development indicators. We found that subjects from developing countries had low IgG galactosylation levels, characteristic for inflammation and ageing. Our results suggest that citizens of developing countries may be exposed to country-specific environmental factors that can cause low-grade chronic inflammation and the apparent increase in biological age.
Occupation and Parkinson disease in Women’s Health Initiative Observational Study
Authors: Burstyn Igor , LaCroix Andrea Z. , Litvan Irene , Wallace Robert B. , Checkoway Harvey 
Published: February 2019

AbstractIntroductionThere is a lack of consistency in associations between workplace factors and risk of Parkinson disease (PD), and paucity of such data on women. We took a classic occupational epidemiology approach that assesses associations with occupational groups in order to derive insights about potential occupation-specific exposures that may be causal.MethodsThe Women’s Health Initiative (WHI-OS) is a prospective cohort that enrolled 91,627 postmenopausal women, 50 to 79 years of age from 10/01/93 to 12/31/98, at 40 clinical centers across the US with average follow-up of 11 years, who reported up to three paid jobs held the longest since age 18; these jobs were coded and duration of employment calculated. We defined the case by self-report of doctor-diagnosed PD (at baseline or follow-up), death attributed to PD, or medication consistent with PD.ResultsAmong 2,590 cases, we report evidence of excess risk among “counselors, social workers, and other community and social service specialists”. There was a suggestion of increase in risk among post-secondary teachers, and “building and grounds cleaning and maintenance”. There was also evidence of deficit in risk among women who worked in sales.Results with ever-employed and duration were similar, except for evidence of excess of risk among “health technologists and technicians” with more than 20 years of employment. Longer duration of life on a farm was associated with higher risk.ConclusionOur findings paint a largely reassuring picture of occupational risks for PD among US women, especially for trades largely unaffected by recent technological advances.
Computational analysis of molecular networks using spectral graph theory, complexity measures and information theory
Authors: Huang Chien-Hung , Tsai Jeffrey J. P. , Kurubanjerdjit Nilubon , Ng Ka-Lok 
Published: February 2019

AbstractMolecular networks are described in terms of directed multigraphs, so-called network motifs. Spectral graph theory, reciprocal link and complexity measures were utilized to quantify network motifs. It was found that graph energy, reciprocal link and cyclomatic complexity can optimally specify network motifs with some degree of degeneracy. Biological networks are built up from a finite number of motif patterns; hence, a graph energy cutoff exists and the Shannon entropy of the motif frequency distribution is not maximal. Also, frequently found motifs are irreducible graphs. Network similarity was quantified by gauging their motif frequency distribution functions using Jensen-Shannon entropy. This method allows us to determine the distance between two networks regardless of their nodes’ identities and network sizes.This study provides a systematic approach to dissect the complex nature of biological networks. Our novel method different from any other approach. The findings support the view that there are organizational principles underlying molecular networks.
LuxUS: DNA Methylation Analysis Using Generalized Linear Mixed Model with Spatial Correlation
Authors: Halla-aho Viivi , Lähdesmäki Harri 
Published: February 2019

AbstractMotivationDNA methylation is an important epigenetic modification, which has multiple functions. DNA methylation and its connections to diseases have been extensively studied in recent years. It is known that DNA methylation levels of neighboring cytosines are correlated and that differential DNA methylation typically occurs rather as regions instead of individual cytosine level.ResultsWe have developed a generalized linear mixed model, LuxUS, that makes use of the correlation between neighboring cytosines to facilitate analysis of differential methylation. LuxUS implements a likelihood model for bisulfite sequencing data that accounts for experimental variation in underlying biochemistry. LuxUS can model both binary and continuous covariates, and mixed model formulation enables including replicate and cytosine random effects. Spatial correlation is included to the model through a cytosine random effect correlation structure. We show with simulation experiments that by utilizing the spatial correlation we gain more power to the statistical testing of differential DNA methylation. Results with real bisulfite sequencing data set show that LuxUS is able to detect biologically significant differentially methylated cytosines.AvailabilityThe tool is available at https://github.com/hallav/LuxUS.Supplementary informationSupplementary data are available at bioRxiv.
Dystrophin and calcium current are decreased in cardiomyocytes expressing Cre enzyme driven by αMHC but not TNT promoter
Authors: Gillet Ludovic , Guichard Sabrina , Essers Maria C. , Rougier Jean-Sébastien , Abriel Hugues 
Published: February 2019

AbstractBackgroundThe Cre/lox system is a potent technology to control gene expression in mouse tissues. However, cardiac alterations following cardiac-specific Cre enzyme expression in non-loxP-flanked genome heart have been reported. Recently, many loxP like sites have been identified in the wild-type mouse genome. Interestingly one of them is localized in the Dmd gene encoding the dystrophin protein known to be crucial for stabilization of cardiac voltage-gated ion channels Nav1.5 and Cav1.2.AimHere, we studied the potential alteration of dystrophin expression in adult alpha-myosin heavy chain (MHC)-Cre mice, which are extensively used for cardiac-specific recombination, and investigated Troponin T (TNT)-Cre mice as a potential alternative.MethodsCardiac-specific MHC-Cre and TNT-Cre mouse lines expressing Cre recombinase under the control of the cardiac-specific alpha-myosin-heavy chain, and rat cardiac troponin T2 promoter respectively were used. Western blots, quantitative RT-PCR, immunostainings, and patch-clamp experiments were performed to characterize MHC-Cre and TNT-Cre mouse hearts and cardiomyocytes.ResultsDystrophin protein level was decreased in hearts from 12-week-old MHC-Cre+ mice compared to MHC-Cre-. Reduction of dystrophin was more pronounced with age. No significant difference was observed between 8-week-old MHC-Cre+ mice and MHC-Cre-. Immunostainings performed on cardiac sections showed reduced dystrophin signal at the lateral membrane of MHC-Cre+ cardiomyocytes. Quantitative RT-PCR showed decreased mRNA levels of Dmd gene encoding dystrophin. Finally, patch-clamp experiments showed a significant decrease in calcium current (ICaL) in adult MHC-Cre+ cardiomyocytes compared to MHC-Cre-. Neither dystrophin nor ICaL was reduced in adult TNT-Cre+ mouse hearts compared to TNT-Cre-.ConclusionIn contrary to TNT-Cre+ mice, the sole expression of Cre recombinase can alter the cardiac phenotype of MHC-Cre+ mice. Thus, researchers should include the “Cre-only” condition as control condition when designing experiments with Cre mouse strains.
Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated
Authors: Picazo Devani Romero , Dagan Tal , Ansorge Rebecca , Petersen Jillian M. , Dubilier Nicole , Kupczok Anne 
Published: February 2019

AbstractEukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated populations. The reconstruction of core genome-wide strain sequences from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel lifespan and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life-cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.
Hif-1α stabilisation polarises macrophages via cyclooxygenase/prostaglandin E2in vivo
Authors: Lewis Amy , Elks Philip M. 
Published: February 2019

AbstractMacrophage subtypes are poorly characterised in disease systemsin vivo. The initial innate immune response to injury and infectious stimuli through M1 polarisation is important for the outcome of disease. Appropriate macrophage polarisation requires complex coordination of local microenvironmental cues and cytokine signalling to influence immune cell phenotypes. If the molecular mechanisms behind macrophage polarisation were better understood then macrophages could be pharmacologically tuned to better deal with bacterial infections, for example tuberculosis. Here, using zebrafishtnfa:GFPtransgenic lines asin vivoreadouts of M1 macrophages, we show that hypoxia and stabilisation of Hif-1α polarises macrophages to atnfaexpressing phenotype. We demonstrate a novel mechanism of Hif-1α mediated macrophagetnfaupregulation via a cyclooxygenase/prostaglandin E2 axis, a mechanism that is conserved in human primary macrophages. These findings uncover a novel macrophage HIF/COX/TNF axis that links microenvironmental cues to macrophage phenotype that may have implications in inflammation, infection and cancer, where hypoxia is a common microenvironmental feature and where cyclooxygenase and Tnfa are major mechanistic players.
Mito-SinCe2 Approach to Quantify Relationships between Mitochondrial Dynamics and Energetics status
Authors: Spurlock Brian , Gupta Priyanka , Basu Malay Kumar , Mukherjee Avik , Hjelmeland Anita B , Darley-Usmar Victor , Parker Danitra , Foxall McKenzie E , Mitra Kasturi 
Published: February 2019

AbstractMitochondrial dynamics primarily refers to the opposing fission and fusion events between individual mitochondria, which maintains steady-state mitochondrial morphology in cells. The details of the bidirectional relationship between mitochondrial dynamics and energetics are unclear as the methods to integrate these mitochondrial aspects are lacking. To study the quantitative relationship between mitochondrial dynamics (fission, fusion, matrix continuity and diameter) and energetics (ATP and redox), we have developed and validated an analytical approach, mito-SinCe2. Application of this approach led to the hypothesis that mitochondria-dependent ovarian tumor initiating cells interconvert between 3 states with distinct relationships between mitochondrial energetics and dynamics. Interestingly, fusion and ATP increase linearly with each other only once a certain level of fusion is attained. Moreover, mitochondrial dynamics status changes linearly either with ATP or with redox, but not simultaneously with both. Furthermore, mito-SinCe2 analyses can potentially predict new quantitative features of the opposing fission vs. fusion relationship and classify cells into functional classes based on their mito-SinCe2 states.