bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of potential microRNAs associated with Herpesvirus family based on bioinformatic analysis
Authors: Lamkiewicz Kevin , Barth Emanuel , Barth Emanuel , Ibrahim Bashar 
Published: September 2018

ABSTRACTMicroRNAs (miRNAs) are known key regulators of gene expression on posttranscriptional level in many organisms encoded in mammals, plants and also several viral families. To date, no homologous gene of a virus-originated miRNA is known in other organisms. To date, only a few homologous miRNA between two different viruses are known, however, no gene of a virus-originated miRNA is known in any organism of other kingdoms. This can be attributed to the fact that classical miRNA detection approaches such as homology-based predictions fail at viruses due to their highly diverse genomes and their high mutation rate.Here, we applied the virus-derived precursor miRNA (pre-miRNA) prediction pipeline ViMiFi, which combines information about sequence conservation and machine learning-based approaches, on Human Herpesvirus 7 (HHV7) and Epstein-Barr virus (EBV). ViMiFi was able to predict 61 candidates in EBV, which has 25 known pre-miRNAs. From these 25, ViMiFi identified 20. It was further able to predict 18 candidates in the HHV7 genome, in which no miRNA had been described yet. We also studied the undescribed candidates of both viruses for potential functions and found similarities with human snRNAs and miRNAs from mammals and plants.
The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs
Authors: Olgeiser Lilli , Haag Carl , Boerner Susan , Ule Jernej , Busch Anke , Koepke Janine , König Julian , Feldbrügge Michael , Zarnack Kathi 
Published: September 2018

AbstractRNA-binding proteins (RBPs) determine spatiotemporal gene expression by mediating active transport and local translation of cargo mRNAs. Here, we cast a transcriptome-wide view on the transported mRNAs and cognate RBP binding sites during endosomal messenger ribonucleoprotein (mRNP) transport in Ustilago maydis. Using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP), we compare the key transport RBP Rrm4 and the newly identified endosomal mRNP component Grp1 that is crucial to coordinate hyphal growth. Both RBPs bind predominantly in the 3’ untranslated region of thousands of shared cargo mRNAs, often in close proximity. Intriguingly, Rrm4 precisely binds at stop codons, which constitute landmark sites of translation, suggesting an intimate connection of mRNA transport and translation. Towards uncovering the code of recognition, we identify UAUG as specific binding motif of Rrm4 that is bound by its third RRM domain. Altogether, we provide first insights into the positional organisation of co-localising RBPs on individual cargo mRNAs.
Tau Secretion and Propagation Is Regulated by p300/CBP via Autophagy-Lysosomal Pathway in Tauopathy
Authors: Chen Xu , Li Yaqiao , Wang Chao , Tang Yinyan , Mok Sue-Ann , Tsai Richard M. , Rojas Julio C. , Karydas Anna , Miller Bruce L. , Boxer Adam L. , Gestwicki Jason E. , Cuervo Ana Maria , Arkin Michelle , Gan Li 
Published: September 2018

SUMMARYThe trans-neuronal propagation of tau has been implicated in the progression of tau-mediated neurodegeneration. Tau secretion from neurons is the first step in tau transmission, but little is known about the cellular mechanism. Here, we report that p300/CBP, the lysine acetyltransferase that acetylates tau and regulates its homeostasis and toxicity, serves as a key regulator of tau secretion by inhibiting the autophagy-lysosomal pathway (ALP). Increased p300/CBP activity was associated with impaired function of this pathway in a tau transgenic mouse model. p300/CBP hyperactivation increased tau secretion by blocking autophagic flux. Conversely, inhibiting p300/CBP genetically or pharmacologically promoted autophagic flux, and reduced tau accumulation, tau secretion, and tau propagation in fibril-induced tau spreading models in vitro and in vivo. Our findings show that p300/CBP-induced impairment in the ALP underlies excessive unconventional secretion and pathogenic spread of tau.
Gut microbiome of an unindustrialized population have characteristic enrichment of SNPs in species and functions with the succession of seasons
Authors: Qin Jiyue , Tan Chongyang , Ning Kang 
Published: September 2018

AbstractMost studies investigating human gut microbiome dynamics are conducted in modern populations. However, unindustrialized populations are arguably better subjects in answering human-gut microbiome coevolution questions due to their lower exposure to antibiotics and higher dependence on natural resources. Hadza hunter-gatherers in Tanzania have been found to exhibit high biodiversity and seasonal patterns in their gut microbiome composition at family level, where some taxa disappear in one season and reappear at later time. However, such seasonal changes have previously been profiled only according to species abundances, with genome-level variant dynamics unexplored. As a result it is still elusive how microbial communities change at the genome-level under environmental pressures caused by seasonal changes. Here, a strain-level SNP analysis of Hadza gut metagenome is performed for 40 Hadza fecal samples collected in three seasons. First, we benchmarked three SNP calling tools based on simulated sequencing reads, and selected VarScan2 that has highest accuracy and sensitivity after a filtering step. Second, we applied VarScan2 on Hadza gut microbiome, with results showing that: with more SNP presented in wet season in general, eight prevalent species have significant SNP enrichments in wet season of which only three species have relatively high abundances. This indicates that SNP characteristics are independent of species abundances, and provides us a unique lens towards microbial community dynamics. Finally, we identify 83 genes with the most characteristic SNP distributions between wet season and dry season. Many of these genes are from Ruminococcus obeum, and mainly from metabolic pathways like carbon metabolism, pyruvate metabolism and glycolysis, as shown by KEGG annotation. This implies that the seasonal changes might indirectly impact the mutational patterns for specific species and functions for gut microbiome of an unindustrialized population, indicating the role of these variants in their adaptation to the changing environment and diets.ImportanceBy analyzing the changes of SNP enrichments in different seasons, we have found that SNP characteristics are independent of species abundances, and could provide us a unique lens towards microbial community dynamics at the genomic level. Many of the genes in microbiome also presented characteristic SNP distributions between wet season and dry season, indicating the role of variants in specific species in their adaptation to the changing environment for an unindustrialized population.
A Nodal/Eph signalling relay drives the transition from apical constriction to apico-basal shortening in ascidian endoderm invagination
Authors: Fiuza Ulla-Maj , Negishi Takefumi , Rouan Alice , Yasuo Hitoyoshi , Lemaire Patrick 
Published: September 2018

AbstractGastrulation is the first major morphogenetic event during animal embryogenesis. Ascidian gastrulation starts with the invagination of 10 endodermal precursor cells between the 64- and late 112-cell stages. This process occurs in the absence of endodermal cell division and in two steps, driven by myosin-dependent contractions of the acto-myosin network. First, endoderm precursors constrict their apex. Second, they shorten apico-basally, while retaining small apical surfaces, thereby causing invagination. The mechanisms controlling the endoderm mitotic delay, the step 1 to step 2 transition, and apico-basal shortening have remained elusive. Here, we demonstrate the conserved role during invagination of Nodal and Eph signalling in two distantly related ascidian species (Phallusia mammillataandCiona intestinalis). We show that the transition to step 2 is controlled by Nodal relayed by Eph signalling and that Eph signalling has a Nodal-independent role in mitotic delay. Interestingly, both Nodal and Eph signals are dispensable for endodermal germ layer fate specification.Summary statementIdentification of a regulatory developmental signalling sub-network driving endoderm cell shape changes during ascidian endoderm invagination, not involved in cell fate specification.
Planned delivery route of preterm breech singletons, and neonatal and 2‐year outcomes: a population‐based cohort study
Authors: Lorthe E , Sentilhes L , Quere M , Lebeaux C , Winer N , Torchin H , Goffinet F , Delorme P , Kayem G ,   the EPIPAGE‐2 Obstetric Writing Group
Published: September 2018

ObjectiveTo assess whether planned route of delivery is associated with perinatal and 2‐year outcomes for preterm breech singletons.DesignProspective nationwide population‐based EPIPAGE‐2 cohort study.SettingFrance, 2011.SampleThree hundred and ninety women with breech singletons born at 26–34 weeks of gestation after preterm labour or preterm prelabour rupture of membranes.MethodsPropensity‐score analysis.Main outcome measuresSurvival at discharge, survival at discharge without severe morbidity, and survival at 2 years of corrected age without neurosensory impairment.ResultsVaginal and caesarean deliveries were planned in 143 and 247 women, respectively. Neonates with planned vaginal delivery and planned caesarean delivery did not differ in survival (93.0 versus 95.7%, P = 0.14), survival at discharge without severe morbidity (90.4 versus 89.9%, P = 0.85), or survival at 2 years without neurosensory impairment (86.6 versus 91.6%, P = 0.11). After applying propensity scores and assigning inverse probability of treatment weighting, as compared with planned vaginal delivery, planned caesarean delivery was not associated with improved survival (odds ratio, OR 1.31; 95% confidence interval, 95% CI 0.67–2.59), survival without severe morbidity (OR 0.75, 95% CI 0.45–1.27), or survival at 2 years without neurosensory impairment (OR 1.04, 95% CI 0.60–1.80). Results were similar after matching on propensity score.ConclusionsNo association between planned caesarean delivery and improved outcomes for preterm breech singletons born at 26–34 weeks of gestation after preterm labour or preterm prelabour rupture of membranes was found. The route of delivery should be discussed with women, balancing neonatal outcomes with the higher risks of maternal morbidity associated with caesarean section performed at low gestational age.
Improving the effectiveness of lifestyle interventions for gestational diabetes prevention: a meta‐analysis and meta‐regression
Authors: Guo X‐Y , Shu J , Fu X‐H , Chen X‐P , Zhang L , Ji M‐X , Liu X‐M , Yu T‐T , Sheng J‐Z , Huang H‐F 
Published: September 2018

BackgroundDiet and exercise during pregnancy have been used to prevent gestational diabetes mellitus (GDM) with some success.ObjectiveTo examine the effectiveness of lifestyle intervention on GDM prevention and to identify key effectiveness moderators to improve the prevention strategy.Search strategyPubmed, Scopus, Cochrane, and cross‐references were searched.Selection criteriaRandomised controlled trials (RCTs) evaluating lifestyle interventions during pregnancy for GDM prevention.Data collection and analysisTwo independent reviewers extracted data. A random‐effects model was used to analyse the relative risk (RR) and 95% confidence interval (95% CI). Meta‐regressions and subgroup analyses were used to investigate important moderators of effectiveness.Main resultsForty‐seven RCTs involving 15 745 participants showed that diet and exercise during pregnancy were preventive of GDM (RR 0.77, 95% CI 0.69–0.87). Four key aspects were identified to improve the preventive effect: targeting the high‐risk population; an early initiation of the intervention; the correct intensity and frequency of exercise; and gestational weight gain management. Although 24 RCTs targeted women who were overweight or obese, body mass index (BMI) failed to predict the effectiveness of an intervention. Instead, interventions are most effective in high‐incidence populations rather than simply in women who are overweight or obese. Furthermore, exercise of moderate intensity for 50–60 minutes twice a week could lead to an approximately 24% reduction in GDM.ConclusionThe best strategy to prevent GDM is to target the high‐risk population predicted by risk evaluation models and to control the gestational weight gain of women through intensified diet and exercise modifications early in their pregnancy.Tweetable abstractFour key effectiveness moderators of lifestyle interventions for GDM prevention.
Microsatellite High‐Resolution Melting (SSR‐HRM) to Track Olive Genotypes: From Field to Olive Oil
Authors: Gomes Sónia , Breia Richard , Carvalho Teresa , Carnide Valdemar , Martins‐Lopes Paula 
Published: September 2018

AbstractThe need to support food labelling has driven to the development of PCR‐based techniques suitable for food analysis. DNA‐based markers have been successfully employed for varietal tracing in Protected Designation of Origin (PDO) olive oils. In this study, we report a fast, sensitive, and easy‐to‐use strategy for PDO olive varietal identification. To achieve this aim four different DNA extraction methods were tested and compared, based on initial volume, extraction time, the gDNA concentration, and quality ratios. The optimized DNA extraction protocol from extra virgin olive oils, based on CTAB–hexane–chloroform extraction, proved to be the most effective. High‐resolution melting (HRM) DNA assay was developed based on nuclear microsatellites (gSSR) and plastid DNA (cpDNA) aiming an accurate identification of the olive varieties present in the olive oil samples. After PCR reproducibility evaluation, six molecular markers: three SSRs and three cpDNA loci were chosen based on their discrimination power. The SSR‐HRM strategy assays were designed to target UDO99‐011, UDO99‐039, UDO99‐024, and ssrOeUA‐DCA16 loci. All SSR‐PCR products generated from these primers were analyzed by capillary electrophoresis (CE) for HRM data validation. The SSR coupled with HRM melting curve analysis generated 14 HRM profiles sufficient to genotype all varieties, highlighting their potential use for varietal discrimination. The locus ssrOeUA‐DCA16 generated a specific melting curve that allow a high‐throughput discrimination of the Picual and Cobrançosa varieties in olive oil samples. Further, the UDO99‐024 was also tested by SSR‐HRM assay in commercial olive oil samples with promising results. Considering time, cost, and performance SSR‐HRM proved to be a reliable method suitable for varietal tracing of olive oils.Practical ApplicationOlive oil authenticity is a form of protecting producers and consumers against fraudulent practices. Herein, we present a DNA barcode suitable for the identification of olive varieties, allowing an accurate identification of the olive varieties in olive oil samples using SSR‐HRM assay. Its applicability in commercial olive oil samples is viable. This methodology can be used as a tool for Extra Virgin Olive Oil (EVOO) adulterations detection.
Analysis of the current preschool vision screening in Denmark
Authors: Sandfeld Lisbeth , Weihrauch Hanne , Tubæk Gitte 
Published: September 2018

AbstractPurposeTo analyse the current vision screening programme for children attending school with respect to identifying children with significant refractive errors.MethodsA total of 950 children from the municipality of Roskilde, Denmark, were invited to participate in a cross‐sectional study of vision screening. 447 children aged 4.5–7 years participated in the study. The children completed a vision screening and a full eye examination. The vision screening consisted of visual acuity at distance (VA), visual acuity at distance with +2.0 glasses (VA+2), visual acuity at near (VAnear) and Lang II stereotest. A LogMAR‐based picture chart was used for the vision testing. Significant refractive errors were defined as hyperopia ≥+3.5 D, myopia >1.0 D, astigmatism ≥1.25 D and anisometropia >1.0 D.ResultsUsing receiver operating characteristic (ROC) curves, we could compare the efficiency of VA, VA+2, VAnear, VA in combination with VA+2 and VA in combination with VAnear. Area under the curve (AUC) for VA, VA combined with VA+2 and VA combined with VAnear was 0.841, 0.857 and 0.857, respectively, that is all classified as ‘very good’ screening tools, whereas VA+2 and VAnear as single screening tools were classified as ‘good’ with AUC of 0.704 and 0.775, respectively. Using the optimal cut‐off limit from the ROC curves, VA above 0.05 LogMAR as cut‐off limit showed a sensitivity of 85.2% with a specificity of 74.9%. A slightly higher sensitivity could be found when combining screening tests, but with declining specificities.ConclusionVisual acuity at distance with the use of LogMAR‐based charts is the optimal screening tool of choice; only minor improvements can be obtained combining with other tests.
Prioritizing recovery funding to maximize conservation of endangered species
Authors: Martin Tara G. , Kehoe Laura , Mantyka‐Pringle Chrystal , Chades Iadine , Wilson Scott , Bloom Robin G. , Davis Stephen K. , Fisher Ryan , Keith Jeff , Mehl Katherine , Diaz Beatriz Prieto , Wayland Mark E. , Wellicome Troy I. , Zimmer Karl P. , Smith Paul A. 
Published: September 2018

AbstractThe absence of a rigorous mechanism for prioritizing investment in endangered species management is a major implementation hurdle affecting recovery. Here, we present a method for prioritizing strategies for endangered species management based on the likelihood of achieving species’ recovery goals per dollar invested. We demonstrate our approach for 15 species listed under Canada's Species at Risk Act that co‐occur in Southwestern Saskatchewan. Without management, only two species have >50% probability of meeting recovery objectives; whereas, with management, 13 species exceed the >50% threshold with the implementation of just five complementary strategies at a cost of $126m over 20 years. The likelihood of meeting recovery objectives rarely exceeded 70% and two species failed to reach the >50% threshold. Our findings underscore the need to consider the cost, benefit, and feasibility of management strategies when developing recovery plans in order to prioritize implementation in a timely and cost‐effective manner.
Amplifying plant disease risk through assisted migration
Authors: Simler Allison B. , Williamson Matthew A. , Schwartz Mark W. , Rizzo David M. 
Published: September 2018

AbstractTranslocation of species, populations, or genotypes beyond their historic ranges (i.e., assisted migration [AM]) is an oft‐debated climate adaptation strategy. Well‐intentioned AM actions could alter disease dynamics for target species and recipient sites, resulting in unanticipated detrimental economic and ecological impacts. Although disease risks are occasionally mentioned in AM debates, current regulations or best practices that reduce or mitigate these complex risks are generally lacking in North America. We use the “Disease Triangle”, a foundational framework in pathology, to illustrate pathways through which AM may impact disease emergence, to identify knowledge gaps, and to suggest best practices to reduce disease risks. We highlight empirical examples in which altering pathogen distributions, host communities, and environment have historically resulted in costly and ecologically damaging diseases in plants. Although guidelines to reduce disease risks in AM are generally lacking, policies governing endangered species, invasive species, and disease management can provide starting points for a more comprehensive policy. We use examples from the United States to identify key strengths and weaknesses that can inform regulations to reduce disease risks associated with AM. We argue that consideration of disease motivates policy development that incorporates improved risk assessments, agency coordination, and accountability mechanisms.
Elevated end‐diastolic wall stress after acute myocardial infarction predicts adverse cardiovascular outcomes and longer hospital length of stay
Authors: Mosleh Wassim , Elango Kalaimani , Shah Tanvi , Chaudhari Milind , Gandhi Sumeet , Kattel Sharma , Karki Roshan , Khalil Charl , Frodey Kevin , Dahal Suraj , Okeeffe Cale , Aljebaje Zaid , Nagahama Makoto , Punnanithinont Natdanai , Sharma Umesh C. 
Published: September 2018

BackgroundAcute myocardial infarction (MI) leads to ventricular remodeling in response to oxygen demand. Such changes include left ventricular (LV) dilatation and increased myocardial wall stress. Prior studies showed that wall stress is a vital parameter of cardiac remodeling. However, outcome data are lacking. We aim to investigate wall stress post‐MI in relation to biomarkers of cardiac remodeling and cardiovascular outcomes.MethodsPatients presenting with ST‐elevation MI (STEMI) requiring primary percutaneous intervention (PCI) were enrolled prospectively. LVEF and volume‐based end‐diastolic (EDWS) and end‐systolic (ESWS) wall stress were measured from predischarge echocardiograms. Serum samples were collected for measurement of serum biomarkers. We identified 81 patients meeting inclusion criteria (64% men, 36% women) with a mean age of 61. The primary outcome was major adverse cardiovascular events (MACE) defined as 1‐year composite endpoint of cardiac mortality, recurrent MI, revascularization, or stroke. Length of hospitalization (LOH) was recorded.ResultsMajor adverse cardiovascular events‐positive patients (n = 12) had significantly higher EDWS levels (15.87 vs 12.33, P = 0.045), and galectin‐3 levels (19.07 vs 11.75, P = 0.015), and lower LVEF (40.0% vs 48.4%, P = 0.023) compared to MACE‐negative patients. Patients with LOH > 72 hours (n = 33) had significantly higher EDWS, galectin‐3, and peak troponin, and lower LVEF compared to patients with LOH < 72 hours. EDWS positively correlated with LOH and galectin‐3. EDWS was an independent predictor of MACE by binomial regression analysis.ConclusionEnd‐diastolic walls tress is a potential prognostic tool for risk stratifying STEMI patients, providing an assessment of the functional consequences of myocardial remodeling. It is predictive of MACE independent of LVEF, associated with longer hospitalizations, and correlates with galectin‐3, a biomarker of cardiac remodeling.