bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing
Authors: Liu Qi , Ding Changjun , Lang Xiaoqiang , Guo Ganggang , Chen Jiafei , Su Xiaohua 
Published: November 2019

Abstract
Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small-interfering RNAs), Piwi-interacting RNA (piRNAs) and plant-specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all of these diverse sncRNAs. This study presents a novel integrated platform, sRNAtools (https://bioinformatics.caf.ac.cn/sRNAtools), that can be used in conjunction with high-throughput sequencing to identify and functionally annotate sncRNAs, including profiling microRNAss, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and rRNAs and discovering isomiRs, tRFs, phasiRNAs and plant-specific 24-nt siRNAs for up to 21 model organisms. Different modules, including single case, batch case, group case and target case, are developed to provide users with flexible ways of studying sncRNA. In addition, sRNAtools supports different ways of uploading small RNA sequencing data in a very interactive queue system, while local versions based on the program package/Docker/virtureBox are also available. We believe that sRNAtools will greatly benefit the scientific community as an integrated tool for studying sncRNAs.
MDiNE: a model to estimate differential co-occurrence networks in microbiome studies
Authors: McGregor Kevin , Labbe Aurélie , Greenwood Celia M T 
Published: November 2019

Abstract

Motivation
The human microbiota is the collection of microorganisms colonizing the human body, and plays an integral part in human health. A growing trend in microbiome analysis is to construct a network to estimate the co-occurrence patterns among taxa through precision matrices. Existing methods do not facilitate investigation into how these networks change with respect to covariates.

Results
We propose a new model called Microbiome Differential Network Estimation (MDiNE) to estimate network changes with respect to a binary covariate. The counts of individual taxa in the samples are modeled through a multinomial distribution whose probabilities depend on a latent Gaussian random variable. A sparse precision matrix over all the latent terms determines the co-occurrence network among taxa. The model fit is obtained and evaluated using Hamiltonian Monte Carlo methods. The performance of our model is evaluated through an extensive simulation study and is shown to outperform existing methods in terms of estimation of network parameters. We also demonstrate an application of the model to estimate changes in the intestinal microbial network topology with respect to Crohn’s disease.

Availability and implementation
MDiNE is implemented in a freely available R package: https://github.com/kevinmcgregor/mdine.

Supplementary information
Supplementary data are available at Bioinformatics online.
SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies
Authors: Ravichandran Srikanth , Hartmann András , del Sol Antonio 
Published: November 2019

Abstract

Summary
Single-cell RNA-sequencing is increasingly employed to characterize disease or ageing cell subpopulation phenotypes. Despite exponential increase in data generation, systematic identification of key regulatory factors for controlling cellular phenotype to enable cell rejuvenation in disease or ageing remains a challenge. Here, we present SigHotSpotter, a computational tool to predict hotspots of signaling pathways responsible for the stable maintenance of cell subpopulation phenotypes, by integrating signaling and transcriptional networks. Targeted perturbation of these signaling hotspots can enable precise control of cell subpopulation phenotypes. SigHotSpotter correctly predicts the signaling hotspots with known experimental validations in different cellular systems. The tool is simple, user-friendly and is available as web-server or as stand-alone software. We believe SigHotSpotter will serve as a general purpose tool for the systematic prediction of signaling hotspots based on single-cell RNA-seq data, and potentiate novel cell rejuvenation strategies in the context of disease and ageing.

Availability and implementation
SigHotSpotter is at https://SigHotSpotter.lcsb.uni.lu as a web tool. Source code, example datasets and other information are available at https://gitlab.com/srikanth.ravichandran/sighotspotter.

Supplementary information
Supplementary data are available at Bioinformatics online.
Parent and Child Perceptions of Collective Efficacy as Predictors of Delinquency
Authors: Gearhart Michael C 
Published: November 2019

AbstractJuvenile delinquency has a negative effect on victims, communities and the individual who commits a delinquent act. However, exposure to the juvenile justice system can be a traumatic event that results in further delinquency—highlighting a need to develop community-based interventions to prevent delinquency. Collective efficacy theory is a commonly used framework to prevent juvenile delinquency. Although community-level interventions have been developed based on collective efficacy, research suggests that they are limited in their effectiveness. This may be due to limitations in our conceptualisation of collective efficacy, and our limited understanding of how perceptions of collective efficacy differ between youths and parents. The present study utilises data from the Fragile Families Child Wellbeing Study to test parent and youth perceptions of collective efficacy as predictors of self-reported juvenile delinquency. The results indicate that—although collective efficacy is typically associated with lower levels of juvenile delinquency in neighbourhoods—neither parents’ nor youths’ perceptions of collective efficacy are strong predictors of self-reported juvenile delinquency. The findings suggest that focusing on youth, family and neighbourhood characteristics may maximise the effectiveness of interventions aimed at preventing juvenile delinquency.
A Re-enchanted Response to a Communal Call: Toward a Christian Understanding of Medicine as Vocation
Authors: Couch Tyler J 
Published: November 2019

Abstract
Modern concepts of vocation often refer to some ambiguous understanding of personal occupation or religious life. These interpretations appear to be in tension with the Christian understanding of vocation as the call of God given to a community to a certain way of living. Christian physicians live into this communal vocation when they remain present to the suffering as a sign of God’s faithfulness. This vocational practice of medicine is threatened by a distorted understanding of the body that stems from what Max Weber called the “disenchantment” of the world. By bringing an understanding of the medicine that stems from Weber’s disenchantment into conversation with the language and beliefs of the church, this essay will seek to explore practices that might serve to re-enchant an understanding of the body and the practice of medicine as a form of Christian vocation.
Altered Gray Matter Structure and White Matter Microstructure in Patients with Congenital Adrenal Hyperplasia: Relevance for Working Memory Performance
Authors: van’t Westeinde Annelies , Karlsson Leif , Thomsen Sandberg Malin , Nordenström Anna , Padilla Nelly , Lajic Svetlana 
Published: November 2019

AbstractCongenital adrenal hyperplasia (CAH) has been associated with brain structure alterations, but systematic studies are lacking. We explore brain morphology in 37 (21 female) CAH patients and 43 (26 female) healthy controls, aged 16–33 years, using structural magnetic resonance imaging to estimate cortical thickness, surface area, volume, subcortical volumes, and white matter (WM) microstructure. We also report data on a small cohort of patients (n = 8) with CAH, who received prenatal dexamethasone (DEX). Patients with CAH had reduced whole brain volume (4.23%) and altered structure of the prefrontal, parietal, and superior occipital cortex. Patients had reduced mean FA, and reduced RD and MD, but not after correcting for brain volume. The observed regions are hubs of the visuospatial working memory and default mode (DMN) networks. Thickness of the left superior parietal and middle frontal gyri was associated with visuospatial working memory performance, and patients with CAH performed worse on this task. Prenatal treatment with DEX affected brain structures in the parietal and occipital cortex, but studies in larger cohorts are needed. In conclusion, our study suggests that CAH is associated with brain structure alterations, especially in the working memory network, which might underlie the cognitive outcome observed in patients.
Labour market attachment among parents and self-rated health of their offspring: an intergenerational study
Authors: Lindholdt Louise , Lund Thomas , Andersen Johan H , Labriola Merete 
Published: November 2019

Abstract

Background
Unemployment influences the individual’s health, whether this effect passes through generations is less studied. The aim of this intergenerational study was to investigate whether parents’ labour market attachment (LMA) were associated with self-rated health (SRH) among adolescents using preceding labour market events.

Methods
The study was performed using questionnaire data from the Danish Future Occupation of Children and Adolescents cohort (the FOCA cohort) of 13 100 adolescents (mean age 15.8 years) and their accompanying parents identified through registers. Adolescents’ SRH was measured using one item from SF-36. Information on parents’ LMA was obtained from a national register, analyzed on a weekly basis in a 5-year period before the adolescents completed the questionnaire. An integration indicator was calculated from an initial sequence analysis to determine how well the parents were integrated in the labour market. The association between the adolescents’ SRH and parents’ LMA was examined by logistic regression and an extended sequence analysis stratified on adolescents’ SRH.

Results
Totally, 29.1% of the adolescents reported moderate SRH. The adjusted odds ratios (OR) of moderate SRH was higher among adolescents of parents with low labour market integration (OR: 1.5 95% CI: 1.3–1.6 for fathers and OR: 1.4 95% CI: 1.2–1.5 for mothers). Also, adolescents with moderate SRH had parents who were less integrated in the labour market and had more weeks on non-employment benefits compared with the adolescents, who reported high SRH.

Conclusions
Unstable LMA among parents affected SRH among their adolescent children, indicating a negative effect of labour market marginalization across generations.
Atonal homolog 7 (ATOH7) loss-of-function mutations in predominant bilateral optic nerve hypoplasia
Authors: Atac David Grubich , Koller Samuel , Hanson James V M , Feil Silke , Tiwari Amit , Bahr Angela , Baehr Luzy , Magyar István , Kottke Raimund , Gerth-Kahlert Christina , Berger Wolfgang 
Published: November 2019

Abstract
Optic nerve hypoplasia (ONH) is a congenital optic nerve abnormality caused by underdevelopment of retinal ganglion cells (RGCs). Despite being a rare disease, ONH is the most common optic disc anomaly in ophthalmological practice. So far, mutations in several genes have been identified as causative, however many cases of ONH remain without a molecular explanation. The early transcription factor atonal basic-helix-loop-helix (bHLH) transcription factor 7 (ATOH7) is expressed in retinal progenitor cells and has a crucial role in RGC development. Previous studies have identified several mutations in the ATOH7 locus in cases of eye developmental diseases such as nonsyndromic congenital retinal nonattachment and persistent hyperplasia of the primary vitreous.
Here we present two siblings with a phenotype predominated by bilateral ONH, with additional features of foveal hypoplasia and distinct vascular abnormalities, where whole-exome sequencing identified two compound heterozygous missense mutations affecting a conserved amino acid residue within the bHLH domain of ATOH7 (NM_145178.3:c.175G>A; p.(Ala59Thr) and c.176C>T; p.(Ala59Val)). ATOH7 expression constructs with patient single nucleotide variants were cloned for functional characterization. Protein analyses revealed decreased protein amounts and significantly enhanced degradation in the presence of E47, a putative bHLH dimerization partner. Protein interaction assays revealed decreased heterodimerization and DNA-binding of ATOH7 variants, resulting in total loss of transcriptional activation of luciferase reporter gene expression. These findings strongly support pathogenicity of the two ATOH7 mutations, one of which is novel. Additionally, this report highlights the possible impact of altered ATOH7 dimerization on protein stability and function.
Safety and effectiveness of a transaortic approach for TAVI: procedural and midterm outcomes of 265 consecutive patients in a single centre
Authors: Romano Mauro , Daprati Andrea , Saitto Guglielmo , Tizzano Francesco , Le Houérou Daniel , Donzeau-Gouge Patrick , Farge Arnaud , Lefèvre Thierry , Hovasse Thomas , Garatti Andrea 
Published: November 2019

Abstract

OBJECTIVES
Transcatheter aortic valve implantation with a transaortic approach (TAo-TAVI) is an alternative to transapical or femoral access. We studied the procedural and midterm efficacy and safety of TAo-TAVI with Edwards Sapien XT and Medtronic CoreValve devices.

METHODS
Among 901 patients receiving TAVI since 2006, 265 consecutive patients underwent TAo-TAVI between January 2011 and September 2014. Procedural and midterm results were evaluated according to Valve Academic Research Consortium-2 criteria.

RESULTS
The mean age was 83 ± 5 years. Sapien XT and CoreValve were used in 191 (72.1%) and 74 (27.9%) patients, respectively. Full sternotomy made elective concomitant off-pump coronary artery bypass grafting possible in 38 patients (14.3%) with severe coronary artery disease unsuitable for percutaneous coronary intervention. The device success rate was 95.5%. Postprocedural paravalvular leak  ≥2/4 was observed in 16 patients (6.4%). Emergency open chest surgery was required in 10 patients (3.8%) (3 aortic dissections, 3 valve embolizations, 2 LMCA occlusions, 1 aortic annulus rupture and 1 aortic rupture). Cerebrovascular accidents occurred in 3 patients (1.1%). Transfusions  ≥4 units were required in 36 patients (13.6%). New pacemakers were implanted in 26 patients (9.8%). Thirty-day and 1-year mortality were 8.7% and 16.2%, respectively. Mean follow-up duration was 24 ± 6 months. At 3 years, freedom from all-cause death was 80% ± 4%. New York Heart Association class &lt;III included 81% (n = 172) of patients alive and without prosthetic echocardiographic dysfunction at follow-up (mean gradient 10.5 ± 5.6 mmHg).

CONCLUSION
The TAo-TAVI approach confirms its safety and effectiveness with satisfactory procedural and midterm outcomes with both currently available devices.
Ulrich Bundles on Intersections of Two 4-Dimensional Quadrics
Authors: Cho Yonghwa , Kim Yeongrak , Lee Kyoung-Seog 
Published: November 2019

AbstractIn this paper, we investigate the moduli space of Ulrich bundles on a smooth complete intersection of two $4$-dimensional quadrics in $\mathbb P^5$. The main ingredient is the semiorthogonal decomposition by Bondal–Orlov, combined with the categorical methods pioneered by Kuznetsov and Lahoz–Macrì–Stellari. Using these methods, we prove that any smooth intersection of two 4-dimensional quadrics in $\mathbb P^5$ carries an Ulrich bundle of rank $r$ for every $r \ge 2$. Moreover, we provide a description of the moduli space of stable Ulrich bundles.
Cytokine Profile Distinguishes Children With Plasmodium falciparum Malaria From Those With Bacterial Blood Stream Infections
Authors: Struck Nicole S , Zimmermann Marlow , Krumkamp Ralf , Lorenz Eva , Jacobs Thomas , Rieger Toni , Wurr Stephanie , Günther Stephan , Gyau Boahen Kennedy , Marks Florian , Sarpong Nimako , Owusu-Dabo Ellis , May Jürgen , Eibach Daniel 
Published: November 2019

AbstractBackgroundMalaria presents with unspecific clinical symptoms that frequently overlap with other infectious diseases and is also a risk factor for coinfections, such as non-Typhi Salmonella. Malaria rapid diagnostic tests are sensitive but unable to distinguish between an acute infection requiring treatment and asymptomatic malaria with a concomitant infection. We set out to test whether cytokine profiles could predict disease status and allow the differentiation between malaria and a bacterial bloodstream infection.MethodsWe created a classification model based on cytokine concentration levels of pediatric inpatients with either Plasmodium falciparum malaria or a bacterial bloodstream infection using the Luminex platform. Candidate markers were preselected using classification and regression trees, and the predictive strength was calculated through random forest modeling.ResultsAnalyses revealed that a combination of 7–15 cytokines exhibited a median disease prediction accuracy of 88% (95th percentile interval, 73%–100%). Haptoglobin, soluble Fas-Ligand, and complement component C2 were the strongest single markers with median prediction accuracies of 82% (with 95th percentile intervals of 71%–94%, 62%–94%, and 62%–94%, respectively).ConclusionsCytokine profiles possess good median disease prediction accuracy and offer new possibilities for the development of innovative point-of-care tests to guide treatment decisions in malaria-endemic regions.
Reactive oxygen species play a dominant role in all pathways of rapid quinolone-mediated killing
Authors: Hong Yuzhi , Li Qiming , Gao Qiong , Xie Jianping , Huang Haihui , Drlica Karl , Zhao Xilin 
Published: November 2019

AbstractBackgroundQuinolones have been thought to rapidly kill bacteria in two ways: (i) quinolone-topoisomerase-DNA lesions stimulate the accumulation of toxic reactive oxygen species (ROS); and (ii) the lesions directly cause lethal DNA breaks. Traditional killing assays may have underestimated the ROS contribution by overlooking the possibility that ROS continue to accumulate and kill cells on drug-free agar after quinolone removal.MethodsQuinolone-induced, ROS-mediated killing of Escherichia coli was measured by plating post-treatment samples on agar with/without anti-ROS agents.ResultsWhen E. coli cultures were treated with ciprofloxacin or moxifloxacin in the presence of chloramphenicol (to accentuate DNA-break-mediated killing), lethal activity, revealed by plating on quinolone-free agar, was inhibited by supplementing agar with ROS-mitigating agents. Moreover, norfloxacin-mediated lethality, observed with cells suspended in saline, was blocked by inhibitors of ROS accumulation and exacerbated by a katG catalase deficiency that impairs peroxide detoxification. Unlike WT cells, the katG mutant was killed by nalidixic acid or norfloxacin with chloramphenicol present and by nalidixic or oxolinic acid with cells suspended in saline. ROS accumulated after quinolone removal with cultures either co-treated with chloramphenicol or suspended in saline. Deficiencies in recA or recB reduced the protective effects of ROS-mitigating agents, supporting the idea that repair of quinolone-mediated DNA lesions suppresses the direct lethal effects of such lesions.ConclusionsROS are the dominant factor in all modes of quinolone-mediated lethality, as quinolone-mediated primary DNA lesions are insufficient to kill without triggering ROS accumulation. ROS-stimulating adjuvants may enhance the lethality of quinolones and perhaps other antimicrobials.
Phenology of Emerald Ash Borer (Coleoptera: Buprestidae) and Its Introduced Larval Parasitoids in the Northeastern United States
Authors: Jones Michael I , Gould Juli R , Mahon Hope J , Fierke Melissa K 
Published: November 2019

Abstract
Biological control offers a long-term and sustainable option for controlling the destructive forest pest emerald ash borer (EAB), Agrilus planipennis Fairmaire, in North America. Three larval parasitoids, Spathius agrili Yang (Hymenoptera: Braconidae), Tetrastichus planipennisi Yang (Eulophidae), and Spathius galinae Belokobylskij & Strazanac, have been introduced to North America from the native range of EAB (northeastern Asia). While T. planipennisi appears to be persisting where it has been introduced in northern United States, S. agrili failed to establish in northeastern states. The more recently identified parasitoid S. galinae was recovered from the Russian Far East and climate matching suggests it should be suited for release in colder climates. We collected data on the phenology of EAB and its introduced larval parasitoids from colonies established in an insectary, growth chambers, and field-caged trees in Syracuse, New York to determine whether asynchrony between parasitoids and EAB or climate could impact establishment and persistence. Phenological data indicated EAB has one and 2-yr life cycles in New York, with parasitoid-susceptible EAB larvae available spring to fall for parasitism. Insectary and growth chamber studies indicated S. galinae and T. planipennisi were synchronous with EAB phenology, and field studies suggested both species could overwinter in northeastern climates. Spathius agrili was asynchronous with EAB phenology and climate, emerging when fewer parasitoid-susceptible EAB larvae were available and temperatures were not optimal for survival. Our results suggest S. galinae and T. planipennisi are suited for biological control of EAB at the northern limits of its range in North America.
Minimal Duration of Tick Attachment Sufficient for Transmission of Infectious Rickettsia rickettsii (Rickettsiales: Rickettsiaceae) by Its Primary Vector Dermacentor variabilis (Acari: Ixodidae): Duration of Rickettsial Reactivation in the Vector Revisited
Authors: Levin Michael L , Ford Shelby L , Hartzer Kris , Krapiunaya Lnna , Stanley Hannah , Snellgrove Alyssa N 
Published: November 2019

AbstractIt has been reported that starving ticks do not transmit spotted fever group Rickettsia immediately upon attachment because pathogenic bacteria exist in a dormant, uninfectious state and require time for ‘reactivation’ before transmission to a susceptible host. To clarify the length of reactivation period, we exposed guinea pigs to bites of Rickettsia rickettsii-infected Dermacentor variabilis (Say) and allowed ticks to remain attached for predetermined time periods from 0 to 48 h. Following removal of attached ticks, salivary glands were immediately tested by PCR, while guinea pigs were observed for 10–12 d post-exposure. Guinea pigs in a control group were subcutaneously inoculated with salivary glands from unfed D. variabilis from the same cohort. In a parallel experiment, skin at the location of tick bite was also excised at the time of tick removal to ascertain dissemination of pathogen from the inoculation site. Animals in every exposure group developed clinical and pathological signs of infection. The severity of rickettsial infection in animals increased with the length of tick attachment, but even attachments for less than 8 h resulted in clinically identifiable infection in some guinea pigs. Guinea pigs inoculated with salivary glands from unfed ticks also became severely ill. Results of our study indicate that R. rickettsii residing in salivary glands of unfed questing ticks does not necessarily require a period of reactivation to precede the salivary transmission and ticks can transmit infectious Rickettsia virtually as soon as they attach to the host.