bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical outcomes three-year after revascularization with biodegradable polymer stents: ultrathin-strut sirolimus-eluting stent versus biolimus-eluting stent: from the Scandinavian organization for randomized trials with clinical outcome VII trial
Authors: Ellert Julia , Maeng Michael , Raungaard Bent , Hansen Knud Nørregaard , Kahlert Johnny , Jensen Svend Eggert , Bøtker Hans Erik , Hansen Henrik Steen , Lassen Jens Flensted , Christiansen Evald Høj , Jensen Lisette Okkels 
Published: April 2020

Background
Drug-eluting stents with biodegradable polymers have been designed to improve safety and efficacy. However, drug-eluting stents with biodegradable polymers may not be a class effect, as stent strut thickness, polymer coating, and drug resorption differ between these groups of stents. Twelve months results of Scandinavian Organization for Randomized Trials With Clinical Outcome VII showed that ultrathin-strut sirolimus-eluting Orsiro stent was noninferior to the biolimus-eluting Nobori stent. The sirolimus-eluting Orsiro stent was associated with a reduced risk of definite stent thrombosis.

Methods
The Scandinavian Organization for Randomized Trials With Clinical Outcome VII trial is a prospective multicenter randomized clinical trial comparing sirolimus-eluting Orsiro stent and biolimus-eluting Nobori stent in all-comers patients. The endpoint target lesion failure was a composite of cardiac death, myocardial infarction (not related to other than index lesion) and target lesion revascularization.

Results
A total of 1261 patients were randomized to treatment with sirolimus-eluting Orsiro stent and 1264 patients to biolimus-eluting Nobori stent and followed for 3 years. At 3-year the target lesion failure was comparable for sirolimus-eluting Orsiro stent (9.0%) and the biolimus-eluting Nobori stent (9.1%), (rate ratio, 0.99; 95% confidence interval, 0.77–1.29). Cardiac death (sirolimus-eluting Orsiro stent 3.0% vs. biolimus-eluting Nobori stent 2.6% [rate ratio, 1.16; 95% confidence interval, 0.73–1.86]), target lesion revascularization (sirolimus-eluting Orsiro stent 5.2% vs. biolimus-eluting Nobori stent 5.9% [rate ratio, 0.90; 95% confidence interval, 0.64–1.25]), myocardial infarction (sirolimus-eluting Orsiro stent 4.7% vs. biolimus-eluting Nobori stent 4.5% [rate ratio, 1.04; 95% confidence interval, 0.72–1.50]), and definite stent thrombosis (sirolimus-eluting Orsiro stent 1.0% vs. biolimus-eluting Nobori stent 1.7% [rate ratio, 0.59; 95% confidence interval, 0.30–1.18]) did not differ significantly between the two groups.

Conclusion
At 3-year follow-up, target lesion failure did not differ among ultrathin-strut sirolimus-eluting Orsiro stent and biolimus-eluting Nobori stent with biodegradable polymers.
Adolescents' Perceptions of Childbirth
Authors: Anderson Cheryl Ann , Baker Kathy , Harter Lindsay 
Published: April 2020

Abstract

Purpose:
The purpose of this study was to describe adolescents' perception of birth within the first 72 hours postpartum.

Study Design & Methods:
A thematic analysis using qualitative data captured via one overarching question about labor expectations as part of a larger, parent quantitative study exploring psychological birth trauma.

Results:
Forty-two percent (n = 128) of adolescents ages 13 to 19 in the original study responded in writing to one overarching question concerning birth expectations. Four major themes were identified including pain, support, personal control, and fear, with three subthemes. Pain was expressed as a primary theme for all age adolescents and had an impact on all other themes. Expressed fear was general and specific including a fear of dying that emerged as a subtheme along with labor information and emotions.

Clinical Implications:
Lacking a positive birth experience has been linked with poor mental health outcomes (depression and posttraumatic stress) postpartum. Findings offer a guide for nurses and other healthcare providers to promote a positive birth experience for adolescents. Pain management is foremost to adolescents and requires healthcare providers' continued attention. Working together with adolescents to identify and monitor level of pain; assess support needs, feelings of loss of personal control, and signs or verbal expressions of fear; and offer ongoing information about labor progress and necessary procedures can help strengthen bonds between teens and their healthcare provider and create a positive birth experience.
Mattering: How Organizations, Patients, and Peers Can Affect Nurse Burnout and Engagement
Authors: Haizlip Julie , McCluney Courtney , Hernandez Morela , Quatrara Beth , Brashers Valentina 
Published: April 2020

OBJECTIVE
The aim of this study was to explore professional mattering in a broad cohort of nurses.

BACKGROUND
Mattering is a construct from social psychology that describes the feeling that one makes a difference in the lives of others and has significance in one's community.

METHODS
A cross-sectional survey assessing mattering, meaning, social support, burnout, and engagement was administered to nurses and nurse practitioners working in various specialties in the United States.

RESULTS
Higher levels of mattering at work were associated with lower burnout and higher engagement. Mattering was correlated with perceived social support from one's organization, supervisor, peers, and subordinates. Open-ended responses describing experiences of mattering at work included demonstrating professional competence, positive interactions with patients and interprofessional peers, and receiving recognition from one's organization.

CONCLUSIONS
A perception of mattering at work is associated with lower levels of burnout. Our data suggest that affirming interactions with other healthcare team members promote a sense of mattering.
Adult Glioma WHO Classification Update, Genomics, and Imaging
Authors: Bai James , Varghese Jerrin , Jain Rajan 
Published: April 2020

Abstract
Recent advances in the understanding of the genetic makeup of gliomas have led to a paradigm shift in the diagnosis and classification of these tumors. Driven by these changes, the World Health Organization (WHO) introduced an update to its classification system of central nervous system (CNS) tumors in 2016. The updated glioma classification system incorporates molecular markers into tumor subgrouping, which has been shown to better correlate with tumor biology and behavior as well as patient prognosis than the previous purely histology-based classification system. Familiarity with this new classification scheme, the individual molecular markers, and corresponding imaging findings is critical for the radiologists who play an important role in diagnostic and surveillance imaging of patients with CNS tumors. The goals of this article are to review these updates to the WHO classification of CNS tumors with a focus on adult gliomas, provide an overview of key genomic markers of gliomas, and review imaging features pertaining to various genomic subgroups of adult gliomas.
Sequence-based prediction of vaccine targets for inducing T cell responses to SARS-CoV-2 utilizing the bioinformatics predictor RECON
Authors: Poran Asaf , Harjanto Dewi , Malloy Matthew , Rooney Michael S. , Srinivasan Lakshmi , Gaynor Richard B. 
Published: April 2020

AbstractBackgroundThe ongoing COVID-19 pandemic has created an urgency to identify novel vaccine targets for protective immunity against SARS-CoV-2. Consistent with observations for SARS-CoV, a closely related coronavirus responsible for the 2003 SARS outbreak, early reports identify a protective role for both humoral and cell-mediated immunity for SARS CoV-2.MethodsIn this study, we leveraged HLA-I and HLA-II T cell epitope prediction tools from RECON® (Real-time Epitope Computation for ONcology), our bioinformatic pipeline that was developed using proteomic profiling of individual HLA-I and HLA-II alleles to predict rules for peptide binding to a diverse set of such alleles. We applied these binding predictors to viral genomes from theCoronaviridaefamily, and specifically to identify SARS-CoV-2 T cell epitopes.ResultsTo test the suitability of these tools to identify viral T cell epitopes, we first validated HLA-I and HLA-II predictions onCoronaviridaefamily epitopes deposited in the Virus Pathogen Database and Analysis Resource (ViPR) database. We then use our HLA-I and HLA-II predictors to identify 11,776 HLA-I and 7,991 HLA-II candidate binding peptides across all 12 open reading frames (ORFs) of SARS-CoV-2. This extensive list of identified candidate peptides is driven by the length of the ORFs and the significant number of HLA-I and HLA-II alleles that we are able to predict (74 and 83, respectively), providing over 99% coverage for the US, European and Asian populations, for both HLA-I and HLA-II. From our SARS-CoV-2 predicted peptide-HLA-I allele pairs, 368 pairs identically matched previously reported pairs in the ViPR database, originating from other forms of coronaviruses. 320 of these pairs (89.1%) had a positive MHC-binding assay result. This analysis reinforces the validity our predictions.ConclusionsUsing this bioinformatic platform, we identify multiple putative epitopes for CD4+and CD8+T cells whose HLA binding properties cover nearly the entire population and thus may be effective when included in prophylactic vaccines against SARS-CoV-2 to induce broad cellular immunity.
Reduced somatostatin signalling leads to hypersecretion of glucagon in mice fed a high fat diet
Authors: Kellard Joely A. , Rorsman Nils J. G. , Hill Thomas G. , Armour Sarah L , van der Bunt Martijn , Rorsman Patrik , Knudsen Jakob G. , Briant Linford J. B. 
Published: April 2020

AbstractElevated plasma glucagon is an early symptom of diabetes, occurring in subjects with impaired glucose regulation. Here we explored alpha-cell function in female mice fed a high fat diet (HFD) – a widely used mouse model of pre-diabetes.In vivo, HFD-fed mice have increased fed plasma glucagon levels that are unaffected by elevation of plasma glucose. To explore the underlying mechanisms, we conducted experiments on isolated islets and in the perfused pancreas. In both experimental models, glucagon secretion under both hypo- and hyperglycaemic conditions was elevated. Because Ca2+is an important intracellular regulator of glucagon release in alpha-cells, we fed mice expressing the Ca2+indicator GCaMP3 specifically in alpha-cells the HFD. In mice fed a control (CTL) diet, increasing glucose reduced intracellular Ca2+([Ca2+]i) (oscillation frequency and amplitude). This effect was not observed in HFD mice where both the frequency and amplitude of the [Ca2+]ioscillations were higher than in CTL alpha-cells. Given that alpha-cells are under strong paracrine control from neighbouring somatostatin-secreting delta-cells, we hypothesised that this elevation of alpha-cell output was due to a lack of somatostatin (SST) secretion. Indeed, SST secretion in isolated islets from HFD mice was reduced but exogenous SST also failed to suppress glucagon secretion and Ca2+activity from HFD alpha-cells, in contrast to observations in CTL mice. These findings suggest that reduced delta-cell function, combined with intrinsic changes in alpha-cell sensitivity to somatostatin, accounts for the hyperglucagonaemia in mice fed a HFD.
The IMPDH inhibitor merimepodib suppresses SARS-CoV-2 replicationin vitro
Authors: Bukreyeva Natalya , Mantlo Emily K. , Sattler Rachel A. , Huang Cheng , Paessler Slobodan , Zeldis Jerry 
Published: April 2020

AbstractThe ongoing COVID-19 pandemic continues to pose a major public health burden around the world. The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected over one million people worldwide as of April, 2020, and has led to the deaths of nearly 300,000 people. No approved vaccines or treatments in the USA currently exist for COVID-19, so there is an urgent need to develop effective countermeasures. The IMPDH inhibitor merimepodib (MMPD) is an investigational antiviral drug that acts as a noncompetitive inhibitor of IMPDH. It has been demonstrated to suppress replication of a variety of emerging RNA viruses. We report here that MMPD suppresses SARS-CoV-2 replication in vitro. After overnight pretreatment of Vero cells with 10 μM of MMPD, viral titers were reduced by 4 logs of magnitude, while pretreatment for 4 hours resulted in a 3-log drop. The effect is dose-dependent, and concentrations as low as 3.3 μM significantly reduced viral titers when the cells were pretreated prior to infection. The results of this study provide evidence that MMPD may be a viable treatment option for COVID-19.
Feedback Between Coevolution and Epidemiology Can Help or Hinder the Maintenance of Genetic Variation in Host-Parasite Models
Authors: MacPherson Ailene , Keeling Matthew J. , Otto Sarah P. 
Published: April 2020

AbstractUnderstanding if and when coevolution helps maintains genetic variation in hosts of a directly-transmissible pathogen is fundamental to quantifying the prevalence and impact of coevolution on disease epidemiology. Here, we extend our previous work on the maintenance of genetic variation in a classic matching-alleles coevolutionary model by exploring the effects of ecological and epidemiological feedbacks, where both allele frequencies and population sizes are allowed to vary over time. In general, we find that coevolution rarely maintains more host genetic variation than expected under neutral genetic drift alone. When and if coevolution maintains or depletes genetic variation relative to neutral drift is determined, predominantly, by two factors: the deterministic stability of the Red Queen allele frequency cycles and the frequency at which pathogen fixation occurs, as this results in directional selection and the depletion of genetic variation in the host. Compared to purely coevolutionary models with constant host and pathogen population sizes, ecological and epidemiological feedbacks stabilize Red Queen cycles deterministically, but population fluctuations in the pathogen increase the rate of pathogen fixation, especially in epidemiological models. Taken together our results illustrate the importance of considering the ecological and epidemiological context in which coevolution occurs when examining the impact of Red Queen cycles on genetic variation.
Prolonged exposure to constant environmental conditions prompts nonrandom genetic variation
Authors: Catania Francesco , Hagen Rebecca , Vitali Valerio 
Published: April 2020

ABSTRACTLong-term environmental exposure under selection-free conditions has no consequences for fitness under the neo-Darwinian paradigm but it may provoke adaptive developmental buffering if environmental pressures foster directional organismal changes. To test this hypothesis, we revisited a Mutation Accumulation (MA) experiment where isogenic lines of the ciliateParameciumwere propagated for >40 sexual cycles (∼4 years) in a nearly selection-free and nutrient-rich environment. We find that these MA lines’ somatic genome is enriched with intervening segments of DNA (IESs), which are normally eliminated during germline-soma differentiation. Across independent replicate MA lines, an excess of these somatic IESs fall into a class of epigenetically controlled sequences, map to the same genomic locations, and preferentially disrupt loci that regulate nutrient metabolism. Although further work is needed to assess the phenotypic consequences of somatic IESs, these findings support a model where environmentally induced developmental variants may restore an adaptive fit between phenotype and environment. In this model, positive selection is surprisingly dispensable for adaptation.
Gene knockdown via electroporation of short hairpin RNAs in embryos of the marine hydroidHydractinia symbiolongicarpus
Authors: Quiroga-Artigas Gonzalo , Duscher Alexandrea , Lundquist Katelyn , Waletich Justin , Schnitzler Christine E. 
Published: April 2020

AbstractPerforming gene function analyses in a broad range of research organisms is crucial for understanding the biological functions of genes and their evolution. Recent studies have shown that short hairpin RNAs (shRNAs) can induce gene-specific knockdowns in two cnidarian species. We have developed a detailed, straightforward, and scalable method to deliver shRNAs into fertilized eggs of the hydrozoan cnidarianHydractinia symbiolongicarpusvia electroporation, yielding gene-targeted knockdowns that can be assessed throughout embryogenesis, larval settlement, and metamorphosis. Our electroporation protocol allows for the transfection of shRNAs into hundreds of fertilizedH.symbiolongicarpuseggs simultaneously with minimal embryo death and no long-term harmful consequences on the developing animals. We show RT-qPCR and detailed phenotypic evidence of our method successfully inducing significant knockdowns of an exogenous gene (eGFP) and an endogenous gene (Nanos2). We also provide visual confirmation of successful shRNA transfection inside embryos through electroporation. This is the first time that electroporation as a delivery system has been developed forHydractinia. Our detailed protocol for electroporation of shRNAs inH. symbiolongicarpusembryos constitutes an important experimental resource for the hydrozoan community while also serving as a successful model for the development of similar methods for interrogating gene function in other marine invertebrates.
IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring
Authors: Kalantar Katrina L. , Carvalho Tiago , de Bourcy Charles F.A. , Dimitrov Boris , Dingle Greg , Egger Rebecca , Han Julie , Holmes Olivia B. , Juan Yun-Fang , King Ryan , Kislyuk Andrey , Mariano Maria , Reynoso Lucia V. , Cruz David Rissato , Sheu Jonathan , Tang Jennifer , Wang James , Zhang Mark A. , Zhong Emily , Ahyong Vida , Lay Sreyngim , Chea Sophana , Bohl Jennifer A. , Manning Jessica E. , Tato Cristina M. , DeRisi Joseph L. 
Published: April 2020

ABSTRACTBackgroundMetagenomic next generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, ora prioriknowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource limited environments.FindingsWe present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics which are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences, and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2.ConclusionThe IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.
Sampling requirements and approaches to detect ecosystem shifts
Authors: Bruel Rosalie , White Easton R. 
Published: April 2020

AbstractEnvironmental monitoring is a key component of understanding and managing ecosystems. Given that most monitoring efforts are still expensive and time-consuming, it is essential that monitoring programs are designed to be efficient and effective. In many situations, the expensive part of monitoring is not sample collection, but instead sample processing, which leads to only a subset of the samples being processed. For example, sediment or ice cores can be quickly obtained in the field, but they require weeks or months of processing in a laboratory setting. Standard sub-sampling approaches often involve equally-spaced sampling. We use simulations to show how many samples, and which types of sampling approaches, are the most effective in detecting ecosystem change. We test these ideas with a case study of Cladocera community assemblage reconstructed from a sediment core. We demonstrate that standard approaches to sample processing are less efficient than an iterative approach. For our case study, using an optimal sampling approach would have resulted in savings of 195 person-hours—thousands of dollars in labor costs. We also show that, compared with these standard approaches, fewer samples are typically needed to achieve high statistical power. We explain how our approach can be applied to monitoring programs that rely on video records, eDNA, remote sensing, and other common tools that allow re-sampling.
Lithium directs embryonic stem cell differentiation versus hemogenic endothelium
Authors: Mnatsakanyan Hayk , Salmeron-Sanchez Manuel , Rico Patricia 
Published: April 2020

AbstractThe discovery that the definitive hematopoietic stem cells (HSCs) derive from specialized regions of the endothelium, known as thehemogenic endothelium(HE), shed a good deal of light on HSC embryonic developmental processes. This knowledge opened up new possibilities for the design of new strategies to obtain HSCsin vitrofrom pluripotent stem cells (PSCs). Previous advances in this field have shown that the Wnt/β-catenin signaling pathway plays a key role in PSC-derived HSC formation. In this work, we identified lithium, a GSK3 inhibitor, as an element capable of stabilizing β-catenin and inducing ESC differentiation in the mesoderm lineage and subsequently in the HE, highly consistent with the role of Wnt agonists on ESC differentiation. ESCs treated with 10 mM lithium express CD31+, Sca-1+, Nkx2-5+ and Runx1+ cells characteristic of HE cells. The ability of lithium-treated ESCs to further derive into HSCs was confirmed after defined maturation, resulting in rounded cell aggregates positive for fetal and mature HSCs markers, confirming the endothelial to hematopoietic transition. Our results represent a novel strategy for generating HSCin vitroas a multipotent source of stem cells for blood and muscle disease therapies.
Chromosome 1 trisomy overcomes the block of sphingolipid biosynthesis caused by aureobasidin A and confers pleiotropic effects on susceptibility to antifungals inCandida albicans
Authors: Xu Yi , Yang Feng 
Published: April 2020

AbstractSphingolipids are important membrane lipid components of eukaryotic cells. InCandida albicans, chromosome 1 trisomy not only overcame the block of sphingolipid biosynthesis caused by aureobasidin A, but also altered tolerance to three of the four major classes of antifungal drugs. Two haploinsufficient genes on chromosome 1,PDR16andIPT1, were associated with tolerance to aureobasidin A. This study illustrates an example of multi-drug tolerance caused by aneuploidy in the human fungal pathogenC. albicans.