bluuebunny/crossref_metadata_2025_split huggingface dataset:
Young bilateral supernova remnants evolving into a turbulent interstellar magnetic field
Authors: Ávila-Aroche A , Velázquez P F , Camps-Fariña A , Toledo-Roy J C , Esquivel A 
Published: May 2020

ABSTRACT
We employ 3D magnetohydrodynamic simulations to study the morphology and synchrotron emission of young supernova remnants evolving in a turbulent interstellar magnetic field, seeking to shed new light on to the polarization structure of the emission and on the debate concerning the quasi-parallel and quasi-perpendicular acceleration mechanisms. In the simulations, we consider a non-homogeneous interstellar medium magnetic field by introducing small random perturbations in the direction and intensity of the field. In order to analyse the dependence of the radio morphology on the degree of magnetic field perturbation and the observer’s point of view, we compute synthetic maps of the polarized intensity, position-angle, polarization fraction, and the polar-reference angle. By comparing the distribution of this angle to the polarization intensity, we show that it is possible to identify what type of acceleration mechanism is taking place at the main shock front.
Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses
Authors: Kapun Martin , Barrón Maite G , Staubach Fabian , Obbard Darren J , Wiberg R Axel W , Vieira Jorge , Goubert Clément , Rota-Stabelli Omar , Kankare Maaria , Bogaerts-Márquez María , Haudry Annabelle , Waidele Lena , Kozeretska Iryna , Pasyukova Elena G , Loeschcke Volker , Pascual Marta , Vieira Cristina P , Serga Svitlana , Montchamp-Moreau Catherine , Abbott Jessica , Gibert Patricia , Porcelli Damiano , Posnien Nico , Sánchez-Gracia Alejandro , Grath Sonja , Sucena Élio , Bergland Alan O , Guerreiro Maria Pilar Garcia , Onder Banu Sebnem , Argyridou Eliza , Guio Lain , Schou Mads Fristrup , Deplancke Bart , Vieira Cristina , Ritchie Michael G , Zwaan Bas J , Tauber Eran , Orengo Dorcas J , Puerma Eva , Aguadé Montserrat , Schmidt Paul , Parsch John , Betancourt Andrea J , Flatt Thomas , González Josefa 
Published: May 2020

AbstractGenetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi
Authors: Gluck-Thaler Emile , Haridas Sajeet , Binder Manfred , Grigoriev Igor V , Crous Pedro W , Spatafora Joseph W , Bushley Kathryn , Slot Jason C 
Published: May 2020

AbstractEcological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.
RPS28B mRNA acts as a scaffold promoting cis-translational interaction of proteins driving P-body assembly
Authors: Fernandes Nikita , Buchan J Ross 
Published: May 2020

AbstractP-bodies (PBs) are cytoplasmic mRNA-protein (mRNP) granules conserved throughout eukaryotes which are implicated in the repression, storage and degradation of mRNAs. PB assembly is driven by proteins with self-interacting and low-complexity domains. Non-translating mRNA also stimulates PB assembly, however no studies to date have explored whether particular mRNA transcripts are more critical than others in facilitating PB assembly. Previous work revealed that rps28bΔ (small ribosomal subunit-28B) mutants do not form PBs under normal growth conditions. Here, we demonstrate that the RPS28B 3′UTR is important for PB assembly, consistent with it harboring a binding site for the PB assembly protein Edc3. However, expression of the RPS28B 3′UTR alone is insufficient to drive PB assembly. Intriguingly, chimeric mRNA studies revealed that Rps28 protein, translated in cis from an mRNA bearing the RPS28B 3′UTR, physically interacts more strongly with Edc3 than Rps28 protein synthesized in trans. This Edc3-Rps28 interaction in turn facilitates PB assembly. Our work indicates that PB assembly may be nucleated by specific RNA ‘scaffolds’. Furthermore, this is the first description in yeast to our knowledge of a cis-translated protein interacting with another protein in the 3′UTR of the mRNA which encoded it, which in turn stimulates assembly of cellular structures.
Oviz-Bio: a web-based platform for interactive cancer genomics data visualization
Authors: Jia Wenlong , Li Hechen , Li Shiying , Chen Lingxi , Li Shuai Cheng 
Published: May 2020

Abstract
Genetics data visualization plays an important role in the sharing of knowledge from cancer genome research. Many types of visualization are widely used, most of which are static and require sufficient coding experience to create. Here, we present Oviz-Bio, a web-based platform that provides interactive and real-time visualizations of cancer genomics data. Researchers can interactively explore visual outputs and export high-quality diagrams. Oviz-Bio supports a diverse range of visualizations on common cancer mutation types, including annotation and signatures of small scale mutations, haplotype view and focal clusters of copy number variations, split-reads alignment and heatmap view of structural variations, transcript junction of fusion genes and genomic hotspot of oncovirus integrations. Furthermore, Oviz-Bio allows landscape view to investigate multi-layered data in samples cohort. All Oviz-Bio visual applications are freely available at https://bio.oviz.org/.
Analyzing pre-symptomatic tissue to gain insights into the molecular and mechanistic origins of late-onset degenerative trinucleotide repeat disease
Authors: Chu Yongjun , Hu Jiaxin , Liang Hanquan , Kanchwala Mohammed , Xing Chao , Beebe Walter , Bowman C Bradley , Gong Xin , Corey David R , Mootha V Vinod 
Published: May 2020

Abstract
How genetic defects trigger the molecular changes that cause late-onset disease is important for understanding disease progression and therapeutic development. Fuchs’ endothelial corneal dystrophy (FECD) is an RNA-mediated disease caused by a trinucleotide CTG expansion in an intron within the TCF4 gene. The mutant intronic CUG RNA is present at one–two copies per cell, posing a challenge to understand how a rare RNA can cause disease. Late-onset FECD is a uniquely advantageous model for studying how RNA triggers disease because: (i) Affected tissue is routinely removed during surgery; (ii) The expanded CTG mutation is one of the most prevalent disease-causing mutations, making it possible to obtain pre-symptomatic tissue from eye bank donors to probe how gene expression changes precede disease; and (iii) The affected tissue is a homogeneous single cell monolayer, facilitating accurate transcriptome analysis. Here, we use RNA sequencing (RNAseq) to compare tissue from individuals who are pre-symptomatic (Pre_S) to tissue from patients with late stage FECD (FECD_REP). The abundance of mutant repeat intronic RNA in Pre_S and FECD_REP tissue is elevated due to increased half-life in a corneal cells. In Pre_S tissue, changes in splicing and extracellular matrix gene expression foreshadow the changes observed in advanced disease and predict the activation of the fibrosis pathway and immune system seen in late-stage patients. The absolute magnitude of splicing changes is similar in pre-symptomatic and late stage tissue. Our data identify gene candidates for early drivers of disease and biomarkers that may represent diagnostic and therapeutic targets for FECD. We conclude that changes in alternative splicing and gene expression are observable decades prior to the diagnosis of late-onset trinucleotide repeat disease.
CVCDAP: an integrated platform for molecular and clinical analysis of cancer virtual cohorts
Authors: Guan Xiaoqing , Cai Meng , Du Yang , Yang Ence , Ji Jiafu , Wu Jianmin 
Published: May 2020

Abstract
Recent large-scale multi-omics studies resulted in quick accumulation of an overwhelming amount of cancer-related data, which provides an unprecedented resource to interrogate diverse questions. While certain existing web servers are valuable and widely used, analysis and visualization functions with regard to re-investigation of these data at cohort level are not adequately addressed. Here, we present CVCDAP, a web-based platform to deliver an interactive and customizable toolbox off the shelf for cohort-level analysis of TCGA and CPTAC public datasets, as well as user uploaded datasets. CVCDAP allows flexible selection of patients sharing common molecular and/or clinical characteristics across multiple studies as a virtual cohort, and provides dozens of built-in customizable tools for seamless genomic, transcriptomic, proteomic and clinical analysis of a single virtual cohort, as well as, to compare two virtual cohorts with relevance. The flexibility and analytic competence of CVCDAP empower experimental and clinical researchers to identify new molecular mechanisms and develop potential therapeutic approaches, by building and analyzing virtual cohorts for their subject of interests. We demonstrate that CVCDAP can conveniently reproduce published findings and reveal novel insights by two applications. The CVCDAP web server is freely available at https://omics.bjcancer.org/cvcdap/.
Low-Grade Infection and Implant Failure Following Spinal Instrumentation: A Prospective Comparative Study
Authors: Shiban Ehab , Joerger Ann-Kathrin , Janssen Insa , Issa Mohammed , Lange Nicole , Wagner Arthur , Feihl Susanne , Ringel Florian , Meyer Bernhard 
Published: May 2020

ABSTRACT

BACKGROUND
Spinal instrumentation can be associated with complications, including implant loosening. Hitherto, implant loosening has mainly been attributed to mechanical overload.

OBJECTIVE
To examine the role of low-grade infections as the cause of implant failure in suspected aseptic implant loosening following spinal instrumentation.

METHODS
A prospective single center observational study was performed. All patients who had revision surgery following spinal instrumentation between August 2015 and February 2018 were screened. Patients with revision surgery due to screw loosening on the computed tomograhy scan constituted the study group. Patients in which the screws where not loosened but removal was performed for other reasons formed the comparison group. Intraoperative swabs were taken and sonication was performed with the explanted material. Results of microbiological cultivation were analyzed.

RESULTS
A total of 59 patients were included in the study group and 34 in the comparison group. In the study group in 42.4% of the cultures a bacterium was detected, while in the comparison group only in 17.6%. 84%, and 83.3% of these germs were detected by sonication in the study and comparison group, respectively. The rate of positive cultures was significantly higher in the study group compared to the comparison group (P = .001). The most frequent bacterium cultivated in both groups was Propionibacterium acnes, followed by Staphylococcus species.

CONCLUSION
For patients with screw loosening a high level of suspicion for a low-grade infection should be raised. Cultures should be performed from the sonication fluid of the explanted devices in all patients with symptomatic screw loosening.
Women With First-Hand Tobacco Smoke Exposure Have a Higher Likelihood of Having an Unruptured Intracranial Aneurysm Than Nonsmokers: A Nested Case-Control Study
Authors: Ogilvy Christopher S , Gomez-Paz Santiago , Kicielinski Kimberly P , Salem Mohamed M , Maragkos Georgios A , Lee Michelle , Vergara-Garcia David , Rojas Rafael , Moore Justin M , Thomas Ajith J 
Published: May 2020

Abstract

BACKGROUND
The prevalence of unruptured intracranial aneurysms (UIA) in females who smoke cigarettes and the association between smoking and hypertension with purely incidental UIAs have been unexplored.

OBJECTIVE
To obtain the prevalence of UIA among females and to assess the relationship between smoking and hypertension with a diagnosis of incidental UIAs.

METHODS
A nested case-control study from a cohort of female patients aged between 30 and 60 yr with a brain magnetic resonance angiography (MRA) between 2016 and 2018. Incidental UIAs were compared to patients with normal MRAs. Smoking was characterized as never or former/current smokers. A logistic regression was used to evaluate the association between smoking, hypertension, or both, with a diagnosis of incidental UIAs.

RESULTS
A total of 1977 patients had a brain MRA between 2016 and 2018. From 1572 nonsmoker patients, we encountered 30 with an UIA (prevalence: 1.9%). There were 405 patients with a positive smoking history, and 77 patients harbored an UIA (prevalence: 19%). Of 64 aneurysm patients and 130 random controls eligible for the case control, aneurysm patients were more likely to have a positive smoking history and hypertension compared with healthy controls (60% vs 18%, P ≤ .001; 44% vs 14%, P ≤ .001). A multivariable analysis demonstrated a significant association between a smoking history, hypertension, or both factors with an incidental UIA (odds ratio [OR] 5.8 CI 1.22-11.70; OR 3.8 CI 2.31-14.78; OR 12.6 CI 4.38-36.26; respectively).

CONCLUSION
Females who smoke cigarettes have a higher prevalence of UIAs than the general population. Smoking confers a higher risk for having a silent UIA, aggravated by hypertension. This population is an ideal target for potential screening.
Ependymoma, NOS and anaplastic ependymoma incidence and survival in the United States varies widely by patient and clinical characteristics, 2000-2016
Authors: Achey Rebecca L , Vo Sierra , Cioffi Gino , Gittleman Haley , Schroer Julia , Khanna Vishesh , Buerki Robin , Kruchko Carol , Barnholtz-Sloan Jill S 
Published: May 2020

Abstract

Background
Ependymoma is a rare CNS tumor arising from the ependymal lining of the ventricular system. General differences in incidence and survival have been noted but not examined on a comprehensive scale for all ages and by histology. Despite the rarity of ependymomas, morbidity/mortality associated with an ependymoma diagnosis justifies closer examination.

Methods
Incidence data were obtained from the Central Brain Tumor Registry of the United States in collaboration with the Centers for Disease Control and Prevention and the National Cancer Institute, and survival data from Surveillance Epidemiology and End Results, from 2000 to 2016 for anaplastic ependymoma and ependymoma, not otherwise specified (NOS). Age-adjusted incidence rates (IRs) per 100 000 person-years were analyzed by age, sex, race, and location. Survival analysis was performed with Kaplan-Meier curves and multivariable Cox proportional hazards models.

Results
Incidence of anaplastic ependymoma was highest in ages 0 to 4 years. African American populations had lower incidence but had a 78% increased risk of death compared to white populations (hazard ratio [HR]: 1.78 [95% CI, 1.30-2.44]). Incidence was highest for anaplastic ependymoma in the supratentorial region. Adults (age 40+ years) had almost twice the risk of death compared to children (ages 0-14 years) (HR: 1.97 [95% CI, 1.45-2.66]). For ependymoma, NOS, subtotal resection had a risk of mortality 1.86 times greater than gross total resection ([HR: 1.86 [95% CI, 1.32-2.63]).

Conclusions
African American populations experienced higher mortality rates despite lower incidence compared to white populations. Extent of resection is an important prognostic factor for survival. This highlights need for further evaluation of treatment patterns and racial disparities in the care of patients with ependymoma subtypes.
Rheumatoid arthritis and dietary interventions: systematic review of clinical trials
Authors: Philippou Elena , Petersson Sara Danuta , Rodomar Carrie , Nikiphorou Elena 
Published: May 2020

Abstract

Context
The impact of various dietary interventions on rheumatoid arthritis (RA), characterized by immune-inflammatory response, has been subject to increased attention.

Objective
A systematic review was conducted to update the current knowledge on the effects of nutritional, dietary supplement, and fasting interventions on RA outcomes.

Data Sources
Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, with prespecification of all methods, Medline and Embase were systematically searched for relevant articles.

Data Extraction
Data were extracted by 2 independent reviewers.

Results
A total of 70 human studies were identified. Administration of omega-3 polyunsaturated fatty acids at high doses resulted in a reduction in RA disease activity and a lower failure rate of pharmacotherapy. Vitamin D supplementation and dietary sodium restriction were beneficial on some RA outcomes. Fasting resulted in significant but transient subjective improvements. While the Mediterranean diet demonstrated improvements in some RA disease activity measures, outcomes from vegetarian, elimination, peptide, or elemental diets suggested that responses are very individualized.

Conclusion
Some dietary approaches may improve RA symptoms and thus it is recommended that nutrition should be routinely addressed.
Prevalence and Characteristics of Neuroinfectious Disease Inquiries Within the Emerging Infections Network: A 22-Year Retrospective Study
Authors: Matthews Elizabeth , Diaz-Arias Luisa A , Beekmann Susan E , Polgreen Philip , Waldrop Greer , Yang Vivian , Rimmer Kathryn , Venkatesan Arun , Thakur Kiran T 
Published: May 2020

Abstract

Background
To monitor emerging infectious diseases, the Centers for Disease Control and Prevention and the Infectious Disease Society of America established the Emerging Infections Network (EIN), allowing infectious disease specialists to post inquiries about clinical cases. We describe the frequency and characteristics of neuroinfectious disease-related inquiries.

Methods
The EIN listserv was retrospectively reviewed from February 1997 to December 2019 using search terms associated with neurologic diseases. We recorded case summaries, disease type (ie, meningitis, encephalitis), inquiry type (diagnostic approach, result interpretation, management decisions), unique patient populations, exposures, pathogens, ultimate diagnosis, and change in clinical care based on responses.

Results
Of 2348 total inquiries, 285 (12.1%) related to neuroinfectious diseases. The majority involved meningitis (99, 34.7%) or encephalitis (56, 19.6%). One hundred fifteen inquiries (40%) related to management, 34 (12%) related to diagnostic workup, and 22 (8%) related to result interpretation. Eight (2.8%) specifically involved results of cerebrospinal fluid polymerase chain reaction testing. Sixty-three (22.1%) involved immunosuppressed patients (29 human immunodeficiency virus-positive cases [46%]). The most common pathogens were Treponema pallidum (19, 6.7%) and Cryptococcus neoformans (18, 6.3%). In 74 (25%) inquiries, patients had neurologic symptoms without a clear infection, 38 (51.3%) of which included noninfectious neurologic etiologies in the differential diagnosis.

Conclusions
This study demonstrates the significant challenges of diagnosis and management of neuroinfectious diseases within the field of infectious diseases. It also highlights the importance of curated forums to guide the approach of difficult cases, in particular instances that mimic infectious diseases. Finally, the EIN listserv may assist in identifying areas for research and training to address these complexities.
Long-term Outcomes of Patients With Fungal Infections Associated With Contaminated Methylprednisolone Injections
Authors: Malani Anurag N , Kauffman Carol A , Latham Robert , Peglow Sheree , Ledtke Christopher S , Kerkering Thomas M , Kaufman David H , Triplett Patricia F , Wright Patty W , Bloch Karen C , McCotter Orion , Toda Mitsuru , Jackson Brendan R , Pappas Peter G , Chiller Tom M 
Published: May 2020

Abstract

Background
The largest health care–associated infection outbreak in the United States occurred during 2012–2013. Following injection of contaminated methylprednisolone, 753 patients developed infection with a dematiaceous mold, Exserohilum rostratum. The long-term outcomes of these infections have not been described.

Methods
This retrospective cohort study of 440 of a total of 753 patients with proven or probable Exserohilum infection evaluated clinical and radiographic findings, antifungal therapy and associated adverse effects, and outcomes at 6 weeks, 3, 6, 9, and 12 months after diagnosis. Patients were grouped into 4 disease categories: meningitis with/without stroke, spinal or paraspinal infections, meningitis/stroke plus spinal/paraspinal infections, and osteoarticular infections.

Results
Among the 440 patients, 223 (51%) had spinal/paraspinal infection, 82 (19%) meningitis/stroke, 123 (28%) both, and 12 (3%) osteoarticular infection. Of 82 patients with meningitis/stroke, 18 (22%) died; among those surviving, 87% were cured at 12 months. Only 7 (3%) of 223 patients with spinal/paraspinal infection died, but at 12 months, 68% had persistent or worsening pain and only 47% were cured. For the 123 patients with both meningitis/stroke and spinal/paraspinal infection, 10 (8%) died, pain persisted in 72%, and 52% were cured at 12 months. Only 37% of those with osteoarticular infection were cured at 12 months. Adverse events from antifungal therapy were noted at 6 weeks in 71% of patients on voriconazole and 81% on amphotericin B.

Conclusions
Fungal infections related to contaminated methylprednisolone injections culminated in death in 8% of patients. Persistent pain and disability were seen at 12 months in most patients with spinal/paraspinal infections.