bluuebunny/crossref_metadata_2025_split huggingface dataset:
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species
Authors: Gao Tianshun , Zheng Zilong , Pan Yihang , Zhu Chengming , Wei Fuxin , Yuan Jinqiu , Sun Rui , Fang Shuo , Wang Nan , Zhou Yang , Qian Jiang 
Published: October 2021

AbstractPrevious studies on enhancers and their target genes were largely based on bulk samples that represent ‘average’ regulatory activities from a large population of millions of cells, masking the heterogeneity and important effects from the sub-populations. In recent years, single-cell sequencing technology has enabled the profiling of open chromatin accessibility at the single-cell level (scATAC-seq), which can be used to annotate the enhancers and promoters in specific cell types. A comprehensive resource is highly desirable for exploring how the enhancers regulate the target genes at the single-cell level. Hence, we designed a single-cell database scEnhancer (http://enhanceratlas.net/scenhancer/), covering 14 527 776 enhancers and 63 658 600 enhancer-gene interactions from 1 196 906 single cells across 775 tissue/cell types in three species. An unsupervised learning method was employed to sort and combine tens or hundreds of single cells in each tissue/cell type to obtain the consensus enhancers. In addition, we utilized a cis-regulatory network algorithm to identify the enhancer-gene connections. Finally, we provided a user-friendly platform with seven useful modules to search, visualize, and browse the enhancers/genes. This database will facilitate the research community towards a functional analysis of enhancers at the single-cell level.
The Sequence Read Archive: a decade more of explosive growth
Authors: Katz Kenneth , Shutov Oleg , Lapoint Richard , Kimelman Michael , Brister J Rodney , O’Sullivan Christopher 
Published: October 2021

Abstract
The Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra/) stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis. Here we note changes in storage designed to increase access and highlight analyses that augment metadata with taxonomic insight to help users select data. In addition, we present three unanticipated applications of taxonomic analysis.
Evaluation of health outcomes in patients aged 70 years and above with glioblastoma multiforme in NHS Tayside between 2017-2020
Authors: Finnan Caitlin , Lord Hannah 
Published: October 2021

Abstract

Aims
The aim of this study is to evaluate health-related outcomes in patients aged 70 years and above diagnosed with glioblastoma multiforme (GBM) in NHS Tayside between 2017-2020. Objectives include identification of factors which influence the oncological treatment modalities pursued; disease progression/recurrence and outcomes within each treatment modality category.

Method
Medical databases were reviewed retrospectively to identify patients aged 70 years and above diagnosed with GBM in NHS Tayside, between 2017-2020. Analysed data identified patients' past medical history, symptoms and investigations preceding diagnosis; date of first brain imaging which demonstrated abnormality in-keeping with a likely diagnosis of GBM; factors influencing treatment modalities undertaken, molecular and genetic analysis of tumour samples; disease recurrence/progression, and date of death if applicable.

Results
54 patients diagnosed with GBM. 13 patients were aged over 70 years. 8 males, 5 females. Commonest co-morbid conditions were hypertension and gout. 2/13 received best supportive care only, based on poor performance status and extensive disease burden. 9/13 underwent neurosurgery; 7 debulked; 2 biopsy only. 7 isocitrate dehydrogenase (IDH1) wild-type; 2 IDH classification not known. 3 MGMT methylated; 4 unmethylated; 2 MGMT classification not known.3/13 received temozolomide (TMZ) alone. 2 later received palliative radiotherapy (30Gy in 6 #) to control symptoms. 4/13 received 40Gy in 15 # with concurrent TMZ 4/13 received 60Gy in 30 # with concurrent TMZ. 5 received adjuvant TMZ following initial chemo-radiation: 3 after 40Gy and 2 after 60Gy. As of March 2021, 6/13 were alive, including all 4 who had received hypofractionated radiotherapy. 4 of these continue to demonstrate stable disease on most recent imaging.

Conclusion
Baseline fitness levels of patients were generally high, with few having significant co-morbidity pre-diagnosis. Prognosis and morbidity was significantly poorer in patients who did not undergo any form of radiotherapy. Patients who received hypofractionated radiotherapy demonstrated most favourable health-related outcomes, demonstrating longest survival and least evidence of disease recurrence/progression.Although the sample size for this study is small, it highlights the potential benefits of radiotherapy on survival, particularly hypofractionated courses such as 40Gy in 15 fractions in a real-world population, even during a global pandemic. It would be useful to prospectively follow-up elderly patients with GBM to assess outcomes and quality of life.
Evaluation of an occupational medicine patient consultation note assessment tool
Authors: Spilchuk V , House R , Nisenbaum R , Holness D L 
Published: October 2021

Abstract

Background
Medical education focuses on assessment, diagnosis and management of various clinical entities. The communication of this information, particularly in the written form, is rarely emphasized. Though there have been assessment tools developed to support medical learner improvement in this regard, none are oriented to occupational medicine (OM) practice.

Aims
This study was aimed to develop and evaluate an assessment tool for consultation letters, by modifying a previously validated assessment tool to suit practice in OM.

Methods
Using an iterative process, OM specialists added to the Consultation Letter Rating Scale (CLRS) of the Royal College of Physicians and Surgeons of Canada (henceforth abbreviated as RC) additional questions relevant to communication in the OM context. The tool was then used by two OM specialists to rate 40 anonymized OM clinical consultation letters. Inter-rater agreement was measured by percent agreement, kappa statistic and intraclass correlation.

Results
There was generally good percent agreement (&gt;80% for the majority of the RC and OM questions). Intraclass correlation for the five OM questions total scores was slightly higher than the intraclass correlations for the five RC questions (0.59 versus 0.46, respectively), suggesting that our modifications performed at least as well as the original tool.

Conclusions
This new tool designed specifically for evaluation of patient consultation notes in OM provides a good option for medical educators in a variety of practice areas in providing non-summative, low-stakes assessment and/or feedback to nurture increased competency in written communication skills for postgraduate trainees in OM.
Impact of Choice of Prophylaxis on the Microbiology of Cardiac Implantable Electronic Device Infections: Insights From the Prevention of Arrhythmia Device Infection Trial (PADIT)
Authors: Longtin Yves , Gervais Philippe , Birnie David H , Wang Jia , Alings Marco , Philippon François , Parkash Ratika , Manlucu Jaimie , Angaran Paul , Rinne Claus , Coutu Benoit , Low R Aaron , Essebag Vidal , Morillo Carlos , Redfearn Damian , Toal Satish , Becker Giuliano , Degrâce Michel , Thibault Bernard , Crystal Eugene , Tung Stanley , LeMaitre John , Sultan Omar , Bennett Matthew , Bashir Jamil , Ayala-Paredes Felix , Rioux Leon , Hemels Martin E W , Bouwels Leon H R , Exner Derek V , Dorian Paul , Connolly Stuart J , Krahn Andrew D 
Published: October 2021

Abstract

Background
The Prevention of Arrhythmia Device Infection Trial (PADIT) investigated whether intensification of perioperative prophylaxis could prevent cardiac implantable electronic device (CIED) infections. Compared with a single dose of cefazolin, the perioperative administration of cefazolin, vancomycin, bacitracin, and cephalexin did not significantly decrease the risk of infection. Our objective was to compare the microbiology of infections between study arms in PADIT.

Methods
This was a post hoc analysis. Differences between study arms in the microbiology of infections were assessed at the level of individual patients and at the level of microorganisms using the Fisher exact test.

Results
Overall, 209 microorganisms were reported from 177 patients. The most common microorganisms were coagulase-negative staphylococci (CoNS; 82/209 [39.2%]) and S. aureus (75/209 [35.9%]). There was a significantly lower proportion of CoNS in the incremental arm compared with the standard arm (30.1% vs 46.6%; P = .04). However, there was no significant difference between study arms in the frequency of recovery of other microorganisms. In terms of antimicrobial susceptibility, 26.5% of microorganisms were resistant to cefazolin. CoNS were more likely to be cefazolin-resistant in the incremental arm (52.2% vs 26.8%, respectively; P = .05). However, there was no difference between study arms in terms of infections in which the main pathogen was sensitive to cefazolin (77.8% vs 64.3%; P = .10) or vancomycin (90.8% vs 90.2%; P = .90).

Conclusions
Intensification of the prophylaxis led to significant changes in the microbiology of infections, despite the absence of a decrease in the overall risk of infections. These findings provide important insight on the physiopathology of CIED infections.

Trial registration
NCT01002911.
Socioeconomic Disparities in Severe Acute Respiratory Syndrome Coronavirus 2 Serological Testing and Positivity in New York City
Authors: Lieberman-Cribbin Wil , Galanti Marta , Shaman Jeffrey 
Published: October 2021

Abstract

Background
We characterized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody test prevalence and positive test prevalence across New York City (NYC) in order to investigate disparities in testing outcomes by race and socioeconomic status (SES).

Methods
Serologic data were downloaded from the NYC Coronavirus data repository (August 2020–December 2020). Area-level characteristics for NYC neighborhoods were downloaded from United States census data and a socioeconomic vulnerability index was created. Spatial generalized linear mixed models were performed to examine the association between SES and antibody testing and positivity.

Results
The proportion of Hispanic population (posterior median, 0.001 [95% credible interval, 0.0003–0.002]), healthcare workers (0.003 [0.0001–0.006]), essential workers (0.003 [0.001–0.005]), age ≥65 years (0.003 [0.00002–0.006]), and high SES (SES quartile 3 vs 1: 0.034 [0.003–0.062]) were positively associated with antibody tests per 100000 residents. The White proportion (–0.002 [–0.003 to –0.001]), SES index (quartile 3 vs 1, –0.068 [–0.115 to –0.017]; quartile 4 vs 1, –0.077 [–0.134 to –0.018]) and age ≥65 years (–0.005 [–0.009 to –0.002]) were inversely associated with positive test prevalence (%), whereas the Hispanic (0.004 [0.002–0.006]) and essential worker (0.008 [0.003–0.012]) proportions had positive coefficients.

Conclusions
Disparities in serologic testing and seropositivity exist on SES and race/ethnicity across NYC, indicative of excess coronavirus disease burden in vulnerable and marginalized populations.
Numerical universal solutions in a-gauge in open string field theory
Authors: Kishimoto Isao 
Published: October 2021

Abstract
In bosonic open string field theory, we construct numerical universal solutions in a-gauge corresponding to “double brane” and “ghost brane” solutions in Siegel gauge in addition to the tachyon vacuum solution, and evaluate their gauge invariants, which are energy- and gauge-invariant observables. The a-gauge condition, which contains a real parameter a, was introduced by Asano and Kato. In earlier works it has been applied to find the tachyon vacuum solution with the level truncation method up to level 14. The “double brane” and “ghost brane” solutions were constructed by Kudrna and Schnabl in Siegel gauge, which corresponds to (a = 0)-gauge, up to level 28. Starting from these solutions, by varying a little by little, we have constructed numerical solutions in a-gauge for various values of a including a = ∞ up to level 20. Contrary to naive expectation, the gauge invariants of “double brane” and “ghost brane” solutions in a-gauge seem to be non-constant for a. In particular, although the normalized energy E of the “double brane” solution in a-gauge is approximately two for a ∼ 0, we find that E becomes almost one for 0.5 &lt; a &lt; 1. The gauge-invariant observable behaves similarly. This might imply that the “double brane” solution varies to a single brane solution in such a-gauges.
Exploring the Relationship Between Schizophrenia and Cardiovascular Disease: A Genetic Correlation and Multivariable Mendelian Randomization Study
Authors: Veeneman Rada R , Vermeulen Jentien M , Abdellaoui Abdel , Sanderson Eleanor , Wootton Robyn E , Tadros Rafik , Bezzina Connie R , Denys Damiaan , Munafò Marcus R , Verweij Karin J H , Treur Jorien L 
Published: October 2021

Abstract
Individuals with schizophrenia have a reduced life-expectancy compared to the general population, largely due to an increased risk of cardiovascular disease (CVD). Clinical and epidemiological studies have been unable to unravel the nature of this relationship. We obtained summary-data of genome-wide-association studies of schizophrenia (N = 130 644), heart failure (N = 977 323), coronary artery disease (N = 332 477), systolic and diastolic blood pressure (N = 757 601), heart rate variability (N = 46 952), QT interval (N = 103 331), early repolarization and dilated cardiomyopathy ECG patterns (N = 63 700). We computed genetic correlations and conducted bi-directional Mendelian randomization (MR) to assess causality. With multivariable MR, we investigated whether causal effects were mediated by smoking, body mass index, physical activity, lipid levels, or type 2 diabetes. Genetic correlations between schizophrenia and CVD were close to zero (−0.02–0.04). There was evidence that liability to schizophrenia causally increases heart failure risk. This effect remained consistent with multivariable MR. There was also evidence that liability to schizophrenia increases early repolarization pattern, largely mediated by BMI and lipids. Finally, there was evidence that liability to schizophrenia increases heart rate variability, a direction of effect contrasting clinical studies. There was weak evidence that higher systolic blood pressure increases schizophrenia risk. Our finding that liability to schizophrenia increases heart failure is consistent with the notion that schizophrenia involves a systemic dysregulation of the body with detrimental effects on the heart. To decrease cardiovascular mortality among individuals with schizophrenia, priority should lie with optimal treatment in early stages of psychosis.
Emotions and Ambient Racism in America’s Whitest Big City
Authors: Woody Ashley 
Published: October 2021

AbstractThis article explores the ways communities of color experience racism in Portland, Oregon—the whitest big city in the Unites States. Drawing from 40 in-depth interviews with an ethnically diverse sample of Portlanders of color, the study’s findings demonstrate how emotions are constitutive of racialized lived experiences. Participants’ emotions were deeply intertwined with Portland’s demographics and historical legacies of white supremacy in the city, highlighting the importance of place in structuring racialized emotions. Participants also describe emotional and impression management strategies they used to navigate predominantly white spaces. As a conceptual link between racial structures and racialized emotions, I introduce the concept of ambient racism, which describes how legacies of racism are “baked into” the social environment that racialized people navigate and emotionally contend with daily. Ambient racism bridges structural and emotional dimensions of racism by illustrating how racial structures are felt by racially subordinated groups.
The ‘Curious Effects’ of Acting: Homosexuality, Theatre and Female Impersonation at the University of Cambridge, 1900–39
Authors: Janes Dominic 
Published: October 2021

Abstract
The University of Cambridge educated a significant proportion of Britain’s elite in the early twentieth century. The homosocial environment of the colleges was similar in many ways to that of the single-sex public boarding schools which many of the undergraduates had attended. Student theatre was a popular activity, and because such shows were acted by single-sex ensembles, there was a strong tradition of female impersonation on stage. The interwar diaries of Cecil Beaton, who identified privately as a homosexual man, provide an unusually detailed source of information about a period when sexual controversy began to surround theatrical cross-dressing. In the 1930s, when moves were made to open previously men-only university drama clubs to women, the issue of male homosexuality and its alleged connections with student theatre came to be widely discussed. This reflected significant changes in the ways in which queerness was accommodated within the predominantly male environment of the University.
Blood Neurofilament Light Chain as a Potential Biomarker for Central and Peripheral Nervous Toxicity in Rats
Authors: Sano Tomoya , Masuda Yasushi , Yasuno Hironobu , Shinozawa Tadahiro , Watanabe Takeshi , Kakehi Masaaki 
Published: October 2021

Abstract
Neurotoxicity is a principal concern in nonclinical drug development. However, standardized and universally accepted fluid biomarkers for evaluating neurotoxicity are lacking. Increasing clinical evidence supports the potential use of neurofilament light (NfL) chain as a biomarker of several neurodegenerative diseases; therefore, we investigated changes in the cerebrospinal fluid (CSF) and serum levels of NfL in Sprague Dawley rats treated with central nervous system (CNS) toxicants (trimethyltin [TMT, 10 mg/kg po, single dose], kainic acid [KA, 12 mg/kg sc, single dose], MK-801 [1 mg/kg sc, single dose]), and a peripheral nervous system (PNS) toxicant (pyridoxine, 1200 mg/kg/day for 3 days). Animals were euthanized 1 (day 2), 3 (day 4), or 7 days after administration (day 8). Increased serum NfL was observed in TMT- and KA-treated animals, which indicated neuronal cell death in the brain on days 2, 4, and/or 8. MK-801-treated animals exhibited no changes in the serum and CSF levels of NfL and no histopathological changes in the brain at any time point. Pyridoxine-induced chromatolysis of the dorsal root ganglion on day 2 and degeneration of peripheral nerve fiber on day 4; additionally, serum NfL was increased. A strong correlation was observed between the serum and CSF levels of NfL and brain lesions caused by TMT and KA, indicating that NfL could be a useful biomarker for detecting CNS toxicity. Additionally, PNS changes were correlated with serum NfL levels. Therefore, serum NfL could serve as a useful peripheral biomarker for detecting both CNS and PNS toxicity in rats.
The Private Administrative Law of Technical Standardization
Authors: Vallejo Rodrigo 
Published: October 2021

Abstract
The nature and place of technical standards has remained an enigma for EU law and legal thought, despite their ubiquitous part and growing importance in market-building processes within and beyond Europe. The significance and intractability of this enigma has been heightened by the landmark Fra.bo (2012) and James Elliot (2016) judgments of the ECJ. These judgments have prompted contradictory positions regarding the publicity and justiciability of technical standards among European legal scholarship and even between the European Commission and the European Parliament. The enigma and these contradictory positions have recently reached the ECJ again through the Stichting Rookpreventie case currently under review by its Grand Chamber. Drawing upon a reconstructive analysis of these and other relevant legal sources concerning technical standardization in Europe, this paper surmounts these seeming contradictions by advancing a new account of these legal developments. Contrary to the mainstream positions nowadays in tension, the article argues that these judgments have reaffirmed the New Approach and the distinctive place of technical standardization organizations in the European legal order while avoiding dysfunctional modes of judicialization. It has done so by acknowledging the techno-political character of technical standards and aptly delineating institutional competences between the government and the judiciary throughout technical standardization processes. To guide future legal thinking and reasoning on these processes, the paper recasts these legal developments through the idea of a ‘private administrative law’ as signifying the way that EU Law has transformed the nature and place of technical standardization in the internal market and as an eventual means for the global reach of EU law.
Cell-to-Cell Communication During Plant-Pathogen Interaction
Authors: Tabassum Naheed , Blilou Ikram 
Published: October 2021

Being sessile, plants are continuously challenged by changes in their surrounding environment and must survive and defend themselves against a multitude of pathogens. Plants have evolved a mode for pathogen recognition that activates signaling cascades such as reactive oxygen species, mitogen-activated protein kinase, and Ca2+ pathways, in coordination with hormone signaling, to execute the defense response at the local and systemic levels. Phytopathogens have evolved to manipulate cellular and hormonal signaling and exploit hosts’ cell-to-cell connections in many ways at multiple levels. Overall, triumph over pathogens depends on how efficiently the pathogens are recognized and how rapidly the plant response is initiated through efficient intercellular communication via apoplastic and symplastic routes. Here, we review how intercellular communication in plants is mediated, manipulated, and maneuvered during plant-pathogen interaction. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.