bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATACdb: a comprehensive human chromatin accessibility database
Authors: Wang Fan , Bai Xuefeng , Wang Yuezhu , Jiang Yong , Ai Bo , Zhang Yong , Liu Yuejuan , Xu Mingcong , Wang Qiuyu , Han Xiaole , Pan Qi , Li Yanyu , Li Xuecang , Zhang Jian , Zhao Jun , Zhang Guorui , Feng Chenchen , Zhu Jiang , Li Chunquan 
Published: October 2020

Abstract
Accessible chromatin is a highly informative structural feature for identifying regulatory elements, which provides a large amount of information about transcriptional activity and gene regulatory mechanisms. Human ATAC-seq datasets are accumulating rapidly, prompting an urgent need to comprehensively collect and effectively process these data. We developed a comprehensive human chromatin accessibility database (ATACdb, http://www.licpathway.net/ATACdb), with the aim of providing a large amount of publicly available resources on human chromatin accessibility data, and to annotate and illustrate potential roles in a tissue/cell type-specific manner. The current version of ATACdb documented a total of 52 078 883 regions from over 1400 ATAC-seq samples. These samples have been manually curated from over 2200 chromatin accessibility samples from NCBI GEO/SRA. To make these datasets more accessible to the research community, ATACdb provides a quality assurance process including four quality control (QC) metrics. ATACdb provides detailed (epi)genetic annotations in chromatin accessibility regions, including super-enhancers, typical enhancers, transcription factors (TFs), common single-nucleotide polymorphisms (SNPs), risk SNPs, eQTLs, LD SNPs, methylations, chromatin interactions and TADs. Especially, ATACdb provides accurate inference of TF footprints within chromatin accessibility regions. ATACdb is a powerful platform that provides the most comprehensive accessible chromatin data, QC, TF footprint and various other annotations.
Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals
Authors: Liu Jianheng , Huang Tao , Zhang Yusen , Zhao Tianxuan , Zhao Xueni , Chen Wanying , Zhang Rui 
Published: October 2020

Abstract
mRNA m5C, which has recently been implicated in the regulation of mRNA mobility, metabolism and translation, plays important regulatory roles in various biological events. Two types of m5C sites are found in mRNAs. Type I m5C sites, which contain a downstream G-rich triplet motif and are computationally predicted to be located at the 5′ end of putative hairpin structures, are methylated by NSUN2. Type II m5C sites contain a downstream UCCA motif and are computationally predicted to be located in the loops of putative hairpin structures. However, their biogenesis remains unknown. Here we identified NSUN6, a methyltransferase that is known to methylate C72 of tRNAThr and tRNACys, as an mRNA methyltransferase that targets Type II m5C sites. Combining the RNA secondary structure prediction, miCLIP, and results from a high-throughput mutagenesis analysis, we determined the RNA sequence and structural features governing the specificity of NSUN6-mediated mRNA methylation. Integrating these features into an NSUN6-RNA structural model, we identified an NSUN6 variant that largely loses tRNA methylation but retains mRNA methylation ability. Finally, we revealed a weak negative correlation between m5C methylation and translation efficiency. Our findings uncover that mRNA m5C is tightly controlled by an elaborate two-enzyme system, and the protein-RNA structure analysis strategy established may be applied to other RNA modification writers to distinguish the functions of different RNA substrates of a writer protein.
Secondhand Smoke Exposure at Home and/or in a Vehicle: Differences Between Urban and Non-Urban Adolescents in the United States, From 2015 to 2018
Authors: Mantey Dale S , Omega-Njemnobi Onyinye , Barroso Cristina S 
Published: October 2020

Abstract

Introduction
Secondhand smoke exposure during adolescence is linked to increased risk for cigarette smoking susceptibility and initiation. Non-urban youth may encounter a disproportionate number social and environmental risk factors for secondhand smoke exposure. Research is needed to explore geographic disparities in secondhand smoke exposure.

Aims and Methods
Four years of National Youth Tobacco Survey (2015–2018) data were pooled. Participants were 69 249 middle and high school students. Multivariable logistic regression examined the relationship between geographic region and secondhand smoke exposure (1) at home and (2) in a vehicle. A multivariable, multinomial logistic regression examined the relationship between geographic region and number of sources of secondhand smoke exposure (ie, 0, 1 source, 2 sources). Covariates included sex, race/ethnicity, grade level, past 30-day tobacco use, and living with a tobacco user.

Results
From 2015 to 2018, ~28.4% of middle and high school students reported secondhand smoke exposure either at home, in a vehicle, or both. Non-urban youth had greater odds of reporting secondhand smoke exposure at home (Adj OR: 1.26; 95% CI: 1.15 to 1.38) and in a vehicle (Adj OR: 1.50; 95% CI: 1.35 to 1.65), compared with urban youth. Similarly, non-urban youth had greater odds of reporting secondhand smoke exposure via one source (RRR: 1.21; 95% CI: 1.11 to 1.31) and two sources (RRR: 1.61; 95% CI: 1.42 to 1.82), relative to no exposure, than urban youth.

Conclusion
Secondhand smoke exposure at home and/or in a vehicle varies across geographic region. Targeted interventions should be developed and implemented to reduce secondhand smoke exposure among at-risk youth.

Implications
Findings showcase the need to address secondhand smoke exposure in non-urban areas and how it impacts adolescents. Public health interventions and regulatory policies aimed at improving social norms and expanding health infrastructure in rural communities should be designed and implemented in order to prevent and reduce secondhand smoke exposure among non-urban youth.
Raising ethnicity recording in NHS Lothian from 3% to 90% in 3 years: processes and analysis of data from Accidents and Emergencies
Authors: Davidson Emma M , Douglas Anne , Villarroel Nazmy , Dimmock Katy , Gorman Dermot , Bhopal Raj S 
Published: October 2020

Abstract

Background
The disproportionate burden of COVID-19 on ethnic minority populations has recently highlighted the necessity of maintaining accessible, routinely collected, ethnicity data within healthcare services. Despite 25 years of supportive legislation and policy in the UK, ethnicity data recording remains inconsistent, which has hindered needs assessment, evaluation and decision-making. We describe efforts to improve the completeness, quality and usage of ethnicity data within our regional health board, NHS Lothian.

Methods
The Ethnicity Coding Task Force was established with the aim of increasing ethnicity recording within NHS Lothian secondary care services from 3 to 90% over 3 years. We subsequently analysed these data specifically focusing on Accident and Emergency (A&E) use by ethnic group.

Results
We achieved 91%, 85% and 93% completeness of recording across inpatients, outpatients and A&E, respectively. Analysis of A&E data found a mixed pattern of attendance amongst ethnic minority populations and did not support the commonly perceived relationship between lower GP registration and higher A&E use within this population.

Conclusions
We identified a successful approach to increase ethnicity recording within a regional health board, which could potentially be useful in other settings, and demonstrated the utility of these data in informing assessment of healthcare delivery and future planning.
The role of metrics in peer assessments
Authors: Langfeldt Liv , Reymert Ingvild , Aksnes Dag W 
Published: October 2020

Abstract
Metrics on scientific publications and their citations are easily accessible and are often referred to in assessments of research and researchers. This paper addresses whether metrics are considered a legitimate and integral part of such assessments. Based on an extensive questionnaire survey in three countries, the opinions of researchers are analysed. We provide comparisons across academic fields (cardiology, economics, and physics) and contexts for assessing research (identifying the best research in their field, assessing grant proposals and assessing candidates for positions). A minority of the researchers responding to the survey reported that metrics were reasons for considering something to be the best research. Still, a large majority in all the studied fields indicated that metrics were important or partly important in their review of grant proposals and assessments of candidates for academic positions. In these contexts, the citation impact of the publications and, particularly, the number of publications were emphasized. These findings hold across all fields analysed, still the economists relied more on productivity measures than the cardiologists and the physicists. Moreover, reviewers with high scores on bibliometric indicators seemed more frequently (than other reviewers) to adhere to metrics in their assessments. Hence, when planning and using peer review, one should be aware that reviewers—in particular reviewers who score high on metrics—find metrics to be a good proxy for the future success of projects and candidates, and rely on metrics in their evaluation procedures despite the concerns in scientific communities on the use and misuse of publication metrics.
Can We Panelize Seizure?
Authors: Roberts Ruth , Authier Simon , Mellon R Daniel , Morton Michael , Suzuki Ikuro , Tjalkens Ronald B , Valentin Jean-Pierre , Pierson Jennifer B 
Published: October 2020

Abstract
Seizure liability remains a significant cause of attrition in drug discovery and development, leading to loss of competitiveness, delays, and increased costs. Current detection methods rely on observations made in in vivo studies intended to support clinical trials, such as tremors or other abnormal movements. These signs could be missed or misinterpreted; thus, definitive confirmation of drug-induced seizure requires a follow-up electroencephalogram study. There has been progress in in vivo detection of seizure using automated video systems that record and analyze animal movements. Nonetheless, it would be preferable to have earlier prediction of seizurogenic risk that could be used to eliminate liabilities early in discovery while there are options for medicinal chemists making potential new drugs. Attrition due to cardiac adverse events has benefited from routine early screening; could we reduce attrition due to seizure using a similar approach? Specifically, microelectrode arrays could be used to detect potential seizurogenic signals in stem-cell-derived neurons. In addition, there is clear evidence implicating neuronal voltage-gated and ligand-gated ion channels, GPCRs and transporters in seizure. Interactions with surrounding glial cells during states of stress or inflammation can also modulate ion channel function in neurons, adding to the challenge of seizure prediction. It is timely to evaluate the opportunity to develop an in vitro assessment of seizure linked to a panel of ion channel assays that predict seizure, with the aim of influencing structure-activity relationship at the design stage and eliminating compounds predicted to be associated with pro-seizurogenic state.
Genome Sequence of the Biocontrol Agent Coniothyrium minitans Conio (IMI 134523)
Authors: Patel Denise , Shittu Taiwo A. , Baroncelli Riccardo , Muthumeenakshi Sreenivasaprasad , Osborne Thomas H. , Janganan Thamarai K. , Sreenivasaprasad Surapareddy 
Published: October 2020

Coniothyrium minitans (synonym, Paraphaeosphaeria minitans) is a highly specific mycoparasite of the wide host range crop pathogen Sclerotinia sclerotiorum. The capability of C. minitans to destroy the sclerotia of S. sclerotiorum has been well recognized and it is available as a widely used biocontrol product Contans WG. We present the draft genome sequence of C. minitans Conio (IMI 134523), which has previously been used in extensive studies that formed part of a registration package of the commercial product. This work provides a distinctive resource for further research into the molecular basis of mycoparasitism to harness the biocontrol potential of C. minitans. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Risk Factors for 30- and 90-Day Readmissions Due To Surgical Site Infection Following Posterior Lumbar Fusion
Authors: Taree Amir , Mikhail Christopher M. , Markowitz Jonathan , Ranson William A. , Choi Brian , Schwartz John T. , Cho Samuel K. 
Published: October 2020

Study Design:
This was a retrospective cohort study.

Objective:
Identify the independent risk factors for 30- and 90-day readmission because of surgical site infection (SSI) in patients undergoing elective posterior lumbar fusion (PLF).

Summary of Background Data:
SSI is a significant cause of morbidity in the 30- and 90-day windows after hospital discharge. There remains a gap in the literature on independent risk factors for readmission because of SSI after PLF procedures. In addition, readmission for SSI after spine surgery beyond the 30-day postoperative period has not been well studied.

Methods:
A retrospective analysis was performed on data from the 2012 to 2014 Healthcare Cost and Utilization Project Nationwide Readmissions Database. The authors identified 65,121 patients who underwent PLF. There were 191 patients (0.30%) readmitted with a diagnosis of SSI in the 30-day readmission window, and 283 (0.43%) patients readmitted with a diagnosis of SSI in the 90-day window. Baseline patient demographics and medical comorbidities were assessed. Bivariate and multivariate analyses were performed to examine the independent risk factors for readmission because of SSI.

Results:
In the 30-day window after discharge, this study identified patients with liver disease, uncomplicated diabetes, deficiency anemia, depression, psychosis, renal failure, obesity, and Medicaid or Medicare insurance as higher risk patients for unplanned readmission with a diagnosis of SSI. The study identified the same risk factors in the 90-day window with the addition of diabetes with chronic complications, chronic pulmonary disease, and pulmonary circulation disease.

Conclusions:
Independent risk factors for readmission because of SSI included liver disease, uncomplicated diabetes, obesity, and Medicaid insurance status. These findings suggest that additional intervention in the perioperative workup for patients with these risk factors may be necessary to lower unplanned readmission because of SSI after PLF surgery.
EGFR-mutant NSCLC: emerging novel drugs
Authors: Ye Lingyun , Chen Xiaoxia , Zhou Fei 
Published: October 2020

Purpose of review
Despite the significant advances in EGFR-mutant nonsmall cell lung cancer (NSCLC), some challenges remain. One of the permanent and inevitable issues is the emergence of acquired resistance. Therefore, blocking the activation of EGFR pathway and overcoming drug resistance with novel agents are still in high demand. Here, we review the development of novel drugs in EGFR-mutant, advanced NSCLC, including targeting EGFR exon 20 insertion (EGFR20ins), and novel role of epidermal growth factor receptor, tyrosine kinase inhibitor (EGFR-TKIs) in early-stage NSCLC.

Recent findings
EGFR-TKIs as adjuvant therapy or neoadjuvant therapy in patients with early-stage NSCLC with EGFR-sensitizing mutations have shown promising efficacy. The resistance mechanisms of third-generation EGFR-TKIs can be divided into two types: EGFR dependent and EGFR independent. Several clinical trials have demonstrated that the addition of MET inhibitors to EGFR-TKIs was an effective option for patients who had acquired resistance to EGFR-TKIs caused by hepatocyte growth factor receptor gene (MET) amplification or overexpression. Novel compounds that selectively and potently inhibit EGFR20ins are being investigated in phase III studies.

Summary
A better characterization and understanding of resistance mechanisms to first-line osimertinib and adjuvant osimertinib is helpful to guide further treatment.
Ultrasound increases the success rate of spinal needle placement through the epidural needle during combined spinal-epidural anaesthesia
Authors: Tao Bingdong , Liu Kun , Ding Mengmeng , Xue Hang , Li Xingyue , Zhao Ping 
Published: October 2020

BACKGROUND
Combined spinal-epidural anaesthesia (CSEA) using a needle-through-needle technique is currently widely used. However, successful epidural needle placement does not mean a successful spinal needle placement during CSEA. Whether ultrasound assistance could increase the first-pass success rate of spinal needle placement for CSEA remains unknown.

OBJECTIVE
The aim of this study was to investigate if ultrasound assistance could increase the first-pass success rate of spinal needle placement through the epidural needle during CSEA performed by experienced anaesthesiologists in patients undergoing caesarean section.

DESIGN
A prospective, randomised, double-blind study.

SETTING
Single centre, Department of Anaesthesiology, Shengjing Hospital, China Medical University, China, from June 2019 to September 2019.

PATIENTS
A total of 185 patients (aged 24 years to 52 years, American Society of Anesthesiologists grade (ASA) II-III, 38 to 40 weeks gestation) scheduled to undergo elective caesarean section under CSEA were enrolled.

INTERVENTION
The patients were randomised to either an ultrasound group (patients received a preprocedural ultrasound scan, and the puncture site was identified by ultrasound imaging) and a palpation group (patients received a sham procedural ultrasound scan, and the puncture site was identified by conventional palpation).

MAIN OUTCOME MEASURES
The primary outcome measure was the first-pass success rate for spinal needle placement through the epidural needle. Secondary outcome measures were total duration of CSEA, time required for successful epidural needle and spinal needle placement, number of epidural needle redirections and complications.

RESULTS
Preprocedural ultrasound imaging significantly increased the first-pass success rate of spinal needle placement through the epidural needle compared with conventional palpation (93.8 vs. 68.8%, P < 0.001). Preprocedural ultrasound imaging also decreased the total duration of CSEA (186.9 ± 37.1 vs. 213 ± 60.4 s, P = 0.0015) and the time required for successful spinal needle placement (78.3 ± 22.9 vs. 100.1 ± 53.7 s, P < 0.01) compared with conventional palpation. Fewer patients in the ultrasound group needed epidural needle redirections during the spinal needle placement procedure than in the palpation group (four patients vs. 20 patients, P < 0.01).

CONCLUSION
For experienced anaesthesiologists, preprocedural ultrasound imaging significantly increased the first-pass success rate of spinal needle placement through the epidural needle for obstetric patients undergoing caesarean section under CSEA.

TRIAL REGISTRATION
chictr.org.cn, identifier: ChiCTR1900024132
Local and regional therapy considerations after preoperative therapy in patients with breast cancer
Authors: Untch Michael 
Published: October 2020

Purpose of review
The starting point of neoadjuvant therapy was to use preoperative chemotherapy in order to provide surgeons and radiotherapists with the possibility of local treatment in patients with locally advanced, primary inoperable or inflammatory disease. Since then, this treatment approach has dramatically evolved and is now a standard of care in patients with high-risk early breast cancer.

Recent findings
The role of surgery after neoadjuvant therapy is to remove residual disease in the breast and or in the lymph nodes and to provide further treatment possibilities according to pathohistologic findings at surgery.

Summary
Innovative medical treatments are now being used for neoadjuvant treatment in order to reduce the extent of locoregional surgery in the breast and the axilla and also to adjust further medical treatment after neoadjuvant therapy and surgery.
Use of presbyopia-correcting intraocular lenses in patients with prior corneal refractive surgery
Authors: Moshirfar Majid , Thomson Andrew C. , Thomson Robert J. , Martheswaran Tanisha , McCabe Shannon E. 
Published: October 2020

Purpose of review
Corneal refractive surgery has achieved spectacle-free vision for millions of patients, but this aging population is now developing cataracts. Many of these patients may wish to avoid reliance on glasses after cataract surgery. Presbyopia-correcting intraocular lenses (IOLs) offer a solution, but corneal changes after refractive surgery may compound higher order aberrations and dysphotopic symptoms associated with these IOLs. This review aims to discuss potential factors that could aid in determining suitable postkeratorefractive candidates for presbyopia-correcting IOLs.

Recent findings
Studies investigating which preoperative measures influence outcomes are lacking. The few studies that have examined presbyopia-correcting IOLs in postkeratorefractive patients report that satisfactory outcomes are possible. However, recommendations for preoperative thresholds appear limited to expert opinion and studies involving virgin corneas.

Summary
As the number of presbyopia-correcting IOLs and postkeratorefractive patients grows, continued investigation into relevant preoperative factors and appropriate IOLs is required to make evidence-based decisions. The current literature shows that with rigorous counseling and appropriate patient selection, presbyopia-correcting IOLs can provide postkeratorefractive patients with satisfactory results and spectacle independence. In addition, the development of postoperative modifiable IOLs may prove to be the preferred option.
Changes in the Trend of Sexually Acquired Chlamydia Infections in Sweden and the Role of Testing: A Time Series Analysis
Authors: Veličko Inga , Ploner Alexander , Sparén Pär , Herrmann Björn , Marions Lena , Kühlmann-Berenzon Sharon 
Published: October 2020

Background
We investigated the notification trends of sexually acquired chlamydia (chlamydia) and its association with testing in Sweden before (1992–2004) and after (2009–2018) the discovery of a new variant of Chlamydia trachomatis (nvCT).

Methods
We applied monthly time series analysis to study chlamydia trends and annual time series to study chlamydia rates adjusted for testing. We analyzed incidence nationally and by county group (based on able and unable to detect nvCT at time of discovery).

Results
We present data on 606,000 cases of chlamydia and 9.9 million persons tested. We found a U-shaped chlamydia trend during the period 1992–2004, with an overall increase of 83.7% from 1996 onward. The period 2009–2018 began with a stable trend at a high incidence level followed by a decrease of 19.7% during the period 2015–2018. Peaks were seen in autumn and through during winter and summer. Similar results were observed by groups of county, although with varying levels of increase and decrease in both periods. Furthermore, increased testing volume was associated with increased chlamydia rates during the first period (P = 0.019) but not the second period.

Conclusions
Our results showed that chlamydia trends during the period 2009–2018 were not driven by testing, as they were during the period 1992–2004. This suggests less biased notified chlamydia rates and thus possibly a true decrease in chlamydia incidence rates. It is important to adjust case rates for testing intensity, and future research should target other potential factors influencing chlamydia rates.