bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reference-based QUantification Of gene Dispensability (QUOD)
Authors: Sielemann Katharina , Weisshaar Bernd , Pucker Boas 
Published: February 2021

Abstract
Background
Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as ‘core’ or ‘dispensable’ is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Even when extended to ‘conditionally dispensable’, this concept still requires the assignment of genes to distinct groups.

Results
Here, we present a new method which overcomes this distinct classification by quantifying gene dispensability and present a dedicated tool for reference-based QUantification Of gene Dispensability (QUOD). As a proof of concept, sequence data of 966 Arabidopsis thaliana accessions (Ath-966) were processed to calculate a gene-specific dispensability score for each gene based on normalised coverage in read mappings. We validated this score by comparison of highly conserved Benchmarking Universal Single Copy Orthologs (BUSCOs) to all other genes. The average scores of BUSCOs were significantly lower than the scores of non-BUSCOs. Analysis of variation demonstrated lower variation values between replicates of a single accession than between iteratively, randomly selected accessions from the whole dataset Ath-966. Functional investigations revealed defense and antimicrobial response genes among the genes with high-dispensability scores.

Conclusions
Instead of classifying a gene as core or dispensable, QUOD assigns a dispensability score to each gene. Hence, QUOD facilitates the identification of candidate dispensable genes, associated with high dispensability scores, which often underlie lineage-specific adaptation to varying environmental conditions.
Clarifying the relationship between pulmonary langerhans cell histiocytosis and Alpha 1 antitrypsin deficiency
Authors: McCarthy Cormac , Bugnet Emmanuelle , Benattia Amira , Keane Michael P. , Vedie Benoit , Lorillon Gwenaël , Tazi Abdellatif 
Published: February 2021

AbstractPulmonary Langerhans cell histiocytosis (PLCH) is a rare, smoking related, progressive diffuse cystic lung disease that occurs primarily in smokers. The aim of this study was to determine if there was an increase in alpha-1 antitrypsin deficient alleles or phenotypes in a large series of PLCH patients and whether serum alpha-1 antitrypsin levels correlated with markers of disease severity. Fifty PLCH patients, 24 with a diffuse cystic lung pattern and 26 with a typical nodulo-cystic pattern on imaging were included. The mean alpha-1 antitrypsin levels were in normal range for both the population with diffuse cystic lung pattern population (1.39 g/L ± 0.37) and the nodulo-cystic pattern group (1.41 g/L ± 0.21). Deficiency alleles PiZ and PiS were 1% and 2% respectively in the entire study population of 50 patients, demonstrating no increased incidence of alpha-1 antitrypsin deficiency in PLCH. Alpha-1 antitrypsin levels showed no correlation with lung function parameters or extent of cystic lesions on lung computed tomography.
Causal relationships between genetically determined metabolites and human intelligence: a Mendelian randomization study
Authors: Yang Jian , Zhao Binbin , Qian Li , Gao Fengjie , Fan Yanjuan , He Xiaoyan , Ma Qingyan , Yang Lihong , Yan Bin , Wang Wei , Ma Xiancang 
Published: February 2021

AbstractIntelligence predicts important life and health outcomes, but the biological mechanisms underlying differences in intelligence are not yet understood. The use of genetically determined metabotypes (GDMs) to understand the role of genetic and environmental factors, and their interactions, in human complex traits has been recently proposed. However, this strategy has not been applied to human intelligence. Here we implemented a two-sample Mendelian randomization (MR) analysis using GDMs to assess the causal relationships between genetically determined metabolites and human intelligence. The standard inverse-variance weighted (IVW) method was used for the primary MR analysis and three additional MR methods (MR-Egger, weighted median, and MR-PRESSO) were used for sensitivity analyses. Using 25 genetic variants as instrumental variables (IVs), our study found that 5-oxoproline was associated with better performance in human intelligence tests (PIVW = 9.25 × 10–5). The causal relationship was robust when sensitivity analyses were applied (PMR-Egger = 0.0001, PWeighted median = 6.29 × 10–6, PMR-PRESSO = 0.0007), and repeated analysis yielded consistent result (PIVW = 0.0087). Similarly, also dihomo-linoleate (20:2n6) and p-acetamidophenylglucuronide showed robust association with intelligence. Our study provides novel insight by integrating genomics and metabolomics to estimate causal effects of genetically determined metabolites on human intelligence, which help to understanding of the biological mechanisms related to human intelligence.
Propofol suppresses cell viability, cell cycle progression and motility and induces cell apoptosis of ovarian cancer cells through suppressing MEK/ERK signaling via targeting circVPS13C/miR-145 axis
Authors: Lu Huan , Zheng Guanlin , Gao Xiang , Chen Chanjuan , Zhou Min , Zhang Longxin 
Published: February 2021

Abstract
Background
Propofol is a kind of common intravenous anaesthetic agent that plays an anti-tumor role in a variety of cancers, including ovarian cancer. However, the working mechanism of Propofol in ovarian cancer needs further exploration.

Methods
The viability and metastasis of ovarian cancer cells were assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and transwell assays. Flow cytometry was used to evaluate the cell cycle and apoptosis. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to examine the abundance of circular RNA vacuolar protein sorting 13 homolog C (circVPS13C) and microRNA-145 (miR-145). The target relationship between miR-145 and circVPS13C was predicted by circinteractome database and verified by dual-luciferase reporter assay, RNA-binding protein immunoprecipitation (RIP) assay and RNA-pull down assay. Western blot assay was used to detect the levels of phosphorylated extracellular regulated MAP kinase (p-ERK), ERK, p-MAP kinse-ERK kinase (p-MEK) and MEK, in ovarian cancer cells.

Results
Propofol treatment suppressed the viability, cell cycle and motility and elevated the apoptosis rate of ovarian cancer cells. Propofol up-regulated miR-145 in a dose-dependent manner. Propofol exerted an anti-tumor role partly through up-regulating miR-145. MiR-145 was a direct target of circVPS13C. Propofol suppressed the progression of ovarian cancer through up-regulating miR-145 via suppressing circVPS13C. Propofol functioned through circVPS13C/miR-145/MEK/ERK signaling in ovarian cancer cells.

Conclusion
Propofol suppressed the proliferation, cell cycle, migration and invasion and induced the apoptosis of ovarian cancer cells through circVPS13C/miR-145/MEK/ERK signaling in vitro.
Recent advances on biomass-fueled microbial fuel cell
Authors: Moradian Jamile Mohammadi , Fang Zhen , Yong Yang-Chun 
Published: February 2021

AbstractBiomass is one of the most abundant renewable energy resources on the earth, which is also considered as one of the most promising alternatives to traditional fuel energy. In recent years, microbial fuel cell (MFC) which can directly convert the chemical energy from organic compounds into electric energy has been developed. By using MFC, biomass energy could be directly harvested with the form of electricity, the most convenient, wide-spread, and clean energy. Therefore, MFC was considered as another promising way to harness the sustainable energies in biomass and added new dimension to the biomass energy industry. In this review, the pretreatment methods for biomass towards electricity harvesting with MFC, and the microorganisms utilized in biomass-fueled MFC were summarized. Further, strategies for improving the performance of biomass-fueled MFC as well as future perspectives were highlighted.
The importance of implementing inpatient virtual coverage in an endocrinology practice: lessons learned thus far from the COVID-19 pandemic
Authors: Griebeler Marcio L. , Pantalone Kevin M. , Gambino Ron , Shewmon David , Morrow Jay , Mendlovic Daniel , Makin Vinni , Hamaty Marwan , Hasan Sana , Lansang M. Cecilia , Zhou Keren , Burguera Bartolome 
Published: February 2021

AbstractThe COVID-19 pandemic has rapidly changed the landscape of medical care and the healthcare system needs to quickly adapt in order to continue providing optimal medical care to hospitalized patients in an efficient, effective, and safe manner. Endocrinology diseases are commonly present in patients with COVID-19 and often are major risk factors for development of severe disease. The use of electronic consultation and telemedicine have already been well-established in the outpatient setting but yet not commonly implemented in the inpatient arena. This type of remote medical care has the potential to provide a reliable delivery of endocrine care while protecting providers and patients from spreading infection. This short review intends to provide the initial steps for the development of an inpatient telemedicine endocrine service to patients with endocrine diseases. Telehealth will become part of our daily practices and has a potential to provide a safe and efficient method of consultative service.
Activity patterns of the soprano pipistrelle Pipistrellus pygmaeus throughout the year in southern Norway
Authors: Frafjord Karl 
Published: February 2021

Abstract
Background
Most temperate bats are regular hibernators in the winter. Knowledge about the length of their active season and how they adjust their nightly activity throughout the season, is critical to conservation. The characteristics of these are likely to vary with climate as well as latitude. This study investigated the flight activity of the soprano pipistrelle Pipistrellus pygmaeus in Frafjord, a small valley in the south-western corner of Norway (58° 50′N 6° 18′E) with an oceanic climate.

Results
Activity was recorded with an ultrasound recorder throughout April 2018 to June 2019 at one site, with supplemental recordings in March to June 2020, i.e., covering all months of the year. Recordings at other nearby sites were made in the summers (June–August) of 2016, 2017, 2019 and 2020, as well as some of the last days in December 2019 to the first days of January 2020. Overall, soprano pipistrelles were recorded flying in all months of the year, but very few in December–March. Regular activity was recorded from late April or early May until late October, and some recordings were also made in November. The highest numbers of recordings were made in August and September. Social calls, i.e. male song flights, were recorded from April to November, with the vast majority in August and September. Nearly all recordings were made between sunset and sunrise.

Conclusions
The soprano pipistrelle in this region showed regular activity through 6–7 months of the year. It adjusted its activity to the changing night length throughout the year, closely following sunset and sunrise. It was rarely recorded flying before sunset and almost never after sunrise. Most activity was recorded in the middle of the night, and social calls also followed this trend closely. Harems in late summer and autumn were confirmed in a bat box, which was also used for winter hibernation.
Interplay Between Class II HLA Genotypes and the Microbiome and Immune Phenotypes in Individuals With PTEN Hamartoma Tumor Syndrome
Authors: Jia Margaret , Sangwan Naseer , Tzeng Alice , Eng Charis 
Published: February 2021

PURPOSE We evaluate potential contributors to the development of autoimmunity and other phenotypes consistent with immune dysregulation in individuals with germline mutations in the tumor suppressor gene PTEN in this observational report. MATERIALS AND METHODS Illumina sequencing of bacterial and fungal microbes was carried out on patient-donated fecal samples in a cohort of 67 patients with pathogenic germline PTEN mutations, including 41 individuals with autoimmunity and/or phenotypes consistent with immune dysregulation (cases) and 26 individuals without (controls). From these data, we measured differences in alpha and beta diversity between cases and controls and identified differentially abundant bacterial and fungal taxa using phyloseq and MicrobiomeSeq packages in R. We analyzed correlations between these taxa and specific HLA genotypes, along with correlations between HLA diversity and microbial diversity, by conducting high-resolution HLA genotyping at four class II loci (DRB1, DRB345, DQA1, and DQB1). RESULTS We found that alpha diversity distributions for both bacterial and fungal genera were statistically different between cases and controls. We identified differentially abundant bacterial and fungal taxa between cases and controls. Network analysis of differentially abundant bacterial taxa revealed some co-varying bacterial genera. We additionally found significant correlations between certain HLA genotypes and certain taxa and significant correlations between HLA diversity and alpha diversity. CONCLUSION PTEN-associated immune phenotypes might be influenced by the gut microbiome, and class II HLA molecules, in part, crosstalk with the gut microbiome. These preliminary observations should lay the groundwork for future studies to ultimately derive clinical measures, which could use gut microbiome and HLA molecule biomarkers to predict, and perhaps prevent, immunity and inflammation in patients predisposed to cancer because of germline PTEN mutations.
Hearts in the Hometown: Diaspora Consciousness and Literature of the Tang and Song
Authors: Hor Wendy 
Published: February 2021

Abstract
Originating in the experience of geographical dispersion and survival, the concept of diaspora (lisan 離散) can be extended to diaspora consciousness (lisan yishi 離散意識) and its correlate, return consciousness (huigui yishi 回歸意識). The famous group of Tang and Song intellectuals who were forced to leave hometown political/cultural centers and dream, perennially, of return constitutes the early Chinese embodiment of diaspora-return consciousness. For many “hometown” (guxiang 故鄉) came to mean not just their homeland but their ideal destination or spiritual home, as in Su Shi's 蘇軾 (1037–1101) “wherever my heart is at peace is my home.” The layered features of this diaspora-return (lisan-huigui 離散—回歸) consciousness led to a unique literary style and the development of tropes that would shape Chinese writing for a millennium. Political banishment yielded an unintended yet undeniable cultural value.
The Art of Chinese Prose: A Critical Introduction
Authors: Cai Zong-qi 
Published: February 2021

Abstract
This article opens with a reflection on the extrinsic and intrinsic causes of the neglect of Chinese prose in sinological literary studies, followed by the construction of a patterning-based scheme for codifying Chinese prose forms. An in-depth analysis of eight famous texts, drawn from antiquity through the Qing, reveals how continual innovations in extratextual patterning and textual patterning have given rise to manifold and inherently related prose forms over the millennia. The close reading also sheds light on these prose forms' distinctive artistic features, as well as their symbiotic relationships with the three types of genres (narrative, descriptive, and expository) and with broad sociopolitical and cultural developments. It is hoped that these findings will generate serious interest in prose studies among literary sinologists.
The laparoscopy in emergency general surgery (LEGS) study: a questionnaire survey of UK practice
Authors: Heywood N , Parmar KL , Stott M , Sodde P , Doherty DT , Lim J , Sharma A ,   On behalf of the LEGS Study Group* and the North West Research Collaborative
Published: February 2021

Introduction Recent consensus guidelines suggest that the laparoscopic approach may be a useful, safe and feasible approach in emergency general surgery. Despite this, the UK National Emergency Laparotomy Audit (NELA) suggests the rate of laparoscopy is low (9% fully laparoscopic) and slow to increase over time. A European survey found uptake to be variable. This UK survey was therefore undertaken to establish current UK practice and to determine factors affecting implementation. Materials and methods A questionnaire survey of currently practising UK consultant general surgeons was carried out by the North West Surgical Research Collaborative, using a secure web-based database maintained by the North West Surgical Trials Centre. Results A total of 151 completed questionnaires were returned from 22 UK centres; 18% of respondents were unaware that laparoscopic cases should be reported to NELA. Appendicectomy (97%) and cholecystectomy (87%) were routinely performed laparoscopically. Laparoscopy was infrequently used in perforation, ischaemia or obstructed hernias. There appears to be equipoise regarding laparoscopic compared with open surgery in small-bowel obstruction among all subspecialty emergency general surgeons, in perforated peptic ulcer among upper gastrointestinal surgeons and in Hinchey III diverticulitis among colorectal surgeons. Conclusion Uptake of laparoscopy in UK emergency general surgery is influenced by surgeon preference, subspecialty, patient and operative factors. Further research into outcomes may help to identify areas of greatest potential benefit. The rate of laparoscopy reported by NELA may be an underestimate due to the 18% of surgeons unaware that laparoscopic cases should be reported, which may affect the validity of analyses performed from this dataset.
The provision of a time-critical elective surgical service during the COVID-19 Crisis: a UK experience
Authors: Burden EG , Walker RW , Ferguson DJ , Goubran AMF , Howell JR , John JB , Khan F , McGrath JS , Evans JP 
Published: February 2021

Introduction With the emergence of the COVID-19 pandemic, all elective surgery was temporarily suspended in the UK, allowing for diversion of resource to manage the anticipated surge of critically unwell patients. Continuing to deliver time-critical surgical care is important to avoid excess morbidity and mortality from pathologies unrelated to COVID-19. We describe the implementation and short-term surgical outcomes from a system to deliver time-critical elective surgical care to patients during the COVID-19 pandemic. Materials and methods A protocol for the prioritisation and safe delivery of time-critical surgery at a COVID-19 ‘clean’ site was implemented at the Nuffield Health Exeter Hospital, an independent sector hospital in the southwest of England. Outcomes to 30 days postoperatively were recorded, including unplanned admissions after daycase surgery, readmissions and complications, as well as the incidence of perioperative COVID-19 infection in patients and staff. Results A total of 128 surgical procedures were performed during a 31-day period by a range of specialties including breast, plastics, urology, gynaecology, vascular and cardiology. There was one unplanned admission and and two readmissions. Six complications were identified, and all were Clavien-Dindo grade 1 or 2. All 128 patients had preoperative COVID-19 swabs, one of which was positive and the patient had their surgery delayed. Ten patients were tested for COVID-19 postoperatively, with none testing positive. Conclusion This study has demonstrated the implementation of a safe system for delivery of time-critical elective surgical care at a COVID-19 clean site. Other healthcare providers may benefit from implementation of similar methodology as hospitals plan to restart elective surgery.
Is there a ‘weekend effect’ in elective lower limb arthroplasty?
Authors: Higgins M , Nightingale J , Sehat K 
Published: February 2021

Introduction The weekend effect has been defined as a real or perceived decline in patient care provided on weekends and that provided on weekdays. The primary aim of this study was to investigate the association between day of surgery and length of stay for patients receiving elective lower limb joint arthroplasty in a large NHS teaching hospital. Materials and methods Data were obtained from a prospectively collected database of consecutive patients undergoing elective primary total knee and hip arthroplasty. Patient and clinical variables were collected alongside length of hospital stay. Data were anonymised and analysed using a multiple linear regression model. Results A total of 3,544 knee and 3,277 hip replacements were included. No association was found between length of stay and day of surgery for either procedure. A significant association was noted between longer length of stay and increasing age, higher American Society of Anesthesiologists grade and male compared with female gender. Discussion No evidence of a weekend effect was identified. Certain patient factors predicted longer hospital stay and focussing additional resources on these patient groups may prove a useful strategy in reducing overall length of stay. Conclusions Length of stay reduced across the time period included in this review while maintaining equality between the days of the week, which represents the successful management of weekend services.
Non-persistence with anti-platelet therapy and long-term mortality after ischemic stroke: A nationwide study
Authors: Kim Seung Jae , Kwon Oh Deog , Choi Ho Chun , Lee Eung-Joon , Cho BeLong 
Published: February 2021

Background
We tried to investigate the effect of non-persistence with antiplatelets after ischemic stroke on long-term all-cause mortality (ACM).

Methods and findings
We selected newly diagnosed ischemic stroke patients aged ≥20years who were newly treated with aspirin or clopidogrel from 2003–2010 Korean National Health Insurance Service-National Sample Cohort, a random sample of 2.2% of total population. Subjects were divided into two pairs of groups according to persistence with antiplatelets at 6 and 12 months: those who discontinued antiplatelets within 6 months (DA6M) and those who continued them for 6 or months or more (CA6M); and those who discontinued antiplatelets within 12 months (DA12M) and those who continued them for 12 months or more (CA12M). Those who died within 6 months among DA6M and those who died within 12 months among DA12M were excluded along with those with medication possession ratio<80% among CA6M and CA12M. Subjects were followed-up until death or December 31, 2013. Among 3,559 total subjects, DA6M were 1,080 and CA6M were 2,479 while, out of 3,628 total patients, DA12M were 1,434 and CA12M were 2,194. The risks of ACM [adjusted hazard ratio (aHR), 2.25; 95% confidence interval (CI), 1.94–2.61], cerebro-cardiovascular disease (CVD) death (aHR, 2.52; 95% CI, 1.96–3.24) and non-CVD death (aHR, 2.11; 95% CI, 1.76–2.64) of DA6M were all significantly increased compared to CA6M. DA12M also had significantly higher risks of ACM (aHR, 1.93; 95% CI, 1.65–2.25), CVD mortality (aHR, 2.13; 95% CI; 1.63–2.77) and non-CVD mortality (aHR, 1.83;95% CI 1.51–2.22) than DA12M but aHRs were lower than that between DA6M and CA6M. The difference rates of ACM, CVD death, and non-CVD death between non-persistent and persistent groups all continuously widened over time but the degree of difference was gradually decreased.

Conclusions
Maintaining antiplatelets for the first 12 months after ischemic stroke reduces long-term risks of both CVD death and non-CVD death.