bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq
Authors: Tshiabuila Derek , Giandhari Jennifer , Pillay Sureshnee , Ramphal Upasana , Ramphal Yajna , Maharaj Arisha , Anyaneji Ugochukwu Jacob , Naidoo Yeshnee , Tegally Houriiyah , San Emmanuel James , Wilkinson Eduan , Lessells Richard J. , de Oliveira Tulio 
Published: February 2022

Abstract
Background: Over 4 million SARS-CoV-2 genomes have been sequenced globally in the past 2 years. This has been crucial in elucidating transmission chains within communities, the development of new diagnostic methods, vaccines, and antivirals. Although several sequencing technologies have been employed, Illumina and Oxford Nanopore remain the two most commonly used platforms. The sequence quality between these two platforms warrants a comparison of the genomes produced by the two technologies. Here, we compared the sequence quality produced by the Oxford Nanopore Technology GridION and the Illumina MiSeq for 28 sequencing runs. Results: Our results show that the MiSeq had a significantly higher number of sequences classified by Nextclade as good and mediocre compared to the GridION. The MiSeq also had a significantly higher sequence coverage and mutation counts than the GridION. Conclusion: Due to the low sequence coverage, high number of indels, and sensitivity to viral load noted with the GridION when compared to MiSeq, we can conclude that the MiSeq is more favourable for genomic surveillance, as successful genomic surveillance is dependent on high quality, near-whole genome sequences.
Edmonton Frailty Scale Score Predicts Postoperative Delirium: A Retrospective Cohort Analysis
Authors: Sieber Frederick , Gearhart Susan , Bettick Dianne , Wang Nae-Yuh 
Published: February 2022

Abstract
Background: Frailty has been associated with postoperative delirium (POD). Studies suggest that the Fried phenotype has a stronger association with POD than the Edmonton Frailty Scale (EFS) criteria. Although phenotypic frailty is recognized as a good predictor of delirium, the EFS has higher ratings for feasibility in the surgical setting. Thus, our aim was to determine the association between EFS-assessed vulnerability and POD in an elective surgical population of older adults. A secondary aim was to determine which domains assessed by the EFS were closely associated with POD. Methods: After IRB approval was received, electronic medical records of surgical patients at our institution were downloaded from 12/1/2018 to 3/1/2020. Inclusion criteria included age ≥65 years, preoperative EFS assessment within 6 months of surgery, elective surgery not scheduled for intensive care unit (ICU) stay but followed by at least 1 day postoperative stay, and at least two in-hospital evaluations with the 4 A's test (arousal, attention, abbreviated mental test-4, acute change [4AT]) on the surgical ward. Vulnerability was determined by EFS score ≥6. Patients were stratified into two groups according to highest postoperative 4AT score: 0-3 (no POD) and ≥4 (POD). Odds of POD associated with EFS score ≥6 were evaluated by using logistic regression adjusted for potential confounders. Results: The dataset included 324 patients. Vulnerability was associated with higher incidence of POD (P=0.0007). EFS ≥6 was consistently associated with POD in all bivariate models. Vulnerability predicted POD in multivariable modeling (OR 95%CI = 3.5 [1.1-11.5]; P=0.04). Multivariable analysis of EFS domains revealed an overall trend in which higher scores per domain had a higher odds for POD. The strongest association occurred with presence of incontinence (OR 95%CI = 3.8 [1.2-11.0]; P=0.02). Conclusions: EFS criteria for vulnerability predict POD in older, non-ICU patients undergoing elective surgery.
Variations in Anthropometric Measures of Obesity with Age in the Jackson Heart Study
Authors: Gao Yan , Min Yuan-I , Bell Ronny A. , Bertoni Alain G. , Correa Adolfo 
Published: February 2022

Abstract
Background– Based on body mass index (BMI), the prevalence of obesity has been shown to vary by age and sex. However, age- or sex-related variations in obesity defined by anthropometric measures of central adiposity, which may be better proxies for obesity-related risk, is unclear.Methods– Using data from 4063 African American (AA) participants in the Jackson Heart Study, linear and Poisson regression model analyses were conducted to estimate mean difference of standardized anthropometric measures and prevalence ratios of obesity based on body mass index (BMI), waist circumference (WC), waist-to-height ratio (WHtR) and waist-to-hip ratio (WHR) by age cohort and sex.Results– We found sex- and age-variations in the prevalence of obesity for all measures; however, these patterns varied. In cross-sectional analyses at Visit 2, older cohorts showed a lower prevalence of obesity based on BMI but a higher prevalence of obesity based on WHtR and WHR. In longitudinal analyses, for BMI, and WC, and WHtR, the mean and the prevalence of obesity from Visit 2 to Visit 3 increased only among younger cohorts; however, for WHR, the mean and the prevalence of obesity increased consistently from Visit 2 to 3 across all age cohorts for both sexes. Conclusions–WHR appeared to be a more consistent anthropometric measure for monitoring the prevalence of obesity particularly among elderly AAs. Instead of BMI, WHR would be used to monitor the prevalence of obesity among elderly AAs in clinic.
Trauma Team Training In Norwegian Hospitals: An Observational Study
Authors: Bredin Ida Celine , Gaup Hedi Marina Joks , Brattebø Guttorm , Wisborg Torben 
Published: February 2022

Abstract
Background: Traumatic injuries are a leading cause of deaths in Norway, especially among younger males. Trauma-related mortality can be reduced by structural measures, such as organization of a trauma system. Many hospitals in Norway treat few seriously injured patients, one of the reasons for development of the Norwegian trauma system. Since its implementation, there has been continuous improvement of this system, including trauma team training. Regular trauma team training is compulsory, with the aims of compensating for lack of experience and maintaining competence. The purpose of this study was to present an overview of current trauma team training activities in Norway. Methods: For this observational study, an online questionnaire was sent to local trauma coordinators from 38 Norwegian hospitals—including 4 trauma centers and 34 acute hospitals with trauma function. The study was performed during April–June 2020, with a two-month response window. Results: Of the 38 contacted trauma coordinators, 33 (87%) responded. All respondents had a role in trauma team training. All responding hospitals conducted regular trauma team training, with varying frequency. Additionally, all included hospitals described a quite homogenous approach.Conclusions: All responding hospitals performed regular trauma team training using a homogenous approach, which is in line with previous assessments. We observed a minor improvement in frequency compared to prior assessments. Our findings suggest that Norwegian trauma teams likely maintain their competence through team training. All hospitals followed the current recommendations from the National Trauma Plan.
In vitro assembly, positioning and contraction of a division ring in minimal cells
Authors: Kohyama Shunshi , Merino-Salomon Adrian , Schwille Petra 
Published: February 2022

Abstract
Constructing a minimal machinery for autonomous self-division of synthetic cells is a major goal of bottom-up synthetic biology. One paradigm has been the E. coli divisome, with the MinCDE protein system guiding assembly and positioning of a presumably contractile ring based on FtsZ and its membrane adaptor FtsA. Here, we demonstrate the full in vitro reconstitution of this machinery consisting of five proteins within lipid vesicles, allowing to observe the following sequence of events in real time: 1) Assembly of an isotropic filamentous FtsZ network, 2) its condensation into a ring-like structure, along with pole-to-pole mode selection of Min oscillations resulting in equatorial positioning, and 3) onset of ring constriction, deforming the vesicles from spherical shape. Besides demonstrating these essential features, we highlight the importance of decisive experimental factors, such as macromolecular crowding. Our results provide an exceptional showcase of the emergence of cell division in a minimal system, and may represent a major breakthrough towards developing a synthetic cell.
The Influence of Time on the Sensitivity of SARS-CoV-2 Serological Testing
Authors: Ortiz Arturo Torres , Torrente Fernanda Fenn , Twigg Adam , Hatcher James , Saso Anja , Lam Tanya , Johnson Marina , Wagstaffe Helen , Dhillon Rishi , Mai Anabelle Lea , Goldblatt David , Still Rachel , Buckland Matthew , Gilmour Kimberly , Grandjean Louis 
Published: February 2022

Abstract
Background: Serological testing is used to quantify SARS-CoV-2 seroprevalence, guide booster vaccination and select patients for anti-SARS-CoV-2 antibodies therapy. However, our understanding of how serological tests perform as time passes after infection is limited.Methods: Four assays were compared in parallel: 1) the multiplexed spike, nucleoprotein and receptor binding domain Meso Scale Discovery (MSD) assay 2) the Roche Elecsys-Nucleoprotein assay (Roche-N) 3) the Roche Spike assay (Roche-S) and 4) the Abbott Nucleoprotein assay (Abbott-N) on serial positive monthly samples from hospital staff up to 200 days following infection as part of the Co-Stars study.Results: We demonstrate that 50% of the Abbott-N assays give a negative result after 175 days (median survival time 95% CI 168-185 days) while the Roche-N assay (93% survival probability at 200 days, 95% CI 88-97%) maintained seropositivity. The MSD spike (97% survival probability at 200 days, 95% CI 95-99%) and the Roche-S assay (95% survival probability at 200 days, 95% CI 93-97%) also remained seropositive. The best performing quantitative Roche-S assay showed no evidence of waning Spike antibody titres over 200-days.Conclusions: The Abbott-N assay fails to detect SARS-CoV-2 antibodies as time passes since infection. In contrast the Roche and the MSD assays maintained high sensitivity. The limitations of the Abbott assay must be considered in clinical decision making. The long duration of detectable neutralizing spike antibody titres by the quantitative Roche-S assay provides further evidence in support of long-lasting SARS-CoV-2 protection to pre-existing strains of SARS-CoV-2 following natural infection.Trial registration: Co-STARs study was registered with ClinicalTrials.gov on May 8th, 2020, with trial number NCT04380896 (www.clinicaltrials.gov, NCT04380896)
Timing Selection for Loosened Tooth Fixation Based on Degree of Alveolar Bone Resorption – a Finite Element Analysis
Authors: Ding Xi , Ye Zhang-yan , Ye Hao , Yu Xi-xi , Wang Yong , Wu Li-jun 
Published: February 2022

Abstract
Objective: To make a three-dimensional finite element biomechanical analysis of mandibular dentition and its bone interface with varying degrees of alveolar bone resorption, and evaluate timing of fixation to prevent tooth loosening. Methods: Volunteer CT images in combination with periodontitis classification were used to construct a finite element model of mandibles with varying degrees of alveolar bone resorption. By simulating occlusal force loading, biomechanical analysis was made on the periodontal membrane, tooth root and surrounding bone interface of mandibular dentition with varying degrees of alveolar bone resorption. Results: A finite element model of the mandible with varying degrees of alveolar bone resorption was established. The von Mises stress value of the periodontal cortical bone, cancellous bone, root surface and periodontal membrane of mandibular dentition was positively related with the degree of alveolar bone resorption, and the von Mises stress at the interface between the periodontal membrane and tooth root was increased significantly in moderate to severe periodontitis models. The von Mises stress at the interface between the periodontal cortical bone and cancellous bone was increased significantly in the severe periodontitis model. During oblique loading, the stress value at each interface was significantly higher than during vertical loading. Conclusion: The model established in this study can effectively realize a biomechanical study of a mandible with varying degrees of alveolar bone resorption. In clinical treatment of teeth with moderate to severe periodontitis, loosened tooth fixation can be used to prevent tooth loosening.
A comparative study of removal efficiency of organic contaminant in landfill leachate contaminated groundwater under micro-nano-bubble and common bubble aeration
Authors: Bai Mei , Liu Zhibin , Zhan Liangtong , Liu Zhu , Fan Zhanhuang 
Published: February 2022

Abstract
Landfill leachate contaminated groundwater is widespread all over the world. In order to study the organic contaminant removal efficiency of landfill leachate contaminated groundwater under oxygen micro-nano-bubble (MNB) aeration, a series of lab-scale experiments of oxygen MNB aeration as well as common bubble (CB) aeration were conducted. On the one hand, the difference of mass transfer, microbial activity enhancement and contaminant removal efficiency between MNB and CB aeration were estimated. On the other hand, the composition variations of dissolved organic matter (DOM) in groundwater treated by MNB or CB aeration were characterized by ultraviolet-visible (UV-VIS) absorption spectrum and fluorescence excitation-emission matrix (EEM). The test results showed that the oxygen utilization efficiency and volumetric oxygen transfer coefficient of MNB aeration were 10 and 50 times that of oxygen CB aeration, respectively. On the 30th day after MNB aeration, the dehydrogenase activity (DHA) of groundwater increased by 101.25%. Compared with CB aeration, the chemical oxygen demand (COD), 5-day biochemical oxygen demand (BOD5) and ammonia nitrogen removal efficiency under MNB aeration increased by 29.72%, 13.43% and 138.59%, respectively. With the biodegradation effect of MNB aeration, a large number of protein-like and soluble microbial by-product substances were degraded, and humic and fulvic acid-like substances were degraded to a certain level. Oxygen MNB aeration played a chemical oxidation effect while enhancing the biodegradation of groundwater, and it was an energy-efficient landfill leachate contaminated groundwater treatment method.
Increased El Niño amplitude during the last deglacial warming
Authors: Yseki Marco , Turcq Bruno , Gutierrez Dimitri , Salvatteci Renato , Espinoza-Morriberón Dante , Boucher Hugues , Martinez Philippe , Carré Matthieu 
Published: February 2022

Abstract
It is still unclear how El Niño Southern Oscillation (ENSO), the leading mode of global-scale interannual climate variability, will respond to global warming. The last deglaciation offers natural experimental conditions to observe the behavior of ENSO in a period of abrupt warming and sea level rise. Here we present a record of ENSO-related interannual variability of river discharge in Peru during the last deglaciation (17.3-13 kyr) and the Late Holocene (2.7-1.3 kyr), based on high-resolution records of Titanium concentration in marine sediments from the Peruvian margin (Callao, 12°S and Pisco 14°S). We find that the amplitude of ENSO events was 16 to 100 % larger during the last deglaciation compared to the Late Holocene, which supports the hypothesis that ENSO in the EP is strengthened by ice sheet meltwater discharge. A possible strengthening of ENSO in response to future ice sheet melting should be considered.
National, Regional, and Global Cardiomyopathy Burden from 1990 – 2019
Authors: Guo Guanjun , Chen Hui , Qi Zhanru , Zhang Ning , Yao Jing , Fang Aijuan , Cheng Siyuan 
Published: February 2022

Abstract
Objective: To gauge the incidence of both alcoholic cardiomyopathy (AC) and other cardiomyopathy (OC) in 204 nations and regions over the 1990 – 2019 period. Methods: The Global Burden of Disease Study 2019 was leveraged to gather comprehensive information pertaining to both AC and OC. The calculated prevalence rates, mortality rates, and disability-adjusted life years (DALYs) related to these forms of cardiomyopathy were presented as counts and age-standardized rates (ASRs) per 100,000 persons with percentage change and 95% uncertainty intervals (UIs). The overall burden of cardiomyopathy was established by combining data pertaining to both AC and OC, with calculations and corresponding 95% confidence intervals (CIs) being determined based upon corresponding standard error values determined by dividing the width of 95% UI by 1.96×2.Results: At the national level, ASR rates for cardiomyopathy varied by 144.6-fold among surveyed countries in 2019, while the rates ASR rates for AC and OC respectively varied by 408.0-fold and 380.6-fold. Age-standardized cardiomyopathy-associated mortality rates also varied by 58.4-fold among surveyed nations. The highest such AC-related death rates were observed in Latvia, with an age-standardized mortality rate of 16.3 (95%UI 11.0 to 21.1) per 100,000 persons, whereas some nations reported 0 AC-related deaths in 2019. National age-standardized OC-related mortality rates varied by 105-fold among surveyed nations. Despite overall reductions in cardiomyopathy ASRs from 1990 – 2019, the overall numbers of cases, deaths, years lost in life (YLLs), and years lost due to disability (YLDs) have all increased over this period for both AC and OC.Conclusion: These data suggest that cardiomyopathy, including both AC and OC, remains a persistent threat to global public health as evidenced by increased numbers of cases, deaths, and DALYs over the past three decades, with clear geographic differences in overall cardiomyopathy burden. Additional study will be essential to more fully understand the risk factors associated with the development of this disease in an effort to guide its prevention, early diagnosis, and treatment.
Validating the Quality of Prenatal Care Questionnaire (QPCQ-P) in an Iranian Sample of Pregnant Mothers: A Methodological Study
Authors: Zakeri Mohammad Ali , Khoram Somaye , Bazmandegan Gholamreza , Ramezani Najmeh , Talebi Batol , Dehghan Mahlagha 
Published: February 2022

Abstract
Background: The quality of prenatal care is preventive health care that improves the health outcomes of women and infants. A comprehensive questionnaire can be used to assess the quality of prenatal care as well as to identify and investigate mother-child health outcomes. Method: In this cross-sectional study, 329 mothers were selected in Rafsanjan, Iran, from May 2019 to February 2020. The validity and reliability of the Quality of Prenatal Care Questionnaire- Persian (QPCQ-P) were determined using criterion validity, Cronbach’s alpha, and test-retest reliability. Internal consistency, test-retest reliability, and cross-validation with the Quality of Life-BREF (WHOQOL-BREF) were calculated.Results: The internal consistency of the QPCQ-P is good (α = 0.936) and the item-rest-correlations are fairly good [ICC of 0.476 and confidence interval (CI): 0.20-0.68]. The WHOQOL-BREF and QPCQ-P scores were found to be positively correlated (r = 0.371, p ≤ 0.001). Conclusion: This study demonstrates that the QPCQ-P is a reliable and valid measure for the quality of prenatal care. The QPCQ-P scale can be used to identify appropriate care strategies for pregnant mothers.
Covid-19 Pandemic: A Qualitative Study on Adolescents’ Stress, Anxiety, and Family Communication
Authors: Çetin Zeynep , Ata Samet 
Published: February 2022

Abstract
This study, which included eight adolescents, was planned as a qualitative study on the stress, anxiety and family communication experienced by adolescents during the COVID-19 pandemic. To collect data, this research was conducted in-depth with case-study from qualitative methods, and a questionnaire was carried out through open-ended interviews by taking the opinions of field experts. In this direction, four models were created and an in-depth analysis of the models was made. According to the results, while the COVID-19 pandemic has led to higher levels of stress and anxiety, it has also revealed both positive and negative aspects in the adolescents’ communication with their families. It has been observed that the lack of communication of adolescents’ with their peers because of social isolation may cause negative effects on them.
Construction and validation of a TRP-related long noncoding RNA signature for prognosis prediction in breast cancer patients
Authors: Guo Qiaonan , Qiu Pengjun , Pan Kelun , Chen Jianpeng , Wang Baiwei , Lin Jianqing 
Published: February 2022

Abstract
Background: Breast cancer (BC) is the most diagnosed malignancy in women around the word. Accumulating evidence suggest that transient receptor potential (TRP) channels play significant role in tumor progression and immune cell infiltration. Nevertheless, the relationship between TRP channels and tumor immune microenvironment of BC is still unclear. Hence, we conducted the study to investigate the correlation between TRP-associated lncRNAs and the prognosis of breast carcinoma. Method: 33 TRP-associated genes were selected from a review published by Amrita Samanta et al. and the TRP-related lncRNAs were identified by the Pearson analysis. Based on the sum of the expression levels of 12 lncRNAs, provided by The Cancer Genome Atlas (TCGA), a TRP-associated-lncRNA signature was established by use of Cox regression analysis. According to the median value of risk score in training set, BC patients were separated into high- and low-risk groups. Subsequently, the functional enrichment analysis was conducted in the differential expression genes (DEGs) between different risk groups. The ESTIMATE Score was calculated by ESTIMATE and the immune cell infiltration was evaluated by ssGSEA. Finally, the immune checkpoint genes expression levels, microsatellite instable (MSI) and the immunophenoscore (IPS) were further assessed.Results: The high-risk groups exhibited lower survival rates while the low-risk groups shown higher survival rates. The DEGs between different risk groups were highly enriched in immune cell activation and immunoregulation. Besides, the ESTIMATE scores of patients in low-risk groups were higher than those in high-risk groups. The infiltration levels of several immune cells were remarkably elevated in low-risk groups and various immune signatures were activated with the decreased risk score. Eventually, the TRP-associated lncRNAs signature was confirmed with highly potential ability to evaluate the immunotherapy response in breast carcinoma patients. Conclusion: The outcomes of current study indicated that the 12-TRP-associate-lncRNA risk model was an independent prognostic risk factor for BC patients. This risk model could be closely related to the tumor immune microenvironment in BC. Our findings will provide a new insight for future immunotherapy for BC treatment.