bluuebunny/crossref_metadata_2025_split huggingface dataset:
Psychological Impacts of the COVID-19 Pandemic on Canadian Healthcare Workers
Authors: Turner Brianna J. , Welch Brooke E. , Legg Nicole K. , Phiri Peter , Rathod Shanaya , Paterson Theone S. E. 
Published: June 2023

Objective
The aim of the study is to describe mental health impacts of the COVID-19 pandemic and identify roles that predict distress among Canadian healthcare workers (HCWs).

Methods
Using data from three cross-sectional Canadian surveys, we compared 799 HCWs to demographically matched controls and compared HCWs with and without COVID-19 patient contact. Participants completed validated measures of depression, anxiety, trauma-related stress, alcohol problems, coping self-efficacy, and sleep quality.

Results
Non-HCWs reported more depression and anxiety in Fall 2020 and more alcohol problems in Fall/Winter 2021 than HCWs. In Winter 2020–2021, HCWs reported more trauma-related stress than non-HCWs. As of early 2021, HCWs with direct patient contact reported worse symptoms across nearly all measures than HCWs without.

Conclusions
Although Canadian HCWs did not report worse mental health than demographically similar peers, mental health supports are needed for HCWs providing direct patient care.
Adding Safety Rules to Surgeon-Authored Virtual Reality Training
Authors: Gao Ruiliang , Kurenov Sergei , Black Erik W. , Peters Jörg 
Published: June 2023

Introduction
The Toolkit for Illustration of Procedures in Surgery (TIPS) is an open source virtual reality (VR) laparoscopic simulation-based training environment with force feedback. The TIPS-author is a content creation interface that allows a surgeon educator (SE) to assemble new laparoscopic training modules. New technology enables safety rules to be specified by the SE, automatically tracks specified safety errors, and summarizes and communicates achievements and errors to the surgical trainee.

Methods
The TIPS-author combines and initializes building blocks of anatomy with their physical properties, as selected by the SE from a database. The SE can add any safety rule that can be tested in terms of location, proximity, separation, clip count, and force. Errors are then automatically monitored during simulation and recorded as visual snapshots for feedback to the trainee. The TIPS was field tested at 2 surgical conferences, one before and one after adding the error snapshot feature.

Results
Sixty-four respondents at 2 surgical conferences assessed the utility of TIPS on a Likert scale. While other ratings remained unchanged for an overall score of 5.24 of 7 (7 = very useful), the rating of the statement “The TIPS interface helps learners understand the force necessary to explore the anatomy” improved from 5.04 to 5.35 of 7 after the snapshot mechanism was added.

Conclusions
The ratings indicate the viability of the TIPS open source SE-authored surgical training units with safety rules. Presenting SE-determined procedural missteps via the snapshot mechanism at the end of the training increases perceived utility.
Expansion of a low-cost, saliva-based PCR test for the detection of mpox virus
Authors: Thomas Russell J , Allicock Orchid M. , Yolda-Carr Devyn , Fajardo Katherine , Steel Sydney A. , Blacklock Chessley B. , Zepeda Theresa , Brownlee Maurice , Saladi Shyam , Parkin James , Wyllie Anne L. 
Published: June 2023

ABSTRACTBackgroundCurrent recommendations for the diagnosis of mpox rely on lesion-swabs as the gold-standard specimen type, even though many patients experience symptoms prior to lesion-onset. Alternative sample types, such as saliva, which enable earlier detection could bolster the mpox response by mitigating transmission and facilitating access to antiviral treatments.MethodsWe evaluated five PCR assays and compared their detection of mpox DNA extracted from 30 saliva specimens collected in Spectrum SDNA-1000 tubes. We sequenced seven mpox-positive samples and assessed concordance with the primers and probes of the PCR assays. Following, we incorporated these PCR assays into a simplified, extraction-free protocol to evaluate its feasibility for testing raw (unsupplemented) saliva samples. To further explore the potential of this approach, we investigated the stability of mpox detection in raw saliva diluted 1:10 and 1:100 in mpox-negative saliva, after storage at 4°C, room temperature (∼19°C), 30°C, and 40°C for 72 hours and through simulated shipping conditions.ResultsDespite identifying three nucleotide substitutions in the CDC’s Monkeypox virus Generic Real-Time PCR Test’s primer sequences, we observed no difference in the mean Ct-values generated between assays. We successfully incorporated each assay into our saliva-based extraction-free PCR protocol. Detection in raw saliva following storage at 4°C, ∼19°C, and 30°C remained relatively stable for 24-48 hours and following simulated shipping conditions.ConclusionsThis pilot investigation supports a flexible, saliva-based, extraction-free PCR test as a promising approach for diagnosis, outbreak response or ongoing surveillance of mpox. With detection in raw saliva remaining stable for 24-48 hours and through simulated shipping temperatures, saliva-based sampling and simplified testing could reduce diagnostic costs, increase access to testing and address hurdles in low- and middle-income countries.
Effects of on Low T3 syndrome astrocyte homeostasis in patients with bisphenol A-associated intracerebral hemorrhage
Authors: Wang Guoping , Chen Jinhua , Qiao Zhongdong , Guo Dongxing , Guo Ping , Wang Aiven , Sun Wanli , Lyu Jiyuan 
Published: June 2023

AbstractBackground and PurposeWe aimed to assess sex differences in lipid metabolism disorders in patients with BPA-related intracerebral hemorrhage, as well as changes in β3-adrenoceptors and oxidative stress parameters, and to explore potential mechanisms of intestinal flora on the functional homeostasis of cerebral astrocytes.MethodsHere, a multicenter longitudinal retrospective study was conducted in 200 patients with intracerebral hemorrhage compared with normal controls. Serum thyroid function, blood lipids and subclasses, superoxide dismutase and malondialdehyde were detected. Active oxygen species and reactive oxidative products in brain tissue were detected by fluorescein labeling apparatus. Lipid metabolism and oxidative stress regulate messenger proteins, as well as changes in intestinal flora and astrocyte expression.ResultsSerum lipoprotein β levels of LT3 male patients were significantly increased, with gender differences compared with female patients. β3-adrenergic receptor and Neuregulin –1 expression changes, targeted regulation of fat and reduce oxidative stress response. The increased expression of messenger protein prompts activation of brain astrocytes. The intestinal flora study found that the alpha diversity index in the low T3 group was higher than that in the control group, and Spearman correlation analysis showed that low T3 level was negatively correlated with lipid metabolism disorders and oxidative stress.ConclusionsBisphenol A and oxidative stress were significantly related to the high risk of cerebral hemorrhage. The changes of inflammatory cytokines and the ratio expression of connexin 43/Yes associated proteins in the gut brain axis drive activated astrocytes and microglia to jointly maintain the homeostasis of cerebral vascular microenvironment.Trial registrationThe trial is registered at clinical.gov (www.medresman.ChiCTR1900023626)
Association between Fine Particulate Matter Exposure and Cerebrospinal Fluid Biomarkers of Alzheimer’s Disease among a Cognitively Healthy Population-based Cohort
Authors: Casey Emma , Li Zhenjiang , Liang Donghai , Ebelt Stefanie , Levey Allan I. , Lah James J. , Wingo Thomas S. , Hüls Anke 
Published: June 2023

AbstractBackgroundEpidemiological evidence suggests air pollution adversely affects cognition and increases the risk of Alzheimer’s disease (AD), but little is known about the biological effects of fine particulate matter (PM2.5) on early predictors of future disease risk.ObjectivesWe investigated the association between 1, 3, and 5-year exposure to ambient and traffic-related PM2.5and cerebrospinal fluid (CSF) biomarkers of AD.MethodsWe conducted a cross-sectional analysis using data from 1,113 cognitively healthy adults (aged 45-75 years) from the Emory Healthy Brain Study in Georgia, USA. CSF biomarker concentrations of Aβ42, tTau, and pTau, were collected at enrollment (between 2016-2020) and analyzed with the Roche Elecsys system. Annual ambient and traffic-related residential PM2.5concentrations were estimated at a 1km and 250m resolution, respectively, and 3- and 5-year average exposures were computed for each participant based on time of specimen collection. Associations between PM2.5and CSF biomarker concentrations, considering continuous and dichotomous (dichotomized at clinical cut-offs for AD-biomarker positivity) outcomes, were estimated with multiple linear/logistic regression, respectively, controlling for potential confounders (age, gender, race/ethnicity, body mass index, and neighborhood socioeconomic status).ResultsInterquartile range (IQR; IQR=0.845) increases in 1-year [β: -0.101; 95%-confidence interval (CI): -0.18, -0.02] and 3-year (β: -0.078; 95%-CI: -0.15, -0.00) ambient fine PM2.5exposures were negatively associated with Aβ42CSF concentrations. Associations between ambient PM2.5and Aβ42were similar for 5-year estimates, but not significant (β: -0.076; 95%-CI: -0.160, 0.005). Dichotomized CSF variables revealed similar and significant associations between ambient PM2.5and Aβ42. Associations with traffic-related PM2.5were similar but not significant. PM2.5exposures were not associated with tTau, pTau, tTau/Aβ42, or pTau/Aβ42levels at enrollment.ConclusionIn our cross-sectional study, PM2.5exposure was associated with a significant decrease in CSF Aβ42which suggests an accumulation of amyloid plaques in the brain and an increased risk of developing AD.
Modelling 25-hydroxyvitamin D responses to different recommended daily intakes of vitamin D
Authors: You Tao , Muhamad Nadda , Jenner Joseph , Huang Zhonghui 
Published: June 2023

AbstractThe reference nutrient intake for vitamin D in people aged ≥ 4 years is 10 μg/day in the UK, which contrasts with the recommended daily allowance of 15 μg/day for people aged 1-70 years in the USA. Using modelling of published data, we compared 95% confidence intervals for serum concentrations of 25-hydroxyvitamin D3(25(OH)D3) attained in response to these two doses. 97.5% of those taking 10 μg/day vs. 15 μg/day were predicted to attain circulating 25(OH)D concentrations >44 nmol/L vs. 50 nmol/L, respectively.
Efficient estimation for large-scale linkage disequilibrium patterns of the human genome
Authors: Huang Xin , Zhu Tian-Neng , Liu Ying-Chao , Qi Guo-An , Zhang Jian-Nan , Chen Guo-Bo 
Published: June 2023

AbstractIn this study, we proposed an efficient algorithm (X-LD) for estimating LD patterns for a genomic grid, which can be of inter-chromosomal scale or of small segments. Compared with conventional methods, the proposed method was significantly faster, dropped from 𝒪 (nm2) to 𝒪 (n2m)—nthe sample size andmthe number of SNPs, and consequently we were permitted to explore in depth unknown or reveal long-anticipated LD features of the human genome. Having applied the algorithm for 1000 Genome Project (1KG), we found:I) The extended LD, driven by population structure, was universally existed, and the strength of inter-chromosomal LD was about 10% of their respective intra-chromosomal LD in relatively homogeneous cohorts, such as FIN and to nearly 56% in admixed cohort, such as ASW.II) After splitting each chromosome into upmost more than a half million grids, we elucidated the LD of the HLA region was nearly 42 folders higher than chromosome 6 in CEU and 11.58 in ASW; on chromosome 11, we observed that the LD of its centromere was nearly 94.05 folders higher than chromosome 11 in YRI and 42.73 in ASW.III) We uncovered the long-anticipated inversely proportional linear relationship between the length of a chromosome and the strength of chromosomal LD, and their Pearson’s correlation was on average over 0.80 for 26 1KG cohorts. However, this linear norm was so far perturbed by chromosome 11 given its more completely sequenced centromere region. Uniquely chromosome 8 of ASW was found most deviated from the linear norm than any other autosomes. The proposed algorithm has been realized in C++ (called X-LD) and available athttps://github.com/gc5k/gear2, and can be applied to explore LD features in any sequenced populations.
Identification of a novel HKU4-related coronavirus in single-cell datasets and clade viral host analysis
Authors: Jones Adrian , Massey Steven E. , Nemzer Louis R. , Zhang Daoyu , Deigin Yuri , Quay Steven C. 
Published: June 2023

AbstractHKU4-related coronaviruses (CoVs) are merbecoviruses related to Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV). In 2022 and 2023, two HKU4-related CoV strains were discovered inManis javanica(Malayan pangolin) metagenomic datasets derived from organ samples: HKU4-P251T and MjHKU4r-CoV-1. Together with theTylonycteris robustulabat CoV 162275, which was discovered in 2022, pangolin CoVs HKU4-P251T and MjHKU4r-CoV-1 form a novel phylogenetic clade distinct from all previously documented HKU4-related CoVs. In this study, we identified a novel HKU4-related CoV in a pangolin single-cell sequencing dataset generated by BGI-Shenzhen in Shenzhen, Guangdong, China in 2020. The CoV phylogenetically belongs to the same newly identified clade. The single cell datasets were reported as generated from organ samples of a single pangolin that died of natural causes. 98% of the HKU4-related CoV reads were found in only one of the seven single cell datasets — a large intestine cell dataset, cells of which exhibit low expression of DPP4. Bacterial contamination was found to be moderately correlated with HKU4-related CoV presence. We further identified with high confidence that the RNA-Seq dataset supporting one of four near identical variants of MjHKU4r-CoV-1 is aSus scrofa(wild pig) metagenomic dataset, with only a trace level ofManis javanicagenomic content. The presence of HKU4-related CoV reads in the dataset are almost certainly laboratory research-related and not from a premortal pangolin or pig infection. Our findings raise concerns about the provenance of the novel HKU4-related CoV we identify here, MjHKU4r-CoV-1 and its four near-identical variants.
Predictors of Intense Treatment in the Emergency Department Among Older Adults With Serious Life-Limiting Illnesses: A Five-Year Cross-sectional Analysis of Medicare Claims Data
Authors: Adeyemi Oluwaseun , Siman Nina , Goldfeld Keith , Hill Jacob , Cuthel Allison , DiMaggio Charles , Chodosh Joshua , Grudzen Corita 
Published: June 2023

AbstractBackgroundTreatment intensity of end-of-life care is the degree of aggressiveness of medical care aimed at providing life-prolonging medical care to patients with serious life-limiting illnesses. This study aims to assess the demographic and health characteristics associated with older adults with serious life-limiting illnesses who received highly intense end-of-life care.MethodsFor this cross-sectional analysis, we pooled the 2015 to 2019 Medicare claims data of adults 65 years and older who visited at least one of the 29 emergency departments (EDs) enrolled in the Primary Palliative Care for Emergency Medicine. We identified those with serious life-limiting illnesses using a Gagne score of seven or higher. Our outcome measure was treatment intensity, defined using acute care and intensive care unit (ICU) admissions. Acute care admission was measured as a binary variable and ICU admission was measured as a three-point nominal variable. The predictor variables were age, sex, race/ethnicity, and illness severity (Gagne score). To assess the odds of acute care and ICU admissions, we used a generalized estimating equation model and a multinomial regression model, respectively. We performed the same analyses among the population without serious life-limiting illnesses to observe differences in effect sizes of intense treatment.ResultsOf the 301,083 older adults that visited one of the 29 EDs, 13% had serious life-limiting illnesses. Age was associated with 9% and 7% increased odds of acute care (95% CI: 1.04 – 1.14) and ICU (95% CI: 1.02 – 1.12) admissions. We reported significant associations by sex, race/ethnicity, and illness severity (Gagne score). The effect sizes of the observed association between measures of treatment intensity and the demographic and health characteristics were smaller among those with serious life-limiting illnesses compared to those without serious life-limiting illnesses.ConclusionOlder adults with serious life-limiting illnesses who present to the ED experience intense treatment. Identifying demographic and health characteristics associated with treatment intensity may inform the need for serious illness conversations in the ED.
Diagnostic Accuracy and Risk Stratification of a Trauma Risk Assessment Tool Among those with Fall Injuries
Authors: Adeyemi Oluwaseun John , Konda Sanjit , DiMaggio Charles , Grudzen Corita R. , Pfaff Ashley , Esper Garrett , Arcila-Mesa Mauricio , Cuthel Allison M. , Poracky Helen , Meyman Polina , Wittman Ian , Chodosh Joshua 
Published: June 2023

AbstractAimThe Score for Trauma Triage in the Geriatric and Middle-Aged (STTGMA) is an injury risk-triage tool. This study aims to validate the STTGMA’s accuracy in predicting fall-related mortality among geriatric trauma patients.MethodsUsing a retrospective cohort design, we selected 5,791 geriatric trauma patients (aged 55 years and older) from a single institutional trauma database (2017-2021). The outcome variable was fatal fall injury, measured as a binary variable. The predictor variable was the STTGMA score, measured as a continuous variable and a four-level categorical variable. We report the predictive accuracy (95% confidence interval (CI)) of the STTGMA. We further assessed the relationship between the STTGMA risk categories and hospital length of stay and time-to-death by performing multivariable quantile regression and time-varying Cox proportional hazard analyses, respectively.ResultsA total of 122 patients (2.1%) died during admission and the median hospital length of stay was 2 days. STTGMA exhibited 84% (95% CI: 75.6 – 92.0) accuracy in predicting in-hospital fall-related mortality. Compared to the minimal risk category, geriatric trauma patients classified as low, moderate, and high risks each had significantly longer hospital stays and adjusted mortality risks, in a dose-response pattern.ConclusionSTTGMA can accurately predict in-hospital mortality and risk-stratify the length of stay and the time to death among geriatric patients with fall injuries.
Characterization of copy number alterations in Pakistani patients with colorectal cancer
Authors: Marcinak Clayton T. , McDonald Bradon R. , Zubairi Hina , Siddique Sabeehuddin , Stephens Michelle D. , Moosajee Munira , Ahmed Rashida , Zafar Syed Nabeel , Murtaza Muhammed , Ghias Kulsoom 
Published: June 2023

AbstractPurposeIncidence and mortality rates of colorectal cancer (CRC) in South Asia are expected to rise by 70% between 2020 and 2040. Despite recent advances in the understanding of molecular alterations in CRC, the representation of South Asians in published genomic datasets is very limited. To address this gap, we performed a pilot study based on a transnational collaboration between academic centers in the US and Pakistan to characterize copy number alterations in a Pakistani cohort with CRC.MethodsWe obtained archived formalin-fixed paraffin-embedded (FFPE) tissue samples from 43 CRC patients treated at Aga Khan University (AKU) Hospital. DNA was extracted and evaluated for quality at AKU, and whole genome sequencing library preparation and shallow whole genome sequencing was performed at University of Wisconsin–Madison. Sequencing data was aligned to the human genome, and we used ichorCNA and GISTIC2 to determine relative copy number alterations.ResultsAfter removing 13 samples with insufficient DNA quality or quantity, tumor sequencing data was analyzed from 30 patients. The cohort consisted of 19 (63.3%) males with a mean age of 50.1 years and standard deviation (SD) of 17.8 years. Twenty-one (70.0%) patients had tumor stage T3 or T4, and 15 (50.0%) had tumors of the colon. A mean of 265 ng (SD, 29 ng) of DNA was extracted from each FFPE tumor sample, and each sample was sequenced to a mean depth of 0.22× (0.21×). Analysis of copy number alterations revealed recurrent gains in regions 8q and 13q, as well as losses in region 8p.ConclusionsThis transnational pilot study helped identify the challenges related to FFPE sample quality that can impede similar efforts in the future. Our results revealed similarities in the most common copy number alterations in CRC identified in native Pakistani patients and published datasets.
Prevalence of Bicuspid Aortic Valve: Systematic Review and Meta-Analysis of Prevalence Studies
Authors: Lester G D. , Jeremy R W. 
Published: June 2023

AbstractBicuspid aortic valve (BAV) is frequently reported as the most common congenital cardiac condition, with 1-2% prevalence by citing one or two autopsy studies performed up to forty years ago. Since then, echocardiography population screening studies have reported contemporaneous results, with lower prevalence, given the absence of autopsy selection bias. Therefore, we performed a systematic review and meta-analysis of autopsy and echocardiography studies to provide a more accurate synthesis of BAV prevalence. Following a systematic literature review, we performed a meta-analysis of prevalence studies using MetaXL Software Version 5.3 by EpiGear, St Lucia, Australia. The results of 45,630 autopsy patients reveal a prevalence of 0.81% (0.5-1.2%, p<0.001, n=444) and 296,245 echocardiography screened population of 0.61% (0.39-0.82% p<0.001, n=1,392) BAV prevalence. The average prevalence of 0.61-0.81% between the two studies still shows this is a common congenital cardiac condition, but shows it is less than frequently reported and thus robustly supports the case of cost effectiveness in screening first degree relatives.