bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why were Twitter Users Obsessed with Vitamin D during the first year of the pandemic?
Authors: Mavroeidi Alexandra , Innes Ryan , Miyake Esperanza , Pennington Diane 
Published: April 2022

AbstractThe aim of this study was to explore how the relationship between vitamin D and COVID-19 has been represented on the social media site Twitter. NCapture was used to collect textual Tweets on a weekly basis for three months during the pandemic. In total, 21,140 Tweets containing the keywords “vitamin D” and “COVID” were collected and imported to NVivo12. An inductive thematic analysis was carried out on the Tweets collected on the first (12/2/2021) and last week (21/5/2021) of the recording period to identify themes and subthemes. Quality control of the coding was conducted on a sample of the dataset (20%). Data were also compared to the “ground truth” to explore the accuracy of media outputs. The four main themes identified were “association of vitamin D with COVID-19”, “politically informed views”, “vitamin D deficiency” and “vitamin D sources”. When compared to the ground truth, the majority of information relating to the key findings was ‘incorrect’ for all of the findings. This study contributes to the area of research by highlighting the extent of the issue social media sites face with health-related misinformation. In the context of COVID-19, it is important that sites such as Twitter improve their existing misinformation policies, as misinformation can be detrimental in disease prevention.
How did the COVID-19 Pandemic impact self-reported cancer screening rates in 12 Midwestern states?
Authors: Semprini Jason 
Published: April 2022

AbstractObjectiveIn the early months of the COVID-19 pandemic, the U.S. healthcare system reallocated resources to emergency response and mitigation. This reallocation impacted essential healthcare services, including cancer screenings.MethodsTo examine how the pandemic impacted cancer screenings at the population-level, this study analyzes 2018 and 2020 Behavioral Risk Factor Surveillance System (BRFSS) data to estimate the change in the proportion of eligible adults reporting a recent cancer screen (mammogram, pap smear, colon/sigmoidoscopy, blood stool test). All analyses accounted for response rates and sampling weights, and explored differences by gender and region across 12 Midwestern states.ResultsWe found that the proportion of adult women completing a mammogram declined across all states (−0.9% to -18.1%). The change in colon/sigmoidoscopies, pap smears, and blood stool tests were mixed, ranging from a 9.7% decline in pap smears to a 7.1% increase in blood stool tests. Declines varied considerably between states and within states by gender or metro/urban/rural status.ConclusionsThe COVID-19 pandemic led to delayed breast, cervical, and colorectal cancer detection services. Policymakers should aim to advance cancer control efforts by implementing targeted screening initiatives.
Functional Magnetic Resonance Imaging of the amygdala and subregions at 3 Tesla: A scoping review protocol
Authors: Foster Sheryl L. , Breukelaar Isabella A. , Ekanayake Kanchana , Lewis Sarah , Korgaonkar Mayuresh S. 
Published: April 2022

AbstractBackgroundFunctional Magnetic Resonance Imaging (fMRI) is a widely accepted and utilised method of investigating neural activation within the brain. There has been increasing awareness and understanding in the field of neuropsychology over the last 10-15 years that the amygdala plays an important role in many mental health conditions. Functional connectivity (FC) of the amygdala with other parts of the brain is well-documented in the literature; however the role of the amygdala and its reported connections is still not well understood and this can be attributed, in part, to its very small size. It is challenging to achieve adequate spatial resolution to visualise amygdala activation using 3T MRI systems that are in widespread use for this type of clinical research. Optimisation of protocols for improved data accuracy and reproducibility may potentially lead to standardisation and subsequent advancements in overall image quality in this field.MethodsThe protocol for this scoping review was developed in line with the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) and registered with the Open Science Framework (OSF). A literature search of five databases (Medline, Embase, Web of Science, Google Scholar and Scopus) will be undertaken using a refined search strategy; peer-reviewed publications identified as being relevant will then be imported into Covidence software for abstract screening and data extraction by two reviewers working independently. The quantitative findings will be tabulated to provide an overview of the current methodologies for comparison. This will be accompanied by a narrative report summarising the extracted data in relation to the stated research questions.DiscussionThe objective of this scoping review is to identify and map the range of existing protocols used in fMRI for imaging the activation and FC patterns of the amygdala at 3 Tesla. This will be achieved by collating and presenting quantitative data relating to protocol parameter choices as well as other qualitative aspects of the data acquisition process.RegistrationOpen Science Framework (OSF) – Registration type: OSF Pre-registrationRegistration: https://osf.io/e3c28, DOI: 10.17605/OSF.IO/KW58P
Comprehensive analyses reveal the impacts of vaccination status and physiological variables in early infection on viral persistence in COVID-19 patients: a retrospective single-center cohort study
Authors: Tian Xiangxiang , Zhang Yifan , Wang Wanhai , Fang Fang , Zhang Wenhong , Wan Yanmin , Zhu Zhaoqin 
Published: April 2022

AbstractBACKGROUNDViral persistence is a crucial factor that influences the communicability of SARS-CoV-2 infection. However, the impacts of vaccination status and physiological variables on viral RNA shedding have not been adequately clarified.METHODSIn this study, we retrospectively collected the clinical records of 377 hospitalized COVID-19 patients, which contained unvaccinated patients and patients received two doses of an inactivated vaccine or an mRNA vaccine. Firstly, we analyzed the impacts of vaccination on disease severity and viral RNA persistence. Next, to clarify the impacts of physiological variables on viral RNA shedding in COVID-19 patients, we retrieved 49 laboratory variables and analyzed their correlations with the duration of viral RNA shedding. Finally, we established a multivariate regression model to predict the duration of viral RNA shedding.RESULTSOur results showed that both inactivated and mRNA vaccines significantly reduced the rate of moderate cases, while the vaccine related shortening of viral RNA shedding were only observed in moderate patients. Correlation analysis showed that 10 significant laboratory variables were shared by the unvaccinated mild patients and mild patients inoculated with an inactivated vaccine, but not by the mild patients inoculated with an mRNA vaccine. Moreover, we demonstrated that a multivariate regression model established based on the variables correlating with viral persistence in unvaccinated mild patients could predict the duration of viral shedding for all groups of patients.CONCLUSIONSVaccination contributed limitedly to the clearance viral RNA in COVID-19 patients. While, laboratory variables in early infection could predict the persistence of viral RNA.
The Cerebellum Plays More Than One Role in the Dysregulation of Appetite: Review of Structural Evidence from Typical and Eating Disorder Populations
Authors: Sader Michelle , Waiter Gordon D. , Williams Justin H. G. 
Published: April 2022

AbstractObjectiveDysregulated appetite control is characteristic of anorexia nervosa (AN), bulimia nervosa (BN) and obesity (OB). Studies using a broad range of methods suggest the cerebellum plays an important role in aspects of weight and appetite control, and is implicated in both AN and OB by reports of aberrant grey matter volume (GMV) compared to non-clinical populations. As functions of the cerebellum are anatomically segregated, specific localization of aberrant anatomy may indicate the mechanisms of its relationship with weight and appetite in different states. We sought to determine if there were consistencies in regions of cerebellar GMV changes in AN/BN and OB, as well as across normative variation.MethodSystematic review and meta-analysis using GingerALE.ResultsTwenty-six publications were identified as either case-control studies (nOB=277; nAN/BN=510) or regressed weight from normative (NOR) data against brain volume (total n=3,830). AN/BN and OB analyses both showed consistently decreased GMV within Crus I and Lobule VI, but volume reduction was bilateral for AN/BN and unilateral for OB. Analysis of the normative dataset identified a cluster in right posterior lobe which overlapped with AN/BN cerebellar reduction. Sensitivity analyses indicated robust repeatability for NOR and AN/BN cohorts, but found OB-specific heterogeneity.DiscussionFindings suggest that more than one area of the cerebellum is involved in control of eating behaviour and is differentially affected in normal variation and pathological conditions. Specifically, we hypothesise an association with sensorimotor and emotional learning via Lobule VI in AN/BN, and executive function via Crus I in OB.
Effectiveness of a Fourth Dose of COVID-19 Vaccine among Long-Term Care Residents in Ontario, Canada: Test-Negative Design Study
Authors: Grewal Ramandip , Kitchen Sophie A , Nguyen Lena , Buchan Sarah A , Wilson Sarah E , Costa Andrew P , Kwong Jeffrey C 
Published: April 2022

AbstractBackgroundAs of December 30, 2021, Ontario long-term care (LTC) residents who received a third dose of COVID-19 vaccine ≥84 days previously were offered a fourth dose to prevent a surge in COVID-19-related morbidity and mortality due to the Omicron variant.MethodsWe used a test-negative design and linked databases to estimate the marginal effectiveness (4 versus 3 doses) and vaccine effectiveness (VE; 2, 3, or 4 doses versus no doses) of mRNA vaccines among Ontario LTC residents aged ≥60 years who were tested for SARS-CoV-2 between December 30, 2021 and April 27, 2022. Outcome measures included any Omicron infection, symptomatic infection, and severe outcomes (hospitalization or death).ResultsWe included 13,654 Omicron cases and 205,862 test-negative controls. The marginal effectiveness of a fourth dose (with 95% of fourth dose vaccine recipients receiving mRNA-1273) ≥7 days after vaccination versus a third dose received ≥84 days prior was 19% (95% Confidence Interval [CI], 12-26%) against infection, 31% (95%CI, 20-41%) against symptomatic infection, and 40% (95%CI, 24-52%) against severe outcomes. VE (compared to an unvaccinated group) increased with each additional dose, and for a fourth dose was 49% (95%CI, 43-54%), 69% (95%CI, 61-76%), and 86% (95%CI, 81-90%), against infection, symptomatic infection, and severe outcomes, respectively.ConclusionsOur findings suggest that compared to a third dose received ≥84 days ago, a fourth dose improved protection against infection, symptomatic infection, and severe outcomes caused by Omicron among long-term care residents. Compared to unvaccinated individuals, fourth doses provide strong protection against severe outcomes, but the duration of protection remains unknown.
Urinary tract infections in children: building a causal model-based decision support tool for diagnosis with domain knowledge and prospective data
Authors: Ramsay Jessica A. , Mascaro Steven , Campbell Anita J. , Foley David , Mace Ariel O. , Ingram Paul , Borland Meredith L. , Blyth Christopher , Larkins Nicholas G. , Robertson Tim , Williams Phoebe , Snelling Tom , Wu Yue 
Published: April 2022

AbstractBackgroundDiagnosing urinary tract infections (UTIs) in children in the emergency department (ED) is challenging due to the variable clinical presentations and difficulties in obtaining a urine sample free from contamination. Clinicians need to weigh a range of observations to make timely diagnostic and management decisions, a difficult task to achieve without support due to the complex interactions among relevant factors. Directed acyclic graphs (DAG) and causal Bayesian networks (BN) offer a way to explicitly outline the underlying disease, contamination and diagnostic processes, and to further make quantitative inference on the event of interest thus serving as a tool for decision support.MethodsWe prospectively collected data on children present to ED with suspected UTIs. Through knowledge elicitation workshops and one-on-one meetings, a DAG was co-developed with domain experts (the Expert DAG) to describe the causal relationships among variables relevant to paediatric UTIs. The Expert DAG was combined with prospective data and further domain knowledge to inform the development of an application-oriented BN (the Applied BN), designed to support the diagnosis of UTI. We assessed the performance of the Applied BN using quantitative and qualitative methods.ResultsWe summarised patient background, clinical and laboratory characteristics of 431 episodes of suspected UTIs enrolled from May 2019 to November 2020. The Expert DAG was presented with a narrative description, elucidating how infection, specimen contamination and management pathways causally interact to form the complex picture of paediatric UTIs. Parameterised using prospective data and expert-elicited parameters, the Applied BN achieved an excellent and stable performance in predicting E.coli culture results, with a mean AUROC of 0.86 and a mean log loss of 0.48 based on 10-fold cross-validation. The BN predictions were reviewed via a validation workshop, and we illustrate how they can be presented for decision support using three hypothetical clinical scenarios.ConclusionCausal BNs created from both expert knowledge and data can integrate case-specific information to provide individual decision support during the diagnosis of paediatric UTIs in ED. The model aids the interpretation of culture results and the diagnosis of UTIs, promising the prospect of improved patient care and judicious use of antibiotics.
Clonal diversity determines persistence of SARS-CoV-2 epitope-specific T cell response
Authors: Zornikova Ksenia V. , Khmelevskaya Alexandra , Sheetikov Savely A. , Kiryukhin Dmitry O. , Shcherbakova Olga V. , Titov Aleksei , Zvyagin Ivan V. , Efimov Grigory A. 
Published: April 2022

AbstractT cells play a pivotal role in reducing disease severity during SARS-CoV-2 infection and formation of long-term immune memory. We studied 50 COVID-19 convalescent patients and found that T cell response was induced more frequently and persisted longer than circulating antibodies. To identify epitopes that give rise to long-lived T cell memory, we performed ex vivo T cell expansion, MHC-tetramer cell-sorting, and high-throughput sequencing. We identified 756 clonotypes specific to nine known CD8+ T cell receptor (TCR) epitopes. Some epitopes were recognized by highly similar public clonotypes with restricted variable and joining segment usage. Receptors for other epitopes were extremely diverse, suggesting alternative modes of recognition. We also tracked persistence of epitope-specific response and individual clonotypes for a median of eight months after infection. The number of recognized epitopes per patient and quantity of epitope-specific clonotypes decreased over time, but the studied epitopes were characterized by uneven decline in the number of specific T cells. Epitopes with more clonally diverse TCR repertoires induced more pronounced and durable responses. In contrast, the abundance of specific clonotypes in peripheral circulation had no influence on their persistence. Our study demonstrates the durability of SARS-CoV-2-specific CD8+ memory, and offers important implications for vaccine design.
A comparative analysis of pediatric mental health-related emergency department utilization in Montréal, Canada before and during the COVID-19 pandemic
Authors: Beaudry Gabrielle , Drouin Olivier , Gravel Jocelyn , Smyrnova Anna , Bender Andreas , Orri Massimiliano , Geoffroy Marie-Claude , Chadi Nicholas 
Published: April 2022

ABSTRACTBackgroundReports on longitudinal trends in mental health–related (MHR) emergency department (ED) utilization spanning the pre- and post-pandemic periods are lacking, along with evidence comparing healthcare services utilization by sociodemographic subgroups. The aim of this study was to evaluate COVID-19–associated changes in MHR ED utilization among youth overall and by age, sex, and socioeconomic status (SES).MethodsThis retrospective cross-sectional study analyzed MHR ED utilization before and during the COVID-19 pandemic at a large urban pediatric tertiary care hospital in Montréal, Canada. All ED visits for children (5–11 years) and adolescents (12–17 years) between April 1, 2016 and November 30, 2021 were included. The main outcome was the monthly count of MHR ED visits. Pre-pandemic and pandemic periods were compared using an interrupted time series design. The effect of seasonality (in months), age (in years), sex (male or female), and SES (low, average, high) were compared using a generalized additive model.ResultsThere were a total of 437,147 ED visits (204,215 unique patients) during the five-year study period of which 9,748 (5.8%) were MHR visits (7,686 unique patients). We observed an increase of 69% (95% CI, +53% to +85%; p = .001) in the mean monthly count of MHR ED visits during the pandemic period, which remained significant after adjusting for seasonality (44% increase, 95% CI, +38% to +51%; p = .001). The chance of presenting for a MHR ED visit increased non-linearly with age. There were increased odds of presenting for a MHR ED visit among girls between the pre-pandemic and pandemic periods (OR 1.42, 95% CI 1.29–1.56). No difference by SES group during and before the COVID-19 pandemic was found (OR 1.01, 95% CI 0.89–1.15 [low]; OR 1.09, 95% CI 0.96–1.25 [high]).ConclusionsOur study shows important increases in MHR ED utilization among youth, and especially among girls, during the first 20 months of the COVID-19 pandemic, highlighting the need for sustained, targeted and scalable mental health resources to support youth mental health during the current and future crises.
Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes
Authors: Ghiaci Payam , Jouhten Paula , Martyushenko Nikolay , Roca-Mesa Helena , Vázquez Jennifer , Konstantinidis Dimitrios , Stenberg Simon , Andrejev Sergej , Grkovska Kristina , Mas Albert , Beltran Gemma , Almaas Eivind , Patil Kiran R. , Warringer Jonas 
Published: April 2022

ABSTRACTAdaptive Laboratory Evolution (ALE) of microbes can improve the efficiency of sustainable industrial processes important to the global economy, but chance and genetic background effects often lead to suboptimal outcomes. Here we report an ALE platform to circumvent these flaws through parallelized clonal evolution at an unprecedented scale. Using this platform, we clonally evolved 10^4 yeast populations in parallel from many strains for eight desired wine production traits. Expansions of both ALE replicates and lineage numbers broadened the evolutionary search spectrum and increased the chances of evolving improved wine yeasts unencumbered by unwanted side effects. ALE gains often coincided with distinct aneuploidies and the emergence of semi-predictable side effects that were characteristic of each selection niche. Many high performing ALE strains retained their desired traits upon transfer to industrial conditions and produced high quality wine. Overall, our ALE platform brings evolutionary engineering into the realm of high throughput science and opens opportunities for rapidly optimizing microbes for use in many industrial sectors which otherwise could take many years to accomplish.
US-align: Universal Structure Alignments of Proteins, Nucleic Acids, and Macromolecular Complexes
Authors: Zhang Chengxin , Shine Morgan , Pyle Anna Marie , Zhang Yang 
Published: April 2022

AbstractStructure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules (proteins, RNAs, and DNAs). The pipeline is built on a uniform TM-score objective function coupled with a heuristic alignment searching algorithm. Large-scale benchmarks demonstrated significant advantages of US-align over state-of-the-art methods in pairwise and multiple structure alignments of different molecules. Detailed analyses showed that the major advantage of US-align lies in the extensive optimization of the unified objective function powered by efficient heuristic search iterations, which significantly improve the accuracy and speed of the structural alignment process. Meanwhile, the universal protocol fusing different molecular and structural types helps facilitate the heterogeneous oligomer structure comparison and template-based protein-protein and protein-RNA/DNA docking.
Roles of Clamp Closing and Allosteric Effects of Discriminator and Upstream Interactions on Downstream Elements in Stabilizing an E. coli RNA Polymerase-Promoter Open Complex
Authors: Wang Hao-Che , Stronek Krysta , Record M. Thomas 
Published: April 2022

AbstractE. coli RNA polymerase (α2ββ’ωσ70) forms stable open complexes (OC) at λPR and T7A1 promoters at 37 °C at similar rates but with very different lifetimes. To probe the origins of these differences, we determine OC lifetimes for full-length (FL) and downstream-truncated (DT) λPR and T7A1 promoter variants with eight combinations of discriminators and upstream elements. We find the discriminator is the major determinant of OC lifetime, while upstream elements modulate the discriminator effect. The very different lifetimes of these stable OC arise primarily from differences in , the free energy change for converting I2 (the initial open intermediate) to stable OC. is twice as favorable for λPR-discriminator variants as for T7A1-discriminator variants. Truncation at +6 (DT+6) eliminates most differences in , destabilizing λPR-discriminator variants without affecting T7A1-discriminator variants. All DT+6 OC are much more stable and longer-lived than I2. Urea greatly destabilizes OC, primarily affecting RNAP interactions with +6 and upstream DNA. From these findings we deduce that stabilization of I2 involves closing the β’-clamp with extensive coupled folding to contact the region of promoter DNA from the transcription start-site to +6. Lifetime differences between DT+6, DT+12 and FL promoters allow dissection of contributions to OC stability from interactions of regions of the downstream duplex with downstream mobile elements (DME; β-lobe, β’–clamp, β’-jaw). We propose an allosteric network by which differences in discriminator and −10 sequence are sensed by σ1.2 and β-gate loop and transmitted to σ1.1 and β-lobe to affect DME-duplex interactions that determine OC lifetime.