bluuebunny/crossref_metadata_2025_split huggingface dataset:
Covaxin (BBV152) Vaccine Neutralizes SARS-CoV-2 Delta and Omicron variants
Authors: Edara Venkata-Viswanadh , Patel Mit , Suthar Mehul S. 
Published: January 2022

AbstractThe SARS-CoV-2 vaccine BBV152/Covaxin is well-tolerated and was shown to be 77.8% efficacious against symptomatic and 93.4% efficacious against severe symptomatic COVID-19 disease in adults. Previous studies have shown that sera from Covaxin vaccinated individuals have neutralizing activity against B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), B.1.1.28 (Zeta), and B.1.617.1 (Kappa) SARS-CoV-2 variants. The B.1.1.529 variant (Omicron) recently emerged in November 2021 and has spread throughout the world. The Omicron variant has more than 30 mutations within the spike protein that could impact vaccine-mediated immunity. We used a live virus neutralization assay to evaluate the neutralizing activity against the Omicron variant of sera collected from subjects who received a booster dose (6-month after primary series last dose) of Covaxin. We found that sera from Covaxin boosted individuals showed neutralizing activity against D614G (vaccine strain), Delta, and Omicron variants. One hundred percent of boosted subjects showed neutralizing activity against the Delta variant while over 90% of boosted subjects showed neutralizing activity against the Omicron variant. These findings show that a booster dose of Covaxin can generate robust neutralizing antibody responses against the Omicron variant.
TreatmentPatterns: An R package to analyze treatment patterns of a study population of interest
Authors: Markus Aniek F. , Verhamme Katia M.C. , Kors Jan A. , Rijnbeek Peter R. 
Published: January 2022

ABSTRACTBackground and objectivesThere is an increasing interest to use real-world data to illustrate how patients with specific medical conditions are treated in real life. Insight in the current treatment practices helps to improve and tailor patient care. We aim to provide an easy tool to support the development and analysis of treatment pathways for a wide variety of medical conditions.MethodsWe formally defined the process of constructing treatment pathways and developed an open-source R package TreatmentPatterns (https://github.com/mi-erasmusmc/TreatmentPatterns) to enable a reproducible and timely analysis of treatment patterns.ResultsThe developed package supports the analysis of treatment patterns of specific populations of interest. We demonstrate the functionality of the package by analyzing the treatment patterns of three common chronic diseases (type II diabetes mellitus, hypertension, and depression) in the Dutch Integrated Primary Care Information (IPCI) database.ConclusionTreatmentPatterns is a tool to make the analysis of treatment patterns more accessible, more standardized, and more interpretation friendly. This tool can facilitate and contribute to the accumulation of knowledge on real-world treatment patterns across disease domains. We encourage researchers to further adjust and add custom analysis to the package based on their research needs.
SPATIAL HETEROGENEITY OF NEIGHBORHOOD-LEVEL WATER AND SANITATION ACCESS IN INFORMAL URBAN SETTLEMENTS: A CROSS-SECTIONAL CASE STUDY IN BEIRA, MOZAMBIQUE
Authors: Victor Courtney , Ocasio Denisse Vega , Cumbe Zaida A. , Garn Joshua V. , Hubbard Sydney , Mangamela Magalhaes , McGunegill Sandy , Nalá Rassul , Snyder Jedidiah S. , Levy Karen , Freeman Matthew C 
Published: January 2022

AbstractRapid urbanization, resulting in population growth within informal settlements, has worsened exclusion and inequality in access to water and sanitation (WASH) services in the poorest and most marginalized communities. In this study, we describe the heterogeneity in water service satisfaction and WASH access in low-income, peri-urban neighborhoods of Beira, Mozambique, and examine whether this heterogeneity can be explained by distance to water distribution mains. Using spatial statistics and regression analyses, we identified statistical spatial heterogeneity in household WASH access, as well as consumer-reported satisfaction with water services (services, pressure, quality, and sufficient quantity). We found that as distance from the water main increased, both access to an improved water source at the household and satisfaction with water pressure decreased, controlling for household density and socioeconomic status. The odds of a household having access to a water source at the household or on the compound decreased with every 100-meter increase in distance from a water main pipe (odds ratio [OR] 0.87, 95% confidence interval [CI]: 0.82, 0.92). Satisfaction with water services also decreased with every 100-meter increase in distance from a water main pipe (OR: 0.80; 95% CI: 0.69, 0.94). Findings from this study highlight the unequal household access to water and sanitation in urban informal settlements, even within low-income neighborhoods. Describing this heterogeneity of access to water services, sanitation, and satisfaction – and the factors influencing them - can inform stakeholders and guide the development of infrastructural solutions to reduce water access inequities within urban settings.
A longitudinal seroconversion panel shows anti-SARS-CoV-2 antibody levels up to 6.5 months after vaccination with mRNA-1273 (Moderna)
Authors: Belda Francisco , Mora Oscar , Christie Rebecca , Crowley Michael 
Published: January 2022

AbstractBackgroundVaccines have emerged as a crucial tool in combatting the COVID-19 pandemic particularly those based on SARS-CoV-2 S-protein mRNA. A crucial aspect of vaccine efficacy is the duration of antibody responses. In this study, a seroconversion panel was created to assess antibody responses to the mRNA-1273 vaccine over time (6.5 months).MethodsBlood samples collected from 15 healthy adult participants prior to and up to 6.5 months after vaccination with the mRNA-1273 vaccine (Moderna). Serum from these blood samples were analyzed for anti-SARS-CoV-2 antibody activity by chemiluminescent immunoassay.ResultsThe immunoassay results showed that one participant was positive for anti-SARS-CoV- 2 antibodies prior to vaccination indicating a prior infection. All participants showed a positive antibody response after the first vaccination. Highest antibody responses were seen after the second dose (41-45 days from the first dose). Subsequent samples collected at 69-75 days, 130-135 days and 221-229 days after the first vaccination showed positive responses but declining levels of anti-SARS-CoV-2 antibodies.ConclusionsDeclining antibody levels in these participants support the use of booster vaccination to increase antibody levels 4-6 months after the initial vaccine series and continued monitoring to assess the durability of COVID-19 vaccine responses. These results are in agreement with other studies showing antibody persistence but declining the antibody levels in the months after immunization with mRNA-based vaccines.
Automatic Identification of Tinnitus Malingering Based on Overt and Covert Behavioral Responses During Psychoacoustic Testing
Authors: Smalt Christopher J. , Sugai Jenna A. , Koops Elouise , Jahn Kelly N. , Hancock Kenneth E. , Polley Daniel B. 
Published: January 2022

AbstractTinnitus, or ringing in the ears, is a prevalent condition that imposes a substantial health and financial burden on the patient and to society. The diagnosis of tinnitus, like pain, relies on patient self-report. Subjective self-report measures can complicate the distinction between actual and fraudulent claims and obscure accurate severity assessments. In this study, we combined tablet-based self-directed hearing assessments with neural network classifiers to objectively determine tinnitus severity, and to differentiate participants with tinnitus (N=24) from a malingering cohort, who were instructed to feign an imagined tinnitus percept (N=28). We identified clear differences between the groups, both in their overt rating of tinnitus severity but also covert differences in their fingertip movement trajectories on the tablet surface as they performed the reporting assay. Using only 10 minutes of data, we achieved 81% accuracy classifying patients vs malingerers (ROC AUC=0.88) with leave-one-participant-out cross validation. Objective measurements of tinnitus will improve estimates of tinnitus prevalence and help to prioritize and direct funds for tinnitus compensation.
Frequency of neutropenia over time in patients on clozapine
Authors: Govind Risha , Jewell Amelia , Whiskey Eromona , Gee Siobhan , Oloyede Ebenezer , Taylor David , MacCabe James H. 
Published: January 2022

ABSTRACTBackgroundClozapine, the only evidence-based drug for treatment-resistant schizophrenia is associated with agranulocytosis. For this reason, all clozapine patients are required to undergo mandatory regular blood monitoring throughout their clozapine treatment. The blood test results are reported using a traffic light system. The clozapine treatment is stopped immediately after a confirmed red result, which is the indication for risk of agranulocytosis. The need for blood tests places a burden on patients and acts as a barrier to clozapine treatment. There is growing evidence that the risk of agranulocytosis falls steeply after the first few months of treatment, raising the possibility that clozapine monitoring could be discontinued after a certain period of treatment.AimTo investigate the frequency density of the confirmed red results from clozapine monitoring across clozapine treatment.MethodBy merging electronic health records (EHR) data with clozapine blood monitoring data, we identified the clozapine treatment dates. The EHR data was from South London and Maudsley NHS Foundation Trust (SLAM). The clozapine blood monitoring data was from Zaponex Treatment Access System (ZTAS). ZTAS is one of the mandatory blood monitoring service providers in the United Kingdom. From these data, Kaplan-Meier survival curve was fitted to determine the time to get confirmed red results. At fixed points in the treatment, the future risk of obtaining a red result were calculated.ResultsBy merging over 301,000 data points that came from the blood monitoring results and EHR data of 1,362 patients, we identified 1,891 clozapine treatment periods. Of these, 75 treatments were stopped due to confirmed red results. The Kaplan-Meier survival curve and the incidence rates data showed that 56 (74.7%) confirmed red results occur within the first 6 months of clozapine treatment.ConclusionWe found a contrast between the relatively high density of the confirmed red results at the beginning of clozapine treatment which significantly reduces after 6 months of treatment which remained low thereafter.
Spectral sparsification helps restore the spatial structure at single-cell resolution
Authors: Wang Jingwan , Li Shiying , Chen Lingxi , Li Shuai Cheng 
Published: January 2022

ABSTRACTSingle-cell RNA sequencing thoroughly quantifies the individual cell transcriptomes but renounces the spatial structure. Conversely, recently emerged spatial transcriptomics technologies capture the cellular spatial structure but skimp cell or gene resolutions. Cell-cell affinity estimated by ligand-receptor interactions can partially reconstruct the quasi-structure of cells but falsely include the pseudo affinities between distant or indirectly interacting cells. Here, we develop a software package, STORM, to reconstruct the single-cell resolution quasi-structure from the spatial transcriptome with diminished pseudo affinities. STORM first curates the representative single-cell profiles for each spatial spot from a candidate library, then reduces the pseudo affinities in the intercellular affinity matrix by partial correlation, spectral graph sparsification, and spatial coordinates refinement. STORM embeds the estimated interactions into a low-dimensional space with the cross-entropy objective to restore the intercellular quasi-structures, which facilitates the discovery of dominant ligand-receptor pairs between neighboring cells at single-cell resolution. STORM reconstructed structures achieved shape Pearson correlations ranging from 0.91 to 0.97 on the mouse hippocampus and human organ tumor microenvironment datasets. Furthermore, STORM can solelyde novoreconstruct the quasi-structures at single-cell resolution,i.e., reaching the cell-type proximity correlations 0.68 and 0.89 between reconstructed and immunohistochemistry-informed spatial structures on a human developing heart dataset and a tumor microenvironment dataset, respectively.
Robust, versatile DNA FISH probes for chromosome-specific repeats in Caenorhabditis elegans and Pristionchus pacificus
Authors: Adilardi Renzo S. , Dernburg Abby F. 
Published: January 2022

ABSTRACTRepetitive DNA sequences are useful targets for chromosomal fluorescence in situ hybridization (FISH). We analyzed recent genome assemblies of Caenorhabditis elegans and Pristionchus pacificus to identify tandem repeats with a unique genomic localization. Based on these findings, we designed and validated sets of oligonucleotide probes for each species targeting at least one locus per chromosome. These probes yielded reliable fluorescent signals in different tissues and can easily be combined with immunolocalization of cellular proteins. Synthesis and labeling of these probes are highly cost-effective and require no hands-on labor. The methods presented here can be easily applied in other model and non-model organisms with a sequenced genome.
Deep Learning Characterization of Brain Tumours With Diffusion Weighted Imaging
Authors: Meaney Cameron , Das Sunit , Colak Errol , Kohandel Mohammad 
Published: January 2022

AbstractGlioblastoma multiforme (GBM) is one of the most deadly forms of cancer. Methods of characterizing these tumours are valuable for improving predictions of their progression and response to treatment. A mathematical model called the proliferation-invasion (PI) model has been used extensively in the literature to model these tumours, though it relies on known values of two key parameters: the tumour cell diffusivity and proliferation rate. Unfortunately, these parameters are difficult to estimate in a patient-specific manner, making personalized tumour projections challenging. In this paper, we develop and apply a deep learning model capable of making accurate estimates of these key GBM-characterizing parameters while simultaneously producing a full projection of the tumour progression curve. Our method uses two sets of multi sequence MRI imaging in order to make predictions and relies on a preprocessing pipeline which includes brain tumour segmentation and conversion to tumour cellularity. We apply our deep learning model to both synthetic tumours and a dataset consisting of five patients diagnosed with GBM. For all patients, we derive evidence-based estimates for each of the PI model parameters and predictions for the future progression of the tumour. Discussion and implications for future work and clinical relevance are included.
Open science policies of medical and health sciences journals before and during the COVID-19 pandemic: a repeat cross-sectional study
Authors: Gardener Antoni D. , Hicks Ellen J. , Jacklin Chloe , Tan Gifford , Cashin Aidan G. , Lee Hopin , Nunan David , Toomey Elaine C. , Richards Georgia C. 
Published: January 2022

ABSTRACTCross-disciplinary openness and transparency of research plays an important role in scientific progress. We evaluated open-science related policies of 19 high ranking health and medical journals before (February 2020) and during (May 2021) the COVID-19 pandemic. The Transparency and Openness Promotion (TOP) guideline and the International Committee of Medical Journal Editors (ICMJE) requirements for disclosing conflicts of interest (COIs) were used to audit journal policies. TOP scores slightly improved during the COVID-19 pandemic, from a median of 5 (IQR: 2-12.5) out of a possible 24 points in February 2020 to 7 (IQR: 4-12) in May 2021. Most journals fulfilled all ICMJE provisions for reporting COIs before (84%; n=16) and during (95%; n=18) the COVID-19 pandemic. The COVID-19 pandemic has highlighted the importance of practising open science, however adherence to open science standards in audited policies was low overall, which may reduce progress in health and medical research.
Social connectedness as a determinant of mental health: A scoping review
Authors: Wickramaratne Priya J. , Yangchen Tenzin , Lepow Lauren , Patra Braja G. , Glicksburg Benjamin , Talati Ardesheer , Adekkanattu Prakash , Ryu Euijung , Biernacka Joanna M. , Charney Alexander , Mann J. John , Pathak Jyotishman , Olfson Mark , Weissman Myrna M. 
Published: January 2022

AbstractPublic health and epidemiologic research have established that social connectedness promotes overall health. Yet there have been no recent reviews of findings from research examining social connectedness as a determinant of mental health. The goal of this review was to evaluate recent longitudinal research probing the effects of social connectedness on depression and anxiety symptoms and diagnoses in the general population. A scoping review was performed of PubMed and PsychInfo databases from January 2015 to December 2020 following PRISMA-ScR guidelines using a defined search strategy. The search yielded 56 articles representing 52 unique studies. In research with other than pregnant women, 84% (16 of 19) studies reported that social support benefited symptoms of depression with the remaining 16% (3 of 19) reporting minimal or no evidence that lower levels of social support predict depression at follow-up. In research with pregnant women, 80% (21 of 26 studies) found that low social support increased postpartum depressive symptoms. Among 3 of 4 studies that focused on loneliness, feeling lonely at baseline was related to adverse outcomes at follow-up including higher risks of major depressive disorder, depressive symptom severity, generalized anxiety disorder, and lower levels of physical activity. In 5 of 7 reports, smaller social network size predicted depressive symptoms or disorder at follow-up. In summary, most recent relevant longitudinal studies have demonstrated that social support protects adults in the general population from depressive symptoms and disorders. The results, which were largely consistent across settings, exposure measures, and populations, support efforts to improve clinical detection of high-risk patients, including adults with low social support and elevated loneliness.
Viral Cultures for Assessing Fomites Transmission of SARS-CoV-2: a Systematic
Authors: Onakpoya Igho J. , Heneghan Carl J. , Spencer Elizabeth A. , Brassey Jon , Rosca Elena C. , Maltoni Susanna , Plüddemann Annette , Evans David H. , Conly John M. , Jefferson Tom 
Published: January 2022

ABSTRACTThis is a protocol for a systematic review to assess fomite transmission in SARS-CoV-2. Our research questions are as follows:
Are fomite samples infectious?If so, what proportion are infectious, and what is the distance and duration of infectiousness in the air?What is the relationship between fomites, infectiousness and PCR cycle threshold (Ct)?Is there evidence of a chain of transmission that establishes an actual instance of fomite transmission of SARS-CoV-2?We will include studies of any design (and in any setting) that investigate fomite transmission (defined as any inanimate object that, when contaminated with or exposed to infectious agents, can transfer the agent to a new host). We will only include studies that performed viral culture which assessed cytopathic effect and verification techniques to ensure the cultured virus is SARS-CoV-2. We will assess the risk of bias using a checklist modified from the QUADAS-2 criteria.
Supportive Mobility Across the Lifespan in Cerebral Palsy: A Modified Delphi Study to Establish Stakeholder Research Priorities
Authors: Feldner Heather A. , Gaebler-Spira Deborah , Awasthi Varun , Bjornson Kristie 
Published: January 2022

AbstractAimThe overarching aim of this research was to 1) Understand the mobility experiences, supported mobility device (SMD) use, and desired participation outcomes of people with cerebral palsy (CP) across the lifespan; and 2) Describe how perspectives of rehabilitation care and professional resources may influence mobility decision-making processes and outcomes. The aim of this study was to co-develop research priorities and identify meaningful research questions with a diverse group of stakeholders representing the CP community for implementation in subsequent research activities.MethodsA modified, three-round Delphi consensus study was conducted with a stakeholder advisory panel consisting of three adults with CP, two parents of children with CP, and four SMD providers.ResultsThe advisory panel identified 13 unique topical categories focused on SMD selection and use, stratified by age group and stakeholder role. Questions or statements within each category were ranked, and top consensus and concordance statements were retained, reviewed, and refined for use in a co-developed focus group guide.InterpretationA modified Delphi process was a useful tool for stakeholders in co-developing research priorities related to SMD use across the lifespan. Drawing on the lived expertise of stakeholders is important in facilitating improved research translation in the CP community.What this Paper AddsNine stakeholders from the CP community participated as Stakeholder Advisory Panelists and co-developers of research toolsStakeholders identified 175 unique responses across 12 SMD related categoriesStakeholders prioritized 38 mobility technology research priorities during consensus-buildingResults from consensus-building will be directly implemented into a qualitative focus group protocol
Spatial and molecular anatomy of germ layers in the gastrulating Cynomolgus monkey embryo
Authors: Cui Guizhong , Feng Su , Yan Yaping , Wang Li , He Xiechao , Li Xi , Duan Yanchao , Chen Jun , Tam Patrick P.L. , Tang Ke , Zheng Ping , Si Wei , Jing Naihe , Peng Guangdun 
Published: January 2022

SummaryDuring mammalian embryogenesis, spatial regulation of gene expression and cell signaling are functionally coupled with lineage specification, patterning of tissue progenitors and germ layer morphogenesis. While the mouse model has been instrumental for our understanding of mammalian development, comparatively little is known about human and non-human primate gastrulation due to the restriction of both technical and ethical issues. Here, we present a morphological and molecular survey of spatiotemporal dynamics of cell types populating the non-human primate embryos during gastrulation. We performed serial sections of Cynomolgus monkeys (Macaca fascicularis) gastrulating embryos at 1-day temporal resolution from E17 to E21, and reconstructed three-dimensional digital models based on high-resolution anatomical atlas that revealed the dynamic changes in the geography of the mesoderm and primitive streaks. Spatial transcriptomics identified unique gene profiles that correspond to distinct germ layers and cross-species spatiotemporal transcriptome analysis revealed a developmental coordinate of germ layer segregation between mouse and primate. Furthermore, we identified species-specific transcription programs during gastrulation. These results offer important insights into evolutionarily conserved and divergent processes during mammalian gastrulation.
HighlightA high-resolution anatomical atlas of Cynomolgus gastrulation embryosCreated a three-dimensional digital template from serial sections of five developmental stagesA two-dimensional spatiotemporal transcriptome of the germ layers of gastrulating embryosCross-species comparison infers conservation of functional attributes of regulome and signaling activity in germ layer formation