bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potentially effective drugs for the treatment of COVID-19 or MIS-C in children: a systematic review
Authors: Wang Zijun , Zhao Siya , Tang Yuyi , Wang Zhili , Shi Qianling , Dang Xiangyang , Gan Lidan , Peng Shuai , Li Weiguo , Zhou Qi , Li Qinyuan , Mafiana Joy James , Cortés Rafael González , Luo Zhengxiu , Liu Enmei , Chen Yaolong 
Published: September 2021

AbstractIntroductionThe purpose of this systematic review is to evaluate the efficacy and safety of using potential drugs: remdesivir and glucocorticoid in treating children and adolescents with COVID-19 and intravenous immunoglobulin (IVIG) in treating MIS-C.MethodsWe searched seven databases, three preprint platform, ClinicalTrials.gov, and Google from December 1, 2019, to August 5, 2021, to collect evidence of remdesivir, glucocorticoid, and IVIG which were used in children and adolescents with COVID-19 or MIS-C.ResultsA total of six cohort studies and one case series study were included in this systematic review. In terms of remdesivir, the meta-analysis of single-arm cohort studies have shown that, after the treatment, 37.1% (95%CI, 0.0% to 74.5%) experienced adverse events, 5.9% (95%CI, 1.5% to 10.2%) died, 37.2% (95%CI, 0% to 76.0%) needed extracorporeal membrane oxygenation or invasive mechanical ventilation. As for glucocorticoids, the results of the meta-analysis showed that the fixed-effect summary odds ratio for the association with mortality was 2.79 (95%CI, 0.13 to 60.87), and the mechanical ventilation rate was 3.12 (95%CI, 0.80 to 12.08) for glucocorticoids compared with the control group. In terms of IVIG, the two included cohort studies showed that for MIS-C patients with more severe clinical symptoms, IVIG combined with methylprednisolone could achieve better clinical efficacy than IVIG alone.ConclusionsOverall, the current evidence in the included studies is insignificant and of low quality. It is recommended to conduct high-quality randomized controlled trials of remdesivir, glucocorticoids, and IVIG in children and adolescents with COVID-19 or MIS-C to provide substantial evidence for the development of guidelines.
Previous COVID-19 infection and antibody levels after vaccination
Authors: Ali Hamad , Alahmad Barrak , Al-Shammari Abdullah A. , Al-Terki Abdelmohsen , Hammad Maha , Cherian Preethi , Alkhairi Irina , Sindhu Sardar , Thanaraj Thangavel Alphonse , Mohammed Anwar , Alghanim Ghazi , Deverajan Sriraman , Ahmad Rasheed , El-Shazly Sherief , Dashti Ali A. , Shehab Mohammad , Al-Sabah Salman , Alkandari Abdullah , Abubaker Jehad , Abu-Farha Mohamed , Al-Mulla Fahd 
Published: September 2021

AbstractBackgroundThe emergence of new COVID-19 variants of concern coupled with a global inequity in vaccine access and distribution, prompted many public health authorities to circumvent the vaccine shortages by altering vaccination protocols and prioritizing high-risk individuals. Those with previous COVID-19 infection may have not been prioritized due to existing humoral immunity.ObjectiveWe aim to study the association between previous COVID-19 infection and antibody levels after COVID-19 vaccination.MethodsA serological analysis to measure SARS-CoV-2 IgG, IgA and neutralizing antibodies was performed on individuals who received one or two doses of either BNT162b2 or ChAdOx1 vaccines in Kuwait. Generalized linear regression models adjusted for individual characteristics and comorbidities were fitted to study the average levels of IgG and neutralizing antibodies in vaccinated individuals based who had previous COVID-19 infection compared to those who had not.ResultsA total of 1025 individuals were recruited. The mean levels of IgG, IgA and neutralizing antibodies were higher in vaccinated subjects with previous COVID-19 infection when compared with those vaccinated without previous COVID-19 infection. Regression analysis showed a steeper slope of decline for IgG in vaccinated individuals without previous COVID-19 infection in comparison with vaccinated individuals with previous COVID-19 infection.ConclusionPrevious COVID-19 infection appears to elicit robust and sustained levels of SARS-CoV-2 antibodies in vaccinated individuals. Given the inconsistent supply of COVID-19 vaccines in many countries due to the global inequity, our results point towards wider vaccination plans to especially cover individuals without previous COVID-19 infection.
Prevalence of Migraine and its associated factors among medical students of Bangladesh: A cross sectional study
Authors: Rafi Abdur , Shahriar Tasnim , Arafat Yeasin , Karmaker Abhishek , Chowdhury Showsan Kabir , Jahangir Benazir , Hossain Meherab , Sultana Mahamoda , Hossain Md. Golam 
Published: September 2021

AbstractIntroductionMedical students are vulnerable group to migraine, one of the most common type of headache worldwide. The aim of the present study was to determine the prevalence of migraine and related disability among medical students of Bangladesh.MethodsThis cross-sectional study was conducted among 1327 students from six medical colleges Bangladesh during March 2021 through a self-administered online survey. ID Migraine™ scale and MIDAS scale were used to screen migraine and migraine related disability respectively. Frequency distribution, and Chi-square test, t-test along with multiple logistic regressions model were used to determine the prevalence and associated factors of migraine respectively.ResultsThe overall prevalence of migraine among the participants was 19%. The prevalence was higher among females (27%) than males (8%). Female sex (aOR 4.11, 95% CI 2.79-6.03) and poor sleep quality (aOR 2.07, 95% CI 1.48-2.91) were identified as independent risk factors of migraine. More than 90% migrainures reported to suffer from moderate to severe headache. Nausea was most commonly reported associated symptom (83.5%) followed by photophobia (72%) and vomiting (53%). Self-reported mental stress (55%), irregular sleep (49%), noise (30.5%), and usage of electronic device (30.5%) were most commonly reported triggering factor of migraine attack. More than half of the sufferers reported severe migraine related disability (MIDAS score ≥ 21).ConclusionsThe prevalence of migraine among medical students of Bangladesh is alarmingly high. Frequent migraine attacks and severe intensity of headache cause a substantial level of disability among the sufferers. Cautious avoidance of the triggering factors through appropriate interventions and prophylactic medication can mitigate the negative impact of migraine as well as improve the quality of life.
Informing behaviour change intervention design using systematic review with Bayesian meta-analysis: physical activity in heart failure
Authors: Amirova A. , Taylor L. , Volkmer B. , Ahmed N. , Chater A.M. , Fteropoulli T. 
Published: September 2021

AbstractEmbracing the Bayesian approach, we aimed to synthesise evidence regarding barriers and enablers to physical activity in heart failure (HF) in a way that can inform behaviour change intervention development. This approach helps in estimating and quantifying the uncertainty in the evidence and facilitates the synthesis of qualitative and quantitative studies. Qualitative and observational studies investigating barriers and enablers to physical activity in adults diagnosed with HF were included in this systematic review with a Bayesian meta-analysis. Qualitative evidence was annotated using the Theoretical Domains Framework and represented as a prior distribution using an expert elicitation task. The maximum a posteriori probability (MAP) was calculated as a summary statistic for the probability distribution for the log OR value estimating the relationship between physical activity and each determinant, according to qualitative evidence alone, quantitative evidence, and qualitative and quantitative evidence combined. The dispersion in the probability distribution for log OR associated with each barrier or enabler was used to evaluate the level of uncertainty in the evidence. Wide, medium, and narrow dispersion (SD) corresponded to high, moderate, and low uncertainty in the evidence, respectively. Evidence from three qualitative and 16 (N = 2739) quantitative studies was synthesised. High pro-b-type natriuretic peptide, pro-BNP (MAP value for log OR = -1.16; 95% CrI: [-1.21; -1.11]) and self-reported symptoms (MAP for log OR = 0.48; 95% CrI: [0.40; 0.55]) were suggested as barriers to physical activity with narrow distribution dispersion (SD = 0.18 and 0.19, respectively). Modifiable barriers were symptom distress (MAP for log OR = -0.46; 95% CrI: [-0.68; -0.24]), and negative attitude (MAP for log OR = -0.40; 95% CrI: [-0.49; -0.31]), SD = 0.36 and 0.26, respectively. Modifiable enablers were social support (MAP for log OR = 0.56; 95% CrI: [0.48; 0.63]), self-efficacy (MAP for log OR = 0.43; 95% CrI: [0.32; 0.54]), positive physical activity attitude (MAP for log OR = 0.92; 95% CrI: [0.77; 1.06]), SD = 0.26, 0.37, and 0.36, respectively. This work extends the limited research on the modifiable barriers and enablers for physical activity by individuals living with HF.
Combining antibody markers for serosurveillance of SARS-CoV-2 to estimate seroprevalence and time-since-infection
Authors: Bhuiyan Md S. , Brintz Ben J. , Whitcombe Alana L. , Markmann Alena J. , Bartelt Luther A. , Moreland Nicole J. , Azman Andrew S. , Leung Daniel T. 
Published: September 2021

SummarySerosurveillance is an important epidemiologic tool for SARS-CoV-2, used to estimate burden of disease and degree of population immunity. Which antibody biomarker, and the optimal number of biomarkers, has not been well-established, especially with the emerging rollout of vaccines globally. Here, we used random forest models to demonstrate that a single spike or receptor-binding domain (RBD) antibody was adequate for classifying prior infection, while a combination of two antibody biomarkers performed better than any single marker for estimating time-since-infection. Nucleocapsid antibodies performed worse than spike or RBD antibodies for classification, but is of utility for estimating time-since-infection, and in distinguishing infection-induced from vaccine-induced responses. Our analysis has the potential to inform the design of serosurveys for SARS-CoV-2, including decisions regarding number of antibody biomarkers measured.
Guidelines for reliable and reproducible functional enrichment analysis
Authors: Wijesooriya Kaumadi , Jadaan Sameer A , Perera Kaushalya L , Kaur Tanuveer , Ziemann Mark 
Published: September 2021

AbstractGene set enrichment tests (a.k.a. functional enrichment analysis) are among the most frequently used methods in computational biology. Despite this popularity, there are concerns that these methods are being applied incorrectly and the results of some peer-reviewed publications are unreliable. These problems include the use of inappropriate background gene lists, lack of false discovery rate correction and lack of methodological detail. An example analysis of public RNA-seq reveals that these methodological errors alter enrichment results dramatically. To ascertain the frequency of these errors in the literature, we performed a screen of 186 open access research articles describing functional enrichment results. We find that 95% of analyses using over-representation tests did not implement an appropriate background gene list or did not describe this in the methods. Failure to perform p-value correction for multiple tests was identified in 43% of analyses. Many studies lacked detail in the methods section about the tools and gene sets used. Only 15% of studies avoided major flaws, which highlights the poor state of functional enrichment rigour and reporting in the contemporary literature. We provide a set of minimum standards that should act as a checklist for researchers and peer-reviewers.
Social belonging: Brain structure and function is linked to membership in sports teams, religious groups and social clubs
Authors: Kieckhaefer Carolin , Schilbach Leonhard , Bzdok Danilo 
Published: September 2021

AbstractHuman behaviour across the life span is driven by the psychological need to belong, from kindergarten to bingo nights. Being part of social groups constitutes a backbone for communal life, and confers many benefits for physical and mental health. Capitalizing on neuroimaging and behavioural data from ~40.000 participants from the UK Biobank population cohort, we used structural and functional analyses to explore how social participation is reflected in the human brain. Across three different types of social groups, structural analyses point towards variance in ventromedial prefrontal cortex, fusiform gyrus and anterior cingulate cortex as structural substrates tightly linked to social participation. Functional connectivity analyses emphasized the importance of default mode and limbic network, but also showed differences for sports teams and religious groups as compared to social clubs.Taken together, our findings establish the structural and functional integrity of the default mode network as a neural signature of social belonging.
Linear superposition of responses evoked by individual glottal pulses explain over 80% of the frequency following response to human speech in the macaque monkey
Authors: Teichert Tobias , Gnanateja G. Nike , Sadagopan Srivatsun , Chandrasekaran Bharath 
Published: September 2021

AbstractThe frequency-following response (FFR) is a scalp-recorded electrophysiological potential that closely follows the periodicity of complex sounds such as speech. It has been suggested that FFRs reflect the linear superposition of responses that are triggered by the glottal pulse in each cycle of the fundamental frequency (F0 responses) and sequentially propagate through auditory processing stages in brainstem, midbrain, and cortex. However, this conceptualization of the FFR is debated, and it remains unclear if and how well a simple linear superposition can capture the spectro-temporal complexity of FFRs that are generated within the highly recurrent and non-linear auditory system. To address this question, we used a deconvolution approach to compute the hypothetical F0 responses that best explain the FFRs in rhesus monkeys to human speech and click trains with time-varying pitch patterns. The linear superposition of F0 responses explained well over 90% of the variance of click train steady state FFRs and well over 80% of mandarin tone steady state FFRs. The F0 responses could be measured with high signal-to-noise ratio and featured several spectro-temporally and topographically distinct components that likely reflect the activation of brainstem (<5ms; 200-1000 Hz), midbrain (5-15 ms; 100-250 Hz) and cortex (15-35 ms; ~90 Hz). In summary, our results in the monkey support the notion that FFRs arise as the superposition of F0 responses by showing for the first time that they can capture the bulk of the variance and spectro-temporal complexity of FFRs to human speech with time-varying pitch. These findings identify F0 responses as a potential diagnostic tool that may be useful to reliably link altered FFRs in speech and language disorders to altered F0 responses and thus to specific latencies, frequency bands and ultimately processing stages.
STAAR Workflow: A cloud-based workflow for scalable and reproducible rare variant analysis
Authors: Gaynor Sheila M. , Westerman Kenneth E. , Ackovic Lea L. , Li Xihao , Li Zilin , Manning Alisa K. , Philippakis Anthony , Lin Xihong 
Published: September 2021

AbstractSummaryWe developed the STAAR WDL workflow to facilitate the analysis of rare variants in whole genome sequencing association studies. The open-access STAAR workflow written in the workflow description language (WDL) allows a user to perform rare variant testing for both gene-centric and genetic region approaches, enabling genome-wide, candidate, and conditional analyses. It incorporates functional annotations into the workflow as introduced in the STAAR method in order to boost the rare variant analysis power. This tool was specifically developed and optimized to be implemented on cloud-based platforms such as BioData Catalyst Powered by Terra. It provides easy-to-use functionality for rare variant analysis that can be incorporated into an exhaustive whole genome sequencing analysis pipeline.Availability and implementationThe workflow is freely available from https://dockstore.org/workflows/github.com/sheilagaynor/STAAR_workflow.
Dual transcriptional analysis of Peronospora belbahrii and Ocimum basilicum in susceptible interactions
Authors: Johnson Eric T. , Kim Hye-Seon , Tian Miaoying , Dudai Nativ , Tal Ofir , Gonda Itay 
Published: September 2021

AbstractBasil downy mildew, caused by the pathogen Peronospora belbahrii, is a major problem for sweet basil growers worldwide. The genome sequences of both Ocimum basilicum and P. belbahrii were recently completed but extensive transcriptome analysis of this pathosystem has not been completed. RNA sequencing was performed using basil leaf samples collected three and six days after inoculation with sporangia from an Illinois isolate of P. belbahrii and differentially expressed genes were identified. Gene enrichment analysis identified 22 genes that were upregulated at day three, in comparison to mock inoculated leaf samples, that were classified as ‘defense response to oomycetes’; among this group were five orthologues of Arabidopsis thaliana DOWNY MILDEW RESISTANCE 6. During the same time interval, many genes contributing to photosynthesis in the infected leaves were downregulated in comparison to control leaf samples. Many more genes were differentially expressed in the inoculated basil leaves at day six, compared to mock inoculated leaves, as the pathogen began to produce sporangiophores. On days three and six, the pathogen produced high transcript levels of secreted glycoside hydrolases, which likely release sugars from the plant cell walls needed for the growth of the pathogen. These results contribute to a better understanding of the infection process of downy mildew and will aid the development of more effective measures for reducing the severity of the disease.
Targeting metabolic adaptations in the breast cancer–liver metastatic niche using dietary approaches to improve endocrine therapy efficacy
Authors: Zuo Qianying , Mogol Ayca Nazli , Liu Yu-Jeh , Casiano Ashlie Santaliz , Chien Christine , Drnevich Jenny , Imir Ozan Berk , Kulkoyluoglu-Cotul Eylem , Park Nicole Hwajin , Shapiro David J , Park Ben Ho , Ziegler Yvonne , Katzenellenbogen Benita S. , Aranda Evelyn , O’Neill John D. , Raghavendra Akshara Singareeka , Tripathy Debu , Erdogan Zeynep Madak 
Published: September 2021

AbstractEstrogen receptor-positive (ER+) metastatic tumors contribute to nearly 70% of breast cancer-related deaths. Most patients with ER+metastatic breast cancer (MBC) undergo treatment with the estrogen receptor antagonist fulvestrant (Fulv) as standard-of-care. Yet, among such patients, metastasis in liver is associated with reduced overall survival compared to other metastasis sites. The factors underlying the reduced responsiveness of liver metastases to ER-targeting agents remain unknown, impeding the development of more effective treatment approaches to improve outcomes for patients with ER+liver metastases. We therefore evaluated site-specific changes in MBC cells and determined the mechanisms through which the liver metastatic niche specifically influences ER+tumor metabolism and drug resistance. We characterized ER activity of MBC cells both in vitro, using a novel system of tissue-specific extracellular matrix hydrogels representing the stroma of ER+tumor metastatic sites (liver, lung and bone), and in vivo, in liver and lung metastasis mouse models. ER+metastatic liver tumors and MBC cells grown in liver hydrogels displayed upregulated expression of glucose metabolism enzymes in response to Fulv. Furthermore, differential ERα activity, but not expression, was detected in liver hydrogels. In vivo, increased glucose metabolism led to increased glycogen deposition in liver metastatic tumors, while a fasting-mimicking diet increased efficacy of Fulv treatment to reduce the metastatic burden.ImplicationsOur findings identify a novel mechanism of endocrine resistance driven by the liver tumor microenvironment. These results may guide the development of dietary strategies to circumvent drug resistance in liver metastasis, with potential applicability in other metastatic diseases.
Superinfection exclusion: a viral strategy with short-term benefits and long-term drawbacks
Authors: Hunter Michael , Fusco Diana 
Published: September 2021

AbstractViral superinfection occurs when multiple viral particles subsequently infect the same host. In nature, several viral species are found to have evolved diverse mechanisms to prevent superinfection (superinfection exclusion) but how this strategic choice impacts the fate of mutations in the viral population remains unclear. Using stochastic simulations, we find that genetic drift is suppressed when superinfection occurs, thus facilitating the fixation of beneficial mutations and the removal of deleterious ones. Interestingly, we also find that the competitive (dis)advantage associated with variations in life history parameters is not necessarily captured by the viral growth rate for either infection strategy. Putting these together, we then show that a mutant with superinfection exclusion will easily overtake a superinfecting population even if the latter has a much higher growth rate. Our findings suggest that while superinfection exclusion can negatively impact the long-term adaptation of a viral population, in the short-term it is ultimately a winning strategy.Author summaryViral social behaviour has recently been receiving increasing attention in the context of ecological and evolutionary dynamics of viral populations. One fascinating and still relatively poorly understood example is superinfection or co-infection, which occur when multiple viruses infect the same host. Among bacteriophages, a wide range of mechanisms have been discovered that enable phage to prevent superinfection (superinfection exclusion) even at the cost of using precious resources for this purpose. What is the evolutionary impact of this strategic choice and why do so many phages exhibit this behaviour? Here, we conduct an extensive simulation study of a phage population to address this question. In particular, we investigate the fate of viral mutations arising in an environment with a constant supply of bacterial hosts designed to mimic a “turbidostat,” as these are increasingly being used in laboratory evolution experiments. Our results show that allowing superinfection in the long-term yields a population which is more capable of adapting to changes in the environment. However, when in direct competition, mutants capable of preventing superinfection experience a very large advantage over their superinfecting counterparts, even if this ability comes at a significant cost to their growth rate. This indicates that while preventing superinfection can negatively impact the long-term prospects of a viral population, in the short-term it is ultimately a winning strategy.