bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroprevalence and attainment of herd immunity against SARS CoV-2: A modelling study
Authors: Paul Abhijit , Kadnur Harshith B , Ray Animesh , Chatterjee Samrat , Wig Naveet 
Published: January 2021

AbstractObjectiveThe present study is aims to predict the likelihood of and likely time required to attain herd immunity against COVID-19 in New Delhi due to natural infection.MethodAn ODE based mathematical model was constructed by extending the classical SEIR model to predict the seroprevalence rate in Delhi. We estimated the parameter values for Delhi using available data (reported cases and the seroprevalence rate) and used them for future prediction. We also attempted to capture the changes in the seroprevalence rate with different possibilities of reinfection.ResultsMaximum seroprevalence rate obtained through our model is 31.65% and also a reduction in the seroprevalence rate was observed for the upcoming one month (month of January, 2021) due to the reduced transmission rate. After increasing the transmission rate to the value same as the third wave in New Delhi, we obtained a maximum value of 54.96%. This maximum value significantly decreased with the reduction in the reinfection possibilities. Also, a little impact of the duration of persistence of antibodies, 180 vs 105 days, was observed on the maximum seroprevalence.ConclusionThis modelling study suggests that natural infection alone, as gauged by serial sero-surveys, will not result in attainment of herd immunity in the state of Delhi.
Sexual dimorphism in outcomes of non-muscle invasive bladder cancer: a role of CD163+ M2 macrophages, B cells and PD-L1 immune checkpoint
Authors: Chenard Stephen , Jackson Chelsea , Vidotto Thiago , Chen Lina , Hardy Céline , Jamaspishvilli Tamara , Berman David , Siemens D. Robert , Koti Madhuri 
Published: January 2021

AbstractNon-muscle invasive bladder cancer (NMIBC) is significantly more common in men than women. However, female patients with NMIBC often present with more aggressive disease and do not respond as well to immunotherapy treatments. We hypothesized that sexual dimorphism in the tumor immune microenvironment (TIME) may contribute to the inferior clinical outcomes observed in female patients. To test this hypothesis, we interrogated the expression patterns of genes associated with specific immune cell types and immune regulatory pathways using tumor whole transcriptome profiles from male (n=357) and female (n=103) patients with NMIBC. High-grade tumors from female patients exhibited significantly increased expression ofCD40, CTLA4, PDCD1, LAG3andICOSimmune checkpoint genes. Based on the significant differences in expression profiles of these genes and the cell types that most commonly express these in the TIME, we evaluated the density and spatial distribution of CD8+Ki67+ (activated cytotoxic T cells), FoxP3+ (regulatory T cells), CD103+ (tissue resident T cells), CD163+ (M2-like tumor associated macrophages), CD79a+ (B cells), PD-L1+ (Programmed-Death Ligand-1) and PD-1+ cells using multiplexed immunofluorescence in an independent cohort of 332 patient tumors on a tissue microarray (n=259 males and n=73 females). Tumors from female patients showed significantly higher infiltration of CD163+ macrophages and PD-L1+ cells compared to tumors from male patients. Notably, increased infiltration of CD163+ macrophages and CD79a+ B cells independently associated with decreased recurrence free survival. Not only do these results have the potential to inform the rational utilization of immunomodulatory therapies based on the TIME of both male and female patients with NMIBC, these novel findings highlight the necessity of considering sexual dimorphism in the design of future immunotherapy trials.
Deep Learning for Predicting Cognitive Gap as a Reliable Biomarker of Dementia
Authors: Habuza Tetiana , Zaki Nazar , Statsenko Yauhen , Alnajjar Fady , Elyassami Sanaa 
Published: January 2021

AbstractNeuroimaging data may reflect the mental status of both cognitively preserved individuals and patients with neurodegenerative diseases. To find the relationship between cognitive performance and the difference between predicted and observed functional test results, we developed a Convolutional Neural Network (CNN) based regression model to estimate the level of cognitive decline from preprocessed T1-weighted MRI images. In this study, we considered the Predicted Cognitive Gap (PCG) as the biomarker to accurately classify Healthy Control (HC) subjects versus Alzheimer disease (AD) subjects. The proposed model was tested on a dataset that includes 422 HC and 377 AD cases. The performance of the proposed solution was measured using Receiver Operating Characteristic (ROC) Area Under the Curve (AUC) and achieved 0.987 (ADAS-cog), 0.978 (MMSE), 0.898 (RAVLT), 0.848 (TMT), 0.829 (DSST) for averaged brain images; and 0.985 (ADAS-cog), 0.987 (MMSE), 0.901 (RAVLT), 0.8474 (TMT), 0.796 (DSST) for middle slice skull stripped brain images. The results achieved indicate that PCG can accurately separate healthy subjects from demented ones and thus, the structure of the brain contributes to the level of human cognition and their functional abilities. Therefore, PCG could be used as a biomarker for dementia.
A behavioral paradigm for cortical control of a robotic actuator by freely moving rats in a one-dimensional two-target reaching task
Authors: Zaidi Syed Muhammad Talha , Kocatürk Samet , Baykaş Tunçer , Kocatürk Mehmet 
Published: January 2021

AbstractControlling the trajectory of a neuroprosthetic device to reach multiple targets is a commonly used brain-machine interface (BMI) task in primates and has not been available for rodents yet. Here, we describe a novel experimental paradigm which enables this task for rats in one-dimensional space for reaching two distant targets depending on their limited cognitive and visual capabilities compared to primates. An online transform was used to convert the activity of a pair of primary motor cortex (M1) units into two robotic actions. The rats were shaped to adapt to the transform and direct the robotic actuator toward the selected target by modulating the activity of the M1 neurons. All three rats involved in the study were capable of achieving randomly selected targets with at least 78% accuracy. A total of 9 out of 16 pairs of units examined were eligible for exceeding this success criterion. Two out of three rats were capable of reversal learning, where the mapping between the activity of the unit pairs and the robotic actions were reversed. The present work is the first demonstration of trajectory-based control of a neuroprosthetic device by rodents to reach two distant targets using visual feedback. The paradigm introduced here may be used as a cost-effective platform for elucidating the information processing principles in the neural circuits related to neuroprosthetic control and for studying the performance of novel BMI technologies using freely moving rats.
Undersampling correction methods to control γ-dependence for comparing β-diversity between regions
Authors: Cao Ke , Svenning Jens-Christian , Yan Chuan , Zhang Jintun , Mi Xiangcheng , Ma Keping 
Published: January 2021

AbstractMeasures of β-diversity are known to be highly constrained by the variation in γ-diversity across regions (i.e., γ-dependence), making it challenging to infer underlying ecological processes. Undersampling correction methods have attempted to estimate the actual β-diversity in order to minimize the effects of γ-dependence arising from the problem of incomplete sampling. However, no study has systematically tested their effectiveness in removing γ-dependence, and examined how well undersampling-corrected β-metrics reflect true β-diversity patterns that respond to ecological gradients. Here, we conduct these tests by comparing two undersampling correction methods with the widely used individual-based null model approach, using both empirical data and simulated communities along a known ecological gradient across a wide range of γ-diversity and sample sizes. We found that undersampling correction methods using diversity accumulation curves were generally more effective than the null model approach in removing γ-dependence. In particular, the undersampling-corrected β-Shannon diversity index was most independent on γ-diversity and was the most reflective of the true β-diversity pattern along the ecological gradient. Moreover, the null model-corrected Jaccard-Chao index removed γ-dependence more effectively than either approach alone. Our validation of undersampling correction methods as effective tools for accommodating γ-dependence greatly facilitates the comparison of β-diversity across regions.
Chinese medicine (Q-14) in the Treatment of Patients with Coronavirus Disease 2019 (COVID-19): A Single-center, Open label, Randomised Controlled Trial
Authors: Liu Jia , Yang Wei , Liu Yue , Lv Cheng , Ruan Lianguo , Zhao Chen , Huo Ruili , Shen Xin , Miao Qing , Lv Wenliang , Li Hao , Shi Huaxin , Hu Lijie , Yang Zhixu , Zhang Li , Wang Bing , Dong Guoju , Xian Yongyue , Li Bin , Zhou Zhenqi , Xu Chunyan , Chen Yingying , Bian Yongjun , Guo Jing , Yang Jinliang , Wang Jian , Qi Wensheng , Chen Suping , Chen Yang , Yan Bei , Wang Wei , Li Jing , Xie Xiaolei , Xu Ming , Jiang Jianxin , Wang Gang , Cong Xiaodong , Zhu Haoning , Shi Jiaheng , Leng Luxing , Li Dongxu , Guo Lanping , Huang Luqi 
Published: January 2021

ABSTRACTOBJECTIVETo evaluate the efficacy and safety of Chinese medicine (Q-14) plus standard care compared with standard care alone in adult with coronavirus disease 2019 (COVID-19).Study DESIGNSingle-center, open label, randomised controlled trial.SETTINGWuhan Jinyintan Hospital, Wuhan, China, February 27 to March 27, 2020.PARTICIPANTS204 patients with laboratory confirmed COVID-19 were randomised in to treatment group and control group, which was 102 patients each group.INTERVENTIONSIn treatment group, Q-14 was administrated at 10g (granules), twice daily for 14 days and plus standard care. In control group, patients were given standard care alone for 14 days.MAIN OUTCOME MEASUREThe primary outcome was conversion time of SARS-CoV-2 viral assay. Adverse events were analyzed in the safety population.RESULTSAmong 204 patients, 195 were analyzed according to the intention to treat principle. There were 149 patients (71 vs. 78 in treatment group and control group respectively) turning to negative via SARS-CoV-2 viral assay. No statistically significance showed in conversion time between treatment group and control group (FAS: Median (IQR): 10.00 (9.00-11.00) vs. 10.00 (9.00-11.00); Mean rank: 67.92 vs. 81.44; P=0.051.). Time to recovery of fever was shorter in treatment group as compared in control group. The disappearance rate of symptom in cough, fatigue, chest discomfort was significantly higher in treatment group. In chest computed tomography (Chest CT) examinations, overall evaluation of chest CT examination after treatment compared with baseline showed more patients improved in treatment group .There were no significant differences in the other outcomes.CONCLUSIONAdministration of Q-14 on standard care for COVID-19 was useful for improvement of symptoms (such as fever, cough, fatigue and chest discomfort), while did not result in a significantly higher probability of negative conversion of SARS-CoV-2 viral assay. No serious adverse events were reported.TRIAL REGISTRATIONChiCTR2000030288
Dynamic balance recovery in chronic Acquired Brain Injury participants following a perturbation training
Authors: Joubran Katherin , Bar-Haim Simona , Shmuelof Lior 
Published: January 2021

AbstractBackgroundAcquired Brain Injury (ABI) is defined as a damage to the brain that occurs after birth. Subjects post-ABI suffer from dynamic balance impairments that persist years after the injury.ObjectiveTo explore the effect of a perturbation method which is consisted of unexpected balance perturbations using Re-Step™ technology on the recovery of dynamic balance and gait velocity in chronic ABI participants.MethodsIn a clinical trial, 35 chronic ABI participants (stroke and traumatic brain injury) participated in 22 sessions of perturbation-training, twice a week for 3 months. Dynamic balance was assessed pre and post-training using Community Balance and Mobility Scale (CB&M). Gait velocity was also assessed in the stroke participants using the 10-meter walk test (10MWT).ResultsDynamic balance improved significantly post-training (p=0.001). This improvement was greater than the improvement that was observed in a sub-group that was tested twice before training (p=0.04). 16 participants (45.7%) out of 35 met or exceeded minimal detectable change (MDC) of the CB&M Scale. Self-paced velocity also improved significantly (p=0.02) but only 2 participants (9.5%) out of 21 exceeded the MDC of 10MWT post-stroke.ConclusionsUnexpected balance perturbation-training using Re-Step™ technology led to an improvement in dynamic balance and gait velocity in chronic ABI participants. The advantage of Re-Step™ technology training compared to conventional balance training should be further examined.
Non-Congruent SARS-CoV-2 Waves in England
Authors: Brookes Anthony J , Pollock Allyson , Dorling Danny 
Published: January 2021

ABSTRACTExamination of the chronology, location and size of waves of SARS-CoV-2 infection across England could shed light on the inter-play between the 1st and the 2nd Waves. From mid-October onwards such an analysis becomes increasingly difficult due to the emergence of a new strain (VOC-202012/01) and in light of the differential implementation of lockdown measures and tiers. Therefore, we sought to examine trends and correlations in virus prevalence and covid-related deaths spanning the start of the UK pandemic in March 2020 through to early November 2020 – i.e., including the first growth period of the 2nd Wave. We found striking regional relationships between the 1st and the 2nd Wave that are difficult to explain other than by involving some role for changing levels of immunity in the population affecting the progression of the pandemic.
Personalized Perturbation Profiles Reveal Concordance between Autism Blood Transcriptome Datasets
Authors: Laird Jason , Maertens Alexandra 
Published: January 2021

AbstractThe complex heterogeneity of Autism Spectrum Disorder (ASD) has made quantifying disease specific molecular changes a challenge. Blood based transcriptomic assays have been performed to isolate these molecular changes and provide biomarkers to aid in ASD diagnoses, etiological understanding, and potential treatment1–6. However, establishing concordance amongst these studies is made difficult in part by the variation in methods used to call putative biomarkers. Here we use personal perturbation profiles to establish concordance amongst these datasets and reveal a pool of 1,189 commonly perturbed genes and new insights into poorly characterized genes that are perturbed in ASD subjects. We find the resultant perturbed gene pools to include the following unnamed genes: C18orf25, C15orf39, C1orf109, C1orf43, C19orf12, C6orf106, C3orf58, C19orf53, C17orf80, C4orf33, C21orf2, C10orf2, C1orf162, C10orf25 and C10orf90. Investigation into these genes using differential correlation analysis and the text mining tool Chilibot reveal interesting connections to DNA damage, ubiquitination, R-loops, autophagy, and mitochondrial damage. Our results support evidence that these cellular events are relevant to ASD molecular mechanisms. The personalized perturbation profile analysis scheme, as described in this work, offers a promising way to establish concordance between seemingly discordant expression datasets and expose the relevance of new genes in disease.
Disrupting D2-NMDA receptor heteromerization blocks the rewarding effects of cocaine but preserves natural reward processing
Authors: Andrianarivelo Andry , Saint-Jour Estefani , Pousinha Paula , Fernandez Sebastian P. , Petitbon Anna , De Smedt-Peyrusse Veronique , Heck Nicolas , Ortiz Vanesa , Allichon Marie-Charlotte , Kappès Vincent , Betuing Sandrine , Walle Roman , Zhu Ying , Joséphine Charlène , Bemelmans Alexis-Pierre , Turecki Gustavo , Mechawar Naguib , Javitch Jonathan A , Caboche Jocelyne , Trifilieff Pierre , Barik Jacques , Vanhoutte Peter 
Published: January 2021

AbstractAddictive drugs increase dopamine in the nucleus accumbens (NAc), where it persistently shapes excitatory glutamate transmission and hijacks natural reward processing. Herein, we provide evidence, from mice to human, that an underlying mechanism relies on drug-evoked heteromerization of glutamate NMDA receptors (NMDAR) with dopamine receptor 1 (D1R) or 2 (D2R). Using temporally-controlled inhibition of D1R-NMDAR heteromerization, we unraveled their selective implication in early developmental phases of cocaine-mediated synaptic, morphological and behavioral responses. In contrast, preventing D2R-NMDAR heteromerization blocked the persistence of these adaptations. Importantly, interfering with these heteromers spared natural reward processing. Strikingly, we established that D2R-NMDAR complexes exist in human samples and showed that, despite a decreased D2R protein expression in the NAc, psychostimulant-addicts display a higher proportion of D2R forming heteromers with NMDAR. These findings contribute to a better understanding of molecular mechanisms underlying addiction and uncover D2R-NMDAR heteromers as targets with potential therapeutic value.
The CovR regulatory network drives the evolution of Group BStreptococcusvirulence
Authors: Mazzuoli Maria-Vittoria , Daunesse Maëlle , Varet Hugo , Rosinski-Chupin Isabelle , Legendre Rachel , Sismeiro Odile , Gominet Myriam , Kaminski Pierre-Alexandre , Glaser Philippe , Chica Claudia , Trieu-Cuot Patrick , Firon Arnaud 
Published: January 2021

ABSTRACTVirulence of the neonatal pathogen Group BStreptococcusdepends on the master regulator CovR. Inactivation of CovR leads to large-scale transcriptome remodeling and impairs almost every step of the interaction between the pathogen and the host. However, comparative analyses suggested a plasticity of the CovR signalling pathway in clinical isolates, probably due to the host selective pressure and leading to phenotypic heterogeneity in the bacterial population. Here, we characterize the CovR regulatory network in a strain representative of the hypervirulent lineage responsible of the majority of late-onset meningitidis. Genome-wide binding and transcriptome analysis demonstrated that CovR acts as a direct and global repressor of virulence genes, either as a primary regulator or with specialized co-regulators. Remarkably, CovR directly regulates genes of the pan-genome, including the two specific hypervirulent adhesins and horizontally acquired genes, as well as core-genes showing mutational biases in the population. Parallel analysis of the CovR network in a second isolate links strain-specificities to micro-evolutions in CovR-regulated promoters and to broad difference due to variability in CovR activation by phosphorylation. Our results highlight the direct, coordinated, and strain-specific regulation of virulence genes by CovR. This intra-species evolution of the signalling network reshapes bacterial-host interactions, increasing the potential for adaptation and the emergence of clone associated with specific diseases.
Development of ADAF screening tool for emotional and coping problems in cancer patients
Authors: Pérez-Segura Pedro , Francés Santos Enrech , Martel Ignacio Juez , Pérez Escutia Maria Angeles , Hernández Agudo Elena , Mateos Leticia Leon , Corradi Guido , Pérez-Frade Helena Olivera , Sánchez Escamilla Francisco , López Marta Baselga , Baquero Jose Luis , Delgado Marta Redondo 
Published: January 2021

ABSTRACTPurposePsychological screening in patient with cancer is recommended by clinical guidelines, however most of scales have large number of items, difficulty detection and refer from routine consultations. The specific objective of the study was to develop and validate the ADAF screening for anxiety, depression and coping.Methods/PatientsCross-sectional, multicenter study performed in the medical and radiotherapy oncology services of 5 hospitals in Madrid, coordinated by the Medical Oncology Service of the Hospital Clínico San Carlos (CEIC nº19 / 265-E). To determine the psychometric properties, the ADAF screening questionnaire ADAF was administered, including 5 items (one related to anxiety symptoms, two related to depressive symptoms, one for helplessness coping and one for avoidance coping), and as a gold-standard the HADS and the MiniMAC. Intraclass correlation coefficients and receiver operating characteristic curves were performed. The p value <0.05 was considered significant.ResultsA total of 186 patients completed the evaluation. The correlation coefficients were significant for all dimensions (Anxiety, Depression, Helplessness coping, and Avoidance Coping), with p <0.001. The statistical analysis of ROC curves suggests that the cut-off point for screening is equivalent to a score > 2 points (3 in the case of depression, having two items), with a sensitivity and specificity between 62 and 90%, depending on the item, and an area under the curve above 0.8 for the first 4 items.ConclusionsADAF screening has adequate reliability, good sensitivity and specificity. This instrument is useful and easy to use to identify emotional and coping problems in cancer patients.
Prevalence of, and risk factors for, diabetes and prediabetes in Bangladesh: Evidence from the national survey using a multilevel Poisson regression model with a robust variance
Authors: Hossain Mohammad Bellal , Khan Md. Nuruzzaman , Oldroyd John C. , Rana Juwel , Magliago Dianna J. , Chowdhury Enayet K. , Karim Md Nazmul , Islam Rakibul M. 
Published: January 2021

AbstractBackgroundTo estimate the age-standardized prevalence of diabetes and prediabetes and identify factors associated with these conditions at individual, household, and community levels.MethodsData from 11952 Bangladeshi adults aged 18-95 years available from the most recent Bangladesh Demographic and Health Survey 2017-18 were used. Anthropometric measurements and fasting blood glucose samples were taken as part of the survey. Prevalence estimates of diabetes and prediabetes were age-standardized with direct standardization, and risk factors were identified using multilevel mix-effects Poisson regression models with robust variance.ResultsThe overall age-standardised prevalence of diabetes was 9.2% (95%CI 8.7-9.7) (men: 8.8%, women: 9.6%), and prediabetes was 13.3% (95%CI 12.7-13.9) (men: 13.0%, women: 13.6%). Among people with diabetes, 61.5% were unaware that they had the condition. 35.2% were taking treatment regularly, and only 30.4% of them had controlled diabetes. Factors associated with an increased prevalence of having diabetes were increasing age, male, overweight/obesity, hypertension, being in the highest wealth quintile, and living in the Dhaka division. People currently employed and living in the Rangpur division were less likely to have diabetes than those currently not employed and living in the Barishal division.ConclusionsDiabetes and prediabetes affect a substantial proportion (over one-quarter) of the Bangladeshi adult population. Continuing surveillance and effective prevention and control measures, focusing on obesity reduction and hypertension management, are urgently needed.