bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of stability and inactivation methods of SARS-CoV-2 in context of laboratory settings
Authors: Westhaus Sandra , Widera Marek , Rabenau Holger F. , Hoehl Sebastian , Bojkova Denisa , Cinatl Jindrich , Ciesek Sandra 
Published: September 2020

SummaryThe novel coronavirus SARS-CoV-2 is the causative agent of the acute respiratory disease COVID-19, which has become a global concern due to its rapid spread. Laboratory work with SARS-CoV-2 in a laboratory setting was rated to biosafety level 3 (BSL-3) biocontainment level. However, certain research applications in particular in molecular biology require incomplete denaturation of the proteins, which might cause safety issues handling contaminated samples. In particular, it is critical to provide proof of inactivation before samples can be removed from the BSL-3.In this study, the stability of the virus in cell culture media at 4°C and on touch panel surfaces used in laboratory environment was analyzed. In addition, we evaluated common lysis buffers that are used in molecular biological laboratories for their ability to inactivate SARS-CoV-2. We have found that guanidine thiocyanate and most of the tested detergent containing lysis buffers were effective in inactivation of SARS-CoV-2, however, the M-PER lysis buffer containing a proprietary detergent failed to inactivate SARS-CoV-2. Furthermore, we compared chemical and non-chemical inactivation methods including ethanol, acetone-methanol mixture, PFA, UV-C light, and heat inactivation.In conclusion, careful evaluation of the used inactivation methods are required and additional inactivation steps are necessary before removal of lysed viral samples from BSL-3.
Direct Continuous EMG control of a Powered Prosthetic Ankle for Improved Postural Control after Guided Physical Training: a Case Study
Authors: Fleming Aaron , Huang Stephanie , Buxton Elizabeth , Hodges Frank , Huang He (Helen) 
Published: September 2020

AbstractBackgroundDespite the promise of powered lower limb prostheses, the existing control of these modern devices is insufficient to assist many daily activities, such as postural control while lifting weight, that require continuous control of prosthetic joints according to human states and environments. The objective of this case study was to investigate the feasibility and potential of direct, continuous electromyographic (dEMG) control of a powered ankle prosthesis, combined with physical therapist (PT)-guided training, for improved standing postural control in an individual with transtibial amputation.MethodsA powered prosthetic ankle was directly controlled by EMG signals of the residuallateral gastrocnemiusandtibialis anteriormuscles. The participant with transtibial amputation received 4-week PT-guided training on posture while using the dEMG control of powered ankle. A subset of activities in the mini-BESTest (a clinical balance assessment tool) were used in the training and evaluation protocol. We quantified EMG signals in the bilateral shank muscles, biomechanics that captures postural control and stability, and score for the clinical balance evaluation.ResultsCompared to the participant’s daily passive prosthesis, the dEMG-controlled ankle, combined with the training, yielded improved clinical balance score and reduced compensation from the intact joints. In addition, cross correlation coefficient of bilateral CoP excursions, a metric for quantifying standing postural control, increased to0.83(±0.07)when using dEMG ankle control, compared with0.39(±0.29)when using the passive device. Between-limb coordination was also observed as synchronized activation of homologous muscles in the shank. We witnessed rapid improvement in performance on the first day of the training for load transfer tasks, where bilateral CoP synchronization improvement was significantly related to repetition order (R=0.459, p = 0.045). Finally, the participant further improved this performance significantly across training days.ConclusionThis case study showed the feasibility of dEMG control of powered prosthetic ankle by a transtibial amputee after a PT-guided training to assist postural control. This study’s training protocol and dEMG control method that lays the foundation for future study to extend these results through the inclusion of more participants and activities.
Distributional Transformation improves Decoding Accuracy when Predicting Chronological Age from Structural MRI
Authors: Soch Joram 
Published: September 2020

ABSTRACTWhen predicting a certain subject-level variable (e.g. age in years) from measured biological data (e.g. structural MRI scans), the decoding algorithm does not always preserve the distribution of the variable to predict. In such a situation, distributional transformation (DT), i.e. mapping the predicted values to the variable’s distribution in the training data, might improve decoding accuracy. Here, we tested the potential of DT within the 2019 Predictive Analytics Competition (PAC) which aimed at predicting chronological age of adult human subjects from structural MRI data. In a low-dimensional setting, i.e. with less features than observations, we applied multiple linear regression, support vector regression and deep neural networks for out-of-sample prediction of subject age. We found that (i) when the number of features is low, no method outperforms linear regression; and (ii) except when using deep regression, distributional transformation increases decoding performance, reducing the mean absolute error (MAE) by about half a year. We conclude that DT can be advantageous when predicting variables that are non-controlled, but have an underlying distribution in healthy or diseased populations.
Dissociable influences of reward and punishment on adaptive cognitive control
Authors: Leng Xiamin , Yee Debbie , Ritz Harrison , Shenhav Amitai 
Published: September 2020

AbstractTo invest effort into any cognitive task, people must be sufficiently motivated. Whereas prior research has focused primarily on how the cognitive control required to complete these tasks is motivated by the potential rewards for success, it is also known that control investment can be equally motivated by the potential negative consequence for failure. Previous theoretical and experimental work has yet to examine how positive and negative incentives differentially influence the manner and intensity with which people allocate control. Here, we develop and test a normative model of control allocation under conditions of varying positive and negative performance incentives. Our model predicts, and our empirical findings confirm, that rewards for success and punishment for failure should differentially influence adjustments to the evidence accumulation rate versus response threshold, respectively. This dissociation further enabled us to infer how motivated a given person was by the consequences of success versus failure.Author SummaryFrom the school to the workplace, whether someone achieves their goals is determined largely by the mental effort they invest in their tasks. Recent work has demonstrated both why and how people adjust the amount of effort they invest in response to variability in the rewards expected for achieving that goal. However, in the real world, we are motivated both by the positive outcomes our efforts can achieve (e.g., praise)andthe negative outcomes they can avoid (e.g., rejection), and these two types of incentives can motivate adjustments not only in the amount of effort we invest but also thetypesof effort we invest (e.g., whether to prioritize performing the taskefficientlyorcautiously). Using a combination of computational modeling and a novel task that measures voluntary effort allocation under varying incentive conditions, we show that people should and do engage dissociable forms of mental effort in response to positive versus negative incentives. With increasing rewards for achieving their goal, they prioritize efficient performance, whereas with increasing penalties for failure they prioritize performing cautious performance. We further show that these dissociable strategies enable us to infer how motivated a given person was based on the positive consequences of success relative to the negative consequences of failure.
Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data
Authors: Vaughan Timothy G. , Sciré Jérémie , Nadeau Sarah A. , Stadler Tanja 
Published: September 2020

We estimate the basic reproductive number and case counts for 15 distinct SARS-CoV-2 outbreaks, distributed across 10 countries and one cruise ship, based solely on phylodynamic analyses of genomic data. Our results indicate that, prior to significant public health interventions, the reproductive numbers for a majority (10) of these outbreaks are similar, with median posterior estimates ranging between 1.4 and 2.8. These estimates provide a view which is complementary to that provided by those based on traditional line listing data. The genomic-based view is arguably less susceptible to biases resulting from differences in testing protocols, testing intensity, and import of cases into the community of interest. In the analyses reported here, the genomic data primarily provides information regarding which samples belong to a particular outbreak. We observe that once these outbreaks are identified, the sampling dates carry the majority of the information regarding the reproductive number. Finally, we provide genome-based estimates of the cumulative case counts for each outbreak, which allow us to speculate on the amount of unreported infections within the populations housing each outbreak. These results indicate that for the majority (7) of the populations studied, the number of recorded cases is much bigger than the estimated cumulative case counts, suggesting the presence of unsequenced pathogen diversity in these populations.Significance StatementSince the beginning of the COVID-19 outbreak in late 2019, researchers around the globe have sought to estimate the rate at which the disease spread through populations prior to public health intervention, as quantified by the parameter R0. This is often estimated based on case count data and may be biased due to the presence of import cases. To overcome this, we estimate R0 by applying Bayesian phylodynamic methods to SARS-CoV-2 genomes which have been made available by laboratories worldwide. We provide R0 and absolute infection count estimates for 15 distinct outbreaks. These estimates contribute to our understanding of the baseline transmission dynamics of the disease, which will be critical in guiding future public health responses to the pandemic.
Analysis of the Interventions Adopted Due to the COVID-19 on Ari Morbility for Colombia
Authors: Quijano-Angarita Á. , Espinosa O. , Mercado M. , Walteros D. , Malo D. 
Published: September 2020

AbstractAcute Respiratory Infections are among the leading causes of death globally, particularly in developing countries, and are highly correlated with the quality of health and surveillance systems and effective early interventions in high-risk age groups. According to the World Health Organization, about four million people die each year from mostly preventable respiratory tract infections, making it a public health concern. The official declaration of a pandemic in March 2020 due to the Sars-CoV-2 virus coincided with the influenza season in Colombia and with environmental alerts about low air quality that increase its incidence. The objective of this document is the application of a flexible model for the identification of the pattern and monitoring of ARI morbility for Colombia by age group that shows atypical patterns in the reported series for 5 departments and that coincide with the decisions implemented to contain the COVID-19.
High-resolution two-photon transcranial imaging of brain using direct wavefront sensing
Authors: Chen Congping , Qin Zhongya , He Sicong , Liu Shaojun , Lau Shun-Fat , Wu Wanjie , Zhu Dan , Ip Nancy Y. , Qu Jianan Y. 
Published: September 2020

AbstractImaging of the brain in its native state at high resolution poses major challenges to visualization techniques. Two-photon microscopy integrated with the thinned-skull or optical clearing skull technique provides a minimally invasive tool forin vivoimaging of the cortex of mice without activating immune response and inducing brain injury. However, the imaging contrast and resolution are severely compromised by the optical heterogeneity of the skull, limiting the imaging depth to the superficial layer. Here, we develop adaptive optics two-photon microscopy for high-resolution transcranial imaging of layer 5 pyramidal neurons up to 700 μm below pia in living mice. In particular, an optimized configuration of imaging system and new wavefront sensing algorithm are proposed for accurate correction for the aberrations induced by the skull window and brain tissue. We investigated microglia-plaque interaction in living brain of Alzheimer’s disease and demonstrated high-precision laser dendrotomy and single-spine ablation.
Low lymphocyte count is a risk factor for Parkinson’s disease
Authors: Jensen Melanie P , Jacobs Benjamin Meir , Dobson Ruth , Bandres-Ciga Sara , Blauwendraat Cornelis , Schrag Anette ,   The International Parkinson’s Disease Genomics Consortium (IPDGC), Noyce Alastair J 
Published: September 2020

AbstractImportanceBiomarkers for the early detection of Parkinson’s disease (PD) are needed. Patients with PD display differences in peripheral blood biomarkers of immune function, including leukocyte differential counts and C-reactive protein (CRP), compared to controls. These differences may be useful biomarkers to predict PD, and may shed light on PD pathogenesis.ObjectivesTo identify whether peripheral immune dysregulation is a pre-diagnostic feature of PD, and whether it plays a causal role.DesignCross-sectional association analysis of the relationship between differential leukocyte count and other markers of acute inflammation at enrolment, and incident cases of PD in UK Biobank. We used Mendelian randomization to establish whether differences in leukocyte differential counts have a causal influence on risk of PD.SettingUK Biobank; a population-based cohort with over 500,000 participants aged 40-69 recruited in the UK between 2006 and 2010.ParticipantsPD cases were defined as individuals with an ICD-10 coded diagnosis of PD. Cases were defined as ’incident’ if their age at diagnosis was greater than their age at recruitment to UKB. ’Controls’ were defined as individuals without a diagnosis of PD. After applying exclusion criteria for pre-existing health conditions that can influence blood counts, 507 incident PD cases and 328,280 controls were included in the analysis.ExposureBlood cell markers (absolute and relative counts) and other markers of inflammation were obtained from blood tests of participants taken at the initial visit.ResultsLower lymphocyte count was associated with increased odds of incident PD (odds ratio [OR] 0.77, 95% confidence interval [CI] 0.65-0.90). There was weaker evidence of association between lower eosinophil and monocyte counts, lower CRP, and higher neutrophil counts on risk of incident PD. The association between lymphopenia and incident PD remained robust to sensitivity analyses. Mendelian randomization analyses suggested that the effect of low lymphocyte count on PD risk was causal (OR 0.91, 95% CI 0.85 - 0.99).Conclusions and relevanceIn this large, prospective setting, lower lymphocyte count was associated with higher risk of subsequent PD diagnosis. Furthermore genetic evidence supported a causal role for lymphocyte count on PD risk.Key pointsQuestionIs the leukcoyte differential count a feature of pre-diagnostic Parkinson’s disease?FindingsIn the UK Biobank, a longitudinal cohort study with over 500,000 participants, lower lymphocyte count was associated with a 23% increased odds of incident PD, a significant difference. Mendelian randomisation revealed a convincing causal effect for low lymphocyte count on PD risk.MeaningPre-diagnostic Parkinson’s disease is associated with lower lymphocyte counts; the suggestion of causal effect may shed light on PD pathogenesis.
Single-cell RNA sequencing identifies aberrant transcriptional profiles of cellular populations and altered alveolar niche signalling networks in Chronic Obstructive Pulmonary Disease (COPD)
Authors: Sauler M , McDonough JE , Adams TS , Kothapalli N , Schupp JC , Nouws J , Chioccioli M , Omote N , Cosme C , Poli S , Ayaub EA , Chu SG , Jensen KH , Gomez-Villalobos J , Britto CJ , Raredon MSB , Timshel PN , Kaminski N , Rosas IO 
Published: September 2020

ABSTRACTChronic Obstructive Pulmonary Disease (COPD) pathogenesis involves a failure to maintain alveolar homeostasis due to repetitive injury and inflammation. In order to improve our understanding of cell-specific mechanisms contributing to COPD pathogenesis, we analysed single-cell RNA sequencing (scRNAseq) profiles of explanted parenchymal lung tissue from 17 subjects with advanced COPD requiring transplant and 15 control donor lungs. We identified a subpopulation of alveolar type II epithelial cells that uniquely expressHHIPand have aberrant stress tolerance profiles in COPD. Amongst endothelial cells, we identified overlapping and unique shifts in transcriptional profiles of endothelial subtypes that may contribute to vascular inflammation and susceptibility to injury. We also identified population composition changes amongst alveolar macrophages. Finally, application of integrative analyses to our scRNAseq data identified cell-specific contributions to COPD heritability and dysfunctional cell-cell communication pathways that occur within the COPD alveolar niche. These findings provide cell type-specific resolution of transcriptional changes associated with advanced COPD that may underlie disease pathogenesis.
Differences in innate Intracellular viral suppression competencies may explain variations in morbidity and mortality from SARS-CoV-2 infection
Authors: Bello Shaibu Oricha , Igumbor Ehimario , Deeni Yusuf Yahaya , Ochu Chinwe Lucia , Ayodele Popoola Mustapha 
Published: September 2020

AbstractSARS-CoV-2 infection and COVID-19 ravage the world with wide variations in morbidity and mortality that have remained largely unexplained, even by mutations in protein coding regions. In this study, we analyzed available complete SARS-CoV-2 sequences using the CpG index as a signature of Zinc finger antiviral protein (ZAP) activity to examine population variations in innate intracellular antiviral competencies. The result suggests that differential ZAP activity may be a major determinant of the outcome of SARS-CoV-2 infection. SARS-CoV-2 sequences from Africa, Asia, and pools of asymptomatic patients had I_CpG signature evidence of high ZAP activity, while SARS-CoV-2 sequences from North America and Intensive Care Unit or Deceased patients had I_CpG signature of low ZAP activity. ZAP activity is linked to the interferon system. Low ZAP activity may be part of the explanation for the increased morbidity of SARS-CoV-2 in the elderly and with comorbidities like diabetes, obesity, and hypertension. It may also provide some insight into the discrepancies between invitro anti-SARS-CoV-2 activities of candidate therapies and performance in clinical trials. Furthermore, our results suggest that asymptomatic patients may paradoxically shed a more dangerous virus.
Lack of consideration of sex and gender in clinical trials for COVID-19
Authors: Brady Emer , Nielsen Mathias Wullum , Andersen Jens Peter , Oertelt-Prigione Sabine 
Published: September 2020

AbstractSex and gender differences impact the incidence of SARS-CoV-2 infection and COVID-19 mortality. Furthermore, sex differences characterize the frequency and severity of pharmacological side effects. A large number of clinical trials are ongoing to develop new therapeutic approaches and vaccines for COVID-19. We investigated the inclusion of sex and/or gender in currently registered studies on http://ClinicalTrials.gov. Only 416 (16.7%) of the 2,484 registered SARS-CoV-2/COVID-19 trials mention sex/gender as recruitment criterion and only 103 (4.1%) allude to sex/gender in the description of the analysis phase. None of the 11 clinical trials published in scientific journals on June 2020 reported sex-disaggregated results. Hence, lack of consideration upon registration does not seem to be corrected during trial execution and reporting. Given the biological relevance and the potential risks of unwanted side effects, we urge researchers to focus on sex-disaggregated analyses already at the planning stage of COVID-19 trials.
Mental health service activity during COVID-19 lockdown among individuals with Personality Disorders: South London and Maudsley data on services and mortality from January to May 2020
Authors: Nuzum Eleanor , Martin Evangelia , Broadbent Matthew , Stewart Robert 
Published: September 2020

AbstractThe lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have a widespread impact on mental healthcare for both services themselves and the people accessing those services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemic’s first wave. However, there is a need to understand this further for specific groups, including those diagnosed with a personality disorder who might have particular vulnerabilities. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with personality disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st May 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with personality disorders. In addition, daily deaths are described for all current and previous SLaM service users with personality disorder over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. Liaison and Older Adult teams showed the largest drop in caseloads, whereas Early Intervention in Psychosis service caseloads remained the same. Reduced accepted referrals and inpatient admissions were observed and there was a 28% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March.