bluuebunny/crossref_metadata_2025_split huggingface dataset:
A head-mounted multi-camera system for electrophysiology and behavior in freely-moving mice
Authors: Sattler Nicholas , Wehr Michael 
Published: July 2020

AbstractAdvances in the ability to monitor freely-moving mice may prove valuable for the study of behavior and its neural correlates. Here we describe a head-mounted multi-camera system for mice, comprised of inexpensive miniature analog camera modules. We illustrate the use of this system with several natural behaviors including prey capture, courtship, jumping, and exploration. With a four-camera headset, monitoring the eyes, ears, whiskers, rhinarium, and binocular visual field can all be achieved simultaneously with high-density electrophysiology. With appropriate focus and positioning, all eye movements can be captured, including cyclotorsion. For studies of vision and eye movements, cyclotorsion provides the final degree of freedom required to reconstruct the visual scene in retinotopic coordinates or to investigate the vestibulo-ocular reflex in mice. Altogether, this system allows for comprehensive measurement of freely-moving mouse behavior, enabling a more holistic and multimodal approach to investigate ethological behaviors and other processes of active perception.
Quantifying the impact of US state non-pharmaceutical interventions on COVID-19 transmission
Authors: Korevaar Hannah M. , Becker Alexander D. , Miller Ian F. , Grenfell Bryan T. , Metcalf C. Jessica E. , Mina Michael J. 
Published: July 2020

AbstractCOVID-19 is an ongoing public health emergency. Without a vaccine or effective antivirals, non-pharmaceutical interventions form the foundation of current response efforts. Quantifying the efficacy of these interventions is crucial. Using mortality data and a classification guide of state level responses, we relate the intensity of interventions to statistical estimates of transmission, finding that more stringent control measures are associated with larger reductions in disease proliferation. Additionally, we observe that transmission increases with population density, but not population size. These results may help inform future response efforts.
ClinSV: Clinical grade structural and copy number variant detection from whole genome sequencing data
Authors: Minoche Andre E , Lundie Ben , Peters Greg B , Ohnesorg Thomas , Pinese Mark , Thomas David M , Zankl Andreas , Roscioli Tony , Schonrock Nicole , Kummerfeld Sarah , Burnett Leslie , Dinger Marcel E , Cowley Mark J 
Published: July 2020

AbstractWhole genome sequencing (WGS) has the potential to outperform clinical microarrays for the detection of structural variants (SV) including copy number variants (CNVs), but has been challenged by high false positive rates. Here we present ClinSV, a WGS based SV integration, annotation, prioritisation and visualisation method, which identified 99.8% of pathogenic ClinVar CNVs >10kb and 11/11 pathogenic variants from matched microarrays. The false positive rate was low (1.5–4.5%) and reproducibility high (95–99%). In clinical practice, ClinSV identified reportable variants in 22 of 485 patients (4.7%) of which 35–63% were not detectable by current clinical microarray designs.
Social-distancing effectiveness tracking of the COVID-19 hotspot Stockholm
Authors: Oberhammer Joachim 
Published: July 2020

SummaryBackgroundThe COVID-19 outbreak in Stockholm, Sweden, is characterized by a near-absence of governmental interventions and high fatalities in the care home population. This study analyses the outbreak and the social-distancing effectiveness timeline in the general population and the care homes.MethodsA novel distributed-compartmental, time-variant epidemiological model was designed specifically for COVID-19 transmission characteristics, featuring a/pre/symptomatic transmission, a non-linear hospital model, a weakly-coupled sub-model for the care-home population, and parametrized continuous social-distancing functions. The model parameters and the social-distancing timelines are determined by randomization and Monte-Carlo simulations analysing real-world data.FindingsDespite a high initial reproduction number (3·29) and the near-absence of governmental interventions, the model quantitated that the transmission rate in the general population was suppressed by 73%, and in the care homes by 79%. The measures in the care homes took effect 4·8 days delayed; and if applied 4 or 8 days earlier, the fatalities could have been reduced by 63·2% or 89·9%. The infected population is estimated to 16·2% (June 10). An expected underestimation of population immunity by antibody studies is confirmed. The infection fatality ratio extrapolates to 0·61% (peak: 1·34%). The model indicates a seasonal effect which effectively suppressed a new rise. An analysed large-scale public event had no large influence. The asymptomatic ratio was determined to 35%.InterpretationThe proposed model and methods have proven to analyse a COVID-19 outbreak and to re-construct the social-distancing behaviour with unprecedented accuracy, confirming even minor details indicated by mobility-data analysis, and are applicable to other regions and other emerging infectious diseases of similar transmission characteristics. The self-regulation of the population in Stockholm, influenced by advices by the authorities, was able to suppress a COVID-19 outbreak to a level far beyond that the stringency index of governmental interventions suggests. Proper timing of effective measures in the care homes is important to reduce fatalities.
APOE4 Copy Number-Dependent Proteomic changes in the Cerebrospinal Fluid
Authors: Berger Miles , Cooter Mary , Roesler Alexander S. , Chung Stacey , Park John , Modliszeski Jennifer L. , VanDusen Keith W. , Thompson J. Will , Moseley Arthur , Devinney Michael J. , Smani Shayan , Hall Ashley , Cai Victor , Browndyke Jeffrey N. , Lutz Michael W. , Corcoran David L. ,   Alzheimer’s Disease Neuroimaging Initiative
Published: July 2020

AbstractBackgroundAPOE4 has been hypothesized to increase Alzheimer’s disease risk by increasing neuroinflammation, though the specific neuroinflammatory pathways involved are unclear.ObjectivesTo characterize CSF proteomic changes as a function of APOE4 copy number.MethodsWe analyzed targeted proteomic data obtained on ADNI CSF samples using a linear regression model adjusting for age, sex, and APOE4 copy number, and a second linear model also adjusting for AD clinical status. False Discovery Rate (FDR) was used to correct for multiple comparisons.ResultsIn the first model, increasing APOE4 copy number was associated with significant expression decreases in a CRP peptide (q=0.006), and significant expression increases in peptides from ALDOA, CH3L1 (YKL-40), and FABPH (q<0.05 for each). In the second model (controlling for age, sex, and AD clinical status), increasing APOE4 copy number was associated with significant expression decreases in a CRP peptide (q=0.009). In both models, increased APOE4 copy number was associated with trends towards lower expression of all 24 peptides from all 8 different complement proteins measured here, although none of these differences were statistically significant. The odds of this happening by chance for 24 unrelated peptides would be less than 1 in 16 million.ConclusionsIncreasing APOE4 copy number was associated with decreased CSF CRP levels and increased CSF ALDOA, CH3L1 and FABH levels; the CRP decrease remained significant after controlling for AD clinical status. Increased APOE4 copy number may also be associated with decreased CSF complement pathway protein levels, a hypothesis for investigation in future studies.
Characteristics, outcome and predictors of in-hospital mortality in an elderly population from a SARS-CoV-2 outbreak in a long-term care facility
Authors: Trecarichi Enrico Maria , Mazzitelli Maria , Serapide Francesca , Pelle Maria Chiara , Tassone Bruno , Arrighi Eugenio , Perri Graziella , Fusco Paolo , Scaglione Vincenzo , Davoli Chiara , Lionello Rosaria , Gamba Valentina La , Marrazzo Giuseppina , Busceti Maria Teresa , Giudice Amerigo , Ricchio Marco , Cancelliere Anna , Lio Elena , Procopio Giada , Costanzo Francesco Saverio , Foti Daniela Patrizia , Matera Giovanni , Torti Carlo ,   IDTM UMG COVID-19 Group
Published: July 2020

AbstractSince December 2019, coronavirus disease 2019 (COVID-19) pandemic has spread from China all over the world, many COVID-19 outbreaks have been reported in long-term care facilities (LCTF). However, data on clinical characteristics and prognostic factors in such settings are scarce. We conducted a retrospective, observational cohort study to assess clinical characteristics and baseline predictors of mortality of COVID-19 patients hospitalized after an outbreak of SARS-CoV-2 infection in a LTCF.A total of 50 patients were included. Mean age was 80 years (SD, 12 years), and 24/50 (57.1%) patients were males. A total of 42/50 (84%) patients experienced symptoms of SARS-CoV-2 infection. The overall in-hospital mortality rate was 32%. In Cox regression, significant predictors of in-hospital mortality were: hypernatremia (HR 9.12), lymphocyte count <1000 cells/µL (HR 7.45), cardiovascular diseases other than hypertension (HR 6.41), and higher levels of serum interleukin-6 (IL-6, pg/mL) (HR 1.005).Our study shows a high in-hospital mortality rate in a cohort of elderly patients with COVID-19 and hypernatremia, lymphopenia, CVD other than hypertension, and higher IL-6 serum levels were identified as independent predictors of in-hospital mortality. Further studies are necessary to better understand and confirm our findings in the setting of a LTCF outbreak of COVID-19.
Low-Impact Social Distancing Interventions to Mitigate Local Epidemics of SARS-CoV-2
Authors: Jackson Michael L. 
Published: July 2020

AbstractBackgroundAfter many jurisdictions have implemented intensive social distancing to suppress SARS-CoV-2 transmission, the challenge now is to mitigate the ongoing COVID-19 epidemic without overburdening economic and social activities. This report explores “low-impact” interventions to mitigate SARS-CoV-2 with a minimum of social and economic disruption.MethodsAn agent-based model simulated the population of King County, Washington, with agents that interact in homes, schools, workplaces, and other community sites. SARS-CoV-2 transmission probabilities were estimated by fitting simulated to observed hospital admissions from February – May 2020. Interventions considered were (a) encouraging telecommuting; (b) reducing contacts to seniors and nursing home residents; (c) modest reductions to contacts outside of the home; (d) encouraging self-isolation of persons with COVID-19 symptoms; (e) rapid testing and household quarantining.ResultsIndividual interventions are not expected to have a large impact on COVID-19 hospitalizations. No intervention reduced COVID-19 hospitalizations by more than 12.7% (95% confidence interval [CI], 12.0% to 13.3%). Removing all interventions would result in nearly 42,000 COVID- 19 hospitalizations between June 2020 and January 2021, with peak hospital occupancy exceeding available beds 6-fold. Combining the interventions is predicted to reduce total hospitalizations by 48% (95% CI, 47-49%), with peak COVID-19 hospital occupancy of 70% of total beds. Targeted school closures can further reduce the peak occupancy.ConclusionsCombining low-impact interventions may mitigate the course of the COVID-19 epidemic, keeping hospital burden within the capacity of the healthcare system. Under this approach SARS-CoV-2 can spread through the community, moving toward herd immunity, while minimizing social and economic disruption.
Transmission Dynamics of the COVID-19 Epidemics in England
Authors: Liu Yang , Tang Julian W , Lam Tommy TY 
Published: July 2020

AbstractThe ongoing COVID-19 pandemic has caused a tremendous health burden and impact on the world economy. As one of the European countries experiencing one of the worst COVID-19 epidemics, the UK government at the end of March 2020 implemented the biggest lockdown of society during peacetime in British history, aiming to contain the rapid spread of the virus. While the lockdown has been maintained for seven weeks in UK, the effectiveness of the control measures in suppressing the transmission of the disease remains incompletely understood. Here we applied a Bayesian SEIR (susceptible-exposed-infected-removed) epidemiological model to rebuild the local transmission dynamics of the spread of COVID-19 in nine regions of England. We found that the basic reproduction number (R0) in England is relatively high compared with China. Our estimation of the temporally varying effective reproduction number (Rt) suggests that the control measures, especially the forceful lockdown, were effective to reduce the transmissibility and curb the COVID-19 epidemic. Although the overall incidence rate in the UK has declined, our forecasting highlights the possibility of a second wave of the disease in several regions, which may be currently underway in one of the cities there (e.g. Leicester, East Midlands). This study enhances our understanding of the current outbreak and effectiveness of control measures in the UK.
Investigating the effect of respiratory indices to predict mortality and the status of trauma patients using artificial neural networks
Authors: Hafezi Zahra , Sabouri Mohammad , Shayan Milad , Paydar Shahram 
Published: July 2020

AbstractIntroductionKnowing the final status of trauma patients and clearly understanding their condition are always significant due to the complexity of injuries and the high dependence of the patient’s condition on various factors. That is why it allows doctors to be able to provide required facilities in a broader perspective and perform appropriate action. In addition, it can avoid wasting time and energy and then increasing patient mortality. While, there are several ways to measure and predict the final status of patients but all of them have some defects. Therefore, it is very important for the significance of the system design with high accuracy and reliability to be able to help physicians investigate the final status of trauma patients.MethodIn this study, a method, a sub-branch of data science and artificial intelligence, is presented and studied based on artificial neural networks to estimate the final status of trauma patients and predict their survival and death probabilities during the treatment and care process. In the proposed method, the final status of patients is predicted using 13 respiratory indices. This method is run in Matlab and its efficiency is studied.ResultsResearch subjects include 3073 patients, 494 females and 2579 males, from Shahid Rajaei Medical Center in Shiraz. In general, according to the results from testing the method, it has been able to accurately predict the mortality of patients based on respiratory indices. The proposed structure has been able to predict patients’ survival and death probabilities with an accuracy of %73.75 and %99.71 respectively. Therefore, we can conclude that the presented and examined method can make a significant relevance between calculated respiratory indices and final status of patients.Discussion and ConclusionDue to the present study and the obtained results and investigating the mortality relevance with the other 13 respiratory indices using artificial intelligence-based methods, it can be stated that these indicators are good criteria for predicting mortality.
Exploring Epidemiological Behavior of Novel Coronavirus Outbreak through the Development and Analysis of COVID-19 Daily Dataset in Bangladesh
Authors: Dey Samrat Kumar , Rahman Md. Mahbubur , Siddiqi Umme Raihan , Howlader Arpita 
Published: July 2020

AbstractBackgroundGlobally, there is an obvious concern about the fact that the evolving 2019-nCoV coronavirus is a worldwide public health threat. The appearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China at the end of 2019 triggered a major global epidemic, which is now a major community health issue. As of April 17, 2020, according to Institute of Epidemiology, Disease Control and Research (IEDCR) Bangladesh has reported 1838 confirmed cases in between 8 March to 17 April 2020, with > 4.08% of mortality rate and >3.15% of recovery rate. COVID-19 outbreak is evolving so rapidly in Bangladesh; therefore, the availability of epidemiological data and its sensible analysis are essential to direct strategies for situational awareness and intervention.MethodThis article presents an exploratory data analysis approach to collect and analyze COVID-19 data on epidemiological outbreaks based on first publicly available COVID-19 Daily Dataset of Bangladesh. Various publicly open data sources on the outbreak of COVID-19 provided by the IEDCR, World Health Organization (WHO), Directorate General of Health Services (DGHS), and Ministry of Health and Family Welfare (MHFW) of Bangladesh have been used in this research.ResultsA Visual Exploratory Data Analysis (V-EDA) techniques have been followed in this research to understand the epidemiological characteristics of COVID-19 outbreak in different districts of Bangladesh in between 8 March 2020 to 12 April 2020 and these findings were compared with those of other countries.ConclusionsIn all, this is extremely important to promptly spread information to understand the risks of this pandemic and begin containment activities in the country.
Potential role of Mercury pollutants in the success of Methicillin-ResistantStaphylococcus aureusUSA300 in Latin America
Authors: Gustave C. A. , Rasigade J.P. , Martins-Simões Patricia , Couzon F. , Bourg Chloe , Tristan Anne , Laurent Frédéric , Wirth T. , Vandenesch F. 
Published: July 2020

AbstractCommunity-acquired methicillin-resistantStaphylococcus aureus(CA-MRSA) lineage known as USA300-North American (NA) has become highly prevalent in North America whilst a USA300 variant known as USA300-LV, harboring a mercury resistance element (COMER), has become dominant in South America. We investigated whether mercury pollution, which is common in South America notably because of artisanal gold mining, may explain the local dominance pattern of USA300-LV. Density-based estimation of epidemic success in 250 genomes of the ST8 lineage revealed that the acquisition of COMER in USA300 progenitors increased success in South American countries but decreased success elsewhere. The fitness of USA300-LV was impairedin vitrocompared with USA300-NA, but the addition of sub-inhibitory concentration of mercury provided a strong fitness advantage to USA300-LV and triggered an overexpression of major virulence factors. The success of USA300-LV in South America may result from low-level mercury exposure selecting resistant and virulent strains.
Hyperrealistic neural decoding: Reconstructing faces from fMRI activations via the GAN latent space
Authors: Dado Thirza , Güçlütürk Yağmur , Ambrogioni Luca , Ras Gabriëlle , Bosch Sander E. , van Gerven Marcel , Güçlü Umut 
Published: July 2020

AbstractNeural decoding can be conceptualized as the problem of mapping brain responses back to sensory stimuli via a feature space. We introduce (i) a novel experimental paradigm which uses well-controlled yet highly naturalistic stimuli with a priori known feature representations and (ii) an implementation thereof for HYPerrealistic reconstruction of PERception (HYPER) of faces from brain recordings. To this end, we embrace the use of generative adversarial networks (GANs) at the earliest step of our neural decoding pipeline by acquiring fMRI data as subjects perceive face images synthesized by the generator network of a GAN. We show that the latent vectors used for generation effectively capture the same defining stimulus properties as the fMRI measurements. As such, GAN latent vectors can be used as features underlying the perceived images that can be predicted for (re-)generation, leading to the most accurate reconstructions of perception to date.
VELCRO-IP RNA-seq explores ribosome expansion segment function in translation genome-wide
Authors: Leppek Kathrin , Byeon Gun Woo , Fujii Kotaro , Barna Maria 
Published: July 2020

SUMMARYRoles for ribosomal RNA (rRNA) in gene regulation remain largely unexplored. With hundreds of rDNA units scattered across multiple chromosomal loci, it is not possible to genetically modify rRNA in mammalian cells, hindering understanding of ribosome function. Emerging evidence suggests that expansion segments (ESs), tentacle-like rRNA extensions that vary in sequence and size across eukaryotic evolution, may provide platforms for the binding of proteins and mRNAs. Here, we develop VELCRO-IP RNA-seq: a versatile methodology to generate species-adapted ESs and map specific mRNA regions across the transcriptome that preferentially associate with ESs. By applying VELCRO-IP RNA-seq to a mammalian ES, ES9S, we identified a large array of mRNAs that are selectively recruited to ribosomes via an ES. We further characterize a set of specific 5’ UTRs that facilitate cap-independent translation through ES9S-mediated ribosome recruitment. These data provide a novel technology for studying the enigmatic ESs of the ribosome in gene-specific translation.
MORT, a locus for apoptosis in the human immunodeficiency virus-type 1 antisense gene: implications for AIDS, Cancer, and Covid-19
Authors: Ludwig Linda B. , Albert Michael S. 
Published: July 2020

AbstractApoptosis, or programmed cell death, is a fundamental requirement for life in multicellular organisms, including humans, and a mechanism to maintain homeostasis and prevent unwarranted cellular proliferations such as cancer. An antisense gene in HIV-1 (Hap) induces apoptosis in human cells. Apoptotic T cell death following HIV-1 infection leads to a compromised immune system and eventually AIDS (acquired immunodeficiency syndrome). A review of several studies that focused on long-term survivors of HIV-1 reveals that these survivors had deletion-mutations inHap. A subset of these survivors changed course and experienced CD4+ T cell death and progression to AIDS. These individuals had virus that regainedHapgene sequence that had previously been deleted. Analysis of the changes in the genetic sequences within vivoprogression of the revertant HIV-1 virus allowed identification of a specific region inHapwe are calling MORT. MORT, inHapRNA forms a primary microRNA-like structure. Potential human mRNAs targeted by MORT mi/siRNAs include gene/RNA sequences of X-linked inhibitor of apoptosis (XIAP), survivin, and apollon, along with many other human gene sites/RNAs. Thus MORT may be acting as an RNA antagonist to cellular IAPs thereby inducing apoptotic cell death. Surprisingly, additional potential MORT targets include viral sites in human SARS-CoV-2, including the protease, nsp5 RNA. Future uses for RNA therapy and a hypothesis for an HIV intrinsic mechanism utilizing MORT for viral anti-viral (or anti-microbial) and HIV anti-immune cell defense are proposed.