bluuebunny/crossref_metadata_2025_split huggingface dataset:
The spatial spread of HIV in Malawi: An individual-based mathematical model
Authors: Estill Janne , Ng’ambi Wingston , Rozanova Liudmila , Keiser Olivia 
Published: December 2020

AbstractThe prevalence of HIV varies greatly between and within countries. We therefore developed a flexible individual-based mathematical model for HIV transmission, that comprises a spatial representation and individual-level determinants. We tested this model by calibrating it to the HIV epidemic in Malawi and exploring whether the heterogeneity in HIV prevalence could be caused without accounting for heterogeneity in behaviour. We ran the model for Malawi between years 1975-2030 with five alternative realizations of the geographical structure and mobility: (I) no geographical structure; 28 administrative districts including (II) only permanent relocations between districts, (III) permanent relocations and between-district casual sexual relationships, or (IV) permanent relocations between districts and to/from abroad and between-district casual sex; and (V) a grid of 10×10km2 cells, with permanent relocations and between-cell casual relationships. We assumed HIV was present in 1975 in the districts with >10% prevalence in 2010. We calibrated the models to national and district-level prevalence estimates.Reaching the national prevalence required all adults to have at least 20 casual sex acts/year until 1990. Models II, III and V reproduced the geographical heterogeneity in prevalence to some extent if between-district relationships were either excluded (Model II) or restricted to minimum (Models III, V). Long-distance casual partnership mixing (Models III-V) mitigated the differences in prevalence substantially; with international migration the differences disappeared completely (Model IV). National prevalence was projected to decrease to 4-5% by 2030. Our model sustained the major differences in HIV prevalence across Malawi, if casual relationships between districts were kept at sufficiently low level. An earlier introduction of HIV into the Southern part of Malawi may thus be one of the explanations to the present heterogeneity in HIV prevalence.Author summaryThe prevalence of HIV varies greatly across the settings, both globally and within countries. The ability of the commonly used compartmental models to account for the geographical structure and individual-level determinants that cause this heterogeneity is limited. In this project, we developed an individual-based simulation framework for modelling HIV transmission in a real setting. We built the model to take into account an unlimited number of individual-level characteristics, and a geographical representation of the setting that can be defined using an arbitrary resolution and distance matrices. We demonstrate the use of this model by simulating the HIV epidemic of Malawi 1975-2030 and exploring whether the observed heterogeneity could be preserved without taking into account any spatial heterogeneity in sexual behaviour. A relatively simple version of the model reproduced the broad-scale differences in HIV prevalence, but the detailed differences will need further investigation.
Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa
Authors: Colson Philippe , Levasseur Anthony , Gautret Philippe , Fenollar Florence , Hoang Van Thuan , Delerce Jeremy , Bitam Idir , Saile Rachid , Maaloum Mossaab , Padane Abdou , Bedotto Marielle , Brechard Ludivine , Bossi Vincent , Khedher Mariem Ben , Chaudet Hervé , Million Matthieu , Tissot-Dupont Hervé , Lagier Jean-Christophe , Mboup Souleymane , Fournier Pierre-Edouard , Raoult Didier 
Published: December 2020

ABSTRACTBACKGROUNDIn Marseille, France, the COVID-19 incidence evolved unusually with several successive epidemic episodes. The second outbreak started in July, was associated with North Africa, and involved travelers and an outbreak on passenger ships. This suggested the involvement of a new viral variant.METHODSWe sequenced the genomes from 916 SARS-CoV-2 strains from COVID-19 patients in our institute. The patients’ demographic and clinical features were compared according to the infecting viral variant.RESULTSFrom June 26th to August 14th, we identified a new viral variant (Marseille-1). Based on genome sequences (n=89) or specific qPCR (n=53), 142 patients infected with this variant were detected. It is characterized by a combination of 10 mutations located in the nsp2, nsp3, nsp12, S, ORF3a, ORF8 and N/ORF14 genes. We identified Senegal and Gambia, where the virus had been transferred from China and Europe in February-April as the sources of the Marseille-1 variant, which then most likely reached Marseille through Maghreb when French borders reopened. In France, this variant apparently remained almost limited to Marseille. In addition, it was significantly associated with a milder disease compared to clade 20A ancestor strains.CONCLUSIONOur results demonstrate that SARS-CoV-2 can genetically diversify rapidly, its variants can diffuse internationally and cause successive outbreaks.
Discrepancies in automated, electronic medical record-based CHA2DS2-VASc scores and clinician assessment for atrial fibrillation patients
Authors: Jones Aubrey E. , Abedin Zameer , Ilkun Olesya , Mukherjee Rebeka , Zhang Mingyuan , White Michael , Steinberg Benjamin A. , Shah Rashmee U. 
Published: December 2020

AbstractBackgroundClinical decision support tools for atrial fibrillation (AF) should include CHA2DS2- VASc scores to guide oral anticoagulant (OAC) treatment.ObjectiveWe compared automated, electronic medical record (EMR) generated CHA2DS2- VASc scores to clinician-documented scores, and report the resulting proportions of patients in the OAC treatment group.MethodsPatients were included if they had both a clinician documented and EMR-generated CHA2DS2-VASc score on the same day. EMR scores were based on billing codes, left ventricular ejection fraction from echocardiograms, and demographics; documented scores were identified using natural language processing. Patients were deemed “re-classified” if the EMR score was ≥2 but the documented score was <2, and vice versa. For the overall cohort and subgroups (sex and age group), we compared mean scores using paired t-tests and re-classification rates using chi-squared tests.ResultsAmong 5,767 patients, the mean scores were higher using EMR compared to documented scores (4.05 [SD 2.1] versus 3.13 [SD 1.8]; p<0.01) for the full cohort, and all subgroups (p<0.01 for all comparisons). If EMR scores were used to determine OAC treatment instead of documented scores, 8.3% (n=479, p<0.01) of patients would be re-classified, with 7.2% moving into and 1.1% moving out of the treatment group. Among 2,322 women, 4.7% (n=109, p<0.01) would be re-classified, with 4.1% into and 0.7% out of the treatment group. Among 3,445 men, 10.7% (n=370, p<0.01) would be re-classified, with 9.2% into and 1.5% out of the treatment group. Among 2,060 patients <65 years old, 18.1% (n=372, p<0.01) would be re-classified, with 15.8% into and 2.3% out of the treatment group. Among 1,877 patients 65-74 years old, 5.4% (n=101, p<0.01) would be re-classified, with 4.4% into and 1.0% out of the treatment group. Among 1,830 patients ≥75 years old, <1% would move into to the treatment group and none would move out of the treatment group.ConclusionsEMR-based CHA2DS2-VASc scores were, on average, almost a full point higher than the clinician-documented scores. Using EMR scores in lieu of documented scores would result in a significant proportion of patients moving into the treatment group, with the highest re-classifications rates in men and patients <65 years old.
The experience of European hospital-based health care workers on following infection prevention and control procedures for COVID-19
Authors: van Hout Denise , Hutchinson Paul , Wanat Marta , Pilbeam Caitlin , Goossens Herman , Anthierens Sibyl , Tonkin-Crine Sarah , Gobat Nina 
Published: December 2020

ABSTRACTBackgroundWorking under pandemic conditions exposes health care workers (HCWs) to infection risk and psychological strain. Protecting the physical and psychological health of HCWs is a key priority. This study assessed the perceptions of European hospital HCWs of local infection prevention and control (IPC) procedures during the COVID-19 pandemic and the impact on their emotional wellbeing.MethodsWe performed two rounds of an international cross-sectional survey, between 31 March and 17 April 2020 via existing research networks (round 1), and between 14 May and 31 August 2020 via online convenience sampling (round 2). Main outcome measures were (1) behavioural determinants of HCW adherence with IPC procedures, (2) WHO-5 Well-Being Index, a validated scale of 0-100 reflecting emotional wellbeing. The WHO-5 was interpreted as a score below or above 50 points, a cut-off score used in previous literature to screen for depression.Results2,289 HCWs (round 1: n=190, round 2: n=2,099) from 40 countries in Europe participated. Mean age of respondents was 42 (±11) years, 66% were female, 47% and 39% were medical doctors and nurses, respectively. 74% (n=1699) of HCWs were directly treating patients with COVID-19, of which 32% (n=527) reported they were fearful of caring for these patients. HCWs reported high levels of concern about COVID-19 infection risk to themselves (71%) and their family (82%) as a result of their job. 40% of HCWs considered that getting infected with COVID-19 was not within their control. This was more common among junior than senior HCWs (46% versus 38%, P value <.01). Sufficient COVID-19-specific IPC training, confidence in PPE use and institutional trust were positively associated with the feeling that becoming infected with COVID-19 was within their control. Female HCWs were more likely than males to report a WHO-5 score below 50 points (aOR 1.5 (95% confidence interval (CI) 1.2-1.8).ConclusionsIn Europe, the COVID-19 pandemic has had a differential impact on those providing direct COVID-19 patient care, junior staff and women. Health facilities must be aware of these differential impacts, build trust and provide tailored support for this vital workforce during the current COVID-19 pandemic.
Reducing contacts to stop SARS-CoV-2 transmission during the second pandemic wave in Brussels, Belgium
Authors: Ingelbeen Brecht , Peckeu Laurène , Laga Marie , Hendrix Ilona , Neven Inge , van der Sande Marianne A. B. , van Kleef Esther 
Published: December 2020

AbstractBackgroundReducing contacts is a cornerstone of containing SARS-CoV-2. We evaluated the effect of physical distancing measures and of school reopening on contacts and consequently on SARS-CoV-2 transmission in Brussels, a hotspot during the second European wave.MethodsUsing SARS-CoV-2 case reports and contact tracing data during August-November 2020, we estimated changes in the age-specific number of reported contacts. We associated these trends with changes in the instantaneous reproduction number Rt and in age-specific transmission-events during distinct intervention periods in the Brussels region. Furthermore, we analysed trends in age-specific case numbers, pre- and post-school opening.FindingsWhen schools reopened and physical distancing measures relaxed, the weekly mean number of reported contacts surged from 2.01 (95%CI 1.73-2.29) to 3.04 (95%CI 2.93-3.15), increasing across all ages. The fraction of cases aged 10-19 years started increasing before school reopening, with no further increase following school reopening (risk ratio 1.23, 95%CI 0.79-1.94). During the subsequent month, 8.9% (67/755) of infections identified were from teenagers to other ages, while 17.0% (131/755) from other ages to teenagers. Rt peaked mid-September at 1.48 (95%CI 1.35-1.63). Reintroduction of physical distancing measures reduced reported contacts to 1.85 (95%CI 1.78-1.91), resulting in Rt dropping below 1 within 3 weeks.InterpretationThe second pandemic wave in Brussels was the result of increased contacts across all ages following school reopening. Stringent physical distancing measures, including closure of bars and limiting close contacts while schools remain open, reduced social mixing, in turn controlling SARS-CoV-2 transmission.FundingEuropean Commission H2020. GGC Brussel.
Plasmodiophora brassicaechitin-binding effectors guard and mask spores during infection
Authors: Muirhead Kevin , Pérez-López Edel 
Published: December 2020

ABSTRACTPlants have a sophisticated and multilayered immune system. However, plant pathogens, helped by effector proteins, have found several strategies to evade plant immunity. For instance, the clubroot pathogen,Plasmodiophora brassicae,is able to turn the roots of the susceptible hosts into nutrient-sink galls surpassing patterns-triggered immunity (PTI) and effector-triggered immunity (ETI). Chitin, the main component ofP. brassicaespores cell walls and a well-known pathogens-associated molecular pattern (PAMP), can elicit PTI but is also the target of plant chitinases and chitin deacetylases. The fact thatP. brassicaedoes not trigger PTI during the infection of the susceptible hosts motivated a genome-wide search of genes coding for secreted chitin-related proteins. We found thatP. brassicaegenome encodes a large repertoire of candidate-secreted effectors containing the chitin-binding domain carbohydrate-binding module family 18 (CBM18), along with chitinases and chitin deacetylases domains. The role of such proteins in the pathogenicity of the clubroot pathogen is unknown. Here, we characterized the function of two effectors,PbChiB2 andPbChiB4, which are transcriptionally activated during the spores transition to uninucleate primary plasmodium and during the spore formation. Through co-precipitation, we found that recombinantPbChiB2 andPbChiB4 bind to the spores and to chitin oligomersin vitro. We also showed that both proteins suppress chitin-triggered activation of the immune MPK3 and MPK6 in the hostBrassica napus. These findings suggest a dual role for theP. brassicaeCBM18 proteins as effectors for protecting zoospores and resting spores formation and for suppressing chitin-triggered immunity during the infection.
Comparative assessment of allelopathic herbicidal actions and total phenolics content of seven Indian medicinal plants
Authors: Goswami Souren , Ray Sanjib 
Published: December 2020

AbstractAllelopathy is a vital ecological process that influences the dynamics of ecological succession, structure, and composition of plant communities. The present study aimed to evaluate a comparative account of allelopathic inhibitory actions in relation to total phenolic contents of aqueous extracts from seven traditionally used medicinal plants of India.Triticum aestivumandCicer arietinumseedlings were used to test seed germination inhibition, seedling growth retardation and branch root sprouting inhibition.Allium ceparoot tip cells were used for mitotic index inhibition and abnormal cell percentage analysis. The correlation between the total phenolics content and allelopathic activities was analyzed. The different extracts show the varied degree of allelopathic inhibitory activity. Out of these seven used extracts,Crinum asiaticumleaf extract (CaLAE) showed the highest allelopathic inhibitory action and it could reduce 94.3 and 79.59% root and shoot growth respectively at 96 h of treatment (1 mg/mL) and that was increased to 96.18 and 93.78% respectively with 2 mg/mL. The quantitative phytochemical analysis also revealed that CaLAE also possess relatively higher amounts of total phenolics. The growth retardation effects of the extract are in accordance with the mito-depression and increased chromosomal abnormality inA. ceparoot tip cells. In conclusion,Crinum asiaticummay be considered as a prospective source of allelochemicals for plant growth regulation and a source of commercial herbicidal products.
The hidden state-dependency of transcranial alternating current stimulation (tACS)
Authors: Kasten Florian H. , Herrmann Christoph S. 
Published: December 2020

AbstractNon-invasive techniques to electrically stimulate the brain such as transcranial direct and alternating current stimulation (tDCS/tACS) are increasingly used in human neuroscience and offer potential new avenues to treat brain disorders. However, their often weak and variable effects have also raised concerns in the scientific community. A possible factor influencing the efficacy of these methods is the dependence on brain-states. Here, we utilized Hidden Markov Models (HMM) to decompose concurrent tACS-magnetoencephalography data into transient brain-states with distinct spatial, spectral and connectivity profiles. We found that out of four spontaneous brain-states only one was susceptible to tACS. No or only marginal effects were found in the remaining states. TACS did not influence the time spent in each state. Our results suggest, that tACS effects may be mediated by a hidden, spontaneous state-dependency and provide novel insights to the changes in oscillatory activity underlying aftereffects of tACS.
Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein
Authors: Tetter Stephan , Terasaka Naohiro , Steinauer Angela , Bingham Richard J. , Clark Sam , Scott Andrew J. P. , Patel Nikesh , Leibundgut Marc , Wroblewski Emma , Ban Nenad , Stockley Peter G. , Twarock Reidun , Hilvert Donald 
Published: December 2020

AbstractViruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution to convert a bacterial enzyme lacking affinity for nucleic acids into an artificial nucleocapsid that efficiently packages and protects multiple copies of its own encoding mRNA. Revealing remarkable convergence on the molecular hallmarks of natural viruses, the accompanying changes reorganized the protein building blocks into an interlaced 240-subunit icosahedral capsid impermeable to nucleases, while emergence of a robust RNA stem-loop packaging cassette ensured high encapsidation yields and specificity. In addition to evincing a plausible evolutionary pathway for primordial viruses, these findings highlight practical strategies for developing non-viral carriers for diverse vaccine and delivery applications.
Genetically engineered retina for improved retinal reconstruction after transplantation
Authors: Matsuyama Take , Tu Hung-Ya , Sun Jianan , Hashiguchi Tomoyo , Akiba Ryutaro , Sho Junki , Fujii Momo , Onishi Akishi , Takahashi Masayo , Mandai Michiko 
Published: December 2020

AbstractES/iPS-retinal sheet transplantation, which supplies photoreceptors as well as other retinal cells, has been shown able to restore visual function in mice with end-stage retinal degeneration. Here, by introducing a novel type of genetically engineered ES/iPS-retinal sheet with reduced numbers of secondary retinal neurons but intact photoreceptor cell layer structure, we reinforced the evidence that ES/iPS-retinal sheet transplantation can establish synaptic connections with the host, restore light responsiveness and reduce aberrant RGC spiking. Furthermore, we show that genetically engineered grafts can substantially improve the outcome of the treatment by improving neural integration. We speculate that this leads to reduced spontaneous activity in the host which in turn contributes to a better visual recovery.
The singleMarchantia polymorpha FERONIAhomolog reveals an ancestral role in regulating cellular expansion and integrity
Authors: Mecchia Martin A. , Rövekamp Moritz , Giraldo-Fonseca Alejandro , Meier Dario , Gadient Philippe , Vogler Hannes , Limacher Daria , Bowman John L. , Grossniklaus Ueli 
Published: December 2020

AbstractPlant cells are surrounded by a cell wall, a rigid structure that is not only important for cell and organ shape, but crucial for intercellular communication and interactions with the environment. In the flowering plantArabidopsis thaliana, the 17 members of theCatharanthus roseusRLK1-like (CrRLK1L) receptor kinase family are involved in a multitude of physiological and developmental processes, making it difficult to assess their primary or ancestral function. To reduce genetic complexity, we characterized the singleCrRLK1L gene ofMarchantia polymorpha, MpFERONIA(MpFER). Plants with reduced MpFERlevels show defects in vegetative development, i.e., rhizoid formation and cell expansion, and have reduced male fertility. In contrast, Mpfernull mutants and overexpression lines severely affect cell integrity and morphogenesis of the gametophyte. Thus, theCrRLK1L gene family originated from a single gene with an ancestral function in cell expansion and the maintenance of cellular integrity. During land plant evolution, this ancestral gene diversified to fulfil a multitude of specialized physiological and developmental and roles in the formation of both gametophytic and sporophytic structures essential to the life cycle of flowering plants.Summary statementTheCrRLK1L family arose in land plants and theMarchantia polymorpha genomecontains a single copy, MpFER,which is broadly expressed and regulates cell expansion and cell wall integrity.
Narratives: fMRI data for evaluating models of naturalistic language comprehension
Authors: Nastase Samuel A. , Liu Yun-Fei , Hillman Hanna , Zadbood Asieh , Hasenfratz Liat , Keshavarzian Neggin , Chen Janice , Honey Christopher J. , Yeshurun Yaara , Regev Mor , Nguyen Mai , Chang Claire H. C. , Baldassano Christopher , Lositsky Olga , Simony Erez , Chow Michael A. , Leong Yuan Chang , Brooks Paula P. , Micciche Emily , Choe Gina , Goldstein Ariel , Vanderwal Tamara , Halchenko Yaroslav O. , Norman Kenneth A. , Hasson Uri 
Published: December 2020

AbstractThe “Narratives” collection aggregates a variety of functional MRI datasets collected while human subjects listened to naturalistic spoken stories. The current release includes 345 subjects, 891 functional scans, and 27 diverse stories of varying duration totaling ~4.6 hours of unique stimuli (~43,000 words). This data collection is well-suited for naturalistic neuroimaging analysis, and is intended to serve as a benchmark for models of language and narrative comprehension. We provide standardized MRI data accompanied by rich metadata, preprocessed versions of the data ready for immediate use, and the spoken story stimuli with time-stamped phoneme- and word-level transcripts. All code and data are publicly available with full provenance in keeping with current best practices in transparent and reproducible neuroimaging.