bluuebunny/crossref_metadata_2025_split huggingface dataset:
Close contact infection dynamics over time: insights from a second large-scale social contact survey in Flanders, Belgium, in 2010-2011
Authors: Van Hoang Thang , Coletti Pietro , Kiffe Yimer Wasihun , Van Kerckhove Kim , Vercruysse Sarah , Willem Lander , Beutels Philippe , Hens Niel 
Published: October 2020

AbstractBackgroundIn 2010-2011, we conducted a social contact survey in Flanders, Belgium, aimed at improving and extending the design of the first social contact survey conducted in Belgium in 2006. This second social contact survey aimed to enable, for the first time, the estimation of social mixing patterns for an age range of 0 to 99 years and the investigation of whether contact rates remain stable over this 5-year time period.MethodsDifferent data mining techniques are used to explore the data, and the age-specific number of social contacts and the age-specific contact rates are modelled using a GAMLSS model. We compare different matrices using assortativeness measures. The relative change in the basic reproduction number (R0) and the ratio of relative incidences with 95% bootstrap confidence intervals (BCI) are employed to investigate and quantify the impact on epidemic spread due to differences in gender, day of the week, holiday vs. regular periods and changes in mixing patterns over the 5-year time gap between the 2006 and 2010-2011 surveys. Finally, we compare the fit of the contact matrices in 2006 and 2010-2011 to Varicella serological data.ResultsAll estimated contact patterns featured strong homophily in age and gender, especially for small children and adolescents. A 30% (95% BCI [17%; 37%] ) and 29% (95% BCI [14%; 40%] ) reduction in R0 was observed for weekend versus weekdays and for holiday versus regular periods, respectively. Significantly more interactions between people aged 60+ years and their grandchildren were observed on holiday and weekend days than on regular weekdays. Comparing contact patterns using different methods did not show any substantial differences over the 5-year time period under study.ConclusionsThe second social contact survey in Flanders, Belgium, endorses the findings of its 2006 predecessor and adds important information on the social mixing patterns of people older than 60 years of age. Based on this analysis, the mixing patterns of people older than 60 years exhibit considerable heterogeneity, and overall, the comparison of the two surveys shows that social contact rates can be assumed stable in Flanders over a time span of 5 years.
Epidemiological and clinical characteristics of COVID-19 in Brazil using digital technology
Authors: Hajar Faissal N. , Fernandes-Silva Miguel M. , Pereira da Cunha Gustavo S. , Hamud Ali B. , Herrera Geny H. , Azevedo Valderílio F. 
Published: October 2020

ABSTRACTBackgroundBrazil has the third-highest number of Coronavirus disease 2019 (COVID-19) cases worldwide. Understanding the epidemiology of COVID-19 from reported cases is challenging due to heterogeneous testing rates. We estimated the number of COVID-19 cases in Brazil on a national and regional level using digital technology.MethodsWe used a web-based application to perform a population-based survey from March 21st to August 29th, 2020 in Brazil. We obtained responses from 243 461 individuals across all federative units, who answered questions on COVID-19-related symptoms, chronic diseases and address of residence. COVID-19 was defined as at least one of the following: fever, cough, dyspnea and nasal flaring, associated with a history of close contact with a suspect or confirmed COVID-19 case in the previous 14 days. A stratified two-stage weighted survey analysis was performed to estimate the population level prevalence of COVID-19 cases.ResultsAfter calibration weighing, we estimated that 10 339 461 cases of COVID-19 occurred, yielding a 2.75 estimated infection per officially reported case. Estimated/reported ratios varied across Brazilian states and were higher in states with lower human development indexes. Areas with lower income levels displayed higher rates of COVID-19 cases (66 vs 38 cases/1000 people in the lowest and highest income strata respectively, p<0.001), but presented lower rates of COVID-19 testing.ConclusionIn this population-based survey using digital technology in Brazil, we estimated that the COVID-19 case rates were 2.75 times higher than officially reported. The estimated per reported case ratios were higher in areas with worse socioeconomic status.
Tumor cell total mRNA expression shapes the molecular and clinical phenotype of cancer
Authors: Cao Shaolong , Wang Jennifer R. , Ji Shuangxi , Yang Peng , Montierth Matthew D. , Guo Shuai , Shen John Paul , Zhao Xiao , Chen Jingxiao , Lee Jaewon James , Guerrero Paola A , Spetsieris Nicholas , Engedal Nikolai , Taavitsainen Sinja , Yu Kaixian , Livingstone Julie , Bhandari Vinayak , Hubert Shawna M , Daw Najat C. , Futreal P. Andrew , Efstathiou Eleni , Lim Bora , Viale Andrea , Zhang Jianjun , Nykter Matti , Czerniak Bogdan A , Msaouel Pavlos , Maitra Anirban , Kopetz Scott , Campbell Peter , Speed Terence P. , Boutros Paul C. , Zhu Hongtu , Urbanucci Alfonso , Demeulemeester Jonas , Van Loo Peter , Wang Wenyi 
Published: October 2020

AbstractCancers can vary greatly in their transcriptomes. In contrast to alterations in specific genes or pathways, differences in tumor cell total mRNA content have not been comprehensively assessed. Technical and analytical challenges have impeded examination of total mRNA expression at scale across cancers. To address this, we developed a model for quantifying tumor-specific total mRNA expression (TmS) from bulk sequencing data, which performs transcriptomic deconvolution while adjusting for mixed genomes. We used single-cell RNA sequencing data to demonstrate total mRNA expression as a feature of tumor phenotype. We estimated and validated TmS in 5,015 patients across 15 cancer types identifying significant inter-individual variability. At a pan-cancer level, high TmS is associated with increased risk of disease progression and death. Cancer type-specific patterns of genetic alterations, intra-tumor genetic heterogeneity, as well as pan-cancer trends in metabolic dysregulation and hypoxia contribute to TmS. Taken together, our results suggest that measuring cell-type specific total mRNA expression offers a broader perspective of tracking cancer transcriptomes, which has important biological and clinical implications.
Automatic Measurement of Inner Ear in Different Mammals1
Authors: Du Yi , Qin Han-dai , Liu Chen , Liu Da , Yuan Shuo-long , Jiang Qing-qing , Yang Jun , Li Gang , Xie Hong-lan , Zhao Jian-guo , Yu Ning , Yang Shi-ming 
Published: October 2020

AbstractObjectiveThe aim of this research is to develop an accurate and automatic measuring method based on the aid of centerline to construct three dimensional models of inner ear in different mammals and to assess the morphological variations.MethodsThree adult healthy mice, three adult guinea pigs, three adult mini pigs and one left temporal bone of human were included in this research. All 18 animal specimens and the human sample were scanned with the use of Micro-CT. After being segmented, three-dimensional models of the inner ear in different mammals were reconstructed using Mimics. A novel method with the use of centerline was established to estimate the properties of 3D models and to calculate the length, volume and angle parameters automatically.ResultsMorphological models of inner ears in different mammals have been built, which describe detailed shape of cochlear, vestibule, semicircular canals and common crus. Mean value of lengths and volumes of the cochlear, lateral semicircular canal, superior semicircular canal and posterior semicircular canal, tended to increase with the body size of the mammals, showed the proximity to the human data in mini pig. The angles between the semicircular canal planes showed differences between mammals. The mean values of semicircular canals of mice and mini pigs closely resembled to human data in numerical assessment.ConclusionThe automatic measurement of the inner ear based on centerline builds an effective way to assess lengths, volumes and angles of three-dimensional structures. This study provides a theoretical basis for mechanical analysis of inner ear in different mammals and proves the similarity between mini pig and human.
Stabilization demands of walking modulate the vestibular contributions to gait
Authors: Magnani Rina M. , Bruijn Sjoerd M. , van Dieën Jaap H. , Forbes Patrick A. 
Published: October 2020

AbstractStable walking relies critically on motor responses to signals of head motion provided by the vestibular system, which are phase-dependent and modulated differently within each muscle. It is unclear, however, whether these vestibular contributions also vary according to the stability of the walking task. Here we investigate how vestibular signals influence muscles relevant for gait stability (medial gastrocnemius, gluteus medius and erector spinae) – as well as their net effect on ground reaction forces – while humans walked normally, with mediolateral stabilization, wide and narrow steps. We estimated local dynamic stability of trunk kinematics together with coherence of electrical vestibular stimulation (EVS) with muscle activity and mediolateral ground reaction forces. Walking with external stabilization increased local dynamic stability and decreased coherence between EVS and all muscles/forces compared to normal walking. Wide-base walking also decreased vestibulomotor coherence, though local dynamic stability did not differ. Conversely, narrow-base walking increased local dynamic stability, but produced muscle-specific increases and decreases in coherence that resulted in a net increase in vestibulomotor coherence with ground reaction forces. Overall, our results show that while vestibular contributions may vary with gait stability, they more critically depend on the stabilization demands (i.e. control effort) needed to maintain a stable walking pattern.
EEG-based decoding and recognition of imagined music
Authors: Tibo Marthe , Geirnaert Simon , Bertrand Alexander 
Published: October 2020

The authors have withdrawn their manuscript because they discovered an error in the analysis code after publication of the preprint, which turns out to have a major impact on the main results in the paper. The results on the imagination data become non-significant after correcting for the mistake. Significant results on the perception data are preserved, although the classification results are worse than what is reported.Therefore, the authors do not wish this work to be cited as a reference.If you have any questions, please contact the last author.
The PEDtracker: an automatic staging approach forDrosophila melanogasterlarvae
Authors: Schumann Isabell , Triphan Tilman 
Published: October 2020

AbstractThe post-embryonal development of arthropod species, including crustaceans and insects, is characterized by ecdysis or molting. This process defines growth stages and is controlled by a conserved neuroendocrine system. Each molting event is divided in several critical time points, such as pre-molt, molt and post-molt, and leaves the animals in a temporarily highly vulnerable state while their cuticle is re-hardening. The molting events occur in an immediate ecdysis sequence within a specific time window during the development. Each sub-stage takes only a short amount of time, which is generally in the order of minutes. To find these relatively short behavioral events, one needs to follow the entire post-embryonal development over several days. As the manual detection of the ecdysis sequence is time consuming and error prone, we designed a monitoring system to facilitate the continuous observation of the post-embryonal development of the fruit flyDrosophila melanogaster. Under constant environmental conditions we are able to observe the life cycle from the embryonic state to the adult, which takes about ten days in this species. Specific processing algorithms developed and implemented in Fiji and R allow us to determine unique behavioral events on an individual level – including egg hatching, ecdysis and pupation. In addition, we measured growth rates and activity patterns for individual larvae. Our newly created RPackage PEDtracker can predict critical developmental events and thus offers the possibility to perform automated screens that identify changes in various aspects of larval development. In conclusion, the PEDtracker system presented in this study represents the basis for automated real-time staging and analysis not only for the arthropod development.
Positive but variable effects of crop diversification on biodiversity and ecosystem services
Authors: Beillouin D. , Ben-Ari T. , Malézieux E. , Seufert V. , Makowski D. 
Published: October 2020

AbstractEcological theory suggests that biodiversity has a positive and stabilizing effect on the delivery of ecosystem services. Yet, the impacts of increasing the diversity of cultivated crop species or varieties in agroecosystems are still under scrutiny. The empirical evidence available is scattered in scope, agronomic and geographical contexts and impacts on ecosystem services may depend on the type of diversification strategy used. To robustly assess the effects of crop diversification in agroecosystems, we compiled the results of 95 meta-analyses integrating 5,156 experiments conducted over 84 experimental years and representing more than 54,500 paired observations on 120 crop species in 85 countries. Overall, our synthesis of experimental data from across the globe shows that crop diversification enhances not only crop production (median effect +14%), but also the associated biodiversity (+24%, i.e. the biodiversity of non-cultivated plants and animals), and several supporting and regulating ecosystem services including water quality (+51%), pest and disease control (+63%) and soil quality (+11%). However, there was substantial variability in the results for each individual ecosystem service between different diversification strategies like agroforestry, intercropping, cover-crops, crop rotation or variety mixtures. Agroforestry is particularly effective in delivering multiple ecosystem services, i.e. water use and quality, pest and diseases regulation, associated biodiversity, long-term soil productivity and quality. Variety mixtures, instead, provide the lowest benefits, while the other strategies show intermediate results. Our results highlight that while increasing the diversity of cultivated crop species or varieties in agroecosystems represents a very promising strategy for more sustainable land management, contributing to enhanced yields, enhanced biodiversity and ecosystem services, some crop diversification strategies are more effective than others in supporting key ecosystem services.
Nonlinear post-selection inference for genome-wide association studies
Authors: Slim Lotfi , Chatelain Clément , Azencott Chloé-Agathe 
Published: October 2020

To address the lack of statistical power and interpretability of genome-wide association studies (GWAS), gene-level analyses combine the p-values of individual single nucleotide polymorphisms (SNPs) into gene statistics. However, using all SNPs mapped to a gene, including those with low association scores, can mask the association signal of a gene.We therefore propose a new two-step strategy, consisting in first selecting the SNPs most associated with the phenotype within a given gene, before testing their joint effect on the phenotype. The recently proposed kernelPSI framework for kernel-based post-selection inference makes it possible to model non-linear relationships between features, as well as to obtain valid p-values that account for the selection step.In this paper, we show how we adapted kernelPSI to the setting of quantitative GWAS, using kernels to model epistatic interactions between neighboring SNPs, and post-selection inference to determine the joint effect of selected blocks of SNPs on a phenotype. We illustrate this tool on the study of two continuous phenotypes from the UKBiobank.We show that kernelPSI can be successfully used to study GWAS data and detect genes associated with a phenotype through the signal carried by the most strongly associated regions of these genes. In particular, we show that kernelPSI enjoys more statistical power than other gene-based GWAS tools, such as SKAT or MAGMA.kernelPSI is an effective tool to combine SNP-based and gene-based analyses of GWAS data, and can be used successfully to improve both statistical performance and interpretability of GWAS.
The CoREST Repressor Complex Mediates Phenotype Switching and Therapy Resistance in Melanoma
Authors: Wu Muzhou , Hanly Ailish , Gibson Frederick , Kuang Kevin , Kalin Jay , Nocco Sarah , Collard Marianne , Cole Matthew , Xiao Amy , Agus Filisia , Labadorf Adam , Cole Philip A , Alani Rhoda M. 
Published: October 2020

AbstractVirtually all patients with BRAF-mutant melanoma develop resistance to MAPK inhibitors largely through non-mutational events1,2. Although the epigenetic landscape has been shown to be altered in therapy-resistant melanomas and other cancers3,4, a specific targetable epigenetic mechanism regulating treatment resistance has not been validated to date. Here we evaluate the CoREST repressor complex and the novel inhibitor, corin5, within the context of melanoma phenotype plasticity and therapeutic resistance in order to define epigenetic mechanisms underlying these processes. We find that CoREST is a critical mediator of the major distinct melanoma phenotypes and that corin treatment of melanoma cells leads to phenotype reprogramming. We further demonstrate that treatment of BRAF inhibitor (BRAFi)-resistant melanomas with corin leads to resensitization of tumor cells to BRAFi. Among the transcriptional targets of CoREST in melanoma are the dual-specificity phosphatases (DUSPs). DUSP1 is shown to be consistently downregulated in BRAFi-resistant melanomas which can be reversed by corin treatment, thereby leading to downstream inhibition of p38 MAPK activity and resensitization of resistant cells to targeted BRAFi therapies. These findings identify the CoREST repressor complex as a central mediator of melanoma phenotype plasticity and resistance to targeted therapy and suggest that CoREST inhibitors may prove beneficial to patients with BRAF-mutant melanomas who have acquired BRAFi-resistance.
A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits
Authors: Davidson Gabrielle L. , Somers Shane E. , Wiley Niamh , Johnson Crystal N. , Reichert Michael S. , Ross R. Paul , Stanton Catherine , Quinn John L. 
Published: October 2020

AbstractNatal body mass is a key predictor of viability and fitness in many animals. While variation in body mass and therefore juvenile viability may be explained by genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. The gut microbiota is known to change during development, but it remains unclear whether the microbiome predicts fitness, and if it does, at which developmental stage it affects fitness traits.We collected data on two traits associated with fitness in wild nestling great tits (Parus major): weight and survival to fledging. We characterised the gut microbiome using 16S rRNA sequencing from nestling faeces and investigated temporal associations between the gut microbiome and fitness traits across development at day 8 (D8) and day 15 (D15) post-hatching. We also explored whether particular microbial taxa were ‘indicator species’ that reflected whether nestlings survived or not.There was no link between mass and microbial diversity on D8 or D15. However, we detected a time-lagged relationship where weight at D15 was negatively associated with the microbial diversity at D8, controlling for weight at D8, therefore reflectingrelativeweight gain over the intervening period.Indicator species analysis revealed that specificity values were high and fidelity values were low, suggesting that indicator taxa were primarily detected within either the survived or not survived groups, but not always detected in birds that either survived or died. Therefore these indicator taxa may be sufficient, but not necessary for determining either survival or mortality, perhaps owing to functional overlap in microbiota.We highlight that measuring microbiome-fitness relationships at just one time point may be misleading, especially early in life. Instead, microbial-host fitness effects may be best investigated longitudinally to detect critical development windows for key microbiota and host traits associated with neonatal weight. Our findings should inform future hypothesis testing to pinpoint which features of the gut microbial community impact on host fitness, and when during development this occurs. Such confirmatory research will shed light on population level processes and could have the potential to support conservation.
Probing universal protein dynamics using residue-level Gibbs free energy
Authors: Smit Jochem H. , Krishnamurthy Srinath , Srinivasu Bindu Y. , Parakra Rinky , Karamanou Spyridoula , Economou Anastassios 
Published: October 2020

AbstractHydrogen Deuterium Exchange Mass Spectrometry is a powerful monitor of protein intrinsic dynamics, yet the interpretation, visualization and cross-comparison of HDX-MS datasets is challenging. Here we present PyHDX, an open-source python package and web server, that batch-extracts the universal quantity Gibbs free energy at residue level over multiple protein conditions and homologues. ΔGvalues relate to protein normal modes and together provide a universal measure of protein flexibility.AvailabilityPyHDX source code is released under the MIT license and can be accessed onGitHub.