Sleep, substance misuse and addictions: a nationwide observational survey on smoking, alcohol, cannabis and sleep in 12,637 adults.

For a good night's sleep, we consensually recommend avoiding alcohol, smoking and drugs. However, these addictions are highly prevalent in the general population, and it is difficult to estimate their real impact on sleep. The aim of this study is to clarify the association between sleep habits and disorders, and addictions. The design was a telephone crossover national recurrent health poll survey (Santé publique France, Baromètre santé, 2017; Questionnaire, pp. 53; Saint Maurice) in a representative sample of French adults. There were 12,367 subjects (18-75 years old) who answered the survey. Sleep log items assessed sleep schedules (total sleep time) on work and leisure days: at night, while napping, and over 24 hr using a sleep log. Retained items include: (1) short sleep (≤ 6 hr/24 hr); (2) chronic insomnia (International Classification of Sleep Disorders, 3rd edition criteria); and (3) chronotype (evening-morning-neutral). Psychoactive substances retained included tobacco (current or former users), alcohol (daily consumption and weekly binge drinking), cannabis (Cannabis Abuse Screening Test), and other drugs (consumption during the past year). We found that: (1) daily smokers (lightly or heavily dependent) were more frequently short sleepers than occasional smokers and non-smokers; (2) heavily dependent daily smokers were more likely to suffer from insomnia than other smokers or non-smokers; (3) short sleep and insomnia were not significantly associated with the consumption of alcohol, cannabis or any other drug; (4) the evening chronotype was significantly associated with the consumption of tobacco, alcohol and cannabis. In conclusion, our study highlights significant relationships between the use of psychoactive substances and sleep characteristics among adults, emphasizing the need to take into account each subject individually.

The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community.

MOTIVATION: Recent advances in transcriptomics have enabled unprecedented insight into gene expression analysis at a single-cell resolution. While it is anticipated that the number of publications based on such technologies will increase in the next decade, there is currently no public resource to centralize and enable scientists to explore single-cell datasets published in the field of reproductive biology. RESULTS: Here, we present a major update of the ReproGenomics Viewer, a cross-species and cross-technology web-based resource of manually-curated sequencing datasets related to reproduction. The redesign of the ReproGenomics Viewer's architecture is accompanied by significant growth of the database content including several landmark single-cell RNA-sequencing datasets. The implementation of additional tools enables users to visualize and browse the complex, high-dimensional data now being generated in the reproductive field. AVAILABILITY AND IMPLEMENTATION: The ReproGenomics Viewer resource is freely accessible at http://rgv.genouest.org. The website is implemented in Python, JavaScript and MongoDB, and is compatible with all major browsers. Source codes can be downloaded from https://github.com/fchalmel/RGV. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

TOXsIgN: a cross-species repository for toxicogenomic signatures.

Motivation: At the same time that toxicologists express increasing concern about reproducibility in this field, the development of dedicated databases has already smoothed the path toward improving the storage and exchange of raw toxicogenomic data. Nevertheless, none provides access to analyzed and interpreted data as originally reported in scientific publications. Given the increasing demand for access to this information, we developed TOXsIgN, a repository for TOXicogenomic sIgNatures. Results: The TOXsIgN repository provides a flexible environment that facilitates online submission, storage and retrieval of toxicogenomic signatures by the scientific community. It currently hosts 754 projects that describe more than 450 distinct chemicals and their 8491 associated signatures. It also provides users with a working environment containing a powerful search engine as well as bioinformatics/biostatistics modules that enable signature comparisons or enrichment analyses. Availability and implementation: The TOXsIgN repository is freely accessible at http://toxsign.genouest.org. Website implemented in Python, JavaScript and MongoDB, with all major browsers supported. Supplementary information: Supplementary data are available at Bioinformatics online.

The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community.

We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

Migration of dendritic cells: physical principles, molecular mechanisms, and functional implications.

Dendritic cells (DCs) constitute a complex cell population that resides in both peripheral tissues and lymphoid organs. Their major function in tissues is to patrol their environment in search of danger-associated antigens to transport to lymph nodes and present to T lymphocytes. This process constitutes the first step of the adaptive immune response and relies on specific DC properties, including a high endocytic capacity as well as efficient motility in confined three-dimensional environments. Although cell motility has been widely studied, little is known on how the geometric characteristics of the environment influence DC migration and function. In this review, we give an overview of the basic physical principles and molecular mechanisms that control DC migration under confinement and discuss how such mechanisms impact the environment-patrolling capacity of DCs.

CyanoLyase: a database of phycobilin lyase sequences, motifs and functions.

CyanoLyase (http://cyanolyase.genouest.org/) is a manually curated sequence and motif database of phycobilin lyases and related proteins. These enzymes catalyze the covalent ligation of chromophores (phycobilins) to specific binding sites of phycobiliproteins (PBPs). The latter constitute the building bricks of phycobilisomes, the major light-harvesting systems of cyanobacteria and red algae. Phycobilin lyases sequences are poorly annotated in public databases. Sequences included in CyanoLyase were retrieved from all available genomes of these organisms and a few others by similarity searches using biochemically characterized enzyme sequences and then classified into 3 clans and 32 families. Amino acid motifs were computed for each family using Protomata learner. CyanoLyase also includes BLAST and a novel pattern matching tool (Protomatch) that allow users to rapidly retrieve and annotate lyases from any new genome. In addition, it provides phylogenetic analyses of all phycobilin lyases families, describes their function, their presence/absence in all genomes of the database (phyletic profiles) and predicts the chromophorylation of PBPs in each strain. The site also includes a thorough bibliography about phycobilin lyases and genomes included in the database. This resource should be useful to scientists and companies interested in natural or artificial PBPs, which have a number of biotechnological applications, notably as fluorescent markers.

High-resolution profiling of novel transcribed regions during rat spermatogenesis.

Mammalian spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the production of mature spermatozoa. If recent genome-wide studies have contributed to the in-depth analysis of the male germline protein-encoding transcriptome, little effort has yet been devoted to the systematic identification of novel unannotated transcribed regions expressed during mammalian spermatogenesis. We report high-resolution expression profiling of male germ cells in rat, using next-generation sequencing technology and highly enriched testicular cell populations. Among 20 424 high-confidence transcripts reconstructed, we defined a stringent set of 1419 long multi-exonic unannotated transcripts expressed in the testis (testis-expressed unannotated transcripts [TUTs]). TUTs were divided into 7 groups with different expression patterns. Most TUTs share many of the characteristics of vertebrate long noncoding RNAs (lncRNAs). We also markedly reinforced the finding that TUTs and known lncRNAs accumulate during the meiotic and postmeiotic stages of spermatogenesis in mammals and that X-linked meiotic TUTs do not escape the silencing effects of meiotic sex chromosome inactivation. Importantly, we discovered that TUTs and known lncRNAs with a peak expression during meiosis define a distinct class of noncoding transcripts that exhibit exons twice as long as those of other transcripts. Our study provides new insights in transcriptional profiling of the male germline and represents a high-quality resource for novel loci expressed during spermatogenesis that significantly contributes to rat genome annotation.

GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development.

We present gene prioritization system (GPSy), a cross-species gene prioritization system that facilitates the arduous but critical task of prioritizing genes for follow-up functional analyses. GPSy's modular design with regard to species, data sets and scoring strategies enables users to formulate queries in a highly flexible manner. Currently, the system encompasses 20 topics related to conserved biological processes including male gamete development discussed in this article. The web server-based tool is freely available at http://gpsy.genouest.org.

Contractility of the cell rear drives invasion of breast tumor cells in 3D Matrigel.

Cancer cells use different modes of migration, including integrin-dependent mesenchymal migration of elongated cells along elements of the 3D matrix as opposed to low-adhesion-, contraction-based amoeboid motility of rounded cells. We report that MDA-MB-231 human breast adenocarcinoma cells invade 3D Matrigel with a characteristic rounded morphology and with F-actin and myosin-IIa accumulating at the cell rear in a uropod-like structure. MDA-MB-231 cells display neither lamellipodia nor bleb extensions at the leading edge and do not require Arp2/3 complex activity for 3D invasion in Matrigel. Accumulation of phospho-MLC and blebbing activity were restricted to the uropod as reporters of actomyosin contractility, and velocimetric analysis of fluorescent beads embedded within the 3D matrix showed that pulling forces exerted to the matrix are restricted to the side and rear of cells. Inhibition of actomyosin contractility or ß1 integrin function interferes with uropod formation, matrix deformation, and invasion through Matrigel. These findings support a model whereby actomyosin-based uropod contractility generates traction forces on the ß1 integrin adhesion system to drive cell propulsion within the 3D matrix, with no contribution of lamellipodia extension or blebbing to movement.

UTAUT2-based questionnaire: cross-cultural adaptation to Canadian French.

PURPOSE: The extended version of the Unified Theory of Acceptance and Use of Technology (UTAUT2) aims to better understand acceptance of technology. The objective of this study was to translate the English UTAUT2-based questionnaire to Canadian French. METHODS: The translation included five steps: (1) Forward translation, (2) Synthesis of the translated versions, (3) Backward translation, (4) Synthesis by a multidisciplinary committee and proposal of the Pre-final Canadian French version, and (5) Cognitive debriefing. Cognitive debriefing included the assessment of the questionnaire items' clarity by (1) a sample of workers, and (2) rehabilitation professionals. Any item not reaching an 80% inter-rater agreement for clarity or relevance was re-evaluated. RESULTS: The multidisciplinary committee included six researchers and clinicians from four different backgrounds. Twelve workers and 12 experts participated in the cognitive debriefing. Each item (n = 40) was judged as "clear" by at least 92% of the worker sample. Six and four items were reviewed following clarity and relevance assessments. The final version was approved unanimously. CONCLUSION: A Canadian French version of the UTAUT2-based questionnaire has been developed. Studies are necessary to examine cultural and semantic equivalence of the original and translated versions, and the cultural appropriateness of the questionnaire.IMPLICATIONS FOR REHABILITATIONThere is an exponential growth in technology, including in the rehabilitation field.Implementing rehabilitation technology into clinical practice remains a challenge.The UTAUT model, and its extension, help to better understand the acceptance of technology before its implementation.The UTAUT2-based questionnaire evaluates the acceptability of rehabilitation technology prior to implementation.

Spatiotemporal organization, regulation, and functions of tractions during neutrophil chemotaxis.

Despite recent advances in our understanding of biochemical regulation of neutrophil chemotaxis, little is known about how mechanical factors control neutrophils' persistent polarity and rapid motility. Here, using a human neutrophil-like cell line and human primary neutrophils, we describe a dynamic spatiotemporal pattern of tractions during chemotaxis. Tractions are located at both the leading and the trailing edge of neutrophils, where they oscillate with a defined periodicity. Interestingly, traction oscillations at the leading and the trailing edge are out of phase with the tractions at the front leading those at the back, suggesting a temporal mechanism that coordinates leading edge and trailing edge activities. The magnitude and periodicity of tractions depend on the activity of nonmuscle myosin IIA. Specifically, traction development at the leading edge requires myosin light chain kinase-mediated myosin II contractility and is necessary for α5ß1-integrin activation and leading edge adhesion. Localized myosin II activation induced by spatially activated small GTPase Rho, and its downstream kinase p160-ROCK, as previously reported, leads to contraction of actin-myosin II complexes at the trailing edge, causing it to de-adhere. Our data identify a key biomechanical mechanism for persistent cell polarity and motility.

Self-organized podosomes are dynamic mechanosensors.

Podosomes are self-organized, dynamic, actin-containing structures that adhere to the extracellular matrix via integrins [1-5]. Yet, it is not clear what regulates podosome dynamics and whether podosomes can function as direct mechanosensors, like focal adhesions [6-9]. We show here that myosin-II proteins form circular structures outside and at the podosome actin ring to regulate podosome dynamics. Inhibiting myosin-II-dependent tension dissipated podosome actin rings before dissipating the myosin-ring structure. As podosome rings changed size or shape, tractions underneath the podosomes were exerted onto the substrate and were abolished when myosin-light-chain activity was inhibited. The magnitudes of tractions were comparable to those generated underneath focal adhesions, and they increased with substrate stiffness. The dynamics of podosomes and of focal adhesions were different. Torsional tractions underneath the podosome rings were generated with rotations of podosome rings in a nonmotile, nonrotating cell, suggesting a unique feature of these circular structures. Stresses applied via integrins at the apical surface directly displaced podosomes near the basal surface. Stress-induced podosome displacements increased nonlinearly with applied stresses. Our results suggest that podosomes are dynamic mechanosensors in which interactions of myosin tension and actin dynamics are crucial for regulating these self-organized structures in living cells.

Rapid signal transduction in living cells is a unique feature of mechanotransduction.

It is widely postulated that mechanotransduction is initiated at the local force-membrane interface by inducing local conformational changes of proteins, similar to soluble ligand-induced signal transduction. However, all published reports are limited in time scale to address this fundamental issue. Using a FRET-based cytosolic Src reporter in a living cell, we quantified changes of Src activities as a local stress via activated integrins was applied. The stress induced rapid (<0.3 s) activation of Src at remote cytoplasmic sites, which depends on the cytoskeletal prestress. In contrast, there was no Src activation within 12 s of soluble epidermal growth factor (EGF) stimulation. A 1.8-Pa stress over a focal adhesion activated Src to the same extent as 0.4 ng/ml EGF at long times (minutes), and the energy levels for mechanical stimulation and chemical stimulation were comparable. The effect of both stress and EGF was less than additive. Nanometer-scale cytoskeletal deformation analyses revealed that the strong activation sites of Src by stress colocalized with large deformation sites of microtubules, suggesting that microtubules are essential structures for transmitting stresses to activate cytoplasmic proteins. These results demonstrate that rapid signal transduction via the prestressed cytoskeleton is a unique feature of mechanotransduction.

Napping and weekend catchup sleep do not fully compensate for high rates of sleep debt and short sleep at a population level (in a representative nationwide sample of 12,637 adults).

INTRODUCTION: Short total sleep time (TST < 6 h) is a strong major health determinant that correlates with numerous metabolic, cardiovascular and mental comorbidities, as well as accidents. Our aim was to better understand, at a population level, how adults adapt their TST during the week, and how short sleepers and those with sleep debt and sleep restriction use napping or catching up on sleep during weekends (ie, sleep debt compensation by sleeping longer), which may prevent these comorbidities. METHODS: A large representative sample of 12,367 subjects (18-75 years old) responded by phone to questions about sleep on a national recurrent health poll (Health Barometer, Santé Publique France 2017) assessing sleep schedules (TST) at night, when napping, and over the course of a 24-h period while using a sleep log on workdays and weekends. Retained items were: (1) short sleep (TST ≤ 6 h/24 h); (2) chronic insomnia (international classification of sleep disorders third edition, ICSD-3 criteria); (3) sleep debt (self-reported ideal TST - TST > 60 min, severe > 90 min); and (4) sleep restriction (weekend TST - workday TST = 1-2 h, severe > 2 h). RESULTS: Average TST/24 h was 6h42 (± 3 min) on weekdays and 7h26 (± 3 min) during weekends. In addition, 35.9% (± 1.0%) of the subjects were short sleepers, 27.7% (± 1.0%) had sleep debt (18.8% (± 0.9%) severe), and 17.4% (± 0.9%) showed sleep restriction (14.4% (± 0.8%) severe). Moreover, 27.4% (± 0.9%) napped at least once per week on weekdays (average: 8.3 min (± 0.5 min)) and 32.2% (± 1.0%) on weekend days (13.7 min (± 0.7 min)). Of the 24.2% (± 0.9%) of subjects with severe sleep debt (> 90 min), only 18.2% (± 1.6%) balanced their sleep debt by catching up on sleep on weekends (14.9% (± 0.8%) of men and 21.5% (± 0.9%) of women), and 7.4% (± 1.2%) of these subjects balanced their sleep debt by napping (7.8% (± 0.5%) of men and 6.6% (± 0.4%) of women). The remaining 75.8% (± 5.4%) did not do anything to balance their severe sleep debt during the week. DISCUSSION AND CONCLUSIONS: Short sleep, sleep debt, and sleep restriction during weekdays affected about one third of adults in our study group. Napping and weekend catch-up sleep only compensated for severe sleep debt in one in four subjects.

Stretch-induced hypoalgesia: a pilot study.

Objectives Stretching is an intervention often used in various kinds of rehabilitation protocols and the effects on pain sensitivity has sparsely been investigated, especially when addressing potential effects on pain. The objective is to investigate the immediate effects of an axial and peripheral prolonged stretch on pressure pain sensitivity (PPT) and temporal summation (TS) on local and distal sites in healthy subjects. Methods Twenty-two healthy volunteers were recruited to participate in this pilot study. Two prolonged stretching protocols were performed: low back and wrist extensors stretches. PPT and pinprick TS were measured pre- and post-intervention at local and remote sites. Repeated measures analysis of variance (ANOVA) was used to examine the effects and significance of the interventions. Results The low back stretch induced an increase in PPT for both local and remote sites, and the wrist stretch produced a PPT increase only at the local site. TS did not change. Conclusions Low back stretching induced an increase in PPT at both local and remote sites whereas the wrist stretch only increased PPT locally, suggesting hypoalgesia at these sites. Further studies are needed to confirm the effect and mechanisms using randomised, controlled and parallel study design. Considering that pain sensitivity is different than clinical pain, results are difficult to extrapolate to clinical practice. Future studies testing clinical pain are needed to better understand the clinical implication of these results.

MIMAS 3.0 is a Multiomics Information Management and Annotation System.

BACKGROUND: DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen years. However, very recently novel technologies for Ultra High-Throughput DNA Sequencing (UHTS) have been harnessed to study these phenomena with unprecedented precision. As a consequence, the extensive bioinformatics environment available for array data management, analysis, interpretation and publication must be extended to include these novel sequencing data types. DESCRIPTION: MIMAS was originally conceived as a simple, convenient and local Microarray Information Management and Annotation System focused on GeneChips for expression profiling studies. MIMAS 3.0 enables users to manage data from high-density oligonucleotide SNP Chips, expression arrays (both 3'UTR and tiling) and promoter arrays, BeadArrays as well as UHTS data using MIAME-compliant standardized vocabulary. Importantly, researchers can export data in MAGE-TAB format and upload them to the EBI's ArrayExpress certified data repository using a one-step procedure. CONCLUSION: We have vastly extended the capability of the system such that it processes the data output of six types of GeneChips (Affymetrix), two different BeadArrays for mRNA and miRNA (Illumina) and the Genome Analyzer (a popular Ultra-High Throughput DNA Sequencer, Illumina), without compromising on its flexibility and user-friendliness. MIMAS, appropriately renamed into Multiomics Information Management and Annotation System, is currently used by scientists working in approximately 50 academic laboratories and genomics platforms in Switzerland and France. MIMAS 3.0 is freely available via http://multiomics.sourceforge.net/.

BioMAJ: a flexible framework for databanks synchronization and processing.

UNLABELLED: Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks. AVAILABILITY: http://biomaj.genouest.org. BioMAJ is free open software. It is freely available under the CECILL version 2 license.

The bio.tools registry of software tools and data resources for the life sciences.

Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.