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.

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.

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.

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.

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.

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.

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

BACKGROUND: The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. RESULTS: To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. CONCLUSIONS: Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.

PepPSy: a web server to prioritize gene products in experimental and biocuration workflows.

Among the 20 000 human gene products predicted from genome annotation, about 3000 still lack validation at protein level. We developed PepPSy, a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein. PepPSy can also be used by biocurators to revisit the annotation of specific categories of proteins based on the 'omics' data housed by the system. In this study, it was used to prioritize 21 dubious protein-coding genes among the 616 annotated in neXtProt for reannotation. PepPSy is freely available at http://peppsy.genouest.orgDatabase URL: http://peppsy.genouest.org.

Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.

BACKGROUND: With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. FINDINGS: Dedicated to 'whole-genome assembly-free' treatments, the Colib'read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. CONCLUSIONS: With the Colib'read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective.

Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material and example curricula. As university education at the Bachelor's level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master's level, as it offers a more flexible framework. Our team of experts and active performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master's programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii) a description of possible career paths for students who undergo such an education, (iv) conditions that should improve the recruitment of students to such programmes and (v) mechanisms for collaboration and excellence spreading among education professionals. With the growing interest of industry in applying Systems Biology approaches in their fields, a concerted action between academia and industry is needed to build this expertise. Here we present a reflection of the European situation and expertise, where most of the challenges we discuss are universal, anticipating that our suggestions will be useful internationally. We believe that one of the overriding goals of any Systems Biology education should be a student's ability to phrase and communicate research questions in such a manner that they can be solved by the integration of experiments and modelling, as well as to communicate and collaborate productively across different experimental and theoretical disciplines in research and development.

BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ.

BACKGROUND: Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. Galaxy offers multiple ways to give access to this data through its web interface. However, the process of adding new reference data was customarily manual and time consuming, even more so when this data needed to be indexed in a variety of formats (e.g. Blast, Bowtie, BWA, or 2bit). BioMAJ is a widely used and stable software that is designed to automate the download and transformation of data from various sources. This data can be used directly from the command line, in more complex systems, such as Mobyle, or by using a REST API. FINDINGS: To ease the process of giving access to reference data in Galaxy, we have developed the BioMAJ2Galaxy module, which enables the gap between BioMAJ and Galaxy to be bridged. With this module, it is now possible to configure BioMAJ to automatically download some reference data, to then convert and/or index it in various formats, and then make this data available in a Galaxy server using data libraries or data managers. CONCLUSIONS: The developments presented in this paper allow us to integrate the reference data in Galaxy in an automatic, reliable, and diskspace-saving way. The code is freely available on the GenOuest GitHub account (https://github.com/genouest/biomaj2galaxy).

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.

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.

LIMLE, a new molecule over-expressed following activation, is involved in the stimulatory properties of dendritic cells.

Dendritic cells are sentinels of the immune system distributed throughout the body, that following danger signals will migrate to secondary lymphoid organs to induce effector T cell responses. We have identified, in a rodent model of graft rejection, a new molecule expressed by dendritic cells that we have named LIMLE (RGD1310371). To characterize this new molecule, we analyzed its regulation of expression and its function. We observed that LIMLE mRNAs were rapidly and strongly up regulated in dendritic cells following inflammatory stimulation. We demonstrated that LIMLE inhibition does not alter dendritic cell maturation or cytokine production following Toll-like-receptor stimulation. However, it reduces their ability to stimulate effector T cells in a mixed leukocyte reaction or T cell receptor transgenic system. Interestingly, we observed that LIMLE protein localized with actin at some areas under the plasma membrane. Moreover, LIMLE is highly expressed in testis, trachea, lung and ciliated cells and it has been shown that cilia formation bears similarities to formation of the immunological synapse which is required for the T cell activation by dendritic cells. Taken together, these data suggest a role for LIMLE in specialized structures of the cytoskeleton that are important for dynamic cellular events such as immune synapse formation. In the future, LIMLE may represent a new target to reduce the capacity of dendritic cells to stimulate T cells and to regulate an immune response.

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.

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.