Galaxy Training: A powerful framework for teaching!

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Etude de la réponse immunitaire dans l' hidrosadénite suppurée Interleukine 22

L hidrosadénite suppurée (HS) est une dermatose inflammatoire chronique récurrente de physiopathologie inconnue. L efficacité inconstante de traitements antibiotiques ou immunosuppresseurs nous a fait poser l hypothèse que l'HS est liée à une réponse immunitaire anormale à la flore commensale cutanée. L homéostasie des muqueuses est assurée par un équilibre dynamique entre la réponse inflammatoire et la réponse régulatrice vis-à-vis de la flore. Le rôle majeur des lymphocytes Th17 et des Th22 dans cette réponse vis-à-vis de la flore suggère l implication de la voie inflammatoire IL-22/IL-17/peptides anti-microbiens (PAM) dans la physiopathologie de l HS. Nos résultats préliminaires ont montré une augmentation significative de production et de sécrétion d IL-17 et d IL-22 dans le sang des patients HS par rapport aux témoins après stimulation. Parallèlement, la fréquence des cellules T régulatrices (Treg) et la sécrétion d IL-10, cytokine anti-inflammatoire, étaient comparables entre témoins et patients HS. In situ, les résultats d immuno-histochimie et de RT-PCR ont retrouvé un infiltrat inflammatoire constitué de Treg et de lymphocytes Th1. La diminution significative de l expression des transcrits RORgt, facteur de transcription caractéristique des Th17, suggère l absence de cellules Th17. L absence de cellules Th17 dans la peau et l augmentation de celles-ci en périphérie sont en faveur d une anomalie de la réponse immunitaire à la flore commensale cutanée dans l HS. Ces résultats posent différentes hypothèses, et, notamment un défaut local de production de PAM, facteurs chimioattractants des cellules T, conduisant à une absence de résolution de l inflammation.PARIS6-Bibl.Pitié-Salpêtrie (751132101) / SudocSudocFranceF

Reevaluation of the University of Wisconsin 2-year protocol for treating canine lymphosarcoma

This retrospective study investigated a population of 96 dogs with newly diagnosed malignant lymphosarcoma that were treated with the commonly used University of Wisconsin-Madison (UW-M) chemotherapy protocol. Pretreatment characteristics were analyzed to determine prognostic factors. Dogs with higher World Health Organization (WHO) stages (including stage IV) and dogs with hypercalcemia were at significantly higher risk of relapse (P=0.018 and P=0.016, respectively). Dose reduction, treatment delays, and prior therapy with cortico-steroids were not associated with clinical outcome. First remission duration of 270 days was similar to historically reported data. Overall survival time of 218 days was much shorter than historical data

Intrinsic Defect in Keratinocyte Function Leads to Inflammation in Hidradenitis Suppurativa

International audienceHidradenitis suppurativa (HS) is a chronic, inflammatory, debilitating, follicular disease of the skin. Despite a high prevalence in the general population, the physiopathology of HS remains poorly understood. The use of antibiotics and immunosuppressive agents for therapy suggests a deregulated immune response to microflora. Using cellular and gene expression analyses, we found an increased number of infiltrating CD4(+) T cells secreting IL-17 and IFN-γ in perilesional and lesional skin of patients with HS. By contrast, IL-22-secreting CD4(+) T cells are not enriched in HS lesions contrasting with increased number of those cells in the blood of patients with HS. We showed that keratinocytes isolated from hair follicles of patients with HS secreted significantly more IL-1β, IP-10, and chemokine (C-C motif) ligand 5 (RANTES) either constitutively or on pattern recognition receptor stimulations. In addition, they displayed a distinct pattern of antimicrobial peptide production. These findings point out a functional defect of keratinocytes in HS leading to a balance prone to inflammatory responses. This is likely to favor a permissive environment for bacterial infections and chronic inflammation characterizing clinical outcomes in patients with HS

Cyclosporine for Epidermal Necrolysis: Absence of Beneficial Effect in a Retrospective Cohort of 174 Patients—Exposed/Unexposed and Propensity Score-Matched Analyses

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Hair follicle stem cell replication stress drives IFI16/STING-dependent inflammation in hidradenitis suppurativa

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