Comparison of Audiovisual and Paper-Based Materials for 1-Time Informed Consent for Research in Prison: A Randomized Clinical Trial.

Importance Few studies are available on informed consent (IC) among detained persons, even with ethics being a critical aspect of prison research. In IC research, audiovisual material seems to improve understanding and satisfaction compared with conventional paper-based material, but findings remain unclear. Objective To compare audiovisual and paper-based materials for 1-time general IC for research in prisons. Design, Setting, and Participants This cross-sectional randomized clinical trial was conducted in 2 corrections facilities in Switzerland (an adult prison and a juvenile detention center). The study was conducted from December 14, 2019, to December 2, 2020, in the adult prison and from January 15, 2020, to September 9, 2021, in the juvenile detention center. In the adult prison, study participation was offered to detained persons visiting the medical unit (response rate, 84.7%). In the juvenile detention center, all newly incarcerated adolescents were invited to participate (response rate, 98.0%). Interventions Participants were randomized to receive paper-based conventional material or to watch a 4-minute video. Materials included the same legal information, as required by the Swiss Federal Act on Research Involving Human Beings. Main Outcomes and Measures The main outcome was acceptance to sign the IC form. Secondary outcomes included understanding, evaluation, and time to read or watch the IC material. Results The study included 190 adults (mean [SD] age, 35.0 [11.8] years; 190 [100%] male) and 100 adolescents (mean [SD] age, 16.0 [1.1] years; 83 [83.0%] male). In the adult prison, no significant differences were found between groups in acceptance to sign the IC form (77 [81.1%] for paper-based material and 81 [85.3%] for audiovisual material; P = .39) and to evaluate it (mean [SD] correct responses, 5.09 [1.13] for paper-based material and 5.01 [1.07] for audiovisual material; P = .81). Understanding was significantly higher in the audiovisual material group (mean [SD] correct responses, 5.09 [1.84]) compared with the paper-based material group (mean [SD] correct responses, 4.61 [1.70]; P = .04). In the juvenile detention center, individuals in the audiovisual material group were more likely to sign the IC form (44 [89.8%]) than the paper-based material group (35 [68.6%], P = .006). No significant difference was found between groups for understanding and evaluation. Adults took a mean (SD) of 5 (2) minutes to read the paper material, and adolescents took 7 (3) minutes. Conclusions and Relevance Given the small benefit of audiovisual material, these findings suggest that giving detained adults and prison health care staff a choice regarding IC material is best. For adolescents, audiovisual material should be provided. Future studies should focus on increasing understanding of the IC process. Trial Registration ClinicalTrials.gov Identifier: NCT05505058

neXtProt: a knowledge platform for human proteins

neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human protein

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

Développement, optimisation et utilisation d'un système cellulaire de l'épithélium épididymaire murin : approches moléculaires

In mammals, the epididymal epithelium, through its activities and secretion reabsorption, participates in post-testicular maturation of sperm by creating a luminal environment particularly along the epididymal course. Studies to characterize the activities of secretion of this organ and to analyze gene regulation involved, have been hampered by the absence of cells in culture to this very epithelium differentiated. Despite numerous attempts, the systems of cultured cells developed so far do not reflect the state of cell differentiation epididymis in vivo. In particular, genes, which can be considered as terminal differentiation markers of epididymal, not expressed in cells in culture. GPX5, laboratory model gene, encoding a secreted protein of the family of glutathione peroxidases is a good example of epididymis-specific gene, that are not found in cells in culture systems available today. In this study, we used GPX5, PEA3 and indoleamine 2, 3-dioxygenase (IDO) and other genes expressed in the epididymis of mammals, as indicators of the state of differentiation of established cell lines head epididymis murine. These are derived from primary cultures, which are naturally immortalized by accumulation of random mutations. In a second step, we have tried to optimize the culture conditions of these cells to improve the level of epididymal gene expression, particularly GPX5, taken as reference.Chez les mammifères, l'épithélium épididymaire, via ses activités de sécrétion et de réabsorption, participe à la maturation post-testiculaire des spermatozoïdes en créant un environnement luminal particulier, tout au long du trajet épididymaire. Les études visant à caractériser les activités de sécrétion de cet organe et à analyser la régulation des gènes impliqués, ont été freinées par l'absence de cellules en culture pour cet épithelium très différencié. Malgré de nombreuses tentatives, les systèmes de cellules en culture développés jusqu'à présent ne reflètent pas l'état de différenciation des cellules épididymaires in vivo. En particulier, des gènes, que l'on peut considérer comme des marqueurs terminaux de la différenciation épididymaire, ne sont pas exprimés dans les cellules en culture. gpx5, gène modèle du laboratoire, codant pour une protéine sécrétée de la famille des glutathion peroxydases est un bon exemple de gène épididyme-spécifique, que l'on ne retrouve pas dans les systèmes de cellules en culture disponibles à ce jour. Dans cette étude, nous avons utilisé gpx5, PEA3 et l'indoleamine 2, 3-dioxygénase (IDO) et divers autres gènes, exprimés dans l'épididyme des mammifères, comme indicateurs de l'état de différenciation de lignées cellulaires établies de tête d'épididyme murin. Ces dernières sont issues de cultures primaires, qui se sont naturellement immortalisées par accumulation de mutations aléatoires. Dans un deuxième temps, nous avons tenté d'optimiser les conditions de culture de ces cellules afin d'améliorer le niveau d'expression de certains gènes épididymaires, en particulier gpx5, pris comme référence

ICEPO: the ion channel electrophysiology ontology

Ion channels are transmembrane proteins that selectively allow ions to flow across the plasma membrane and play key roles in diverse biological processes. A multitude of diseases, called channelopathies, such as epilepsies, muscle paralysis, pain syndromes, cardiac arrhythmias or hypoglycemia are due to ion channel mutations. A wide corpus of literature is available on ion channels, covering both their functions and their roles in disease. The research community needs to access this data in a user-friendly, yet systematic manner. However, extraction and integration of this increasing amount of data have been proven to be difficult because of the lack of a standardized vocabulary that describes the properties of ion channels at the molecular level. To address this, we have developed Ion Channel ElectroPhysiology Ontology (ICEPO), an ontology that allows one to annotate the electrophysiological parameters of the voltage-gated class of ion channels. This ontology is based on a three-state model of ion channel gating describing the three conformations/states that an ion channel can adopt: closed, open and inactivated. This ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. Here, we present ICEPO (ICEPO ftp site:ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/), as well as examples of its use

Malignant ascites: a source of therapeutic protein against ovarian cancer?

Ovarian cancer is the fifth leading cause of cancer-related death in the world. Some ovarian cancer patients present large amount of ascites at the time of diagnosis which may play an active role in tumor development. In earlier studies, we demonstrated that the acellular fraction of ascites can induce apoptosis of ovarian cancer cells. The current study identifies pigment epithelium derived factor (PEDF) as the molecule responsible for the apoptotic effect of ascites and evaluates the Sleeping Beauty transposon (SBT) system as a new tool for PEDF gene therapy against ovarian cancer. We utilize gel filtration, mass spectrometry, affinity column, cell viability assay, tumor development on chick chorioallantoic membrane and molecular biology techniques for these purposes. PEDF was thus identified as the agent responsible for the effects of ascites on ovarian cancer cell viability and tumor growth. Interestingly,the PEDF expression is decreased in ovarian cancer cells compared to healthy ovarian cells. However, the level of PEDF is higher in ascites than in serum of ovarian cancer patients suggesting that cells present in the tumor environment are able to secrete PEDF. We then used the SBT system to stably induce PEDF expression in ovarian cancer cells. The overexpression of PEDF significantly reduced the tumor growth derived from these cells. In conclusion, the results presented here establish that PEDF is a therapeutic target and that PEDF from ascites or SBT could be utilized as a therapeutic strategy for the treatment of ovarian cancer

Annotation of functional impact of voltage-gated sodium channel mutations.

Voltage-gated sodium channels are pore-forming transmembrane proteins that selectively allow sodium ions to flow across the plasma membrane according to the electro-chemical gradient thus mediating the rising phase of action potentials in excitable cells and playing key roles in physiological processes such as neurotransmission, skeletal muscle contraction, heart rhythm, and pain sensation. Genetic variations in the nine human genes encoding these channels are known to cause a large range of diseases affecting the nervous and cardiac systems. Understanding the molecular effect of genetic variations is critical for elucidating the pathologic mechanisms of known variations and in predicting the effect of newly discovered ones. To this end, we have created a Web-based tool, the Ion Channels Variants Portal, which compiles all variants characterized functionally in the human sodium channel genes. This portal describes 672 variants each associated with at least one molecular or clinical phenotypic impact, for a total of 4,658 observations extracted from 264 different research articles. These data were captured as structured annotations using standardized vocabularies and ontologies, such as the Gene Ontology and the Ion Channel ElectroPhysiology Ontology. All these data are available to the scientific community via neXtProt at https://www.nextprot.org/portals/navmut

GPX5, the selenium-independent glutathione peroxidase-encoding single copy gene is differentially expressed in mouse epididymis

International audienc

Beta cell coupling and connexin expression change during the functional maturation of rat pancreatic islets

AIMS/HYPOTHESIS: Cell-cell coupling mediated by gap junctions formed from connexin (CX) contributes to the control of insulin secretion in the endocrine pancreas. We investigated the cellular production and localisation of CX36 and CX43, and gap junction-mediated beta cell coupling in pancreatic islets from rats of different ages, displaying different degrees of maturation of insulin secretion. METHODS: The presence and distribution of islet connexins were assessed by immunoblotting and immunofluorescence. The expression of connexin genes was evaluated by RT-PCR and quantitative real-time PCR. The ultrastructure of gap junctions and the function of connexin channels were assessed by freeze-fracture electron microscopy and tracer microinjection, respectively. RESULTS: Young and adult beta cells, which respond to glucose, expressed significantly higher levels of Cx36 (also known as Gjd2) than fetal and newborn beta cells, which respond poorly to the sugar. Accordingly, adult beta cells also showed a significantly higher membrane density of gap junctions and greater intercellular exchange of ethidium bromide than newborn beta cells. Cx43 (also known as Gja1) was not expressed by beta cells, but was located in various cell types at the periphery of fetal and newborn islets. CONCLUSIONS/INTERPRETATION: These findings show that the pattern of connexins, gap junction membrane density and coupling changes in islets during the functional maturation of beta cells