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.

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.

Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt.

The development of efficient text-mining tools promises to boost the curation workflow by significantly reducing the time needed to process the literature into biological databases. We have developed a curation support tool, neXtA5, that provides a search engine coupled with an annotation system directly integrated into a biocuration workflow. neXtA5 assists curation with modules optimized for the thevarious curation tasks: document triage, entity recognition and information extraction.Here, we describe the evaluation of neXtA5 by expert curators. We first assessed the annotations of two independent curators to provide a baseline for comparison. To evaluate the performance of neXtA5, we submitted requests and compared the neXtA5 results with the manual curation. The analysis focuses on the usability of neXtA5 to support the curation of two types of data: biological processes (BPs) and diseases (Ds). We evaluated the relevance of the papers proposed as well as the recall and precision of the suggested annotations.The evaluation of document triage by neXtA5 precision showed that both curators agree with neXtA5 for 67 (BP) and 63% (D) of abstracts, while curators agree on accepting or rejecting an abstract ~80% of the time. Hence, the precision of the triage system is satisfactory.For concept extraction, curators approved 35 (BP) and 25% (D) of the neXtA5 annotations. Conversely, neXtA5 successfully annotated up to 36 (BP) and 68% (D) of the terms identified by curators. The user feedback obtained in these tests highlighted the need for improvement in the ranking function of neXtA5 annotations. Therefore, we transformed the information extraction component into an annotation ranking system. This improvement results in a top precision (precision at first rank) of 59 (D) and 63% (BP). These results suggest that when considering only the first extracted entity, the current system achieves a precision comparable with expert biocurators.

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.

The neXtProt knowledgebase on human proteins: 2017 update.

The neXtProt human protein knowledgebase (https://www.nextprot.org) continues to add new content and tools, with a focus on proteomics and genetic variation data. neXtProt now has proteomics data for over 85% of the human proteins, as well as new tools tailored to the proteomics community.Moreover, the neXtProt release 2016-08-25 includes over 8000 phenotypic observations for over 4000 variations in a number of genes involved in hereditary cancers and channelopathies. These changes are presented in the current neXtProt update. All of the neXtProt data are available via our user interface and FTP site. We also provide an API access and a SPARQL endpoint for more technical applications.

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 proteins.

Connexins protect mouse pancreatic ß cells against apoptosis.

Type 1 diabetes develops when most insulin-producing ß cells of the pancreas are killed by an autoimmune attack. The in vivo conditions modulating the sensitivity and resistance of ß cells to this attack remain largely obscure. Here, we show that connexin 36 (Cx36), a trans-membrane protein that forms gap junctions between ß cells in the pancreatic islets, protects mouse ß cells against both cytotoxic drugs and cytokines that prevail in the islet environment at the onset of type 1 diabetes. We documented that this protection was at least partially dependent on intercellular communication, which Cx36 and other types of connexin channels establish within pancreatic islets. We further found that proinflammatory cytokines decreased expression of Cx36 and that experimental reduction or augmentation of Cx36 levels increased or decreased ß cell apoptosis, respectively. Thus, we conclude that Cx36 is central to ß cell protection from toxic insults.

Involvement of microRNAs in the cytotoxic effects exerted by proinflammatory cytokines on pancreatic beta-cells.

OBJECTIVE: Pancreatic beta-cells exposed to proinflammatory cytokines display alterations in gene expression resulting in defective insulin secretion and apoptosis. MicroRNAs are small noncoding RNAs emerging as key regulators of gene expression. Here, we evaluated the contribution of microRNAs to cytokine-mediated beta-cell cytotoxicity. RESEARCH DESIGN AND METHODS: We used global microarray profiling and real-time PCR analysis to detect changes in microRNA expression in beta-cells exposed to cytokines and in islets of pre-diabetic NOD mice. We assessed the involvement of the microRNAs affected in cytokine-mediated beta-cell failure by modifying their expression in insulin-secreting MIN6 cells. RESULTS: We found that IL-1beta and TNF-alpha induce the expression of miR-21, miR-34a, and miR-146a both in MIN6 cells and human pancreatic islets. We further show an increase of these microRNAs in islets of NOD mice during development of pre-diabetic insulitis. Blocking miR-21, miR-34a, or miR-146a function using antisense molecules did not restore insulin-promoter activity but prevented the reduction in glucose-induced insulin secretion observed upon IL-1beta exposure. Moreover, anti-miR-34a and anti-miR-146a treatment protected MIN6 cells from cytokine-triggered cell death. CONCLUSIONS: Our data identify miR-21, miR-34a, and miR-146a as novel players in beta-cell failure elicited in vitro and in vivo by proinflammatory cytokines, notably during the development of peri-insulitis that precedes overt diabetes in NOD mice.

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

Using various molecular approaches, including reverse transcription-polymerase chain reaction (RT-PCR), rapid amplification of cDNA ends-PCR, sequencing, northern and western blotting, we found that the mouse GPX5 gene gives rise to at least three different transcripts that are not expressed at the same levels in the mouse epididymis. In addition to the major GPX5 transcript, we show that minor GPX5 transcripts exist, arising either from precocious termination of transcription or an alternative splicing event within intron 4 of the 5 exon-encoding GPX5 single copy gene. Furthermore, we demonstrate that variants of the GPX5 protein that are correlated with the shorter GPX5 transcripts can be detected in caput epididymidis protein extracts and that the various GPX5 isoforms are subject to differential post-transcriptional maturation processes in the mouse epididymis that essentially involve the addition of O-glycosyl extensions. Using a sensitive poly-A+ mRNA tissue blot, as well as RT-PCR and northern assays, we further show that in addition to being expressed in the epididymis, the GPX5 gene is also expressed, albeit at lower levels, in other tissues of the male genital tract, including the testis and prostate. Finally, we present evidence suggesting that the GPX5 gene is expressed in a temporally regulated manner during mouse embryonic development.

Quantitative and spatial differences in the expression of tryptophan-metabolizing enzymes in mouse epididymis.

Previous reports have suggested that indoleamine 2,3-dioxygenase (IDO) activity is particularly important in mouse epididymis tissue. We show here, using reverse transcription/polymerase chain reaction assays, Northern assays, Western blotting experiments, and immunohistochemistry that IDO is indeed highly expressed in mouse epididymis, and that IDO mRNA distribution and protein location are precisely regionalized within the organ and within sub-territories of the proximal part of the epididymal duct, the so-called caput epididymidis. Within the caput epididymidis, both the principal and the apical cells have been shown to express IDO. On the contrary, tryptophan dioxygenase (TDO), a sister enzyme of IDO, is weakly and uniformly expressed in mouse epididymis and, in contrast to IDO, is also expressed in testis. In the epididymis, TDO protein expression has been found in a totally different cell type in the smooth muscle layer surrounding the epididymal tubules. Finally, IDO is not secreted into the epididymal lumen, whereas the testis-expressed TDO is present on the head of spermatozoa retrieved from the cauda epididymidis. On the basis of the various functions that have been associated with IDO/TDO, we discuss the putative impacts of IDO/TDO expression on the physiology of mammalian epididymis and spermatozoa.

Dietary magnesium depletion does not promote oxidative stress but targets apical cells within the mouse caput epididymidis.

It is well documented that a dietary deficiency in magnesium can induce oxidative stress and an inflammatory response in animal models. In our study, we have investigated these responses in the mouse epididymis after mice had been fed a magnesium-deficient diet for a 2-week duration. The extracellular and intracellular concentrations of magnesium where shown to be depleted on this diet. This was followed, however, only in the liver of the Mg-deficient animals, by an increase in both alpha 2-macroglobulin (alpha-2m), an acute phase marker, and interleukin-6 transcripts suggesting that an inflammatory response had been initiated. These changes were correlated with a decrease in circulating neutrophils. To address the question of whether or not peroxidation was induced in mouse epididymis following hypomagnesia, we have monitored the level of endogenous peroxidation, their ability to respond to induced peroxidation as well as the expression and activity of the enzymatic glutathione peroxidase (GPX) antioxidant family. To evaluate if the epididymis had evolved specific protections against peroxidation, other organs such as the liver and the kidney were monitored in parallel. We detected no evidence for increased peroxidation in any of the mouse organs tested. However, GPX activity was found to be significantly lower in the liver and the kidney of Mg-deficient animals while it was unchanged in the epididymides of the same animals during the deficiency. Histological analysis of the epididymis showed no major difference in the overall cytological aspect of the organ. Segment 2 of the caput, however presented a significant increase in the number of apically located cells or blebbing cells. Immunohistochemical analysis proved that these cells were epididymal apical cells and not infiltrated leukocytes. These observations suggested that the mouse caput epididymidis segment 2 specifically responded to Mg deficiency via the apical cells. Finally, a comparative analysis of stress response genes was conducted in control and magnesium-deficient caput epididymidis samples. It brought forward some genes that might be involved in the peculiar response of the caput epithelium following hypomagnesia.