Project description:Many modern interactions happen in a digital space, where automated recommendations and homophily can shape the composition of groups interacting together and the knowledge that groups are able to tap into when operating online. Digital interactions are also characterized by different scales, from small interest groups to large online communities. Here, we manipulate the composition of groups based on a large multi-trait profiling space (including demographic, professional, psychological and relational variables) to explore the causal link between group composition and performance as a function of group size. We asked volunteers to search news online under time pressure and measured individual and group performance in forecasting real geo-political events. Our manipulation affected the correlation of forecasts made by people after online searches. Group composition interacted with group size so that composite diversity benefited individual and group performance proportionally to group size. Aggregating opinions of modular crowds composed of small independent groups achieved better forecasts than aggregating a similar number of forecasts from non-modular ones. Finally, we show differences existing among groups in terms of disagreement, speed of convergence to consensus forecasts and within-group variability in performance. The present work sheds light on the mechanisms underlying effective online information gathering in digital environments.
Project description:The Molecular Biology Database Collection represents an effort geared at making molecular biology database resources more accessible to biologists. This online resource, available at http://www.oup.co.uk/nar/Volume_28/Issue_01/html /gkd115_gml.html, is intended to serve as a searchable, up-to-date, centralized jumping-off point to individual Web sites. An emphasis has also been placed on including databases where new value is added to the underlying data by virtue of curation, new data connections, or other innovative approaches.
Project description:A broad body of scientific literature exists on the effects that COVID-19 related confinement has had on the population: mental health problems, isolation, and problems concerning cohesion and employment, among others. However, there is a gap in the literature on the actions that reverse some of the effects generated during lockdown. This article collects the results of a study conducted with 53 people participating in a dialogic gathering of films (DGF) that was held online during two months of confinement. The data from the survey show that the development of this DGF generated improvements in 1) personal welfare and attitudes concerning the management of confinement, 2) living together and online relationships, 3) motivation and creativity in the professional domain, and 4) openness to a diversity of perspectives and realities, which improves the understanding, argumentation and positioning in social, scientific and ethical debates.
Project description:Autophagosomes are double-membrane vesicles generated intracellularly to encapsulate substrates for lysosomal degradation during autophagy. Phase separated p62 body plays pivotal roles during autophagosome formation, however, the underlying mechanisms are still not fully understood. Here we describe a spatial membrane gathering mode by which p62 body functions in autophagosome formation. Mass spectrometry-based proteomics reveals significant enrichment of vesicle trafficking components within p62 body. Combining cellular experiments and biochemical reconstitution assays, we confirm the gathering of ATG9 and ATG16L1-positive vesicles around p62 body, especially in Atg2ab DKO cells with blocked lipid transfer and vesicle fusion. Interestingly, p62 body also regulates ATG9 and ATG16L vesicle trafficking flux intracellularly. We further determine the lipid contents associated with p62 body via lipidomic profiling. Moreover, with in vitro kinase assay, we uncover the functions of p62 body as a platform to assemble ULK1 complex and invigorate PI3KC3-C1 kinase cascade for PI3P generation. Collectively, our study raises a membrane-based working model for multifaceted p62 body in controlling autophagosome biogenesis, and highlights the interplay between membraneless condensates and membrane vesicles in regulating cellular functions.
Project description:The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest. In the area of metabolism, HMDB and Reactome both report new features while PULDB appears in NAR for the first time. This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE. Update papers from the IUPHAR/BPS Guide to Pharmacology and DrugBank are highlights of the drug and drug target section while a number of proteomics databases including proteomicsDB are also covered. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 138 entries, adding 88 new resources and eliminating 47 discontinued URLs, bringing the current total to 1737 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.
Project description:The 2024 Nucleic Acids Research database issue contains 180 papers from across biology and neighbouring disciplines. There are 90 papers reporting on new databases and 83 updates from resources previously published in the Issue. Updates from databases most recently published elsewhere account for a further seven. Nucleic acid databases include the new NAKB for structural information and updates from Genbank, ENA, GEO, Tarbase and JASPAR. The Issue's Breakthrough Article concerns NMPFamsDB for novel prokaryotic protein families and the AlphaFold Protein Structure Database has an important update. Metabolism is covered by updates from Reactome, Wikipathways and Metabolights. Microbes are covered by RefSeq, UNITE, SPIRE and P10K; viruses by ViralZone and PhageScope. Medically-oriented databases include the familiar COSMIC, Drugbank and TTD. Genomics-related resources include Ensembl, UCSC Genome Browser and Monarch. New arrivals cover plant imaging (OPIA and PlantPAD) and crop plants (SoyMD, TCOD and CropGS-Hub). The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Over the last year the NAR online Molecular Biology Database Collection has been updated, reviewing 1060 entries, adding 97 new resources and eliminating 388 discontinued URLs bringing the current total to 1959 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.
Project description:A recent proliferation of Massive Open Online Courses (MOOCs) and other web-based educational resources has greatly increased the potential for effective self-study in many fields. This article introduces a catalog of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. The courses are organized into eleven subject areas modeled on university departments and are accompanied by commentary and career advice.
Project description:Funding agencies and researchers increasingly recognize the importance of patient stakeholder engagement in research. Despite calls for greater patient engagement, few studies have engaged a broad-based online community of patient stakeholders in the early stages of the research development process.The objective of our study was to inform a research priority-setting agenda by using a Web-based survey to gather perceptions of important and difficult aspects of diabetes care from patient members of a social networking site-based community.Invitations to participate in a Web-based survey were sent by email to members of the PatientsLikeMe online diabetes community. The survey asked both quantitative and qualitative questions addressing individuals' level of difficulty with diabetes care, provider communication, medication management, diet and exercise, and relationships with others. Qualitative responses were analyzed using content analysis.Of 6219 PatientsLikeMe members with diabetes who were sent survey invitations, 1044 (16.79%) opened the invitation and 320 (5.15% of 6219; 30.65% of 1044) completed the survey within 23 days. Of the 320 respondents, 33 (10.3%) reported having Type 1 diabetes; 107 (33.4%), Type 2 diabetes and taking insulin; and 180 (56.3%), Type 2 diabetes and taking oral agents or controlling their diabetes with lifestyle modifications. Compared to 2005-2010 National Health and Nutrition Examination Survey data for individuals with diabetes, our respondents were younger (mean age 55.8 years, SD 9.9 vs 59.4 years, SE 0.5); less likely to be male (111/320, 34.6% vs 48.4%); and less likely to be a racial or ethnic minority (40/312, 12.8% vs 37.5%). Of 29 potential challenges in diabetes care, 19 were categorized as difficult by 20% or more of respondents. Both quantitative and qualitative results indicated that top patient challenges were lifestyle concerns (diet, physical activity, weight, and stress) and interpersonal concerns (trying not to be a burden to others, getting support from family/friends). In our quantitative analysis, similar concerns were expressed across patient subgroups.Lifestyle and interpersonal factors were particularly challenging for our online sample of adults with Type 1 or Type 2 diabetes. Our study demonstrates the innovative use of social networking sites and online communities to gather rapid, meaningful, and relevant patient perspectives that can be used to inform the development of research agendas.
Project description:Current methods of pharmacovigilance result in severe under-reporting of adverse drug events (ADEs). Patient forums have the potential to complement current pharmacovigilance practices by providing real-time uncensored and unsolicited information. We are the first to explore the value of patient forums for rare cancers. To this end, we conduct a case study on a patient forum for Gastrointestinal Stromal Tumor patients. We have developed machine learning algorithms to automatically extract and aggregate side effects from messages on open online discussion forums. We show that patient forum data can provide suggestions for which ADEs impact quality of life the most: For many side effects the relative reporting rate differs decidedly from that of the registration trials, including for example cognitive impairment and alopecia as side effects of avapritinib. We also show that our methods can provide real-world data for long-term ADEs, such as osteoporosis and tremors for imatinib, and novel ADEs not found in registration trials, such as dry eyes and muscle cramping for imatinib. We thus posit that automated pharmacovigilance from patient forums can provide real-world data for ADEs and should be employed as input for medical hypotheses for rare cancers.