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Gene-set analysis (GSA) dominates the functional interpretation of omics data and downstream hypothesis generation. Despite its ability to summarise thousands of measurements into semantically interpretable components, GSA often results in hundreds of significantly enriched gene-sets. However, summarisation and effective visualisation of GSA results to facilitate hypothesis generation is still lacking. While some webservers provide gene-set visualization tools, there is still a need for tools that can effectively summarize and guide exploration of GSA results. To enable versatility, webservers accept gene lists as input, however, none provide end-to-end solutions for emerging data types such as single-cell and spatial omics. Here, we present vissE.Cloud, a webserver for end-to-end gene-set analysis, offering gene-set summarisation and highly interactive visualisation. vissE.Cloud uses algorithms from our earlier R package vissE to summarise GSA results by identifying biological themes. We maintain versatility by allowing analysis of gene lists, as well as, analysis of raw single-cell and spatial omics data, including CosMx and Xenium data, making vissE.Cloud the first webserver to provide end-to-end gene-set analysis of sub-cellular localised spatial data. Structuring the results hierarchically allows swift interactive investigations of results at the gene, gene-set, and clusters level. vissE.Cloud is freely available at https://www.vissE.Cloud.

RaftProt (http://lipid-raft-database.di.uq.edu.au/) is a database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms. Given their fundamental roles in cellular regulation, there is a plethora of information on the size, composition and regulation of these membrane microdomains, including a large number of proteomics studies. To facilitate the mining and analysis of published lipid raft proteomics studies, we have developed a searchable database RaftProt. In addition to browsing the studies, performing basic queries by protein and gene names, searching experiments by cell, tissue and organisms; we have implemented several advanced features to facilitate data mining. To address the issue of potential bias due to biochemical preparation procedures used, we have captured the lipid raft preparation methods and implemented advanced search option for methodology and sample treatment conditions, such as cholesterol depletion. Furthermore, we have identified a list of high confidence proteins, and enabled searching only from this list of likely bona fide lipid raft proteins. Given the apparent biological importance of lipid raft and their associated proteins, this database would constitute a key resource for the scientific community.

Large quantities of information describing the mechanisms of biological pathways continue to be collected in publicly available databases. At the same time, experiments have increased in scale, and biologists increasingly use pathways defined in online databases to interpret the results of experiments and generate hypotheses. Emerging computational techniques that exploit the rich biological information captured in reaction systems require formal standardized descriptions of pathways to extract these reaction networks and avoid the alternative: time-consuming and largely manual literature-based network reconstruction. Here, we systematically evaluate the effects of commonly used knowledge representations on the seemingly simple task of extracting a reaction network describing signal transduction from a pathway database. We show that this process is in fact surprisingly difficult, and the pathway representations adopted by various knowledge bases have dramatic consequences for reaction network extraction, connectivity, capture of pathway crosstalk and in the modelling of cell-cell interactions. Researchers constructing computational models built from automatically extracted reaction networks must therefore consider the issues we outline in this review to maximize the value of existing pathway knowledge.

Objective To evaluate the effectiveness of the STARBRIGHT Fitting Cystic Fibrosis Into Your Life Everyday CD-ROM. Data were analyzed to evaluate the effectiveness of the program as an educational tool for children and adolescents with cystic fibrosis (CF). Methods Forty-seven children and adolescents with CF between the ages of 7 and 17 years were enrolled in the study. Participants completed an initial evaluation of CF-related knowledge and coping skills and were then randomly assigned to one of two groups: the treatment group or the wait-list control group. Participants then viewed the CD-ROM, and researchers completed posttest measures. Results Analyses indicated that both disease-related knowledge and coping strategies generated by children and adolescents with CF improved as a result of the intervention and that this effect was replicated in the wait-list group. Conclusions In sum, the results of the current study indicate that the STARBRIGHT CD-ROM program is a promising intervention for increasing CF-related knowledge and the competence of children's and adolescents' coping strategies. These positive results are enhanced by the brief, inexpensive, and portable nature of this educational program.

Objective To reduce young children's distress and increase coping behavior among children undergoing a voiding cystourethrogram (VCU). Methods Three- to seven-year-old children were stratified based on prior VCU experience and randomly assigned to an intervention (n = 20) or a standard care (n = 20) condition. The intervention included provision of information, coping skills training, and parent coaching. We hypothesized that the intervention would reduce children's distress as assessed by child report, parent and technician ratings, and behavioral observations. Results Children in the intervention displayed fewer distress behaviors and greater coping behaviors and were rated as more cooperative than children receiving standard care. Children's fear and pain ratings did not differ significantly between groups. Conclusions A cognitive-behavioral treatment package effectively reduced children's distress, increased coping, and increased cooperation during voiding cystourethrogram procedures. This type of an intervention should be integrated into routine pediatric radiological procedures.

Among the ways corporations use their enormous wealth is to support private justice systems complete with investigative, adjudicatory, and sentencing powers. The present paper advances a sociological analysis of a private corporate justice system and the private police who run it. Our research setting is a full line store of one of the nation's largest corporations. Our focus is private justice for shoplifters in a civil recovery state. Analysis reveals that retail value of the item taken, neighborhood social class, and physical resistance are among the factors determining private corporate justice for shoplifters in a civil recovery state. The findings suggest the part played by private justice systems in shaping public images of crime and criminals.