Deep Learning-based detection of psychiatric attributes from German mental health records.

Background: Health care records provide large amounts of data with real-world and longitudinal aspects, which is advantageous for predictive analyses and improvements in personalized medicine. Text-based records are a main source of information in mental health. Therefore, application of text mining to the electronic health records - especially mental state examination - is a key approach for detection of psychiatric disease phenotypes that relate to treatment outcomes.

Ontology-based identification and prioritization of candidate drugs for epilepsy from literature.

Background: Drug repurposing can improve the return of investment as it finds new uses for existing drugs. Literature-based analyses exploit factual knowledge on drugs and diseases, e.g.

Fast Healthcare Interoperability Resources (FHIR) in a FAIR Metadata Registry for COVID-19 Research.

Adopting international standards within health research communities can elevate data FAIRness and widen analysis possibilities. The purpose of this study was to evaluate the mapping feasibility against HL7® Fast Healthcare Interoperability Resources® (FHIR)® of a generic metadata schema (MDS) created for a central search hub gathering COVID-19 health research (studies, questionnaires, documents = MDS resource types). Mapping results were rated by calculating the percentage of FHIR coverage.

Radical collaboration during a global health emergency: development of the RDA COVID-19 data sharing recommendations and guidelines.

The coronavirus disease 2019 (COVID-19) global pandemic required a rapid and effective response. This included ethical and legally appropriate sharing of data. The European Commission (EC) called upon the Research Data Alliance (RDA) to recruit experts worldwide to quickly develop recommendations and guidelines for COVID-related data sharing.

Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group.

The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby facilitating research and research reproducibility and timely collaboration beyond borders. The Research Data Alliance COVID-19 Working Group recently published a set of recommendations and guidelines on data sharing and related best practices for COVID-19 research.

COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints.

During the current COVID-19 pandemic, the rapid availability of profound information is crucial in order to derive information about diagnosis, disease trajectory, treatment or to adapt the rules of conduct in public. The increased importance of preprints for COVID-19 research initiated the design of the preprint search engine preVIEW. Conceptually, it is a lightweight semantic search engine focusing on easy inclusion of specialized COVID-19 textual collections and provides a user friendly web interface for semantic information retrieval.

Facilitating Study and Item Level Browsing for Clinical and Epidemiological COVID-19 Studies.

COVID-19 poses a major challenge to individuals and societies around the world. Yet, it is difficult to obtain a good overview of studies across different medical fields of research such as clinical trials, epidemiology, and public health. Here, we describe a consensus metadata model to facilitate structured searches of COVID-19 studies and resources along with its implementation in three linked complementary web-based platforms.

The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application.

Recent years have seen great advances in the development of glycoproteomics protocols and methods resulting in a sustainable increase in the reporting proteins, their attached glycans and glycosylation sites. However, only very few of these reports find their way into databases or data repositories. One of the major reasons is the absence of digital standard to represent glycoproteins and the challenging annotations with glycans.

Reprograming of sRNA target specificity by the leader peptide peTrpL in response to antibiotic exposure.

Trans-acting regulatory RNAs have the capacity to base pair with more mRNAs than generally detected under defined conditions, raising the possibility that sRNA target specificities vary depending on the specific metabolic or environmental conditions. In Sinorhizobium meliloti, the sRNA rnTrpL is derived from a tryptophan (Trp) transcription attenuator located upstream of the Trp biosynthesis gene trpE(G). The sRNA rnTrpL contains a small ORF, trpL, encoding the 14-aa leader peptide peTrpL.

Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli.

Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology.

The CARF Protein MM_0565 Affects Transcription of the Casposon-Encoded Gene in Gö1.

Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci are found in bacterial and archaeal genomes where they provide the molecular machinery for acquisition of immunity against foreign DNA. In addition to the genes fundamentally required for CRISPR activity, a second class of genes is associated with the CRISPR loci, of which many have no reported function in CRISPR-mediated immunity. Here, we characterize MM_0565 associated to the type I-B CRISPR-locus of Gö1.

Gene autoregulation by 3' UTR-derived bacterial small RNAs.

Negative feedback regulation, that is the ability of a gene to repress its own synthesis, is the most abundant regulatory motif known to biology. Frequently reported for transcriptional regulators, negative feedback control relies on binding of a transcription factor to its own promoter. Here, we report a novel mechanism for gene autoregulation in bacteria relying on small regulatory RNA (sRNA) and the major endoribonuclease, RNase E.

The Leader Peptide peTrpL Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes.

Bacterial ribosome-dependent attenuators are widespread posttranscriptional regulators. They harbor small upstream open reading frames (uORFs) encoding leader peptides, for which no functions in are known yet. In the plant symbiont , the tryptophan biosynthesis gene is preceded by the uORF and is regulated by transcription attenuation according to tryptophan availability.

Ten simple rules for making training materials FAIR.

Everything we do today is becoming more and more reliant on the use of computers. The field of biology is no exception; but most biologists receive little or no formal preparation for the increasingly computational aspects of their discipline. In consequence, informal training courses are often needed to plug the gaps; and the demand for such training is growing worldwide.

GlyGen data model and processing workflow.

Summary: Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. This application note describes the GlyGen data model, processing workflow and the data access interfaces featuring programmatic use case example queries based on specific biological questions. The GlyGen project is a data integration, harmonization and dissemination project for carbohydrate and glycoconjugate-related data retrieved from multiple international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources.

Differences in the Transcriptomic Response of and to Heat Stress.

spp. are one of the most important food-borne pathogens, which are quite susceptible to environmental or technological stressors compared to other zoonotic bacteria. This might be due to the lack of many stress response mechanisms described in other bacteria.

Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control.

RNA-protein interactions are the crucial basis for many steps of bacterial gene expression, including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in the analysis of Gram-negative bacteria, knowledge about RNA-protein complexes in Gram-positive species remains scarce. Here, we used the Grad-seq approach to draft a comprehensive landscape of such complexes in Streptococcus pneumoniae, in total determining the sedimentation profiles of ~ 88% of the transcripts and ~ 62% of the proteins of this important human pathogen.

YBEY is an essential biogenesis factor for mitochondrial ribosomes.

Ribosome biogenesis requires numerous trans-acting factors, some of which are deeply conserved. In Bacteria, the endoribonuclease YbeY is believed to be involved in 16S rRNA 3'-end processing and its loss was associated with ribosomal abnormalities. In Eukarya, YBEY appears to generally localize to mitochondria (or chloroplasts).

The Application of Internet-Based Sources for Public Health Surveillance (Infoveillance): Systematic Review.

Background: Public health surveillance is based on the continuous and systematic collection, analysis, and interpretation of data. This informs the development of early warning systems to monitor epidemics and documents the impact of intervention measures. The introduction of digital data sources, and specifically sources available on the internet, has impacted the field of public health surveillance.

SEAweb: the small RNA Expression Atlas web application.

We present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms. It contains sRNA and pathogen expression information for over 4200 published samples with standardized search terms and ontologies. In addition, SEAweb allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons.

A conserved RNA seed-pairing domain directs small RNA-mediated stress resistance in enterobacteria.

Small regulatory RNAs (sRNAs) are crucial components of many stress response systems. The envelope stress response (ESR) of Gram-negative bacteria is a paradigm for sRNA-mediated stress management and involves, among other factors, the alternative sigma factor E (σ ) and one or more sRNAs. In this study, we identified the MicV sRNA as a new member of the σ regulon in Vibrio cholerae.

Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications.

The total number of scholarly publications grows day by day, making it necessary to explore and use simple yet effective ways to expose their metadata. Schema.org supports adding structured metadata to web pages via markup, making it easier for data providers but also for search engines to provide the right search results.