Cataloging the phylogenetic diversity of human bladder bacterial isolates.

BACKGROUND: Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity. RESULTS: To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches. CONCLUSIONS: This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.

Principales tecnologías de indización en las ciencias de la salud que se emplean en Occidente / Main indexing healthcare technologies used in West

En la actualidad, las tecnologías de indización en las ciencias de la salud están aportando mu-chos beneficios para el ámbito biomédico y la estandarización de su correspondiente termino-logía, puesto que esta cuestión es fundamental para lograr un diagnóstico médico más preciso e inequívoco Por esta razón, en este artículo se ha explicado con detalle cómo funcionan estas tecnologías: Terminología Anatómica In-ternacional (TAI), Medical Subject Headings y el Systematized Nomenclature of Medicine Cli-nical terminology (SNOMED CT), así como, las razones de la importancia de su uso para los sanitarios y los terminólogos.(AU)

Nowadays, healthcare indexing technologies are profiting the biomedical field and the stand-ardization of its corresponding terminology, since this is essential to achieve a more pre-cise and unequivocal medical diagnosis. Thus, in this article it has been performed a thorough explanation on how these healthcare technolo-gies work: International Anatomical Terminology (TAI), Medical Subject Headings and the Sys-tematised Nomenclature of Medicine Clinical terminology (SNOMED CT), as well as it was elucidated the reasons of its use for healthcare professionals and terminologists.(AU)

Cataloging natural sialic acids and other nonulosonic acids (NulOs), and their representation using the Symbol Nomenclature for Glycans.

Nonulosonic acids or non-2-ulosonic acids (NulOs) are an ancient family of 2-ketoaldonic acids (α-ketoaldonic acids) with a 9-carbon backbone. In nature, these monosaccharides occur either in a 3-deoxy form (referred to as "sialic acids") or in a 3,9-dideoxy "sialic-acid-like" form. The former sialic acids are most common in the deuterostome lineage, including vertebrates, and mimicked by some of their pathogens. The latter sialic-acid-like molecules are found in bacteria and archaea. NulOs are often prominently positioned at the outermost tips of cell surface glycans, and have many key roles in evolution, biology and disease. The diversity of stereochemistry and structural modifications among the NulOs contributes to more than 90 sialic acid forms and 50 sialic-acid-like variants described thus far in nature. This paper reports the curation of these diverse naturally occurring NulOs at the NCBI sialic acid page (https://www.ncbi.nlm.nih.gov/glycans/sialic.html) as part of the NCBI-Glycans initiative. This includes external links to relevant Carbohydrate Structure Databases. As the amino and hydroxyl groups of these monosaccharides are extensively derivatized by various substituents in nature, the Symbol Nomenclature For Glycans (SNFG) rules have been expanded to represent this natural diversity. These developments help illustrate the natural diversity of sialic acids and related NulOs, and enable their systematic representation in publications and online resources.

Functional interpretation, cataloging, and analysis of 1,341 glucose-6-phosphate dehydrogenase variants.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency affects over 500 million individuals who can experience anemia in response to oxidative stressors such as certain foods and drugs. Recently, the World Health Organization (WHO) called for revisiting G6PD variant classification as a priority to implement genetic medicine in low- and middle-income countries. Toward this goal, we sought to collect reports of G6PD variants and provide interpretations. We identified 1,341 G6PD variants in population and clinical databases. Using the ACMG standards and guidelines for the interpretation of sequence variants, we provided interpretations for 268 variants, including 186 variants that were not reported or of uncertain significance in ClinVar, bringing the total number of variants with non-conflicting interpretations to 400. For 414 variants with functional or clinical data, we analyzed associations between activity, stability, and current classification systems, including the new 2022 WHO classification. We corroborated known challenges with classification systems, including phenotypic variation, emphasizing the importance of comparing variant effects across individuals and studies. Biobank data made available by All of Us illustrate the benefit of large-scale sequencing and phenotyping by adding additional support connecting variants to G6PD-deficient anemia. By leveraging available data and interpretation guidelines, we created a repository for information on G6PD variants and nearly doubled the number of variants with clinical interpretations. These tools enable better interpretation of G6PD variants for the implementation of genetic medicine.

Molecular Network Guided Cataloging of the Secondary Metabolome of Selected Egyptian Red Sea Soft Corals.

Soft corals are recognized as an abundant source of diverse secondary metabolites with unique chemical features and physiologic capabilities. However, the discovery of these metabolites is usually hindered by the traditional protocol which requires a large quantity of living tissue for isolation and spectroscopic investigations. In order to overcome this problem, untargeted metabolomics protocols have been developed. The latter have been applied here to study the chemodiversity of common Egyptian soft coral species, using only minute amounts of coral biomass. Spectral similarity networks, based on high-resolution tandem mass spectrometry data, were employed to explore and highlight the metabolic biodiversity of nine Egyptian soft coral species. Species-specific metabolites were highlighted for future prioritization of soft coral species for MS-guided chemical investigation. Overall, 79 metabolites were tentatively assigned, encompassing diterpenes, sesquiterpenes, and sterols. Simultaneously, the methodology assisted in shedding light on newly-overlooked chemical diversity with potential undescribed scaffolds. For instance, glycosylated fatty acids, nitrogenated aromatic compounds, and polyketides were proposed in Sinularia leptoclados, while alkaloidal terpenes and N-acyl amino acids were proposed in both Sarcophyton roseum and Sarcophyton acutum.

Advances and challenges in cataloging the human gut virome.

The human gut virome, which is often referred to as the "dark matter" of the gut microbiome, remains understudied. A better understanding of the composition and variations of the gut virome across populations is critical for exploring its impact on diseases and health. A series of advances in the characterization of human gut virome have unveiled high genetic diversity and various functional potentials of gut viruses. Here, we summarize the recently available human gut virome databases and discuss their features, procedures, and challenges with the intention to provide a reference to researchers to use while choosing a profiling database. We also propose a "best practice" for cataloging the viral population.

Advanced Cataloging of Lysine-63 Polyubiquitin Networks by Genomic, Interactome, and Sensor-Based Proteomic Analyses.

The lack of resolution when studying the many different ubiquitin chain types found in eukaryotic cells has been a major hurdle to our understanding of their specific roles. We currently have very little insight into the cellular and physiological functions of Lys-63 (K63)-linked ubiquitin chains, although they are the second most abundant forms of ubiquitin in plant cells. To overcome this problem, we developed several large-scale approaches to characterize (1) the E2-E3 ubiquitination machinery driving K63-linked ubiquitin chain formation and (2) K63 polyubiquitination targets to provide a comprehensive picture of K63 polyubiquitin networks in Arabidopsis (Arabidopsis thaliana). Our work identified the ubiquitin-conjugating enzymes (E2s) UBC35/36 as the major drivers of K63 polyubiquitin chain formation and highlights the major role of these proteins in plant growth and development. Interactome approaches allowed us to identify many proteins that interact with the K63 polyubiquitination-dedicated E2s UBC35/36 and their cognate E2 variants, including more than a dozen E3 ligases and their putative targets. In parallel, we improved the in vivo detection of proteins decorated with K63-linked ubiquitin chains by sensor-based proteomics, yielding important insights into the roles of K63 polyubiquitination in plant cells. This work strongly increases our understanding of K63 polyubiquitination networks and functions in plants.

Campos MARC21 para interoperabilidade com a base de dados LILACS / MARC21 fields for interoperability with LILACS database

Tabela de conversão de dados para fins de interoperabilidade entre formato MARC21 e Metodologia LILACS para criação de registros bibliográficos

Evaluating a historical medical book collection.

BACKGROUND: After several years of storing a large number of historical medical books that had been weeded from the general collection, the University of New Mexico Health Sciences Library and Informatics Center developed a set of evaluation criteria to determine whether the material should be kept and included in the library catalog or discarded. The purpose of this article is to share lessons learned in evaluating and processing a historical medical book collection. The authors share how we determined review criteria as well as cataloging and processing procedures. CASE PRESENTATION: Best practices for evaluating, cataloging, and processing historical library material were determined through a literature search and then reviewed and adapted for application to this project. Eight hundred sixty-two titles were selected to add to the catalog and were added to a shelving location in our offsite storage facility. CONCLUSIONS: These materials are now discoverable in the library's catalog for library users who are interested in historical research, and the materials have been processed for easy retrieval as well as preservation purposes.

Real-time geotracking and cataloging of mass casualty incident markers in a search and rescue training simulation: Pilot study.

OBJECTIVE: Search and rescue after mass casualty incidents relies on robust data infrastructure. Federal Emergency Management Agency (FEMA's) Task Force 1 (TF1) trains its volunteers to locate and virtually tag scene incidents using a global positioning satellite (GPS) device programmed with markers for each incident (Iron Sights). The authors performed a pilot study comparing Iron Sights™ to a Wi-Fi-based real-time incident geolocation and virtual tagging dashboard (Panacea™) in creating a dynamic common operating picture. DESIGN: Twenty-nine stations were placed at a predefined scene incident, each featuring a set of varying waypoint markers using standard FEMA/TF1 nomenclature. Two volunteers performed the experiment for both the Iron Sights and Panacea systems, digitally tagging all station waypoints. SETTING: TF1 simulation training field. MAIN OUTCOME MEASURE(S): Metrics compared included GPS location precision, marker accuracy, and delay between scene sweep and common operational picture (COP) generation. RESULTS: Two hundred and sixty-one waypoints were digitally tagged after excluding three stations for missing data. The average GPS location difference for all waypoints between Iron Sights and Panacea was 3.65 m. Marker tagging accuracy between Iron Sights and Panacea was equivalent and not statistically different (78.8 percent vs 66.2 percent, respectively, p = 0.11). Waypoints were tagged in 26.59 minutes and 10.55 minutes on average, respectively. Time from scene sweep to virtual COP generation was 7.97 minutes for Iron Sights after complete scene sweep and 37 seconds for Panacea for each waypoint posting in real-time. CONCLUSIONS: Panacea generated the COP in real-time compared to a delay with Iron Sights while maintaining the same location precision and marker accuracy. This pilot trial successfully demonstrated the ability to provide real-time actionable intelligence to incident commanders during mass casualty search and rescue missions. Larger field trials are recommended to refine the system and broaden its capabilities.

Guía rápido: Repositorio REA CVSP / BVS - utilizando el FI-Admin

Al final de este guía, el usuario es capaz de: - Acceder el sistema FI-Admin para ingresar y editar registros de recursos educativos de un repositorio del nodo país del CVSP. - Reconocer los principales componentes y funciones del sistema FI-Admin, permitiendo describir, indizar, enlazar y relacionar los registros de recursos educativos.

AutophagySMDB: a curated database of small molecules that modulate protein targets regulating autophagy.

Macroautophagy/autophagy is a complex self-degradative mechanism responsible for clearance of non functional organelles and proteins. A range of factors influences the autophagic process, and disruptions in autophagy-related mechanisms lead to disease states, and further exacerbation of disease. Despite in-depth research into autophagy and its role in pathophysiological processes, the resources available to use it for therapeutic purposes are currently lacking. Herein we report the Autophagy Small Molecule Database (AutophagySMDB; http://www.autophagysmdb.org/ ) of small molecules and their cognate protein targets that modulate autophagy. Presently, AutophagySMDB enlists ~10,000 small molecules which regulate 71 target proteins. All entries are comprised of information such as EC50 (half maximal effective concentration), IC50 (half maximal inhibitory concentration), Kd (dissociation constant) and Ki (inhibition constant), IUPAC name, canonical SMILE, structure, molecular weight, QSAR (quantitative structure activity relationship) properties such as hydrogen donor and acceptor count, aromatic rings and XlogP. AutophagySMDB is an exhaustive, cross-platform, manually curated database, where either the cognate targets for small molecule or small molecules for a target can be searched. This database is provided with different search options including text search, advanced search and structure search. Various computational tools such as tree tool, cataloging tools, and clustering tools have also been implemented for advanced analysis. Data and the tools provided in this database helps to identify common or unique scaffolds for designing novel drugs or to improve the existing ones for autophagy small molecule therapeutics. The approach to multitarget drug discovery by identifying common scaffolds has been illustrated with experimental validation. Abbreviations: AMPK: AMP-activated protein kinase; ATG: autophagy related; AutophagySMDB: autophagy small molecule database; BCL2: BCL2, apoptosis regulator; BECN1: beclin 1; CAPN: calpain; MTOR: mechanistic target of rapamycin kinase; PPARG: peroxisome proliferator activated receptor gamma; SMILES: simplified molecular input line entry system; SQSTM1: sequestosome 1; STAT3: signal transducer and activator of transcription.

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.

FAMILY SCATOPSIDAE.

An updated catalogue of the family Scatopsidae in Colombia is presented. Seven species of six genera have being recorded for the country, but four of these species are still undescribed. The Ectaetiinae genus Ectaetia, the Psectrosciarinae genera Anapausis and Psectrosciara, and at least the Scatopsinae genera Scatopse, Efcookella, and Abrhexoza are expected to be present in the fauna of the family in Colombia.

FAMILY RHAGIONIDAE.

The family Rhagionidae is one of the oldest Brachyeran lineages. Its monophyly is still uncertain. There are four rhagionid genera distributed in Neotropical Region but only three species of Chrysopilus are found in Colombia.

FAMILY XYLOPHAGIDAE.

This family is recorded for the first time to Colombia, with only one undescribed species of genus Rachicerus.

FAMILY PANTOPHTHALMIDAE.

This catalogue features 11 species distributed in 2 genera recorded to Colombia. Three species of Pantophthalmus are recorded for the first time to the country.