CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

MOTIVATION: Combining multiple layers of information underlying biological complexity into a structured framework represent a challenge in systems biology. A key task is the formalization of such information in models describing how biological entities interact to mediate the response to external and internal signals. Several databases with signalling information, focus on capturing, organizing and displaying signalling interactions by representing them as binary, causal relationships between biological entities. The curation efforts that build these individual databases demand a concerted effort to ensure interoperability among resources. RESULTS: Aware of the enormous benefits of standardization efforts in the molecular interaction research field, representatives of the signalling network community agreed to extend the PSI-MI controlled vocabulary to include additional terms representing aspects of causal interactions. Here, we present a common standard for the representation and dissemination of signalling information: the PSI Causal Interaction tabular format (CausalTAB) which is an extension of the existing PSI-MI tab-delimited format, now designated PSI-MITAB 2.8. We define the new term 'causal interaction', and related child terms, which are children of the PSI-MI 'molecular interaction' term. The new vocabulary terms in this extended PSI-MI format will enable systems biologists to model large-scale signalling networks more precisely and with higher coverage than before. AVAILABILITY AND IMPLEMENTATION: PSI-MITAB 2.8 format and the new reference implementation of PSICQUIC are available online (https://psicquic.github.io/ and https://psicquic.github.io/MITAB28Format.html). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

BACKGROUND: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. RESULTS: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

Bacterial septicemia and herpesvirus infection in Antarctic fur seals (Arctocephalus gazella) stranded in the São Paulo coast, Brazil.

In August 2021, two juvenile male Antarctic fur seals (Arctocephalus gazella) stranded in the southeastern Brazilian coast and were referred to rehabilitation centers. The animals presented increased body temperature, prostration, respiratory distress and despite treatment died. A necropsy following a standardized protocol was performed, and formalin-fixed tissues were processed for microscopic examination. Samples were screened for morbillivirus, herpesvirus, and Brucella spp. by molecular analyses (PCR, RT-PCR). Bacteriological culture was performed in samples collected from the lungs, trachea, and lymph nodes of both cases. The main histopathologic findings were of infectious nature, including multifocal necrotizing and fibrinous mixed interstitial pneumonia, bronchiolitis, and bronchitis, with intralesional myriad bacteria associated with vascular fibrinoid necrosis. Pseudomonas aeruginosa was isolated from tracheal and lung swabs of Case 1, and Klebsiella oxytoca was found in nostril swabs, tracheobronchial lymph nodes, and lung of Case 2. Gammaherpesvirus infection was detected in both cases, and the sequences retrieved were classified into the genus Percavirus. All tested samples were PCR-negative for Brucella spp. and morbillivirus. We hypothesize that the deficient immunological status in association with starvation predisposed the reactivation of herpesvirus and secondary bacterial co-infections. To the authors' knowledge, this is the first molecular detection of herpesvirus in an Antarctic pinniped. These findings reinforce that Otariid gammaherpesvirus circulating in the Southern Hemisphere are likely endemic in the Arctocephalus genus. This report contributes to the current knowledge of health aspects affecting wild pinnipeds, especially in the poorly studied Antarctic species.

Ultrasound and microwave techniques for assisting ageing on lees of red wines.

Ageing on lees is a slow process that carries microbiological and economic risks in the wineries. This study evaluates the possibility of enhancing the extraction of different compounds from the lees, using combined strategies, such as ultrasound (US) or microwaves (MW) and the addition of inactive dry yeasts (IDY), to reduce the lees ageing time. The complete chemical analysis of the wine was done, amino acids, polysaccharides, colour and volatile compounds, together with the sensory analysis. The combined treatments increased the release of total polysaccharides, mannoproteins and total monosaccharides in the wines, and some amino acids like proline. However, wines treated with US and MW, with and without lees, showed a decrease in tannins and colour intensity, and in some volatile compounds like fatty acid esters, acetates and terpenes. The wines treated with IDY and MW were the best valued for their floral and red berry flavours and less astringency.

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions.

The current coronavirus disease of 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions can provide fine-grained resolution of the mechanisms behind the virus biology and the human organism response. We present a curated dataset of physical molecular interactions focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family that has been manually extracted by International Molecular Exchange (IMEx) Consortium curators. Currently, the dataset comprises over 4400 binarized interactions extracted from 151 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (https://www.ebi.ac.uk/intact) and will be continuously updated as research on COVID-19 progresses.

The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions.

The current Coronavirus Disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions enables studying fine-grained resolution of the mechanisms behind the virus biology and the human organism response. Here we present a curated dataset of physical molecular interactions, manually extracted by IMEx Consortium curators focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family. Currently, the dataset comprises over 2,200 binarized interactions extracted from 86 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website ( www.ebi.ac.uk/intact ), and will be continuously updated as research on COVID-19 progresses.

[Morphological characteristics of cerebral aneurysm of Willis' circle: a direct anatomical study]. / Características morfológicas de aneurimas cerebrales del polígono de Willis: estudio anatómico directo.

OBJECTIVE: To determine the prevalence and morphologic characteristics of unruptured aneurysms of Willis' circle in a sample of mestizo Colombian population. MATERIALS AND METHODS: A mixture of resin and mineral red was injected into cerebral arteries by dissection and canalization of common carotids and vertebral arteries of the encephalons of 125 mestizo male cadavers of 16 to 65 years old. The procedure was carried out during the autopsy course at the Legal Medicine Institute, Bucaramanga - Colombia. Then the encephalons were extracted and fixed. After that, the Willis' circles were identified and the presence of aneurysms at this level was determined with magnifying glass. RESULTS: A total of nine aneurysms were observed in six brains (4.8%). The most frequent location was the supraclinoid segment of the intern carotid artery, with 4 cases (44.4%), three of which were localized in the origin of the anterior choroidal artery. Additionally, three aneurysms were found in the anterior communicating artery (33.3%). From the remaining cases, one (11.1%) was localized in the pre-communicating segment of the anterior cerebral artery, and the other in the bifurcation of the basilar artery. The average size of the aneurysms was 2.49 mm SD 0.37. The affected encephalons presented concomitant variations of the Willis' circle configuration, being predominant the presence of hypoplasic posterior communicanting arteries. CONCLUSION: The aneurysm prevalence in the evaluated sample was similar to the reported in other populations. In this work, the presence of aneurysms on the origin of the anterior chorioid artery, an unusually reported localization, was prominent.

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

In the original HTML version of this Article, the order of authors within the author list was incorrect. The IMEx Consortium contributing authors were incorrectly listed as the last author and should have been listed as the first author. This error has been corrected in the HTML version of the Article; the PDF version was correct at the time of publication.

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule's interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.

Expression of glutaredoxin (thioltransferase) in the rat ovary during the oestrous cycle and postnatal development.

Glutaredoxins (Grxs) are low-molecular-weight proteins which participate in redox events in association with glutathione (GSH) and are involved in a variety of cellular processes. It is known that oxidative stress plays important physiological roles within the ovary. In the present study, we have prepared specific antibodies against rat Grx and have used them to localize the protein in the ovaries of rats during postnatal development and during the oestrous cycle, by immunohistochemical methods. We have also performed a quantitative analysis of Grx by ELISA and Western blotting in homogenates of whole ovaries of cycling and pseudopregnant rats. We have found a prominent presence of Grx in the oocytes and in corpora lutea (CL) during developmental and oestrous cycle changes. Grx was absent from the oocytes in the first days of postnatal life when marked oocyte degeneration takes place, but its presence was very conspicuous in the cytoplasm of oocytes in healthy and attretic follicles in rats from 10 days of age onward, independently of the day of oestrous cycle. Follicular cells were negative. Grx immunostaining in the CL was strong in infiltrating macrophages and in a population of steroidogenic cells that survived the apoptotic burst in regressing CL and in CL remnants, but was faint or absent in young CL of the current cycle and in CL during pseudopregnancy. Grx content and oxidoreductase activity in whole ovaries increased significantly during the phase transition from proestrous to oestrous along the cycle. These results support a role of Grx in the maintenance of functional oocytes and in luteal cells surviving the regression process, probably as a consequence of the demonstrated deglutathionylating function of this protein in an antioxidant and antiapoptotic context.

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in a cellular environment. Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental evidence. We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative-molecular interaction standards. In this manuscript, we introduce these two algorithms and provide community access to the tool suite, describe examples of how these tools are useful to selectively present molecular interaction data and demonstrate a case where the algorithms were successfully used to identify a systematic error in an existing dataset.

Nutritional state of beta-carotene and retinol in institutionalized elderly individuals of México City.

A study of the nutritional status of beta-carotene and retinol of 228 institutionalized elderly individuals, in four elderly homes of México City was carried out. Subjects varied between 61 and 101 years of age (151 were females and 77 were males). High pressure liquid chromatography was used to quantitate retinol and beta-carotene. Ninety eight percent of elderly individuals showed beta-carotene levels less than acceptable (at risk); 85.2% were deficient (high risk), and 12.9% were low (medium risk), only 1.85% had acceptable values (low risk). Ninety two percent of subjects had acceptable values (low risk) of retinol, while 6.0% and 2.0% were low (medium risk) and deficient (high risk) respectively. There were not significant differences among the four elderly homes. No significant correlation with age was found for any of the two vitamins. No sex related difference (p > 0.05) was observed in serum vitamin A and beta-carotene in either group.

Trombofilia primaria: mejoramiento del diagnóstico basado en evidencia / Thrombophilia: improving diagnosis with an evidence-based approach

El tromboembolismo venoso, que involucra que trombosis venosa profunda (TVP) y el tromboembolismo pulmonar (TEP)es uno de los síndromes con mayor morbi-mortalidad en pacientes ambulatorios y hospitalizados. Los factores de riesgogenéticos tienen un papel aún discutido en la génesis de enfermedades como la trombosis venosa profunda ya que existeuna gran variabilidad gen-gen y gen-ambiente. Existe debate desde hace muchos años sobre la utilidad de realizar estudiosgenéticos para detectar poblaciones de riesgo, sin embargo, la tendencia a medida que se publica nueva informaciónes limitar su uso para casos en los cuales proporcionará información valiosa capaz de modificar la estrategia terapéutica.El único método confiable para el diagnóstico de las mutaciones en trombofilia es por medio de la biología molecular, locual incurre en costes elevados para un sistema de salud como el nuestro, motivo por el cual se hace necesario efectuar unanálisis de la literatura acerca de la utilidad real del tamizaje por trombofilia y diseñar una estrategia basada en evidenciapara seleccionar pacientes que van a obtener un beneficio al someterse a este tipo de estudios.

Thromboembolic disorders are one of the leading causes of morbidity and mortality among patients hospitalized aswell as outpatients. There is an active debate about the contribution of genetic causes to thrombotic events such asdeep vein trombosis mainly because of the great variability between gene-gene and gene-environment interactions.Due to growing new evidence, there is a trend toward limiting thrombophilia testing to patients in whom the resultcould influence the treatment strategy. The only reliable method to diagnose mutations in thrombophilia is by means ofmolecular biology tests which incurrs in a high cost to our nacional social security. For this reasons, a revision of currentliterature is necessary to develop a evidence based- approach to patients with these diseases.

Medicamentos en un servicio de cirugía hospitalaria / Drugs in a hospital surgery service

Un estudio que se llevó a cabo en el servicio de cirugía de mujeres del Hospital Universitario del Valle en Cali, Colombia, en mayo de 1980 puso de manifiesto una utilización inadecuada de los medicamentos que ascendía al 62% del costo de los mismos. Tal uso inadecuado correspondía a robo, deterioro o pérdida, ya que los medicamentos no se devolvían a la farmacia ni se entregaban a los pacientes cuando abandonaban el servicio. Se implantaron ciertas medidas de control entre las que se destacan el empleo de un formulario único que recogía en un solo pedido todas las órdenes médicas diarias individuales para cada paciente y supervisión de los medicamentos más utilizados por parte de la enfermera jefa del servicio. En mayo y junio de 1981 se repitió un estudio similiar y se comprobó que la utilización inadecuada había descendido al 29%. Si bien esto representa una mejora existe la necesidad de establecer sistemas de control en todo el proceso de adquisición, distribución y uso de los medicamentos con el fin de que la cantidad que prescribe el médico coincida con la que despachaba la farmacia y la que se administra a los enfermos