WormBase 2024: status and transitioning to Alliance infrastructure.

WormBase has been the major repository and knowledgebase of information about the genome and genetics of C. elegans and other nematodes of experimental interest for over two decades. We have three goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.

Consenso colombiano de Falla Intestinal Crónica en Síndrome de Intestino Corto / Colombian Consensus on Chronic Intestinal Failure in Short Bowel Syndrome

Introducción. Los términos falla intestinal crónica, síndrome de intestino corto (SIC) y nutrición parenteral total son muy frecuentes en la práctica clínica cotidiana.El objetivo de esta guía fue establecer un marco de referencia de práctica clínica basado en el mejor de nivel de evidencia en pacientes con falla intestinal crónica secundaria a síndrome de intestino corto. Métodos. Se estableció un grupo de expertos interdisciplinarios en el manejo de la falla intestinal crónica quienes, previa revisión de la literatura escogida, se reunieron de manera virtual acogiendo el método Delphi para discutir una serie de preguntas seleccionadas, enfocadas en el contexto terapéutico de la falla intestinal crónica asociada al síndrome de intestino corto. Resultados. La recomendación del grupo de expertos colombianos es que se aconseje a los pacientes con SIC consumir dietas regulares de alimentos integrales que genere hiperfagia para compensar la malabsorción. Las necesidades proteicas y energéticas dependen de las características individuales de cada paciente; la adecuación del régimen debe ser evaluada a través de pruebas clínicas, antropométricas y parámetros bioquímicos. Se sugiere, especialmente a corto plazo después de la resección intestinal, el uso de análogos de somatostatina para pacientes con yeyunostomía de alto gasto en quienes el manejo de líquidos y electrolitos es problemático. En pacientes con SIC, que son candidatos a tratamiento con enterohormonas, Teduglutida es la primera opción. Conclusión. Existen recomendaciones en el manejo integral de la rehabilitación intestinal respaldadas ampliamente por este consenso y es importante el reconocimiento de alternativas terapéuticos enmarcadas en el principio de buenas prácticas clínicas.

Introduction. The terms chronic intestinal failure, short bowel syndrome (SBS), and total parenteral nutrition are very common in daily clinical practice. The objective of this guideline was to establish a reference framework for clinical practice based on the best level of evidence in patients with chronic intestinal failure secondary to short bowel syndrome. Methods. A group of interdisciplinary experts in the management of chronic intestinal failure was established who, after reviewing the selected literature, met virtually using the Delphi method to discuss a series of selected questions, focused on the therapeutic context of chronic intestinal failure associated with short bowel syndrome. Results. The recommendation of the Colombian expert group is that patients with SBS be advised to consume regular diets of whole foods that generate hyperphagia to compensate malabsorption. Protein and energy needs depend on the individual characteristics of each patient; the adequacy of the regimen must be evaluated through clinical, anthropometric tests and biochemical parameters. The use of somatostatin analogue is suggested, especially in the short term after bowel resection, for patients with high-output jejunostomy in whom fluid and electrolyte management is problematic. In SBS, who are candidates for enterohormonal therapy, Teduglutide is the first choice. Conclusion. There are recommendations on the comprehensive management of intestinal rehabilitation that are widely supported by this consensus and it is important to recognize therapeutic alternatives framed in the principle of good clinical practice.

WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans.

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.

Prehospital and First Hospital System Response to a Terrorist Attack in Bogotá, Colombia.

Background: Assembling an effective medical response for an overwhelming number of casualties has become a priority worldwide. Terrorist attacks have been part of the Colombian contemporaneous history. On February 7, 2003, a terrorist car bomb explosion occurred inside a private club in Bogotá, causing the largest number of casualties of all terrorist attacks for over 15 years. The present study analyses the hospital and prehospital responses to this mass casualty event by characterizing the patterns of injury, resource allocation, and outcome in a tertiary-level hospital where most of the casualties were treated. Materials and methods: This is a retrospective chart review of the patients brought to a single hospital (La Clínica del Country), which was the nearest to the terrorist attack. Demographics, severity of injury, patterns of injury, prehospital care, and outcomes were determined from the hospital medical records and government registries. Results: Of the 240 victims, 35 died at the explosion site (immediate mortality 17%). The 205 survivors were dispersed throughout the city, of whom 63 patients came to La Clínica del Country hospital. Most of these patients were evaluated only clinically and deemed not serious. The main mechanism of trauma was blunt (81.4%). The mean injury severity score (ISS) was 5.6 ± 8.3. Ten patients required emergent surgical intervention and 14 patients were admitted. The in-hospital mortality was 20%. Conclusion: This mass casualty event was a true test for the Colombian emergency medical system and disaster preparedness. The medical response and resource optimization resulted in an overall mortality rate similar to those observed in the recent European and North American bombings. Despite the limited resources, the continuous challenge of terrorist's attacks in Colombia made the country feel the need for training and preparing the healthcare professionals, allowing effective delivery of medical care.

Introducción: La organización de una respuesta médica efectiva a un número excesivo de víctimas de ataques terroristas se ha convertido en una prioridad en el mundo. Los ataques terroristas han sido parte de la historia colombiana contemporánea. El 7 de Febrero de 2003, un carro bomba explotó en el interior de un club privado en Bogotá, resultando en el ataque terrorista con mayor numero de víctimas durante los últimos 15 años. El objetivo de este estudio es determinar la respuesta del sistema pre y hospitalario a un ataque terrorista masivo, caracterizar los patrones de lesión, utilización de recursos y desenlaces en un hospital de primer nivel, donde la mayoría de las víctimas fueron atendidas. Métodos: Este es un estudio retrospectivo de la revisión de 43 historias clínicas de 63 pacientes que fueron llevados al hospital privado más cercano después de un ataque terroristas. La información demográfica, la severidad, el patrón de las lesiones y los desenlaces fueron determinados a partir de las historias clínicas y los registros gubernamentales. Resultados: Treinta y cinco personas murieron en la escena y 205 personas fueron lesionadas (mortalidad inmediata de 17%). 63 pacientes fueron transferidos a nuestros hospitales. La mayoría de los pacientes fueron valorados clínicamente y no tenían lesiones serias. El principal mecanismos de trauma fue cerrado. El promedio de ISS fue 5.6 ± 8.3. Diez pacientes requirieron intervenciones quirúrgicas de urgencia y 14 fueron admitidos al hospital. La mortalidad crítica fue de 20%. Conclusione: Este incidente fue un verdadero examen a nuestro sistema médico de emergencias y plan de desastres hospitalario. Nuestro sistema médico optimizó los recursos resultando en una mortalidad crítica similar a la de las bombas ocurridas en Europa y Norte América. El desafío permanente de confrontar los ataques terroristas en Colombia ha proporcionado entrenamiento y preparación para asegurar un cuidado médico efectivo, aun con recursos limitados. Palabras clave: Ataque terrorista, Bomba, Evento con lesionados masivos, Respuesta medica.

Meningioma cordoide: revisión de la literatura y reporte de un caso / Cordoid meningioma: review of the literature and report of a case

RESUMEN El meningioma es una neoplasia común que representa entre el 13 % al 19% de todos los tumores primarios, su variante, el meningioma cordoide es un raro subtipo representando solo el 0,5 % a 1,0 % de todos los meningiomas intracraneales, una entidad de interés por su baja prevalencia comparada con los demás subtipos de meningioma. Presentamos el caso clínico de un hombre de 51 años con cuadro clínico de 18 meses de evolución, consistente en parestesias en miembro inferior derecho y cefalea. Quien mostró en la resonancia magnética nuclear (RNM) una gran masa tumoral extra axial de 6,0 x 5,0 cm sobre el área motora izquierda, región parietal, bien vascularizada con efecto compresivo. Se llevó a cirugía en donde se encontró lesión dependiente de la hoz del cerebelo que fue removida en su totalidad con desaparición progresiva de los cambios neurológicos descritos.

SUMMARY Meningioma is a common malignancy that accounts for 13 to 19% of all primary tumors, meningioma Chordoid variant is a rare subtype representing only 0.5% to 1.0% of all intracranial meningiomas resulting in a entity of interest by its low prevalence compared with other subtype of meningioma. We report the case of a 51-year clinical evolution of 18 months, consisting of paresthesia and headache right lower limb. RNM who showed a large tumor in extra-axial mass of 6.0x5.0 cm on left motor area, parietal region, well-vascularized with compressive effect. It takes surgery where dependent injury Sickle of the cerebellum that is removed entirely with progressive disappearance of neurological changes described is.

Prediction of virus-host protein-protein interactions mediated by short linear motifs.

BACKGROUND: Short linear motifs in host organisms proteins can be mimicked by viruses to create protein-protein interactions that disable or control metabolic pathways. Given that viral linear motif instances of host motif regular expressions can be found by chance, it is necessary to develop filtering methods of functional linear motifs. We conduct a systematic comparison of linear motifs filtering methods to develop a computational approach for predicting motif-mediated protein-protein interactions between human and the human immunodeficiency virus 1 (HIV-1). RESULTS: We implemented three filtering methods to obtain linear motif sets: 1) conserved in viral proteins (C), 2) located in disordered regions (D) and 3) rare or scarce in a set of randomized viral sequences (R). The sets C,D,R are united and intersected. The resulting sets are compared by the number of protein-protein interactions correctly inferred with them - with experimental validation. The comparison is done with HIV-1 sequences and interactions from the National Institute of Allergy and Infectious Diseases (NIAID). The number of correctly inferred interactions allows to rank the interactions by the sets used to deduce them: D∪R and C. The ordering of the sets is descending on the probability of capturing functional interactions. With respect to HIV-1, the sets C∪R, D∪R, C∪D∪R infer all known interactions between HIV1 and human proteins mediated by linear motifs. We found that the majority of conserved linear motifs in the virus are located in disordered regions. CONCLUSION: We have developed a method for predicting protein-protein interactions mediated by linear motifs between HIV-1 and human proteins. The method only use protein sequences as inputs. We can extend the software developed to any other eukaryotic virus and host in order to find and rank candidate interactions. In future works we will use it to explore possible viral attack mechanisms based on linear motif mimicry.

Electronic Structure and Potential Reactivity of Silaaromatic Molecules.

Silicon-based materials are crucial for conventional electronics. The fascinating properties of the new two-dimensional material silicene, the silicon analogue of graphene (one atom-thick silicon sheets), offer a potential bridge between conventional and molecular electronics. The ground-state configuration of silicene is buckled, which compromises optimal constructive overlap of p orbitals. Because silicene is not planar like graphene, it has a lower intrinsic electron/hole mobility than graphene. This motivates a search for improved, alternative, planar materials. Miniaturization of silicene/graphene hybrid monolayers affords diverse silicon-organic and -inorganic molecules, whose potential as building blocks for molecular electronics is unexplored. Additionally, hybridization of pure silicon rings (or sheets) is a versatile way to control the geometrical and electronic characteristics of the aromatic ring. In this work we systematically investigate, computationally, architectures and electronic structures of a series of hybrid silaaromatic monomers and fused-ring oligomers. This includes the thermochemistry of representative reactions: hydrogenation and oxidation. The effect of various skeletal substituents of interest is elucidated as well. We show that the specific location of carbon and silicon atoms, and their relative populations in the rings are crucial factors controlling the molecular geometry and the quasi-particle gap. Furthermore, we suggest that electron-withdrawing substituents such as CN, F, and CF3 are promising candidates to promote the air-stability of silaaromatics. Finally, on the basis of the analysis of benzene-like silaaromatic molecules, we discuss a set of alternative, prototype ring molecules that feature planarity and delocalized π bonds. These motifs may be useful for designing new extended materials.