Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data.

Efficient sharing and integration of phenotypic data is crucial for advancing biomedical research and enhancing patient outcomes in precision medicine and public health. To achieve this, the health data community has developed standards to promote the harmonization of variable names and values. However, the use of diverse standards across different research centers can hinder progress. Here we present Convert-Pheno, an open-source software toolkit that enables the interconversion of common data models for phenotypic data such as Beacon v2 Models, CDISC-ODM, OMOP-CDM, Phenopackets v2, and REDCap. Along with the software, we have created a detailed documentation that includes information on deployment and installation.

Síndrome de Ramsay Hunt en paciente epiléptico en Santander, Colombia: Reporte de caso / Ramsay Hunt Syndrome in an epileptic patient in Santander, Colombia: Case report

El Síndrome de Ramsay Hunt es una entidad infrecuente, con una incidencia de 5 por cada 100.000 personas por año. Esta condición se caracteriza por una reactivación del virus de la varicela-zoster en el nervio facial. Su diagnóstico implica un reto para el médico puesto que suele ser netamente clínico, con la aparición de una triada consistente en: otalgia, parálisis facial ipsilateral y vesículas en el canal auditivo. El objetivo del artículo es presentar el caso de una mujer de 49 años de edad, con antecedente de epilepsia en tratamiento anticonvulsivante, quien ingresa con la triada clínica antes descrita, asociada a visión borrosa derecha y vértigo. La paciente fue tratada con antivirales y corticoides orales, presentando una resolución clínica favorable dado una reducción de más del 50% de las lesiones cutáneas. No se identificaron diferencias respecto a la presentación clínica de este síndrome al compararse con pacientes no epilépticos.

Ramsay Hunt Syndrome is a rare entity, with an incidence of 5 per 100,000 people per year. This condition is characterized by a reactivation of the varicella-zoster virus in the facial nerve. Its diagnosis implies a challenge for the physician since it is usually a clinical diagnosis, with the appearance of a clinical triad consisting of: otalgia, ipsilateral facial paralysis and vesicles in the ear canal. The objective of the article is to present the case of a 49-year-old woman, with a history of epilepsy receiving anticonvulsant treatment, who was admitted with the aforementioned clinical triad, associated with blurred right vision and vertigo. The patient was treated with oral antiviral management and oral corticosteroids, presenting a favorable clinical resolution given a reduction of more than 50% of the skin lesions. No differences were identified regarding the clinical presentation of this syndrome when compared with non-epileptic patients.

Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data.

SUMMARY: Beacon v2 is an API specification established by the Global Alliance for Genomics and Health initiative (GA4GH) that defines a standard for federated discovery of genomic and phenotypic data. Here, we present the Beacon v2 Reference Implementation (B2RI), a set of open-source software tools that allow lighting up a local Beacon instance 'out-of-the-box'. Along with the software, we have created detailed 'Read the Docs' documentation that includes information on deployment and installation. AVAILABILITY AND IMPLEMENTATION: The B2RI is released under GNU General Public License v3.0 and Apache License v2.0. Documentation and source code is available at: https://b2ri-documentation.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Gene expression profiles of beta-adrenergic receptors in canine vascular tumors: a preliminary study.

Beta adrenergic receptors (ß-AR) play a key role in regulating several hallmark pathways of both benign and malignant human and canine tumors. There is scarce information on the expression of ß-AR in canine vascular tumors. Therefore, the purpose of the present research work was to study the mRNA expression levels of the three subtypes of the ß-AR genes (ADRB1, ADRB2, ADRB3) in hemangiosarcoma (HSA) and hemangioma (HA), as well as in vascular hamartomas (VH) from dogs.Fifty samples (n = 50) were obtained from 38 dogs. Twenty-three animals had HSA, eight animals HA and seven animals VH. HSA were auricular (n = 8), splenic (n = 5), cutaneous (n = 6), auricular and splenic (n = 2), cutaneous-muscular (n = 1) and disseminated (n = 1). There were seven cases of HSA that were divided into primary tumor and secondary (metastatic) tumor. Skin and muscle samples with a normal histological study were used as control group. ADRB gene expression was determinate in all samples by real-time quantitative PCR. Results showed that ADRB1, ADRB2 and ADRB3 were overexpressed in HSA when compared to the control group. ADRB2 was overexpressed in HA when compared to the control group. HSA express higher values of ADBR1 (p = 0.0178) compared to VH. There was a high inter-individual variability in the expression of the three subtypes of ADBR. No statistically significant difference in the expression of ADBR genes were observed between HSA primary when compared to metastatic or in different anatomical locations. In conclusion, canine HSA overexpress the three ß-AR subtypes and canine HA ß2-AR. High variability was observed in ß-AR mRNA levels amongst HSA cases.

A quality control portal for sequencing data deposited at the European genome-phenome archive.

Since its launch in 2008, the European Genome-Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data. In this regard, one of the community concerns is the potential usability of the stored data, as of now, data submitters are not mandated to perform any quality control (QC) before uploading their data and associated metadata information. Here, we present a new File QC Portal developed at EGA, along with QC reports performed and created for 1 694 442 files [Fastq, sequence alignment map (SAM)/binary alignment map (BAM)/CRAM and variant call format (VCF)] submitted at EGA. QC reports allow anonymous EGA users to view summary-level information regarding the files within a specific dataset, such as quality of reads, alignment quality, number and type of variants and other features. Researchers benefit from being able to assess the quality of data prior to the data access decision and thereby, increasing the reusability of data (https://ega-archive.org/blog/data-upcycling-powered-by-ega/).

Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond.

Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple "yes" or "no" responses to queries about the presence of a given variant in datasets hosted by Beacon providers. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a "lingua franca" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects.

Successful Closure of Paravalvular Leak Using Computed Tomography Image Fusion and Planning With 3-Dimensional Printing.

The presence of moderate to severe paravalvular leak increases mortality. We present a case of giant paravalvular leak closure using the 3-dimensional printing model to assess the success of the device to be used for its closure, computed tomography was performed for planning and guiding the procedure by image fusion. (Level of Difficulty: Advanced.).

The European Genome-phenome Archive in 2021.

The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is to foster hosted data reuse, enable reproducibility, and accelerate biomedical and translational research in line with the FAIR principles. Launched in 2008, the EGA has grown quickly, currently archiving over 4,500 studies from nearly one thousand institutions. The EGA operates a distributed data access model in which requests are made to the data controller, not to the EGA, therefore, the submitter keeps control on who has access to the data and under which conditions. Given the size and value of data hosted, the EGA is constantly improving its value chain, that is, how the EGA can contribute to enhancing the value of human health data by facilitating its submission, discovery, access, and distribution, as well as leading the design and implementation of standards and methods necessary to deliver the value chain. The EGA has become a key GA4GH Driver Project, leading multiple development efforts and implementing new standards and tools, and has been appointed as an ELIXIR Core Data Resource.

Description of the Step-by-Step Technique With Snare Catheter for TAVR in Horizontal Aorta.

The presence of a horizontal aorta in patients treated with transcatheter aortic valve replacement increases the difficulty of the procedure. We present 5 cases with aortic stenosis with a horizontal aorta who underwent transcatheter aortic valve replacement using a self-expanding prostheses, with the objective of describing the techniques used and obtaining success with a snare catheter. (Level of Difficulty: Intermediate.).

Ecosystem services show variable responses to future climate conditions in the Colombian páramos.

BACKGROUND: The páramos, the high-elevation ecosystems of the northern Andes, are well-known for their high species richness and provide a variety of ecosystem services to local subsistence-based communities and regional urbanizations. Climate change is expected to negatively affect the provision of these services, but the level of this impact is still unclear. Here we assess future climate change impact on the ecosystem services provided by the critically important páramos of the department of Boyacá in Colombia, of which over 25% of its territory is páramo. METHODS: We first performed an extensive literature review to identify useful species of Boyacá, and selected 103 key plant species that, based on their uses, support the provision of ecosystem services in the páramos. We collated occurrence information for each key species and using a Mahalanobis distance approach we applied climate niche modelling for current and future conditions. RESULTS: We show an overall tendency of reduction in area for all ecosystem services under future climate conditions (mostly a loss of 10% but reaching up to a loss of 40%), but we observe also increases, and responses differ in intensity loss. Services such as Food for animals, Material and Medicinal, show a high range of changes that includes both positive and negative outcomes, while for Food for humans the responses are mostly substantially negative. Responses are less extreme than those projected for individual species but are often complex because a given ecosystem service is provided by several species. As the level of functional or ecological redundancy between species is not yet known, there is an urgency to expand our knowledge on páramos ecosystem services for more species. Our results are crucial for decision-makers, social and conservation organizations to support sustainable strategies to monitor and mitigate the potential consequences of climate change for human livelihoods in mountainous settings.

Preoperative Use of Intra-Aortic Balloon Pump Support Reduced 30-Day Mortality in a Population with LVEF >35% and High Surgical Risk after Coronary Artery Bypass Graft Surgery.

INTRODUCTION: The intra-aortic balloon pump (IABP) is used to prevent complications after coronary artery bypass grafting (CABG) surgery, although some results are controversial and basal ventricular function may play a role. This study assessed the benefit of preoperative use of IABP, as stratified by the ventricular function, in a population submitted to high-surgical-risk CABG. METHODS: Patients >18 years old, with multiple coronary artery disease and thus candidates for CABG, were included. Cardiogenic shock, acute myocardial infarction (AMI), acute ventricle mechanical dysfunction, severe aortic regurgitation, tachyarrhythmia, massive pulmonary embolism, coagulopathy, or low life expectancy were exclusion criteria. RESULTS: One hundred and twenty-nine patients aged 65 years old with hypertension, dyslipidemia, type 2 diabetes mellitus, and mean left ventricular ejection fraction (LVEF) 46% constituted the study population. No difference was observed at 30-day mortality endpoint (IABP vs. no IABP, 17 vs. 24%, OR 0.63, p = 0.20; AMI 25 vs. 31%, OR 0.75, p = 0.29). After LVEF stratification, the subgroup of 48 (75%) patients under IABP support and LVEF >35% had a reduced 30-day mortality risk (LVEF ≤35% vs. LVEF >35%, 37.5 vs. 10.4%, OR 0.3, p = 0.03), independently from potential confounders and showing an interaction with European System for Cardiac Operative Risk Evaluation-II (EuroSCORE-II). At secondary endpoints, IABP use was associated with a lower prevalence of acute renal failure and renal replacement therapy, but with a longer stay in the intensive care unit and longer hospitalization time. CONCLUSION: The preoperative use of IABP was associated with an independent reduction of 30-day mortality risk in cases with LVEF >35% in a population submitted to high-surgical-risk CABG. Likewise, the use of IABP was associated with a lower risk of postoperative renal complications.

Leptolegnia chapmanii como alternativa biológica para el control de Aedes aegypti

Leptolegnia chapmanii is a facultative pathogen of many species of mosquitoes, among which species of the genus Aedes, Culex and Anopheles stand out for their medical and sanitary importance. The potential of L. chapmanii as an alternative to control lies in its virulence, pathogenicity and specificity against the larval stages of mosquitoes, and because of its harmlessness to non-target species such as fish and amphibians, among others. The natural presence of L. chapmanii had been reported in Argentina, Brazil and the United States. Its presence is possible in other countries throughout the American continent. The development of protocols to produce, formulate, store and apply products based on this microorganism is one of the objectives proposed for the group of Entomopathogenic Fungi at the Centro de Estudios Parasitológicos y de Vectores, Universidad Nacional de La Plata. The efficacy of L. chapmanii as controller is affected by external factors such as temperature, pH, salinity and radiation among others. The process of transfer from the research centers to industry implies many phases. In this way, our project with L. chapmanii is in an initial phase, where we are working on a laboratory scale in proof of concept. We hope to begin soon with the efficacy, efficiency, stability and ecotoxicological safety tests, at the laboratory, semi-field and field scale.

Leptolegnia chapmanii es un microorganismo patógeno facultativo de diversas especies de mosquito, entre las que se destacan, por su importancia médica y sanitaria, especies de los géneros Aedes, Culex y Anopheles. El potencial de L. chapmanii como alternativa de control radica en la virulencia, capacidad patógena y grado de especificidad que presenta hacia los estadios larvales de las diferentes especies de mosquito, y por su inocuidad frente a organismos acuáticos no blanco como, por ejemplo, peces y anfibios. Su presencia natural ha sido reportada en Argentina, Brasil, y Estados Unidos, pensándose como posible en otros países dentro del continente americano. La eficacia de L. chapmanii como controlador se ve influenciada por factores externos, como la temperatura, la radiación y el pH, entre otros. Uno de los objetivos de trabajo del Grupo de Hongos Entomopatógenos del Centro de Estudios Parasitológicos y de Vectores de la Universidad Nacional de La Plata, corresponde al desarrollo de protocolos para la producción, formulación, almacenamiento y aplicación de productos basados en este microorganismo. Con este referente, estamos desarrollando un proyecto con L. chapmanii que se encuentra en la fase inicial, en la que se está trabajando la prueba de concepto a escala de laboratorio. Se espera continuar en el futuro con estudios de eficacia, eficiencia, estabilidad y seguridad ecotoxicológica, a diferentes escalas.

Re-analysis of whole-exome sequencing data uncovers novel diagnostic variants and improves molecular diagnostic yields for sudden death and idiopathic diseases.

BACKGROUND: Whole-exome sequencing (WES) has become an efficient diagnostic test for patients with likely monogenic conditions such as rare idiopathic diseases or sudden unexplained death. Yet, many cases remain undiagnosed. Here, we report the added diagnostic yield achieved for 101 WES cases re-analyzed 1 to 7 years after initial analysis. METHODS: Of the 101 WES cases, 51 were rare idiopathic disease cases and 50 were postmortem "molecular autopsy" cases of early sudden unexplained death. Variants considered for reporting were prioritized and classified into three groups: (1) diagnostic variants, pathogenic and likely pathogenic variants in genes known to cause the phenotype of interest; (2) possibly diagnostic variants, possibly pathogenic variants in genes known to cause the phenotype of interest or pathogenic variants in genes possibly causing the phenotype of interest; and (3) variants of uncertain diagnostic significance, potentially deleterious variants in genes possibly causing the phenotype of interest. RESULTS: Initial analysis revealed diagnostic variants in 13 rare disease cases (25.4%) and 5 sudden death cases (10%). Re-analysis resulted in the identification of additional diagnostic variants in 3 rare disease cases (5.9%) and 1 sudden unexplained death case (2%), which increased our molecular diagnostic yield to 31.4% and 12%, respectively. CONCLUSIONS: The basis of new findings ranged from improvement in variant classification tools, updated genetic databases, and updated clinical phenotypes. Our findings highlight the potential for re-analysis to reveal diagnostic variants in cases that remain undiagnosed after initial WES.

Leptolegnia chapmanii como alternativa biológica para el control de Aedes aegypti / Leptolegnia chapmanii as a biological alternative to control Aedes aegypti

Leptolegnia chapmanii es un microorganismo patógeno facultativo de diversas especies de mosquito, entre las que se destacan, por su importancia médica y sanitaria, especies de los géneros Aedes, Culex y Anopheles. El potencial de L. chapmanii como alternativa de control radica en la virulencia, capacidad patógena y grado de especificidad que presenta hacia los estadios larvales de las diferentes especies de mosquito, y por su inocuidad frente a organismos acuáticos no blanco como, por ejemplo, peces y anfibios. Su presencia natural ha sido reportada en Argentina, Brasil, y Estados Unidos, pensándose como posible en otros países dentro del continente americano. La eficacia de L. chapmanii como controlador se ve influenciada por factores externos, como la temperatura, la radiación y el pH, entre otros. Uno de los objetivos de trabajo del Grupo de Hongos Entomopatógenos del Centro de Estudios Parasitológicos y de Vectores de la Universidad Nacional de La Plata, corresponde al desarrollo de protocolos para la producción, formulación, almacenamiento y aplicación de productos basados en este microorganismo. Con este referente, estamos desarrollando un proyecto con L. chapmanii que se encuentra en la fase inicial, en la que se está trabajando la prueba de concepto a escala de laboratorio. Se espera continuar en el futuro con estudios de eficacia, eficiencia, estabilidad y seguridad ecotoxicológica, a diferentes escalas.

Leptolegnia chapmanii is a facultative pathogen of many species of mosquitoes, among which species of the genus Aedes, Culex and Anopheles stand out for their medical and sanitary importance. The potential of L. chapmanii as an alternative to control lies in its virulence, pathogenicity and specificity against the larval stages of mosquitoes, and because of its harmlessness to non-target species such as fish and amphibians, among others. The natural presence of L. chapmanii had been reported in Argentina, Brazil and the United States. Its presence is possible in other countries throughout the American continent. The development of protocols to produce, formulate, store and apply products based on this microorganism is one of the objectives proposed for the group of Entomopathogenic Fungi at the Centro de Estudios Parasitológicos y de Vectores, Universidad Nacional de La Plata. The efficacy of L. chapmanii as controller is affected by external factors such as temperature, pH, salinity and radiation among others. The process of transfer from the research centers to industry implies many phases. In this way, our project with L. chapmanii is in an initial phase, where we are working on a laboratory scale in proof of concept. We hope to begin soon with the efficacy, efficiency, stability and ecotoxicological safety tests, at the laboratory, semi-field and field scale.