6,823 research outputs found

    Pancreatic surgery outcomes: multicentre prospective snapshot study in 67 countries

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    The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

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    Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch\u27s APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch\u27s data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch\u27s analytic tools by developing a customized plugin for OpenAI\u27s ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app

    The Human Phenotype Ontology in 2024: phenotypes around the world.

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    The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

    The Human Phenotype Ontology in 2024: phenotypes around the world

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    \ua9 The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

    DOES THE TYPE OF CONTRACTION PERFORMED DURING MIRROR ILLUSION ALTER HEMISPHERIC COMMUNICATION? A PRELIMINARY ANALYSIS

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    Shawn Reese1, Claire Smith1, Alex Olmos1, Jocarol Shields1, Caleb Voskuil2, Xin Ye3, Matt Stock4, Joshua Carr2 and Jason DeFreitas1 1Oklahoma State University, Stillwater, OK 2Texas Christian University, Fort Worth, TX 3University of Hartford, West Hartford, CT 4University of Central Florida, Orlando, FL Mirror illusions are utilized in the rehabilitation of impaired limbs due to injury and stroke to stimulate the affected limb’s associated motor cortex and peripheral neural pathways during movements with the healthy limb without actual movement of the affected limb. However, how mirror illusions affect communication between the two hemispheres, and whether the type of contraction in the healthy limb plays a role are still unknown. PURPOSE: To determine the effects of mirror illusion during different contraction types on interhemispheric inhibition. METHODS: Ten healthy individuals have completed this study so far. A figure-eight transcranial magnetic stimulation coil was used to stimulate the hand area of the right primary motor cortex during dynamic and isometric contractions of the right hand. Ipsilateral silent period (iSP) was used as a measure of interhemispheric inhibition. Participants were instructed to fix their gaze in the same location for 2 visual conditions: No mirror, and Bilateral mirror illusion. The effect of the mirror illusion was defined as the change in iSP from the no mirror to the bilateral condition. Since the data is currently too underpowered for standard null-hypothesis testing, we utilized Cohen’s d as an estimate of the preliminary effect sizes. RESULTS: Mirror illusions during dynamic contractions show a rise in interhemispheric inhibition, with mean iSP increasing from 35.4ms to 36.7ms (3.5% change; d = 0.15). However, mirror illusions during isometric contractions show a reduction in inhibition, with mean iSP decreasing from 39.6ms to 37.5ms (-5.4% change; d = -0.27). CONCLUSION: The effects of mirror illusions on interhemispheric inhibition seems to be dependent on the type of contraction (dynamic vs. isometric). If these results hold firm with further sampling, then contraction type may be an important consideration for how hemispheric communication is modulated in mirror illusion therapy and upper extremity rehabilitation

    RUBIS: a simple tool for calculating the centrifugal deformation of stars and planets

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    In this article we present RUBIS (Rotation code Using Barotropy conservation over Isopotential Surfaces), a fully Python-based centrifugal deformation program available at https://github.com/pierrehoudayer/RUBIS. The code has been designed to calculate the centrifugal deformation of a star or planet resulting from a given cylindrical rotation profile, starting from a spherically symmetric non-rotating model. Furthermore, it can handle models with discontinuities in the density profile. The underlying assumption in RUBIS is that the relationship between density and pressure is preserved during the deformation process. This leads to many procedural simplifications. For instance, RUBIS only needs to solve Poisson' equation, either in spheroidal or spherical coordinates depending on whether the 1D model has discontinuities or not. In this paper, we present the benefits of using RUBIS to deform polytropic models and more complex barotropic structures, thus providing, to a certain extent, insights into baroclinic models. The resulting structures can be used for a wide range of applications, including the seismic study of models. Finally, we illustrate how RUBIS is beneficial specifically in the analysis of Jupiter's gravitational moments, thanks to its ability to handle discontinuous models while retaining a high accuracy compared to current methods

    A global assessment of actors and their roles in climate change adaptation

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    An assessment of the global progress in climate change adaptation is urgently needed. Despite a rising awareness that adaptation should involve diverse societal actors and a shared sense of responsibility, little is known about the types of actors, such as state and non-state, and their roles in different types of adaptation responses as well as in different regions. Based on a large n-structured analysis of case studies, we show that, although individuals or households are the most prominent actors implementing adaptation, they are the least involved in institutional responses, particularly in the global south. Governments are most often involved in planning and civil society in coordinating responses. Adaptation of individuals or households is documented especially in rural areas, and governments in urban areas. Overall, understanding of institutional, multi-actor and transformational adaptation is still limited. These findings contribute to debates around ‚Äėsocial contracts‚Äô for adaptation, that is, an agreement on the distribution of roles and responsibilities, and inform future adaptation governance
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