513 research outputs found

    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

    Artificial Intelligence and International Conflict in Cyberspace

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    This edited volume explores how artificial intelligence (AI) is transforming international conflict in cyberspace. Over the past three decades, cyberspace developed into a crucial frontier and issue of international conflict. However, scholarly work on the relationship between AI and conflict in cyberspace has been produced along somewhat rigid disciplinary boundaries and an even more rigid sociotechnical divide – wherein technical and social scholarship are seldomly brought into a conversation. This is the first volume to address these themes through a comprehensive and cross-disciplinary approach. With the intent of exploring the question ‘what is at stake with the use of automation in international conflict in cyberspace through AI?’, the chapters in the volume focus on three broad themes, namely: (1) technical and operational, (2) strategic and geopolitical and (3) normative and legal. These also constitute the three parts in which the chapters of this volume are organised, although these thematic sections should not be considered as an analytical or a disciplinary demarcation

    Digital agriculture: research, development and innovation in production chains.

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    Digital transformation in the field towards sustainable and smart agriculture. Digital agriculture: definitions and technologies. Agroenvironmental modeling and the digital transformation of agriculture. Geotechnologies in digital agriculture. Scientific computing in agriculture. Computer vision applied to agriculture. Technologies developed in precision agriculture. Information engineering: contributions to digital agriculture. DIPN: a dictionary of the internal proteins nanoenvironments and their potential for transformation into agricultural assets. Applications of bioinformatics in agriculture. Genomics applied to climate change: biotechnology for digital agriculture. Innovation ecosystem in agriculture: Embrapa?s evolution and contributions. The law related to the digitization of agriculture. Innovating communication in the age of digital agriculture. Driving forces for Brazilian agriculture in the next decade: implications for digital agriculture. Challenges, trends and opportunities in digital agriculture in Brazil

    Metal Cations in Protein Force Fields: From Data Set Creation and Benchmarks to Polarizable Force Field Implementation and Adjustment

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    Metal cations are essential to life. About one-third of all proteins require metal cofactors to accurately fold or to function. Computer simulations using empirical parameters and classical molecular mechanics models (force fields) are the standard tool to investigate proteins’ structural dynamics and functions in silico. Despite many successes, the accuracy of force fields is limited when cations are involved. The focus of this thesis is the development of tools and strategies to create system-specific force field parameters to accurately describe cation-protein interactions. The accuracy of a force field mainly relies on (i) the parameters derived from increasingly large quantum chemistry or experimental data and (ii) the physics behind the energy formula. The first part of this thesis presents a large and comprehensive quantum chemistry data set on a consistent computational footing that can be used for force field parameterization and benchmarking. The data set covers dipeptides of the 20 proteinogenic amino acids with different possible side chain protonation states, 3 divalent cations (Ca2+, Mg2+, and Ba2+), and a wide relative energy range. Crucial properties related to force field development, such as partial charges, interaction energies, etc., are also provided. To make the data available, the data set was uploaded to the NOMAD repository and its data structure was formalized in an ontology. Besides a proper data basis for parameterization, the physics covered by the terms of the additive force field formulation model impacts its applicability. The second part of this thesis benchmarks three popular non-polarizable force fields and the polarizable Drude model against a quantum chemistry data set. After some adjustments, the Drude model was found to reproduce the reference interaction energy substantially better than the non-polarizable force fields, which showed the importance of explicitly addressing polarization effects. Tweaking of the Drude model involved Boltzmann-weighted fitting to optimize Thole factors and Lennard-Jones parameters. The obtained parameters were validated by (i) their ability to reproduce reference interaction energies and (ii) molecular dynamics simulations of the N-lobe of calmodulin. This work facilitates the improvement of polarizable force fields for cation-protein interactions by quantum chemistry-driven parameterization combined with molecular dynamics simulations in the condensed phase. While the Drude model exhibits its potential simulating cation-protein interactions, it lacks description of charge transfer effects, which are significant between cation and protein. The CTPOL model extends the classical force field formulation by charge transfer (CT) and polarization (POL). Since the CTPOL model is not readily available in any of the popular molecular-dynamics packages, it was implemented in OpenMM. Furthermore, an open-source parameterization tool, called FFAFFURR, was implemented that enables the (system specific) parameterization of OPLS-AA and CTPOL models. Following the method established in the previous part, the performance of FFAFFURR was evaluated by its ability to reproduce quantum chemistry energies and molecular dynamics simulations of the zinc finger protein. In conclusion, this thesis steps towards the development of next-generation force fields to accurately describe cation-protein interactions by providing (i) reference data, (ii) a force field model that includes charge transfer and polarization, and (iii) a freely-available parameterization tool.Metallkationen sind für das Leben unerlässlich. Etwa ein Drittel aller Proteine benötigen Metall-Cofaktoren, um sich korrekt zu falten oder zu funktionieren. Computersimulationen unter Verwendung empirischer Parameter und klassischer Molekülmechanik-Modelle (Kraftfelder) sind ein Standardwerkzeug zur Untersuchung der strukturellen Dynamik und Funktionen von Proteinen in silico. Trotz vieler Erfolge ist die Genauigkeit der Kraftfelder begrenzt, wenn Kationen beteiligt sind. Der Schwerpunkt dieser Arbeit liegt auf der Entwicklung von Werkzeugen und Strategien zur Erstellung systemspezifischer Kraftfeldparameter zur genaueren Beschreibung von Kationen-Protein-Wechselwirkungen. Die Genauigkeit eines Kraftfelds hängt hauptsächlich von (i) den Parametern ab, die aus immer größeren quantenchemischen oder experimentellen Daten abgeleitet werden, und (ii) der Physik hinter der Kraftfeld-Formel. Im ersten Teil dieser Arbeit wird ein großer und umfassender quantenchemischer Datensatz auf einer konsistenten rechnerischen Grundlage vorgestellt, der für die Parametrisierung und das Benchmarking von Kraftfeldern verwendet werden kann. Der Datensatz umfasst Dipeptide der 20 proteinogenen Aminosäuren mit verschiedenen möglichen Seitenketten-Protonierungszuständen, 3 zweiwertige Kationen (Ca2+, Mg2+ und Ba2+) und einen breiten relativen Energiebereich. Wichtige Eigenschaften für die Entwicklung von Kraftfeldern, wie Wechselwirkungsenergien, Partialladungen usw., werden ebenfalls bereitgestellt. Um die Daten verfügbar zu machen, wurde der Datensatz in das NOMAD-Repository hochgeladen und seine Datenstruktur wurde in einer Ontologie formalisiert. Neben einer geeigneten Datenbasis für die Parametrisierung beeinflusst die Physik, die von den Termen des additiven Kraftfeld-Modells abgedeckt wird, dessen Anwendbarkeit. Der zweite Teil dieser Arbeit vergleicht drei populäre nichtpolarisierbare Kraftfelder und das polarisierbare Drude-Modell mit einem Datensatz aus der Quantenchemie. Nach einigen Anpassungen stellte sich heraus, dass das Drude-Modell die Referenzwechselwirkungsenergie wesentlich besser reproduziert als die nichtpolarisierbaren Kraftfelder, was zeigt, wie wichtig es ist, Polarisationseffekte explizit zu berücksichtigen. Die Anpassung des Drude-Modells umfasste eine Boltzmann-gewichtete Optimierung der Thole-Faktoren und Lennard-Jones-Parameter. Die erhaltenen Parameter wurden validiert durch (i) ihre Fähigkeit, Referenzwechselwirkungsenergien zu reproduzieren und (ii) Molekulardynamik-Simulationen des Calmodulin-N-Lobe. Diese Arbeit demonstriert die Verbesserung polarisierbarer Kraftfelder für Kationen-Protein-Wechselwirkungen durch quantenchemisch gesteuerte Parametrisierung in Kombination mit Molekulardynamiksimulationen in der kondensierten Phase. Während das Drude-Modell sein Potenzial bei der Simulation von Kation - Protein - Wechselwirkungen zeigt, fehlt ihm die Beschreibung von Ladungstransfereffekten, die zwischen Kation und Protein von Bedeutung sind. Das CTPOL-Modell erweitert die klassische Kraftfeldformulierung um den Ladungstransfer (CT) und die Polarisation (POL). Da das CTPOL-Modell in keinem der gängigen Molekulardynamik-Pakete verfügbar ist, wurde es in OpenMM implementiert. Außerdem wurde ein Open-Source-Parametrisierungswerkzeug namens FFAFFURR implementiert, welches die (systemspezifische) Parametrisierung von OPLS-AA und CTPOL-Modellen ermöglicht. In Anlehnung an die im vorangegangenen Teil etablierte Methode wurde die Leistung von FFAFFURR anhand seiner Fähigkeit, quantenchemische Energien und Molekulardynamiksimulationen des Zinkfingerproteins zu reproduzieren, bewertet. Zusammenfassend lässt sich sagen, dass diese Arbeit einen Schritt in Richtung der Entwicklung von Kraftfeldern der nächsten Generation zur genauen Beschreibung von Kationen-Protein-Wechselwirkungen darstellt, indem sie (i) Referenzdaten, (ii) ein Kraftfeldmodell, das Ladungstransfer und Polarisation einschließt, und (iii) ein frei verfügbares Parametrisierungswerkzeug bereitstellt

    Towards the implementation of a fully-fledged electronic service for citizens: the case for local government in South Africa

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    The current literature on e-government implementation in South Africa informs this research that there is no framework to guide the implementation of e-government for local municipalities. The public sector does not adopt models that are designed and developed for their context. SA as a developing nation still battles with the implementation of e-government for local government. The research findings in this research depict that the implementation of electronic services is complicated, stagnant, and incoherent due to various factors that hinder its swift implementation. The research commenced its pursuit to identify the factors that hinder the implementation of e-government through conducting four areas of investigations, firstly, the study investigated 205 existing municipal electronic portals to establish the extent to which eportal offers the relevant e-services to the citizens; secondly, the study conducted a research survey and a sample of 579 citizens gave their perspective about e-government services that they receive from local municipalities; thirdly, the study also evaluated the City of Cape Town electronic services to ascertain its adoption; and finally, the study conducted in-depth interviews with 35 e-government experts to understand the factors that hinder the implementation of e-government in SA. The study selected three social theoretical approaches, namely structuration, activity, and agency theories to address the different contexts of the research. Structuration theory has aided the research to ask critical questions about the social structures in local government that affect implementation. The activity theory was used to provide some guidelines to investigate how e-government activities are implemented within the identified social structure. Finally, the agency theory was used to develop a model to guide the implementation of a successful egovernment model by employing a deductive approach. Keywords: e-government, collaboration, citizens, agents, actors, implementation, structuration theory, activity theory, agency theory, and municipalitie

    Computerized Clinical Decision Support Systems for decision support in patients with breast, lung, colorectal or prostate cancer

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    Sistemes electrònics; Càncer; Presa de decisionsSistemas electrónicos; Cáncer; Toma de decisionesElectronic systems; Cancer; Decision makingEl objetivo general de este informe de ETS es evaluar la seguridad, eficacia, efectividad y eficiencia de los sistemas electrónicos de apoyo a las decisiones clínicas (computerized Clinical Decision Support Systems o cCDSS), específicamente de los considerados de nivel medio (p. ej. calculadoras pronósticas o GPC automatizadas) y de nivel alto (aquellos que utilizan la IA para formular recomendaciones específicas para un paciente), para el apoyo a la toma de decisiones clínicas relativas al manejo terapéutico, seguimiento o pronóstico de pacientes con cáncer de mama, pulmón, colon-recto o próstata. También se propone evaluar el impacto de los cCDSS en cáncer a nivel organizativo, legal, ético y social/de pacientes.L'objectiu general d'aquest informe d'ETS és avaluar la seguretat, eficàcia, efectivitat i eficiència dels sistemes electrònics de suport a les decisions clíniques (computeritzed Clinical Decision Support Systems o cCDSS), específicament dels considerats de nivell mitjà (p. ex. calculadores pronòstiques o GPC automatitzades) i de nivell alt (aquells que utilitzen la IA per formular recomanacions específiques per a un pacient), per al suport a la presa de decisions clíniques relatives al maneig terapèutic, seguiment o pronòstic de pacients amb càncer de mama, pulmó, còlon-recte o pròstata. També es proposa avaluar l'impacte dels cCDSS en càncer a nivell organitzatiu, legal, ètic i social/de pacients.The overall objective of this HTA report is to evaluate the safety, efficacy, effectiveness, and efficiency of (computeritzed Clinical Decision Support Systems (cCDSS), specifically those considered medium level (e.g. prognostic calculators or automated CPGs) and high level (those that use AI to formulate patient-specific recommendations), for clinical decision support regarding the therapeutic management, follow-up, or prognosis of patients with breast, lung, colon-rectum or prostate cancer. It is also proposed to assess the impact of cCDSS in cancer at organizational, legal, ethical, and social/patient level

    Contributions to time series analysis, modelling and forecasting to increase reliability in industrial environments.

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    356 p.La integración del Internet of Things en el sector industrial es clave para alcanzar la inteligencia empresarial. Este estudio se enfoca en mejorar o proponer nuevos enfoques para aumentar la confiabilidad de las soluciones de IA basadas en datos de series temporales en la industria. Se abordan tres fases: mejora de la calidad de los datos, modelos y errores. Se propone una definición estándar de métricas de calidad y se incluyen en el paquete dqts de R. Se exploran los pasos del modelado de series temporales, desde la extracción de características hasta la elección y aplicación del modelo de predicción más eficiente. El método KNPTS, basado en la búsqueda de patrones en el histórico, se presenta como un paquete de R para estimar datos futuros. Además, se sugiere el uso de medidas elásticas de similitud para evaluar modelos de regresión y la importancia de métricas adecuadas en problemas de clases desbalanceadas. Las contribuciones se validaron en casos de uso industrial de diferentes campos: calidad de producto, previsión de consumo eléctrico, detección de porosidad y diagnóstico de máquinas

    Metaverse. Old urban issues in new virtual cities

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    Recent years have seen the arise of some early attempts to build virtual cities, utopias or affective dystopias in an embodied Internet, which in some respects appear to be the ultimate expression of the neoliberal city paradigma (even if virtual). Although there is an extensive disciplinary literature on the relationship between planning and virtual or augmented reality linked mainly to the gaming industry, this often avoids design and value issues. The observation of some of these early experiences - Decentraland, Minecraft, Liberland Metaverse, to name a few - poses important questions and problems that are gradually becoming inescapable for designers and urban planners, and allows us to make some partial considerations on the risks and potentialities of these early virtual cities
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