Using Machine Learning to Collect and Facilitate Remote Access to Biomedical Databases: Development of the Biomedical Database Inventory

[Abstract] Background: Currently, existing biomedical literature repositories do not commonly provide users with specific means to locate and remotely access biomedical databases. Objective: To address this issue, we developed the Biomedical Database Inventory (BiDI), a repository linking to biomedical databases automatically extracted from the scientific literature. BiDI provides an index of data resources and a path to access them seamlessly. Methods: We designed an ensemble of deep learning methods to extract database mentions. To train the system, we annotated a set of 1242 articles that included mentions of database publications. Such a data set was used along with transfer learning techniques to train an ensemble of deep learning natural language processing models targeted at database publication detection. Results: The system obtained an F1 score of 0.929 on database detection, showing high precision and recall values. When applying this model to the PubMed and PubMed Central databases, we identified over 10,000 unique databases. The ensemble model also extracted the weblinks to the reported databases and discarded irrelevant links. For the extraction of weblinks, the model achieved a cross-validated F1 score of 0.908. We show two use cases: one related to “omics” and the other related to the COVID-19 pandemic. Conclusions: BiDI enables access to biomedical resources over the internet and facilitates data-driven research and other scientific initiatives. The repository is openly available online and will be regularly updated with an automatic text processing pipeline. The approach can be reused to create repositories of different types (ie, biomedical and others).Proyecto colaborativo de integración de datos genómicos; PI17/0156

Nanoinformática: retos e iniciativas para la gestión de la información generada en la investigación nanomédica

Durante la última década la investigación en nanomedicina ha generado gran cantidad de datos, heterogéneos, distribuidos en múltiples fuentes de información. El uso de las Tecnologías de la Información y la Comunicación (TIC) puede facilitar la investigación médica a escala nanométrica, proporcionando mecanismos y herramientas que permitan gestionar todos esos datos de una manera inteligente. Mientras que la informática biomédica comprende el procesamiento y gestión de la información generada desde el nivel de salud pública y aplicación clínica hasta el nivel molecular, la nanoinformática extiende este ámbito para incluir el “nivel nano”, ocupándose de gestionar y analizar los resultados generados durante la investigación en nanomedicina y desarrollar nuevas líneas de trabajo en este espacio interdisciplinar. En esta nueva área científica, la nanoinformática (que podría consolidarse como una auténtica disciplina en los próximos años), elGrupo de Informática Biomédica (GIB) de la Universidad Politécnica de Madrid (UPM) participa en numerosas iniciativas, que se detallan a continuación

La disfunción familiar como predisponente de la enfermedad mental. ¿Existe tal asociación?

ObjetivosEl objetivo principal es conocer la relación entre la disfunción familiar y la presencia de trastorno mental. El objetivo secundario es conocer la prevalencia y la distribución de los principales tipos de patología mental en la población atendida en atención primaria.Diseño y emplazamientoEstudio descriptivo y transversal realizado en 6 consultas de medicina de familia de un área básica de salud semiurbana.MétodoSe seleccionaron 280 sujetos mediante muestreo aleatorio sistemático de los que acudieron espontáneamente a la consulta. Mediante entrevista se recogieron las variables de estudio: dinámica familiar (medida mediante el test de APGAR familiar), estructura familiar, variables sociodemográficas y presencia de trastorno mental detectado mediante la Mini International Neuropsyquiatric Interview (MINI-DSM IV).ResultadosAceptaron participar 264 sujetos. Un 64,4% era mujer y la media de edad fue de 45,6 años (DE, 16,7). Se detectó patología mental en 87 participantes (33%), siendo la patología más frecuente trastorno de ansiedad generalizada, distimia y depresión mayor. Se encontró alteración de la dinámica familiar en 32 personas (12,3%). No se observaron diferencias significativas en la frecuencia de presentación de patología mental entre el grupo con disfunción familiar y el resto.ConclusionesLos trastornos de salud mental son frecuentes entre los pacientes que acuden a las consultas de atención primaria. No encontramos asociación entre las alteraciones de la dinámica familiar y los trastornos de salud mental, lo que podría deberse a la dificultad para detectar disfunción familiar con el test de APGAR.ObjectivesThe main purpose is to describe the relationship between family disfunction and mental disorder. The secondary objective is to know the prevalence and distribution of mental disorders in primary care attended population.DesignA cross-sectional study was conducted in a primary care setting.Patients and methodsRandom sample was selected over 280 subjects from consultant population. The variables (family function, family structure, social and economic conditions and mental disorders) were collected through interview. APGAR test and Mini International Neuropsychiatric Interview test were performed.Results264 patients were finally included (64% women). Mean age was 45,6 years (SD 16,7). Mental disorders were detected in 87 patients (33%). The most prevalent disorders were generalized anxiety disorder, dysthymia and major depression. family disfunction was found in 32 patients (12,3%). Prevalence of mental disorders wasn't statistically different in the group with family disfunction.ConclusionMental disorders are a common problem between primary care attended population. There wasn't any association between family disfunction and mental disorders, because of the limitations in the APGAR test in detecting family disfunction

e-MIR2: a public online inventory of medical informatics resources

Background. Over the last years, the number of available informatics resources in medicine has grown exponentially. While specific inventories of such resources have already begun to be developed for Bioinformatics (BI), comparable inventories are as yet not available for Medical Informatics (MI) field, so that locating and accessing them currently remains a hard and time-consuming task. Description. We have created a repository of MI resources from the scientific literature, providing free access to its contents through a web-based service. Relevant information describing the resources is automatically extracted from manuscripts published in top-ranked MI journals. We used a pattern matching approach to detect the resources? names and their main features. Detected resources are classified according to three different criteria: functionality, resource type and domain. To facilitate these tasks, we have built three different taxonomies by following a novel approach based on folksonomies and social tagging. We adopted the terminology most frequently used by MI researchers in their publications to create the concepts and hierarchical relationships belonging to the taxonomies. The classification algorithm identifies the categories associated to resources and annotates them accordingly. The database is then populated with this data after manual curation and validation. Conclusions. We have created an online repository of MI resources to assist researchers in locating and accessing the most suitable resources to perform specific tasks. The database contained 282 resources at the time of writing. We are continuing to expand the number of available resources by taking into account further publications as well as suggestions from users and resource developers

Nanoinformatics: a new area of research in nanomedicine

Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and ?omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings

Water-Gas Shift Reaction on K/Cu(111) and Cu/K/TiO2(110) Surfaces: Alkali Promotion of Water Dissociation and Production of H2

The addition of potassium atoms to Cu(111) and Cu/TiO2(110) surfaces substantially enhances the rate for water dissociation and the production of hydrogen through the water-gas shift reaction (WGS, CO + H2O → H2 + CO2). In the range of temperatures investigated, 550-625 K, Cu/K/TiO2(110) exhibits a WGS activity substantially higher than those of K/Cu(111), Cu(111), and Cu/ZnO(0001̄) systems used to model an industrial Cu/ZnO catalyst. The apparent activation energy for the WGS drops from 18 Kcal/mol on Cu(111) to 12 Kcal/mol on K/Cu(111) and 6 Kcal/mol on Cu/K/TiO2(110). The results of density functional calculations show that K adatoms favor the thermochemistry for water dissociation on Cu(111) and Cu/TiO2(110) with the cleavage of an O-H bond occurring at room temperature. Furthermore, at the Cu/K/TiO2 interface, there is a synergy, and this system has a unique ability to dissociate the water molecule and catalyze hydrogen production through the WGS process. Therefore, when optimizing a regular catalyst, it is essential to consider mainly the effects of an alkali promoter on the metal-oxide interface.US Department of Energy DE-SC0012704Ministerio de Economía y Competitividad CTQ2015-64669-

Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and side effects. Due to their special properties, nanoparticles are suitable for cellular-level diagnostics and therapy, offering numerous applications in medicine, e.g. development of biomedical devices, tissue repair, drug delivery systems and biosensors. In nanomedicine, recent studies are producing large amounts of structural and property data, highlighting the role for computational approaches in information management. While in vitro and in vivo assays are expensive, the cost of computing is falling. Furthermore, improvements in the accuracy of computational methods (e.g. data mining, knowledge discovery, modeling and simulation) have enabled effective tools to automate the extraction, management and storage of these vast data volumes. Since this information is widely distributed, one major issue is how to locate and access data where it resides (which also poses data-sharing limitations). The novel discipline of nanoinformatics addresses the information challenges related to nanotechnology research. In this paper, we summarize the needs and challenges in the field and present an overview of extant initiatives and efforts

Disnea progresiva en varón de 47 años

We report the case of a 47 year old male whose cardinal symptom was progressive dyspnea. We describe the diag- nostic process highlighting the usefulness of pulmonary and cardiac ultrasound. We stress the importance in this patient to take into account their personal history (Hodgkin’s lymphoma treated more than 10 years earlier) and the finding of a left bundle branch block in the electrocardiogram.Presentamos el caso de un varón de 47 años cuyo síntoma cardinal era la disnea progresiva. Describimos su proceso diagnóstico destacando la utilidad de la ecografía pulmonar y cardíaca. Resaltamos la importancia en este enfermo de tener en cuenta sus antecedentes (linfoma de Hodgkin tratado hacía más de 10 años) y el hallazgo de un bloqueo de rama izquierda en el electrocardiograma