Exploración de Bases de Datos Genómicas Dirigida por Modelos Conceptuales

Cada día los doctores, genetistas e investigadores enfrentan grandes retos al momento de buscar información y querer sintetizar los resultados obtenidos luego de una consulta de información médica en la web. No obstante, internamente quedan las dudas sobre: > o > o > entre otras. Pues muchas de las veces lo que se espera es abarcar todas las fuentes de información para generar así un reporte médico completo. De manera similar sucede en el ámbito del genoma humano, donde se pueden encontrar cientos de páginas con bases de datos genómicas. Varios de estos sitios son desconocidos, ya sea porque son nuevos o no han sido publicitados. Ahora bien, la interrogante del investigador en el momento de sintetizar información es >, >. La aplicación del modelado conceptual aplicado en este caso al ámbito médico permite considerar los diferentes procesos y detallar las tareas y actividades que se desarrollan. Pues ahí es donde el modelado conceptual juega un rol muy importante, puesto que, luego de abstraer los elementos que se desea obtener se permite encontrar coincidencias desde varias fuentes y que estas apunten a un mismo concepto. Es así que, el modelado del genoma humano es una pieza fundamental que permite considerar las entidades involucradas y sus relaciones. Por este motivo, el presente trabajo de fin de máster pretende ser una herramienta de ayuda para las personas involucradas con el área del genoma humano. Al crearse un mapeo, es decir al establecerse los vínculos entre la información las bases de datos genómicas contrastadas con cada uno de los elementos del Esquema Conceptual del Genoma Humano (ECGH), se establecen los enlaces necesarios para que los usuarios tengan un soporte sus búsquedas. Este trabajo presenta el desarrollo de la exploración de las bases de datos genómicas que se han encontrado en listados avalados por Institutos de investigación en el área genómica. Se indica el proceso de verificación de los sitios que se han encontrado, puesto que algunos sitios han sufrido cambios en los servidores o simplemente ya dejaron de funcionar. Así también se exponen las tareas de depuración que se ha generado, debido a que cada una de las bases de datos genómicas presentan diferentes estructuras, organizaciones de la información, incluso en algunos de los casos se utiliza nomenclatura distinta a la que habitualmente el investigador está acostumbrado a encontrar. Posteriormente se presenta el mapeo de cada base de datos genómica con los elementos del ECGH. Finalmente se muestra los resultados obtenidos con estadísticas que se pudieron establecer en la exploración de las bases de datos genómicas y un interfaz resultado como herramienta de ayuda para el usuario. Para finalizar, se exponen los problemas encontrados en el desarrollo de este trabajo, así como también las conclusiones a las que se han podido llegar. Se indican los posibles trabajos futuros que se pueden realizar a partir de este trabajo.Doctors, geneticists and researchers face huge challenges every day; especially at the time of looking for information and to synthesize the results obtained after checking medical information online. However, there are certain doubts regarding this issue; for example, > or > or >, among others. Most of the time, it is expected to encompass all the sources to generate a complete medical report. It happens in a similar way in the human genome field where hundreds of pages with data bases are found. Many of those are unknown since they are either new or have been advertised. So the questions for the researcher at the time of synthesizing information is, How to unify results if the searches done have brought different information? Which pieces of information are the same or have the same meaning? In this case, the application of the conceptual model in the medical field allows to consider different processes to detail the tasks and activities that are developed. It is there where the conceptual model plays an important role, given that once the elements are abstracted and that the desired information is obtained, it is possible to find information from many sources so that they match one single concept. Thereof is the fact that the human genome modeling is a fundamental piece that allows to consider the different entities and their relationships. For this reason, this master¿s degree work aims to be a tool for those professionals involved in the human genome field. Setting up a map, that is to say, establishing links among the genomic data bases contrasted to each one of the elements from the Human Genomic Conceptual Scheme (HGCS), the necessary links are established so that the users find support when searching information. This work presents the development of the genomic data bases exploration that has been found on validated sources; that is, by research institutions in the area of genetics. The verification process of the sites that were found is shown because several sites have been changed in the servers or they simply stopped working. In addition, the debugging tasks are mentioned in this work because each one of the genomic data bases presents different structures, information organization, and in some cases, they used different naming compared to the one the researcher is used to find. After that, a genomic data base mapping is presented with the HGCS. Finally, the obtained results are shown in this work, including statistics that were established through the genomic data bases exploration and the interface that was the result as a tool for the user. In a nutshell, the problems found during the development of this work are shown along with the conclusions that arose. Possible future researches on the bases of this work are indicated.Solis Cabrera, VA. (2018). Exploración de Bases de Datos Genómicas Dirigida por Modelos Conceptuales. http://hdl.handle.net/10251/114954TFG

Generación de un modelo de calidad para la evaluación de objetos de aprendizaje utilizando notación i* e ISO/IEC 25010

Este trabajo describe el proceso para la creación de un modelo de calidad que evalúe Objetos de Aprendizaje (OA) en aspectos tecnológicos y didácticos utilizando la notación i*. Para cumplir con este objetivo se revisaron modelos de calidad en ambos aspectos y conjuntamente con los conceptos de OA y calidad se han determinado las características que debe cumplir un OA. Para entender el contexto de un OA se definió un modelo de Dependencias Estratégicas (SD) utilizando la notación i*. Con el modelo SD creado se establece la trazabilidad entre sus criterios y los elementos de calidad incluidos en el estándar ISO/IEC 25010. El modelo de calidad resultante fue enriquecido con las características y los atributos identificados en la literatura utilizando el método IQMC. A cada propiedad de calidad incluida se le asignaron métricas apropiadas para su evaluación. Como resultado se obtuvo un modelo genérico para la evaluación de distintos tipos de OAThis study describes the process for the creation of a quality model that evaluates Learning Objects in terms of technology and didactics by using i* notation. In order to achieve the objective, quality models from both aspects were reviewed along with LO concepts and quality characteristics that a LO must accomplish were determined in order to consider the evaluation characteristics. The IQMC method was used to construct the diagram for strategic (SD) i* sections for the final quality model. With the SD model created, it was established the traceability between the generated model criteria and the ISO/IEC 25010 matrix to keep a correlation between the i* notation characteristics and the standard ISO matrix mentioned before. The matrix obtained was enriched with conceptual characteristics and with the attributes that a LO should fulfill. For each quality property included in final model was asigned appropiate metrics for your evaluation. As a result, a model through LO evaluation with each one of the selected metrics was generated

Soluciones ante el caos genómico

La investigación acerca del genoma humano ha dejado como resultado muchos datos e información desde su descubrimiento hasta la actualidad. Esta información es útil para investigadores, pero se vuelve un reto la extracción de información genómica por la gran cantidad de recursos disponibles en la web, esto se debe en gran parte a que no se dispone actualmente de herramientas que brinden soporte para automatizar las búsquedas personalizadas y que se discrimine la información repetida. Este trabajo pretende plantear y forjar soluciones que mitiguen los problemas que se tienen en el momento de la investigación genómica. Partiendo de una exploración de bases de datos genómicas orientadas al humano, donde se han podido evidenciar problemas que conllevan al conocido “caos genómico”, y a raíz de ello se plantean soluciones que ayuden a controlarlo y disminuirlo. De esta manera poder integrar la información de mejor manera, filtrar la información según las necesidades de investigación, tener un manejo adecuado de los datos, extraer información sin importar la presentación de estos y finalmente preservar la información actualizada.Research on the human genome has resulted in much data and information from its discovery to the present day. This information is useful for researchers but an extraction of genomic information is retrieved due to the large number of resources available on the web, this is largely due to the fact that tools that provide support to automate personalized searches are not currently available and that repeated information is discriminated. This work aims to propose and forge solutions that mitigate the problems they have at the time of genomic research. Starting from an exploration of human-oriented genomic databases, where evidence of problems that lead to the known “genomic chaos” has been found, and one root of this is solutions that help control and reduce it. In this way, being able to integrate the information in a better way, filter the information according to the research needs, have an adequate handling of the data, extract information regardless of the presentation of the data, and finally preserve the updated informatio

Efectos de la capacitación en el uso de herramientas informáticas en la docencia médica

Objetivo: Evaluar el efecto de una estrategia educativa, dirigida a docentes y estudiantes de pregrado y posgrado del área de la salud, para la aplicación de tecnologías de información y comunicación TICs, como apoyo en el proceso formativo. Material y métodos: Se utilizó el diseño cuasiexperimental en el que participaron 477 estudiantes y 123 docentes, el mismo grupo fue considerado antes de la capacitación como expuesto y después como expuesto. El programa educativo incluyó técnicas para la búsqueda, elaboración, presentación y comunicación de la información. La medida del efecto se estableció en los cambios en el uso de las TICs por los docentes y estudiantes, con base en la prueba de McNemar. Resultados: Luego del proceso de capacitación, los docentes incrementaron de manera significativa sus competencias en el uso del 50% de las herramientas informáticas, así como de equipos y recursos de telemedicina y en 6 de 9 valores éticos. Los estudiantes mejoraron de manera significativa en 80% en el uso de herramientas informáticas, 100% de equipos y recursos de telemedicina y en 5 de 9 valores éticos seleccionados para el estudio.Objective: To evaluate the effect of an educational strategy, aimed at teachers and undergraduate and graduate students in the area of health, for the application of information and communication technologies ICTs as support in the training process. Methods: We used a quasi-experimental design involving 477 students and 123 teachers, the same group was seen before and after training as exposed as above. The educational program included techniques for searching, processing, presentation and communication of information. The measure of effect was established as changes in the use of ICT for teachers and students, based on the McNemar test. Results: After the training process, teachers significantly increased their skills in the use of 50% of the tools and equipment and telemedicine resources and ethical September 6. Students improved significantly by 80% in the use of tools, 100% of telemedicine equipment and resources and September 5 ethical values selected for the study.Cuenc

A comprehensive solution for electrical energy demand prediction based on auto-regressive models

Energy consumption and demand are two widely used terms necessary to understand the functioning of the different mechanisms used in electrical energy transactions. In this article, the design and construction of a comprehensive solution to forecast future trends in electricity transactions using the historical data and two auto-regressive models were considered. Simple linear regression and a complete model such as ARIMA. We compared these models to find which one best suits the type of data considering their strengths and weaknesses for this specific case. Finally, to complete the comprehensive solution, the results are presented to the final user. This solution is mainly aimed at professionals who carry out activities related to contracting and managing electricity supply in public institutions. This solution pretends to collaborate to reduce energy demand and therefore, consumption.Mant

Co-infection and ICU-acquired infection in COIVD-19 ICU patients: a secondary analysis of the UNITE-COVID data set

Background: The COVID-19 pandemic presented major challenges for critical care facilities worldwide. Infections which develop alongside or subsequent to viral pneumonitis are a challenge under sporadic and pandemic conditions; however, data have suggested that patterns of these differ between COVID-19 and other viral pneumonitides. This secondary analysis aimed to explore patterns of co-infection and intensive care unit-acquired infections (ICU-AI) and the relationship to use of corticosteroids in a large, international cohort of critically ill COVID-19 patients.Methods: This is a multicenter, international, observational study, including adult patients with PCR-confirmed COVID-19 diagnosis admitted to ICUs at the peak of wave one of COVID-19 (February 15th to May 15th, 2020). Data collected included investigator-assessed co-infection at ICU admission, infection acquired in ICU, infection with multi-drug resistant organisms (MDRO) and antibiotic use. Frequencies were compared by Pearson's Chi-squared and continuous variables by Mann-Whitney U test. Propensity score matching for variables associated with ICU-acquired infection was undertaken using R library MatchIT using the "full" matching method.Results: Data were available from 4994 patients. Bacterial co-infection at admission was detected in 716 patients (14%), whilst 85% of patients received antibiotics at that stage. ICU-AI developed in 2715 (54%). The most common ICU-AI was bacterial pneumonia (44% of infections), whilst 9% of patients developed fungal pneumonia; 25% of infections involved MDRO. Patients developing infections in ICU had greater antimicrobial exposure than those without such infections. Incident density (ICU-AI per 1000 ICU days) was in considerable excess of reports from pre-pandemic surveillance. Corticosteroid use was heterogenous between ICUs. In univariate analysis, 58% of patients receiving corticosteroids and 43% of those not receiving steroids developed ICU-AI. Adjusting for potential confounders in the propensity-matched cohort, 71% of patients receiving corticosteroids developed ICU-AI vs 52% of those not receiving corticosteroids. Duration of corticosteroid therapy was also associated with development of ICU-AI and infection with an MDRO.Conclusions: In patients with severe COVID-19 in the first wave, co-infection at admission to ICU was relatively rare but antibiotic use was in substantial excess to that indication. ICU-AI were common and were significantly associated with use of corticosteroids

Clinical and organizational factors associated with mortality during the peak of first COVID-19 wave : the global UNITE-COVID study

Purpose To accommodate the unprecedented number of critically ill patients with pneumonia caused by coronavirus disease 2019 (COVID-19) expansion of the capacity of intensive care unit (ICU) to clinical areas not previously used for critical care was necessary. We describe the global burden of COVID-19 admissions and the clinical and organizational characteristics associated with outcomes in critically ill COVID-19 patients. Methods Multicenter, international, point prevalence study, including adult patients with SARS-CoV-2 infection confirmed by polymerase chain reaction (PCR) and a diagnosis of COVID-19 admitted to ICU between February 15th and May 15th, 2020. Results 4994 patients from 280 ICUs in 46 countries were included. Included ICUs increased their total capacity from 4931 to 7630 beds, deploying personnel from other areas. Overall, 1986 (39.8%) patients were admitted to surge capacity beds. Invasive ventilation at admission was present in 2325 (46.5%) patients and was required during ICU stay in 85.8% of patients. 60-day mortality was 33.9% (IQR across units: 20%-50%) and ICU mortality 32.7%. Older age, invasive mechanical ventilation, and acute kidney injury (AKI) were associated with increased mortality. These associations were also confirmed specifically in mechanically ventilated patients. Admission to surge capacity beds was not associated with mortality, even after controlling for other factors. Conclusions ICUs responded to the increase in COVID-19 patients by increasing bed availability and staff, admitting up to 40% of patients in surge capacity beds. Although mortality in this population was high, admission to a surge capacity bed was not associated with increased mortality. Older age, invasive mechanical ventilation, and AKI were identified as the strongest predictors of mortality

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

BackgroundWe previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in similar to 80% of cases.MethodsWe report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.ResultsNo gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P=1.1x10(-4)) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70[95%CI 1.3-8.2], P=2.1x10(-4)). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR=19.65[95%CI 2.1-2635.4], P=3.4x10(-3)), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR=4.40[9%CI 2.3-8.4], P=7.7x10(-8)). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P=1.68x10(-5)).ConclusionsRare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old