Inferring ontology graph structures using OWL reasoning.

BACKGROUND: Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies' semantic content remains a challenge. RESULTS: We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph . CONCLUSIONS: Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

Integrating phenotype ontologies with PhenomeNET.

BACKGROUND: Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization that includes as one of its components an ontology designed to integrate phenotype ontologies. While not applicable to matching arbitrary ontologies, PhenomeNET can be used to identify related phenotypes in different species, including human, mouse, zebrafish, nematode worm, fruit fly, and yeast. RESULTS: Here, we apply the PhenomeNET to identify related classes from two phenotype and two disease ontologies using automated reasoning. We demonstrate that we can identify a large number of mappings, some of which require automated reasoning and cannot easily be identified through lexical approaches alone. Combining automated reasoning with lexical matching further improves results in aligning ontologies. CONCLUSIONS: PhenomeNET can be used to align and integrate phenotype ontologies. The results can be utilized for biomedical analyses in which phenomena observed in model organisms are used to identify causative genes and mutations underlying human disease.

Resultado del cierre incompleto de defecto tipo Gerbode con coil Nit-Occlud Lê VSD: hemolisis grave que precisa reintervención / Effect of incomplete closure of a Gerbode defect with the Nit-Occlud Lê VSD Coil: severe hemolysis requiring a second procedure

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Sentiment Analysis on Tweets about Diabetes: An Aspect-Level Approach.

In recent years, some methods of sentiment analysis have been developed for the health domain; however, the diabetes domain has not been explored yet. In addition, there is a lack of approaches that analyze the positive or negative orientation of each aspect contained in a document (a review, a piece of news, and a tweet, among others). Based on this understanding, we propose an aspect-level sentiment analysis method based on ontologies in the diabetes domain. The sentiment of the aspects is calculated by considering the words around the aspect which are obtained through N-gram methods (N-gram after, N-gram before, and N-gram around). To evaluate the effectiveness of our method, we obtained a corpus from Twitter, which has been manually labelled at aspect level as positive, negative, or neutral. The experimental results show that the best result was obtained through the N-gram around method with a precision of 81.93%, a recall of 81.13%, and an F-measure of 81.24%.

Calidad de vida en pacientes con insuficiencia cardiaca crónica / Quality of life in patients with chronic cardiac failure

OBJETIVO: evaluar la calidad de vida (CV) en pacientes con insuficiencia cardiaca crónica (ICC) pertenecientes a una unidad de insuficiencia cardiaca (UIC) y valorar la asociación con factores clínicos. MÉTODO: estudio descriptivo transversal en 87 enfermos con ICC pertenecientes la UIC del "Complejo Asistencial Universitario de León". Para medir la CV se utilizó el cuestionario 36-Item Short-Form Health Survey (SF-36). La comparación de variables se realizó con el testt-Student. Para evaluar la asociación independiente entre las diferentes dimensiones y las variables, se construyeron modelos de regresión lineal múltiple. RESULTADOS: la edad media de los sujetos estudiados fue de 71,3años, predominó el sexo masculino (70,6%), la etiología no-isquémica(57,6%), el grado funcional de la New York Heart Association (NYHA)III-IV (52,9%) y la IC sistólica (82,4%). La puntuación media de CV en el componente sumario físico (CSF) fue de 33,2 y en el componente sumariomental (CSM) de 48,9. En los análisis multivariantes: para el CSF, un grado funcional III-IV de la NYHA y una etiología no-isquémica, empeoraban la CV en su componente físico; el componente mental de la CV empeoraba en la IC diastólica y con etiología no-isquémica. CONCLUSIONES: la percepción de la CV en pacientes con ICC está considerablemente alterada en todas las dimensiones. Un peor grado funcional y la etiología no isquémica se asociaron independientemente con un mayor deterioro de la CV en las dimensiones físicas, y la IC diastólica y la etiología no isquémica con un mayor deterioro en las emocionales. La etiología es la variable con mayor impacto en todos los dominios

OBJECTIVE: critical patients tend to present hyperglycemia, a fact associated with an increase in morbimortality and infectious complications. According to the Spanish Society of Intensive and Critical Medicine and Coronary Units (SEMICYUC), a safe and good-quality care requires maintaining glycemic levels between80 and 150 mg/dl with insulin therapy. The objective is to obtain an estimation of the adequate maintenance of glycemic levels of patients, as well as to detect any potential for quality improvement, if necessary. METHOD: a descriptive observational study conducted in the Intensive Care Unit of the Hospital Virgen del Rocío during January, February and March, 2014. The sample size was estimated in 108 patients, recruited in 13 days randomly chosen, with all week days represented. The indicator was measured according to the following formula: (Number of patients with glycemia > 150 mg/dl and on insulin treatment / Number of patients with indication for glycemic control and glycemias> 150mg/d) X 100.RESULTS: the mean age of subjects was 64 years, with 73%male and 27% women. A 41% of the sample suffered Type 2diabetes, 1% suffered Type I diabetes, and 58% had no diabetes. A range of glycemias between 151 mg/dl and 323 mg/dl was obtained. The minimum level of the indicator required by the SEMICYUC (80%) was not reached in any of the three months measured, thus being in a sub-standard situation. CONCLUSIONS: there is no adequate maintenance of the glycemi levels in patients managed in our unit; therefore, a review of the current protocol for insulin therapy could improve the quality and safety in this aspect of care

Using data crawlers and semantic Web to build financial XBRL data generators: the SONAR extension approach.

Precise, reliable and real-time financial information is critical for added-value financial services after the economic turmoil from which markets are still struggling to recover. Since the Web has become the most significant data source, intelligent crawlers based on Semantic Technologies have become trailblazers in the search of knowledge combining natural language processing and ontology engineering techniques. In this paper, we present the SONAR extension approach, which will leverage the potential of knowledge representation by extracting, managing, and turning scarce and disperse financial information into well-classified, structured, and widely used XBRL format-oriented knowledge, strongly supported by a proof-of-concept implementation and a thorough evaluation of the benefits of the approach.

La calidad de vida en los enfermos con insuficiencia cardiaca: visión desde atención primaria de salud / Quality of life in patients with heart failure: the perspective of primary health care

Objetivo Medir e identificar las dimensiones y los determinantes de la calidad de vida relacionada con la salud (CVRS) en los enfermos con insuficiencia cardiaca crónica. Métodos Mediante un estudio transversal se midió la CVRS con los cuestionarios SF-36 y MLHFQ, en 544 enfermos con insuficiencia cardiaca crónica, clínicamente estables, de 97 médicos de atención primaria. Resultados La edad media de los enfermos es de 77,6 años (desviación estándar: 9,9), significativamente mayor en las mujeres. El 31,2% están en grado III-IV de la New York Heart Association (NYHA). El 88,6% tiene al menos otra enfermedad crónica. Las dimensiones físicas tienen peor puntuación que las emocionales en ambos cuestionarios. Tras ajustar por regresión múltiple, siete variables entran en alguno de los cinco modelos y explican entre un 22% y un 36% de la varianza. Conclusiones La CVRS en los pacientes con insuficiencia cardiaca crónica está alterada en todos los dominios. Ser mujer, estar en clase funcional de la NYHA III-IV, la presencia de otras afecciones tales como depresión o enfermedad osteoarticular, el ingreso hospitalario, el índice de masa corporal y la edad, se asocian con una peor percepción de la CVRS (AU)

Objective To measure and identify the dimensions and determinants of health-related quality of life (HRQoL) in patients with chronic heart failure. Methods We performed a cross-sectional study, in which HRQoL was measured with the short-form (SF)-36 and the Minnesota Living with Heart Failure Questionnaire (MLHFQ) in 544 clinically-stable patients with chronic heart failure managed by 97 primary care physicians. Results The mean age of the patients was 77.6 years (SD: 9.9) and was significantly higher in women. A total of 31.2% were in New York Heart Association (NYHA) grade III-IV and 88.6% had at least one chronic condition. In both questionnaires, physical dimensions scored worse than emotional dimensions. After adjustment was made for multiple regression, seven variables entered into one of the five models and explained between 22% and 36% of the variance. Conclusions HRQoL in patients with chronic heart failure is impaired across all domains. Being female and being in NYHA functional class III-IV, as well as other factors such as depression, osteoarticular disease, hospital admission, body mass index and age, were associated with poorer self-perceived HRQoL (AU)

[Quality of life in patients with heart failure: the perspective of primary health care]. / La calidad de vida en los enfermos con insuficiencia cardiaca: visión desde atención primaria de salud.

OBJECTIVE: To measure and identify the dimensions and determinants of health-related quality of life (HRQoL) in patients with chronic heart failure. METHODS: We performed a cross-sectional study, in which HRQoL was measured with the short-form (SF)-36 and the Minnesota Living with Heart Failure Questionnaire (MLHFQ) in 544 clinically-stable patients with chronic heart failure managed by 97 primary care physicians. RESULTS: The mean age of the patients was 77.6 years (SD: 9.9) and was significantly higher in women. A total of 31.2% were in New York Heart Association (NYHA) grade III-IV and 88.6% had at least one chronic condition. In both questionnaires, physical dimensions scored worse than emotional dimensions. After adjustment was made for multiple regression, seven variables entered into one of the five models and explained between 22% and 36% of the variance. CONCLUSIONS: HRQoL in patients with chronic heart failure is impaired across all domains. Being female and being in NYHA functional class III-IV, as well as other factors such as depression, osteoarticular disease, hospital admission, body mass index and age, were associated with poorer self-perceived HRQoL.

Estimulación en la insuficiencia cardiaca congestiva. Situación actual y perspectivas / Cardiac pacing in congestive heart disease. Current status and future prospects

La resincronización cardiaca se ha consolidado en sus 10 años de vida como un tratamiento insustituible para determinados pacientes afectados de insuficiencia cardiaca refractaria. Este capítulo pretende transmitir algunos de los avances recientes y líneas de evolución que mantienen a este tipo de estimulación en permanente actualidad. Se revisan seguidamente los parámetros fisiopatológicos que justifican la mejora en la calidad de vida, disminución de las necesidades de tratamiento hospitalario y supervivencia logrados mediante la estimulación biventricular. También se aborda a los grupos de pacientes, fuera de las indicaciones establecidas en las guías de actuación internacionales, que son el centro de atención en importantes ensayos clínicos para ampliar la aplicación de esta terapia. Para optimizar la respuesta a la resincronización es preciso también una correcta planificación del implante incluida una cuidada estrategia de seguimiento y optimización en la programación del estimulador. Las indicaciones de resincronización se basan actualmente en determinados parámetros eléctricos y ecocardiográficos, se comentan también estos conceptos con especial énfasis en algunos datos de imagen que presumiblemente permitirán en un futuro próximo precisar la selección de pacientes y mejorar el porcentaje de respuestas al tratamiento de estimulación (AU)

In the ten years of its existence, cardiac resynchronization therapy has become established as an irreplaceable form of treatment in selected patients with refractory heart failure. This article presents a summary of recent advances and future trends which ensure that this type of pacing remains of continuing relevance. Thereafter, there is a review of the pathophysiologic factors that underlie the improvement in quality of life, the reduction in the need for hospitalization, and the increased survival brought about by biventricular pacing. There is also a discussion of the groups of patients who lie outside the indications listed in international guidelines and who are the focus of large clinical trials aimed at extending the applications of this type of therapy. To ensure an optimum response to resynchronization therapy, device implantation must be fully planned, there should be close follow-up, and device programming should be optimized. Currently, indications for resynchronization therapy are based on specific electrocardiographic and echocardiographic parameters. This article also contains a discussion of these parameters, with particular emphasis on imaging data that will enable more accurate patient selection in the near future, thereby increasing the response rate in cardiac pacing (AU)

Doppler tisular del anillo mitral en pacientes con disfunción sistólica ventricular izquierda. Análisis de la función diastólica / Doppler tissue imaging of the mitral annulus in patients with left ventricular systolic dysfunction. Assessment of diastolic function

Introducción y objetivos. Evaluar el Doppler tisular del anillo mitral lateral en pacientes con disfunción sistólica ventricular izquierda. Esta técnica se ha propuesto para analizar la función diastólica ventricular puesto que los valores obtenidos son relativamente independientes de la precarga. Pacientes y métodos. Se estudiaron 46 pacientes con fracción de eyección < 40 por ciento, en ritmo sinusal y sin regurgitación mitral. Se analizó el Doppler pulsado del flujo transmitral (ondas E y A), el flujo en venas pulmonares (ondas S, D y Ar) y el Doppler tisular del anillo mitral lateral (ondas Ea y Aa).Resultados. Las correlaciones lineales de las medidas Doppler son en conjunto bajas. Cuando los pacientes se agruparon según el cociente E/A (E/A < 1 o grupo 1 y E/A 1 o grupo 2 con patrón seudonormalizado), el valor de Ea no difirió entre los dos grupos: 5,0 cm/s (4,2/6,0) frente a 6,2 cm/s (5,5/8,2); p = 0,129, ni tampoco el de E/Ea: 10,2 (8,2/14,5) frente a 12,9 (9,1/17,4); p = 0,160. El tamaño auricular izquierdo fue significativamente mayor en el grupo 2: 20,0 cm2 (18,0/22,0) frente a 25,0 cm2 (20,0/29,0); p < 0,001. El cociente Ea/Aa se seudonormalizó en el grupo 2: 0,65 (0,48/0,83) frente a 1,15 (0,75/1,71); p = 0,001.Conclusión. En pacientes con disfunción sistólica ventricular izquierda, el valor de Ea/Aa se seudonormaliza cuando la precarga aumenta. Esto no sucede en los valores de Ea, E/Ea ni en el tamaño de la aurícula izquierda. Por tanto, el Doppler tisular del anillo mitral es un método útil para evaluar la función diastólica ventricular izquierda al ser relativamente independiente de la precarga (AU)