Optimització d'una aplicacio bioinformàtica d'alineament de seqüències executada en processadors multi-core i many-core (GPUs)

Las aplicaciones de alineamiento de secuencias son una herramienta importante para la comunidad científica. Estas aplicaciones bioinformáticas son usadas en muchos campos distintos como pueden ser la medicina, la biología, la farmacología, la genética, etc. A día de hoy los algoritmos de alineamiento de secuencias tienen una complejidad elevada y cada día tienen que manejar un volumen de datos más grande. Por esta razón se deben buscar alternativas para que estas aplicaciones sean capaces de manejar el aumento de tamaño que los bancos de secuencias están sufriendo día a día. En este proyecto se estudian y se investigan mejoras en este tipo de aplicaciones como puede ser el uso de sistemas paralelos que pueden mejorar el rendimiento notablemente.Les aplicacions d'alineament de seqüències són una eina important per a la comunitat científica. Aquestes aplicacions bioinformàtiques són utilitzades en molts camps diferents com poden ser la medicina, la biologia, la farmacologia, la genètica, etc. A dia d'avui els algorismes d'alineament de seqüències tenen una complexitat elevada i cada dia han de gestionar un volum de dades més gran. Per això s'han de buscar alternatives per a que aquestes aplicacions siguin capaces de gestionar l'augment de mida que els bancs de seqüències estan patint dia a dia. En aquest projecte s'estudien i s'investiguen millores en aquest tipus d'aplicacions com pot ser l'ús de sistemes paral·leles que poden millorar el rendiment notablement.The sequence alignment applications are an important tool for the scientific community. These bioinformatics applications are used in many different fields such as medicine, biology, pharmacology, genetics, etc. Today the sequence alignment algorithms are highly complex and every day have to handle a large volume of data. For this reason we must find alternatives for these applications are able to handle the increased size of sequences that banks are suffering every day. In this project we study and investigate improvements in these applications such as the use of parallel systems that can improve performance significantly

Galones de librea con escudos de armas de familias cubanas

The heraldic livery ribbons of Cuban colonial families acquired the category of collectibles in a short amount of time due to their high interest as decorative elements. This combined with certain nostalgia evocative of customs and characters from past times gives a distinctive rank to the sugar aristocracy that led the economic development of Cuba in the 18th and 19th century. The heraldic livery ribbons are also a testimony and a valuable source of information of a period in Cuban history.Los galones de librea heráldicos de familias coloniales cubanas, en poco tiempo adquirieron la categoría de objetos coleccionables por su alto interés como elementos decorativos, combinado esto con cierta nostalgia evocadora de costumbres y de personajes de tiempos pasados. Constituyen un rango distintivo de la aristocracia azucarera que lideró el desarrollo económico de Cuba en los siglos XVIII y XIX, son un testimonio y una valiosa fuente de información de una etapa de la historia cubana

Optical imaging of voltage and calcium in isolated hearts: Linking spatiotemporal heterogeneities and ventricular fibrillation initiation

[EN] Background Alternans have been associated with the development of ventricular fibrillation and its control has been proposed as antiarrhythmic strategy. However, cardiac arrhythmias are a spatiotemporal phenomenon in which multiple factors are involved (e.g. calcium and voltage spatial alternans or heterogeneous conduction velocity) and how an antiarrhythmic drug modifies these factors is poorly understood. Objective The objective of the present study is to evaluate the relation between spatial electrophysiological properties (i.e. spatial discordant alternans and conduction velocity) and the induction of ventricular fibrillation (VF) when a calcium blocker is applied. Methods The mechanisms of initiation of VF were studied by simultaneous epicardial voltage and calcium optical mapping in isolated rabbit hearts using an incremental fast pacing protocol. The additional value of analyzing spatial phenomena in the generation of unidirectional blocks and reentries as precursors of VF was depicted. Specifically, the role of action potential duration (APD), calcium transients (CaT), spatial alternans and conduction velocity in the initiation of VF was evaluated during basal conditions and after the administration of verapamil. Results Our results enhance the relation between (1) calcium spatial alternans and (2) slow conduction velocities with the dynamic creation of unidirectional blocks that allowed the induction of VF. In fact, the administration of verapamil demonstrated that calcium and not voltage spatial alternans were the main responsible for VF induction. Conclusions VF induction at high activation rates was linked with the concurrence of a low conduction velocity and high magnitude of calcium alternans, but not necessarily related with increases of APD. Verapamil can postpone the development of cardiac alternans and the apparition of ventricular arrhythmias.This work was funded in part by the CIBERCV (Centro de Investigacion Biomedica en Red Enfermedades Cardiovasculares), Instituto de Salud Carlos III (PI14/00857, PI16/01123, DTS16/0160, PI17/01059, PI17/01106 and IJCI-2014-22178); Spanish Ministry of Ecomomy (TEC2013-46067-R); Generalitat Valenciana Grants (APOSTD/2017 and APOSTD/2018) and projects (GVA/2018/103), EIT-Health 19600 AFFINE and cofound by FEDER.Hernández-Romero, I.; Guillem Sánchez, MS.; Figuera, C.; Atienza, F.; Fernández-Avilés, F.; Martínez Climent, BA. (2019). Optical imaging of voltage and calcium in isolated hearts: Linking spatiotemporal heterogeneities and ventricular fibrillation initiation. PLoS ONE. 14(5):1-15. https://doi.org/10.1371/journal.pone.0215951S115145Hayashi, M., Shimizu, W., & Albert, C. M. (2015). The Spectrum of Epidemiology Underlying Sudden Cardiac Death. 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American Journal of Physiology-Heart and Circulatory Physiology, 308(9), H1112-H1125. doi:10.1152/ajpheart.00556.2014Laughner, J. I., Ng, F. S., Sulkin, M. S., Arthur, R. M., & Efimov, I. R. (2012). Processing and analysis of cardiac optical mapping data obtained with potentiometric dyes. American Journal of Physiology-Heart and Circulatory Physiology, 303(7), H753-H765. doi:10.1152/ajpheart.00404.2012Gizzi, A., Cherry, E. M., Gilmour, R. F., Luther, S., Filippi, S., & Fenton, F. H. (2013). Effects of Pacing Site and Stimulation History on Alternans Dynamics and the Development of Complex Spatiotemporal Patterns in Cardiac Tissue. Frontiers in Physiology, 4. doi:10.3389/fphys.2013.00071VISWESWARAN, R., McINTYRE, S. D., RAMKRISHNAN, K., ZHAO, X., & TOLKACHEVA, E. G. (2013). Spatiotemporal Evolution and Prediction of [Ca2+ ]i and APD Alternans in Isolated Rabbit Hearts. Journal of Cardiovascular Electrophysiology, 24(11), 1287-1295. doi:10.1111/jce.12200Bayly, P. V., KenKnight, B. 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Detección de fibrilación ventricular mediante técnicas de aprendizaje profundo

Detección de fibrilación ventricular mediante técnicas de aprendizaje profundo La detección de arritmias ventriculares, en particular la fibrilación ventricular (FV), es parte fundamental de los algoritmos de clasificación de arritmias de los desfibriladores. Dichos algoritmos deciden si administrar la descarga de desfibrilación, para lo que clasifican los ritmos en desfibrilables (Sh) o no desfibrilables (NSh). Este trabajo propone un nuevo abordaje para la clasificación Sh/NSh de ritmos basado en un sistema de aprendizaje profundo. Para el trabajo se emplearon tres bases de datos públicas de la plataforma Physionet (CUDB, VFDB y AHADB), y se extrajeron segmentos de 4 y 8 segundos. Se anotaron los segmentos como Sh y NSh en base a las anotaciones de las bases de datos, que fueron auditadas por expertos. Los datos se dividieron por paciente en 80% para desarrollar los algoritmos y 20% para evaluación. El sistema de aprendizaje profundo emplea dos etapas convolucionales seguidas de, una red longshort- term-memory y una etapa final de clasificación basada en red neuronal. A modo de referencia se optimizó un clasificador SVM basado en las características de detección de arritmias ventriculares más eficientes publicadas en la literatura. Se calculó la sensibilidad (Se), ritmos desfibrilables, especificidad (Sp), ritmos no desfibrilables, y la precisión (Acc). El método de aprendizaje profundo proporcionó Se, Sp y Acc de 98.5%, 99.4% y 99.2% para segmentos de 4 segundos y 99.7%, 98.9%, 99.1% para segmentos de 8 segundos. El algoritmo permite detectar FV de forma fiable con segmentos de 4 segundos, corrigiendo un 30% de los errores del método basado en SVM.Este trabajo ha sido financiado por el Ministerio de Economía y Competitividad mediante el proyecto TEC2015-64678R junto con el Fondo Europeo de Desarrollo Regional (FEDER), así como por la UPVEHU mediante el proyecto EHU16/18

Mixed convolutional and long short-term memory network for the detection of lethal ventricular arrhythmia

Early defibrillation by an automated external defibrillator (AED) is key for the survival of out-of-hospital cardiac arrest (OHCA) patients. ECG feature extraction and machine learning have been successfully used to detect ventricular fibrillation (VF) in AED shock decision algorithms. Recently, deep learning architectures based on 1D Convolutional Neural Networks (CNN) have been proposed for this task. This study introduces a deep learning architecture based on 1D-CNN layers and a Long Short-Term Memory (LSTM) network for the detection of VF. Two datasets were used, one from public repositories of Holter recordings captured at the onset of the arrhythmia, and a second from OHCA patients obtained minutes after the onset of the arrest. Data was partitioned patient-wise into training (80%) to design the classifiers, and test (20%) to report the results. The proposed architecture was compared to 1D-CNN only deep learners, and to a classical approach based on VF-detection features and a support vector machine (SVM) classifier. The algorithms were evaluated in terms of balanced accuracy (BAC), the unweighted mean of the sensitivity (Se) and specificity (Sp). The BAC, Se, and Sp of the architecture for 4-s ECG segments was 99.3%, 99.7%, and 98.9% for the public data, and 98.0%, 99.2%, and 96.7% for OHCA data. The proposed architecture outperformed all other classifiers by at least 0.3-points in BAC in the public data, and by 2.2-points in the OHCA data. The architecture met the 95% Sp and 90% Se requirements of the American Heart Association in both datasets for segment lengths as short as 3-s. This is, to the best of our knowledge, the most accurate VF detection algorithm to date, especially on OHCA data, and it would enable an accurate shock no shock diagnosis in a very short time.This study was supported by the Ministerio de Economía, Industria y Competitividad, Gobierno de España (ES) (TEC-2015-64678-R) to UI and EA and by Euskal Herriko Unibertsitatea (ES) (GIU17/031) to UI and EA. The funders, Tecnalia Research and Innovation and Banco Bilbao Vizcaya Argentaria (BBVA), provided support in the form of salaries for authors AP, AA, FAA, CF, EG, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the author contributions section

Intervención no farmacológica como estrategia para favorecer el control de la hipertensión arterial y mejorar el cumplimiento antihipertensivo

ResumenObjetivoComprobar la eficacia de una intervención mediante una revista educacional en el cumplimiento antihipertensivo de la hipertensión arterial (HTA) no controlada.DiseñoEstudio clínico controlado, aleatorizado y multicéntrico.EmplazamientoOchenta y siete Centros de Salud de España.ParticipantesSe incluyeron 450 pacientes hipertensos diagnosticados de HTA no controlada.IntervenciónSe formaron 2 grupos con 225 individuos: a) grupo de intervención (GI), los que recibieron una revista educacional domiciliaria bimensual y b) grupo de control (GC), que tuvieron práctica clínica habitual.Mediciones principalesEl cumplimiento se midió mediante monitores electrónicos (MEMS-Aardex). Se calculó el porcentaje de cumplimiento, el porcentaje de cumplidores del total de dosis y de días en los que tomaba una dosis y el NNT (number needed to treat 'número de pacientes que es necesario tratar'). Se definió cumplidor un consumo del 80 al 110%. Se calculó la presión arterial media y los porcentajes de los controlados.ResultadosConcluyeron 393 individuos (edad: 62,4 años [desviación estándar de 11,6 años]), 196 pacientes del GI y 197 pacientes del GC. Ciento ochenta y cuatro eran varones (46,8%).Fueron cumplidores del total de las dosis tomadas el 83,2% en el GI (del 78 al 88,4%) y el 49,2% del GC (IC del 95%: del 42,2 al 56,2%) (p=0,0001) y fueron cumplidores diarios el 74% del GI (IC del 95%: del 67,9 al 80,1%) y el 42,6% del GC (IC del 95%: del 35,7 al 49,5%) (p=0,0001).El control de la HTA fue del 81,6% en el GI (IC del 95%: del 76,2 al 86,5%) y del 56,3% en el GC (IC del 95%: del 49,4 al 63,2%). El NNT con la intervención fue de 3,3 pacientes.ConclusionesEl incumplimiento del tratamiento fue muy alto. La revista educacional es una estrategia eficaz para disminuir el incumplimiento y mejorar el grado de control de la HTA.AbstractObjetiveTo evaluate the efficacy of an intervention by means of an educational magazine on treatment compliance in uncontrolled arterial hypertension (AHT).DesignControlled, randomised clinical trial.Setting87 primary care centres. Spain.ParticipantsA total of 450 patients with uncontrolled hypertension were included.InterventionTwo groups of 225 patients were formed: 1) Control group (CG): standard health intervention; 2) Intervention Group (IG): received a twice monthly educational magazine at home.Main measurementsCompliance was measured using the Medication Event Monitoring System (MEMS-Aardex). Compliance rate (CR) was recorded. Compliers were defined as individuals with a treatment compliance of 80–110%. The percentage of compliers, the mean percentage of doses taken and the percentage of patients taking the medication at the correct times were estimated. The mean blood pressures (BPs) and the percentage of controlled patientswere calculated. The number needed to treat (NNT) was calculated.ResultsA total of 393 individuals were evaluable (Age: 62.4 years), 196 in the IG and 197 in the CG. There were 83.2% (95% CI 78–88.4) and 49.2% (95% CI 42.2–56.2) (P=0.0001) of overall compliers in the IG and CG, respectively and 74% (95% CI: 67.9–80.1) and 42.6% (95% CI=35.7–49.5) (P=0.0001) of correct times compliers. A total of 81.6% (95% CI=76.2–86.5%)) were controlled in the IG and 56.3% (95% CI=49.4–63.2) in the CG. The NNT was 3.3 patients.ConclusionsTherapeutic non-compliance was very high. The educational magazine is an effective strategy to improve the compliance and degree of control of the AHT

Aspectos clínico-epidemiológicos del aborto en un hospital de Upata. Estado Bolívar-Venezuela

Introducción. El aborto se ha convertido en un problema de salud pública. Una las causas que podría estar influyendo para su aumento es la falta de información sobre el control prenatal, por lo anterior, este es un tema que no escapa de la realidad y de la práctica médica. Objetivo. Caracterizar clínica y epidemioló-gicamente el aborto. Materiales y Métodos. Estudio observacional, descriptivo, retrospectivo, realizado en el Hospital Gervasio Vera Custodio Upata- Estado Bolívar, Venezuela, durantel periodo comprendido de enero a diciembre de 2013. Se recolecto datos de 207 historias clínicas de mujeres con diagnóstico de aborto. En el análisis estadístico se aplicó la prueba chi2 de Pearson. Resultados. Se encontró que la edad prevalente de aborto fue de 21 a 30 años con 42%. La edad gestacional más frecuente de las pacientes fue de 1 a 8 semanas con 50%. De estas 93,5% no cumplieron control prenatal. El tipo de aborto más frecuente fue espontáneo con 98,5%. Se realizó legrado uterino a 97%, de las cuales, 8,5% presentaron complicaciones. Se encontraron diferencias estadísticamente significativas al relacionar la edad materna con la edad gestacional. Conclusiones. Existió alta prevalencia de aborto espontáneo en el grupo de 21 a 30 años de edad, presentados entre las semanas 1 a 8 de gestación. La técnica más segura fue el legrado uterino. Finalmente, se encontró bajo cumplimiento del control prenatal

Bullying among adolescent attending school: validation of the nursing diagnosis “risk of violence directed to others”

La adolescencia es una etapa en la cual surgen una serie de cambios físicos, psicológicos y sociales, que  contribuyen a la formación de la personalidad; la manera en que los adolescentes afrontan estos cambios se  ve reflejada en los comportamientos de permisibilidad y violencia que ellos exteriorizan ante las diversas  situaciones de la vida cotidiana. Objetivo: validar el diagnóstico de enfermería “riesgo de violencia dirigida a  otros”, en adolescentes escolarizados. Método: estudio de corte transversal, donde la población eran  adolescentes de una institución media educativa del municipio de Rionegro (Santander, Colombia). La  variable principal fue “riesgo de violencia dirigida a otros”, la recolección de la información se hizo por medio de un instrumento de valoración de tamizaje del adolescente escolarizado. La validez clínica del diagnóstico,  se realizó mediante análisis de factores y análisis Rasch. Resultados: la población conformada por 300  adolescentes, la mediana de edad fue de 14 años, el 58,67% correspondió al género femenino. Los ítems que  ajustaron al modelo de análisis Rasch se encuentran con un INFIT que oscila entre 0,85 el menor y 1,24 el  mayor, y el OUTFIT que oscila entre 0,65 el menor y 1,77 el mayor. Muestra que las mujeres son más  agresoras que los varones, con una media de 1,53 de riesgo de violencia para las mujeres y una media de  1,03 para los hombres, con una probabilidad p=0,0006. Conclusión: validar clínicamente los diagnósticos de  enfermería, aporta a la evidencia y el crecimiento de la profesión como ciencia del cuidado.    Adolescence is a stage in which a series of physical, psychological and social factors arise which contribute to  the personality shaping;, the way in which adolescents face these changes are reflected in the permissibility  and violence behaviors they externalize to various situations of everyday life. Objective: to validate the  nursing diagnosis “risk of violence directed to others” among adolescents attending school. Method: a  cross-sectional study, where the population was teenagers from a Middle School in Rionegro (Santander,  Colombia). The main variable was the “risk of violence directed at others”, the data collection was carried out using an assessment screening instrument for the adolescent attending school. The clinical validity of the  diagnosis, was performed using factor analysis and Rasch analysis. Results: the population comprised 300  adolescents, the median age was 14 years, and 58.67% were female. The items that fitted the Rasch model  analysis with a INFIT are ranging between 0.85 the lowest and 1.24 the the highest, and OUTFIT ranging  between 0.65 the lowest and 1.77 the highest. It shows that women are more assailant than males, with a mean of 1.53 risk of violence for women and an average of 1.03 for men, with a probability p=0.0006.  Conclusion: clinical validation of nursing diagnoses, contributes to the evidence and the growth of the  profession as a science of care

Clinical Characteristics and Electrophysiological Mechanisms Underlying Brugada ECG in Patients With Severe Hyperkalemia

[EN] Background-Several metabolic conditions can cause the Brugada ECG pattern, also called Brugada phenotype (BrPh). We aimed to define the clinical characteristics and outcome of BrPh patients and elucidate the mechanisms underlying BrPh attributed to hyperkalemia. Methods and Results-We prospectively identified patients hospitalized with severe hyperkalemia and ECG diagnosis of BrPh and compared their clinical characteristics and outcome with patients with hyperkalemia but no BrPh ECG. Computer simulations investigated the roles of extracellular potassium increase, fibrosis at the right ventricular outflow tract, and epicardial/endocardial gradients in transient outward current. Over a 6-year period, 15 patients presented severe hyperkalemia with BrPh ECG that was transient and disappeared after normalization of their serum potassium. Most patients were admitted because of various severe medical conditions causing hyperkalemia. Six (40%) patients presented malignant arrhythmias and 6 died during admission. Multiple logistic regression analysis revealed that higher serum potassium levels (odds ratio, 15.8; 95% CI, 3.1-79; P=0.001) and male sex (odds ratio, 17; 95% CI, 1.05-286; P=0.045) were risk factors for developing BrPh ECG in patients with severe hyperkalemia. In simulations, hyperkalemia yielded BrPh by promoting delayed and heterogeneous right ventricular outflow tract activation attributed to elevation of resting potential, reduced availability of inward sodium channel conductance, and increased right ventricular outflow tract fibrosis. An elevated transient outward current gradient contributed to, but was not essential for, the BrPh phenotype. Conclusions-In patients with severe hyperkalemia, a BrPh ECG is associated with malignant arrhythmias and all-cause mortality secondary to resting potential depolarization, reduced sodium current availability, and fibrosis at the right ventricular outflow tract.This work was funded in part by the CIBERCV (Centro de Investigacion Biomedica en Red Enfermedades Cardiovasculares), Instituto de Salud Carlos III (PI14/00857, DTS16/0160, PI17/1059, PI01106), Spanish Ministry of Ecomomy (TEC2013-46067-R) and the ERDF (European Regional Development Fund).Rivera-Juárez, A.; Hernández-Romero, I.; Puertas, C.; Zhang-Wang, S.; Sánchez-Álamo, B.; Martins, R.; Figuera, C.... (2019). Clinical Characteristics and Electrophysiological Mechanisms Underlying Brugada ECG in Patients With Severe Hyperkalemia. Journal of the American Heart Association. 8(3):1-15. https://doi.org/10.1161/JAHA.118.010115S11583Brugada, P., & Brugada, J. (1992). 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