Vergara I

StAR: a simple tool for the statistical comparison of ROC curves

BackgroundAs in many different areas of science and technology, most important problems in bioinformatics rely on the proper development and assessment of binary classifiers. A generalized assessment of the performance of binary classifiers is typically carried out through the analysis of their receiver operating characteristic (ROC) curves. The area under the ROC curve (AUC) constitutes a popular indicator of the performance of a binary classifier. However, the assessment of the statistical significance of the difference between any two classifiers based on this measure is not a straightforward task, since not many freely available tools exist. Most existing software is either not free, difficult to use or not easy to automate when a comparative assessment of the performance of many binary classifiers is intended. This constitutes the typical scenario for the optimization of parameters when developing new classifiers and also for their performance validation through the comparison to previous art.ResultsIn this work we describe and release new software to assess the statistical significance of the observed difference between the AUCs of any two classifiers for a common task estimated from paired data or unpaired balanced data. The software is able to perform a pairwise comparison of many classifiers in a single run, without requiring any expert or advanced knowledge to use it. The software relies on a non-parametric test for the difference of the AUCs that accounts for the correlation of the ROC curves. The results are displayed graphically and can be easily customized by the user. A human-readable report is generated and the complete data resulting from the analysis are also available for download, which can be used for further analysis with other software. The software is released as a web server that can be used in any client platform and also as a standalone application for the Linux operating system.ConclusionA new software for the statistical comparison of ROC curves is released here as a web server and also as standalone software for the LINUX operating system.

A Knowledge-Based Potential with an Accurate Description of Local Interactions Improves Discrimination between Native and Near-Native Protein Conformations

The correct discrimination between native and near-native protein conformations is essential for achieving accurate computer-based protein structure prediction. However, this has proven to be a difficult task, since currently available physical energy functions, empirical potentials and statistical scoring functions are still limited in achieving this goal consistently. In this work, we assess and compare the ability of different full atom knowledge-based potentials to discriminate between native protein structures and near-native protein conformations generated by comparative modeling. Using a benchmark of 152 near-native protein models and their corresponding native structures that encompass several different folds, we demonstrate that the incorporation of close non-bonded pairwise atom terms improves the discriminating power of the empirical potentials. Since the direct and unbiased derivation of close non-bonded terms from current experimental data is not possible, we obtained and used those terms from the corresponding pseudo-energy functions of a non-local knowledge-based potential. It is shown that this methodology significantly improves the discrimination between native and near-native protein conformations, suggesting that a proper description of close non-bonded terms is important to achieve a more complete and accurate description of native protein conformations. Some external knowledge-based energy functions that are widely used in model assessment performed poorly, indicating that the benchmark of models and the specific discrimination task tested in this work constitutes a difficult challenge.

Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression

BackgroundRecent evidence from global studies of gene expression indicates that transcriptomes are more complex than expected. Xenopus has been typically used as a model organism to study early embryonic development, particularly dorso-ventral patterning. In order to identify novel transcripts involved in dorso-ventral patterning, we compared dorsal and ventral transcriptomes of Xenopus tropicalis at the gastrula stage using serial analysis of gene expression (SAGE).ResultsOf the experimental tags, 54.5% were confidently mapped to transcripts and 125 showed a significant difference in their frequency of occurrence between dorsal and ventral libraries. We selected 20 differentially expressed tags and assigned them to specific transcripts using bioinformatics and reverse SAGE. Five mapped to transcripts with known dorso-ventral expression and the frequency of appearance for these tags in each library is in agreement with the expression described by other methods. The other 15 tags mapped to transcripts with no previously described asymmetric expression along the dorso-ventral axis. The differential expression of ten of these novel transcripts was validated by in situ hybridization and/or RT-PCR. We can estimate that this SAGE experiment provides a list of at least 86 novel transcripts with differential expression along the dorso-ventral axis. Interestingly, the expression of some novel transcripts was independent of β-catenin.ConclusionsOur SAGE analysis provides a list of novel transcripts with differential expression in the dorso-ventral axis and a large number of orphan tags that can be used to identify novel transcripts and to improve the current annotation of the X. tropicalis genome.

Unidad de dolor torácico: primera experiencia en Chile

In large series, nearly 60% of admissions forsuspected acute coronary syndrome (ACS) had a non-coronary etiology of the pain. However,short term mortality of non recognized ACS patients, mistakenly discharged from the emergencyroom is at least twice greater than the expected if they would had been admitted. The concept ofa chest pain unit (CPU) is a methodological approach developed to address these issues.

Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile

The thirteen autosomal STR loci of the CODIS system were typed from DNA of 732 unrelated male individuals sampled from different locations in Chile. This is the first report of allele frequencies for the thirteen STRs loci defined in the CODIS system from the Chilean population.

Terapia de resincronización en pacientes con insuficiencia cardiaca: experiencia acumulada de 10 años

BACKGROUND Multiple randomized trials support the clinical benefits of cardiac resynchronization therapy (CRT) in patients with heart failure (HF) and ventricular dyssynchrony. Since the year 2000 this therapy has been increasingly used in Chile. AIM To describe the clinical characteristics and follow-up of HF patients undergoing CRT in a single Chilean university hospital during the last 10 years. PATIENTS AND METHODS All patients undergoing CRT between 2000 and 2010 in our university hospital were included. Clinical and echocardiographic data were extracted from medical records and mortality causes were obtained from the National Identification Service. RESULTS A total of 252 patients underwent CRT during the study period. Seventy five percent were in New York Heart Associatin (NYHA) functional class III and mean ejection fraction was 29 ± 10%. Complete left bundle branch block was present in 55% and 20% had permanent atrial fibrillation (AF). Mean survival was 86% at 1 year and 82% of patients in NYHA class III-IV improved at least one functional class. Survival was poorer in patients with ischemic etiology (hazard ratio (HR) 1.48), functional class IV (HR 2.2), right bundle branch block (RBBB) (HR 3.1) and AF (HR 3.4). No survival differences were observed between patients with and without an implanted cardiodefibrillator. CONCLUSIONS This series show good clinical outcomes, comparable to those reported in randomized trials. Predictors of worse survival included an ischemic etiology, functional class IV, RBBB and AF. Patients with a defibrillator had no better survival, which could be relevant in countries with limited health care resources.

Rehabilitación cardiovascular y ejercicio en prevención secundaria

Exercise and cardiac rehabilitation are indications with type I A evidence in most secondary cardiovascular prevention guidelines. Rehabilitation programs not only include exercise but also provide integral care and education about cardiovascular risk factors. However there is a paucity of such programs in Chile. Moreover there is a lack of awareness about the benefits of exercise and there is lack of knowledge about the details of exercise prescription in secondary prevention. Therefore, the divulgation of this knowledge is of utmost importance.

Impacto de un programa de rehabilitación cardiovascular fase II sobre la calidad de vida de los pacientes

Antecedentes: La rehabilitación cardiovascular (RCV) ha demostrado mejorar la capacidad física (CF) y la calidad de vida. La relación de estos aspectos ha sido escasamente reportada en Chile. Objetivos: 1) Determinar el impacto de la RCV fase II sobre la calidad de vida, medida por la encuesta SF36 y, 2) determinar qué factores, relacionados con el paciente, pueden incidir en esta relación. Método: Estudio prospectivo en sujetos que completaron 36 sesiones de un programa de RCV y Prevención Secundaria (PREV2). Se registraron al ingreso y final de la RCV: antecedentes médicos, factores de riesgo cardiovascular (CV), parámetros antropométricos, previsión de salud, CF (determinada por los metros caminados en test de marcha de 6 minutos-TM6) y puntaje en la encuesta SF36. Resultados: 277 sujetos (78% hombres, edad 59 años). Hubo una mejoría significativa en: a) los metros caminados (diferencia final/inicial= 56 metros, p<0.0001), b) puntaje de salud física (68 vs 79; p<0.0001), c) salud emocional (68 vs 78, p<0.0001) del SF36. Los hombres caminaron más metros promedio (p<0.0001). Hubo una asociación significativa entre los deltas del TM6 final-inicial y SF36 final-inicial, sólo para salud física (p<0.01). Por un aumento de 10 metros caminados en el TM6 final se incrementa el puntaje de la SF36 para salud física (Hombres: 0.38/ Mujeres: 1.52). La mejoría en la salud emocional sólo se asoció significativamente con los cambios en la salud física (p<0.0001). Conclusión: Los pacientes que asisten a un programa de RCV mejoran significativamente su capacidad aeróbica, y su percepción de salud física y emocional. María José Bustamante1, Mónica Acevedo1, Giovanna Valentino1, 2, Cinthia Casasbellas1, María José Saavedra1, Marcela Adasme1, Lorena Orellana1, Ismael Vergara1, Ramón Corbalán1, Carlos Navarrete3.

Tormenta eléctrica en síndrome de Brugada tratada exitosamente con infusión de isoproterenol

We report A 22 years old male who experienced several episodes of syncope within a time frame of few hours. In the emergency room, multiple ventricular fibrillation episodes where documented along with a type 1 Brugada ECG pattern. Isoproterenol in continuous infusion was started, which normalized the ECG pattern and avoided the recurrence of arrhythmias. The patient was implanted with an automated defibrillator and discharged 3 days after admission.We report a 22-year-old male who experienced several episodes of syncope within a timeframe of few hours. In the emergency room, multiple ventricular fibrillation episodes where documented along with a type 1 Brugada ECG pattern. Isoproterenol in continuous infusion was started, normalizing the ECG and avoiding further arrhythmia recurrences. The patient was implanted with an automated defibrillator and discharged 3 days after admission.