Classification and Clustering on Microarray Data for Gene Functional Prediction Using R.

Gene expression data (microarrays and RNA-sequencing data) as well as other kinds of genomic data can be extracted from publicly available genomic data. Here, we explain how to apply multivariate cluster and classification methods on gene expression data. These methods have become very popular and are implemented in freely available software in order to predict the participation of gene products in a specific functional category of interest. Taking into account the availability of data and of these methods, every biological study should apply them in order to obtain knowledge on the organism studied and functional category of interest. A special emphasis is made on the nonlinear kernel classification methods.

[Influence of bullying on the quality of life perception of Chilean students]. / Bullying y calidad de vida relacionada con la salud en adolescentes escolares chilenos.

BACKGROUND: Bullying has a negative impact on the perception of adolescents of their quality of life. AIM: To analyze the association between being bullied and health related quality of life in Chilean adolescents. MATERIAL AND METHODS: The bullying module of the KIDSCREEN 52 survey and the KIDSCREEN 10 survey to assess health related quality of life were applied to 7737 students aged 10 to 18 years. Social and demographic data, information about disability and type of school were also gathered. RESULTS: Fifteen percent of surveyed students were bullied. A lower quality of life perception increased by a factor of 2.6 among bullied students. It also increased by a factor of 4.4 among students with a low self-esteem, by a factor of 3.1 among those who perceived their health status as regular or bad and by a factor of 1.4 among women. CONCLUSIONS: Bullying is associated with a lower quality of life perception among Chilean students.

Bullying y calidad de vida relacionada con la salud en adolescentes escolares chilenos / Influence of bullying on the quality of life perception of Chilean students

Background: Bullying has a negative impact on the perception of adolescents of their quality of life. Aim: To analyze the association between being bullied and health related quality of life in Chilean adolescents. Material and Methods: The bullying module of the KIDSCREEN 52 survey and the KIDSCREEN 10 survey to assess health related quality of life were applied to 7737 students aged 10 to 18 years. Social and demographic data, information about disability and type of school were also gathered. Results: Fifteen percent of surveyed students were bullied. A lower quality of life perception increased by a factor of 2.6 among bullied students. It also increased by a factor of 4.4 among students with a low self-esteem, by a factor of 3.1 among those who perceived their health status as regular or bad and by a factor of 1.4 among women. Conclusions: Bullying is associated with a lower quality of life perception among Chilean students.

[Depressive symptoms and work-related stress in Chilean workers: differential conditions for males and females]. / Síntomas depresivos y distrés laboral en trabajadores chilenos: condiciones diferenciales para hombres y mujeres.

This article assessed depressive symptoms associated with work-related psychosocial risk factors according to gender in Chile, using the demand-control model (Karasek) and effort-reward imbalance (Siegrist). A cross-sectional study was conducted in a random sample of 3,010 workers (35% female and 65% male) from the country. Data analysis determined prevalence and associations through various statistical techniques (χ2, logistic regression). Exposure to psychosocial risk factors at work and prevalence of depressive symptoms were higher in women than men (15% vs. 5%). The adjusted analysis highlighted that female workers exposed to Isostrain (OR = 2.34; 95%CI: 1.42-3.85) and low rewards (OR = 2.13; 95%CI: 1.41-3.21) and male workers exposed to psychological demands (OR = 3.04; 95%CI: 1.94-4.76) and effort-reward imbalance (OR = 2.19; 95%CI: 1.39-3.46) had increased risk of depressive symptoms. Exposure to work-related psychosocial risk factors was associated with depressive symptoms in Chilean workers. Effective prevention in key aspects of work organization is thus needed.

Sintomas depresivos y distres laboral en trabajadores chilenos: condiciones diferenciales para hombres y mujeres / Depressive symptoms and work-related stress in Chilean workers: differential conditions for males and females / Sintomas depressivos e estresse em trabalhadores chilenos: condicoes diferenciais para homens e mulheres

El objetivo fue evaluar sintomatología depresiva, asociada a factores de riesgo psicosocial laboral según sexo en Chile, mediante los modelos demanda-control (Karasek) y desequilibrio esfuerzo-recompensas (Siegrist). El estudio fue transversal con una muestra aleatoria de 3010 trabajadores asalariados (35% mujeres y 65% hombres) de todo el país. Se determinó prevalencias y asociaciones a través de diversas técnicas estadísticas (eg. χ 2 ; regresión logística). La exposición a factores de riesgo psicosocial laboral y la prevalencia de sintomatología depresiva es mayor en mujeres que en hombres (15% vs. 5%). En los análisis ajustados destaca que mujeres expuestas a Isostrain (OR = 2,34; IC95%: 1,42-3,85) y bajas recompensas (OR = 2,13; IC95%: 1,41-3,21), y hombres expuestos a demandas psicológicas (OR = 3,04; IC95%: 1,94-4,76) y desequilibrio esfuerzos-recompensas (OR = 2,19; IC95%: 1,39-3,46), tienen una chance aumentada de sintomatología depresiva al compararse con los no expuestos. La exposición a factores de riesgo psicosocial laboral se asoció con síntomas depresivos en trabajadores chilenos. Resulta clave generar prevención en aspectos de la organización del trabajo.

This article assessed depressive symptoms associated with work-related psychosocial risk factors according to gender in Chile, using the demand-control model (Karasek) and effort-reward imbalance (Siegrist). A cross-sectional study was conducted in a random sample of 3,010 workers (35% female and 65% male) from the country. Data analysis determined prevalence and associations through various statistical techniques (χ 2 , logistic regression). Exposure to psychosocial risk factors at work and prevalence of depressive symptoms were higher in women than men (15% vs. 5%). The adjusted analysis highlighted that female workers exposed to Isostrain (OR = 2.34; 95%CI: 1.42-3.85) and low rewards (OR = 2.13; 95%CI: 1.41-3.21) and male workers exposed to psychological demands (OR = 3.04; 95%CI: 1.94-4.76) and effort-reward imbalance (OR = 2.19; 95%CI: 1.39-3.46) had increased risk of depressive symptoms. Exposure to work-related psychosocial risk factors was associated with depressive symptoms in Chilean workers. Effective prevention in key aspects of work organization is thus needed.

O objetivo foi avaliar os sintomas depressivos associados com fatores de risco ocupacionais psicossociais, por sexo, no Chile, por meio do modelo demanda-controle (Karasek) e desequilíbrio esforço-recompensa (Siegrist). O estudo foi transversal, com uma amostra aleatória de 3.010 empregados (35% mulheres e 65% homens) em todo o país. Prevalência e associações foram determinados por diversas técnicas estatísticas (eg. χ 2 ; regressão logística). A exposição ao fatores de risco ocupacionais psicossociais e prevalência de sintomas depressivos é maior em mulheres do que em homens (15% vs. 5%). Análise ajustada salienta que as mulheres expostas a Isostrain (OR = 2,34; IC95%: 1,42-3,85) e baixa recompensa (OR = 2,13; IC95%: 1,41-3,21) e homens expostos a demandas psicológicas (OR = 3,04; IC95%: 1,94-4,76) e desequilíbrio esforço-recompensa (OR = 2,19; IC95%: 1,39-3,46) têm chance maior de sintomas depressivos quando comparado com o não exposto. A exposição a fatores de risco ocupacionais psicossociais foi associada com sintomas depressivos em trabalhadores chilenos. A geração de cuidados preventivos em aspectos de organização do trabalho é fundamental.

Calidad de vida relacionada con la salud en adolescentes chilenos, según autopercepción de discapacidad, enfermedad o problemas de salud crónicos / Health-Related Quality of Life according to perceivedmorbidity in Chilean adolescents

Objetivo. Relacionar la morbilidad percibida de adolescentes chilenos con su calidad de vida relacionada con la salud. (CVRS). Método. Análisis comparativo en adolescentes chilenos con y sin morbilidad percibida, según la Clasificación Internacional de Enfermedades (CIE10). Información obtenida a través de un estudio nacional, aplicando un cuestionario de medición de calidad de vida relacionada con salud (KIDSCREEN-52), adaptado culturalmente y validado en Chile en 2009. Se analizó por las variables de sexo, edad, tipo de establecimiento escolar y zonas del país. Se analizó las 10 dimensiones de calidad de vida del KIDSCREEN que se expresan como puntajes Rasch. Para el análisis de las diferencias de medias entre las variables se utilizó la prueba de Chi2 y t de Student. Se aplicó el software STATA 10.0 y SAS 9.1 Resultados. Se determina la morbilidad autopercibida a nivel nacional, la cual es más frecuente en mujeres, adolescentes menores, estudiantes de establecimientos escolares particulares y zona norte del país. El cuestionario demuestra que los puntajes Rasch más bajos de CVRS se alcanzan en adolescentes con morbilidad percibida. Conclusión. Las peores CVRS en adolescentes con morbilidad autopercibida , fue en mujeres, adolescentes mayores, del sector público de la educación y de la zona norte del país. La información es un aporte nuevo y útil para futuros programas de salud juveniles del sector público.

Objective. To correlate Chilean adolescents’ perceived morbidity with their Health-Related Quality of Life (HRQoL). Method. Comparative analysis of Chilean adolescents with and without perceived morbidity classified according to the International Classification of Diseases (ICD10). Information was collected through a national study, applying the KIDSCREEN-52 questionnaire, adapted culturally and validated in Chile in 2009. The ten quality life dimensions, expressed as Rasch points, were analyzed by sex, age, type of school and zones of the country. To analyze the mean differences between the variables, the Chi squared and Student’s t-test were used. The software used were STATA 10.0 and SAS 9. Results. The self perceived morbidity was assessed across the country and was more frequent in women, adolescents of younger age, students from private schools and from the north zone of the country. The lowest HRQoL Rasch points were determined in adolescents with perceived morbidity. Conclusion. The worst HRQoL in adolescents was found in those with self perceived morbidity, women, higher adolescent age, students from public schools and from the north of the country. This finding is new and a useful contribution for future national public health programs concerning adolescents.

Psychosocial risk at work and hazardous alcohol consumption among Chile's working adults.

OBJECTIVE: Karasek's demand-control model and Siegrist's effort-reward imbalance model have accumulated solid evidence regarding the associations between exposure to psychosocial risk at work (PSRW) and mental health of workers. However, there is scarce such evidence with regard to its associations with alcohol consumption. This study proposed to estimate the associations between exposure to PSRW and hazardous alcohol consumption (HAC) in Chile's working adult population. METHOD: The study was cross-sectional and a nationally representative survey was applied to 3,010 workers (65% male and 35% female, ages 20 to 65). The analysis included prevalences and logistic regression controlling for covariables. RESULTS: The adjusted analyses show that male workers exposed to low social support (OR=1.47; 95% CI:1.14-1.89), low reward (OR=1.38; 95% CI:1.07-1.78) and effort-reward imbalance (OR=1.34; 95% CI:1.04-1.73) have a higher chance of presenting with HAC compared to those who are not exposed. Female workers exposed to effort-reward imbalance (OR=2.34; 95% CI:1.10-5.58) have twice the risk of HAC compared with their reference group. CONCLUSION: This study shows evidence of the associations between HAC and exposure to a set of psychosocial risk factors from the Karasek and Siegrist models. For future research, it is recommended that HAC and PSRW factors be examined in a longitudinal study in order to control for possible confounding effects on these associations.

How should we assess the fit of Rasch-type models? Approximating the power of goodness-of-fit statistics in categorical data analysis.

We investigate the performance of three statistics, R1, R2 (Glas in Psychometrika 53:525-546, 1988), and M2 (Maydeu-Olivares & Joe in J. Am. Stat. Assoc. 100:1009-1020, 2005, Psychometrika 71:713-732, 2006) to assess the overall fit of a one-parameter logistic model (1PL) estimated by (marginal) maximum likelihood (ML). R1 and R2 were specifically designed to target specific assumptions of Rasch models, whereas M2 is a general purpose test statistic. We report asymptotic power rates under some interesting violations of model assumptions (different item discrimination, presence of guessing, and multidimensionality) as well as empirical rejection rates for correctly specified models and some misspecified models. All three statistics were found to be more powerful than Pearson's X(2) against two- and three-parameter logistic alternatives (2PL and 3PL), and against multidimensional 1PL models. The results suggest that there is no clear advantage in using goodness-of-fit statistics specifically designed for Rasch-type models to test these models when marginal ML estimation is used.

Cambios en el manejo intrahospitalario del infarto del miocardio en hospitales chilenos / Changes in the in-hospital treatment of the acute myocardial infarction in chilean hospitals

Antecedentes: En comunicaciones anteriores se han descrito los cambios en el tratamiento y la evolución del infarto del miocardio (IAM) intrahospitalario durante 2 período de registro en Chile. Objetivo: Evaluar los cambios en el tratamiento farmacológico y las terapias de reperfusión en pacientes con IAM que ingresaron durante 2001 en la red GEMI. Métodos: El registro 2001 (R3) se efectuó entr marzo y diciembre en 23 hospitales de Santiago y regiones. Fue comparado con los registros 93-95 (R1) y 97-98 (R2). Se recolectó información sobre características demográficas, el tratamiento y la evolución intrahospitalaria de los pacientes que ingresaron con el diagnostico de IAM. Resultados: En R3 se incluyeron 1.091 pacientes, cuya edad promedio fue 63 ± 13 años. El 70,4 por ciento fueron hombres. La frecuencia de uso de los medicamentos en R1, R2 y R3 fue respectivamente: aspirina 93 por ciento, 96,1 por ciento y 94,7 por ciento (p=ns); I-ECA 32 por ciento, 53 por ciento y 60 por ciento (p=ns); bloqueadores 37 por ciento, 55,2 por ciento y 60,9 por ciento (p=ns); heparina 59 por ciento, 55 por ciento y 43,5 por ciento (p=ns): nitratos iv 59 por ciento, 67,6 por ciento y 63,7 por ciento (p=ns); antagonista del calcio 23 por ciento, 12,4 por ciento y 6,2 por ciento (p <0,01); trombolíticos 33 por ciento, 33,7 por ciento y 32, por ciento. La angioplastía primaria no se efectuó en R1, pero R2 y R3 fue utilizada en el 9,5 por ciento y el 7,5 por ciento de los pacientes respectivamente. La mortalidad intrahospitalaria fue de 11,6 por ciento durante 2001, comparada con el 10,8 por ciento y el 13,4 por ciento obtenida en los registros 97-98 y 93-95. Conclusión: Se aprecia un aumento de la utilización de los I-ECA y (bloqueadores, fármacos de demostrada eficacia para reducir mortalidad en el IAM. Es racional la reducción del uso del calcio antagonista y probablemente la de antiarrítmicos. No se modifica el empleo de trombolíticos y la angioplastía primaria no aumenta debido a que está limitada a algunos hospitales. Se debe continuar estimulando el uso de terapias que mejoren el pronóstico de los pacientes con IAM, especialmente las orientadas a la reperfusión.

[Reduction of myocardial infarction mortality in Chilean hospitals]. / Reducción de la mortalidad por infarto del miocardio en hospitales chilenos.

BACKGROUND: The characteristics of patients with acute myocardial infarction (MI) admitted to 37 Chilean hospitals (GEMI Registry Group), have been analyzed in the period 1993-1995 and 1997-1998. AIM: To report the changes in hospital mortality between these 2 periods, with a particular emphasis on the impact of treatment. PATIENTS AND METHODS: Between 1993-1995 we collected information from 2,957 patients and between 1997-1998 we registered 1,981 patients with MI. Analysis of the changes in mortality between periods was adjusted by demographic variables, coronary risk factors, MI location, Killip class on admission and the different therapeutic strategies utilized. The effects of different treatments on hospital mortality were adjusted by the previously determined mortality risk variables. RESULTS: Hospital mortality decreased from 13.3% to 10.8% between both periods (Odds Ratio (OR) 0.78, confidence intervals (95%) (CI) 0.65-0.93). A significant reduction in mortality was observed among patients below 60 years of age, in men, in diabetics and in subjects with an infarction classified as Killip class over II. The use of beta blockers (OR 0.65, CI 0.42-0.99) and intravenous nitrates (OR 0.78, CI 0.61-0.99) and the lower use of calcium channel blockers (OR 0.72, CI 0.60-0.87) were significantly associated with a lower mortality. The administration of angiotensin converting enzyme inhibitors was associated with a 29.3% mortality reduction (OR 0.69, CI 0.47-1.02). CONCLUSIONS: There has been a significant reduction in the mortality rate for MI in Chilean hospitals during the 2 registry periods analyzed, which was significant among some high risk patients and was related to treatment changes, according to evidence based guidelines.