GrimoireLab: A toolset for software development analytics.

BACKGROUND: After many years of research on software repositories, the knowledge for building mature, reusable tools that perform data retrieval, storage and basic analytics is readily available. However, there is still room to improvement in the area of reusable tools implementing this knowledge. GOAL: To produce a reusable toolset supporting the most common tasks when retrieving, curating and visualizing data from software repositories, allowing for the easy reproduction of data sets ready for more complex analytics, and sparing the researcher or the analyst of most of the tasks that can be automated. METHOD: Use our experience in building tools in this domain to identify a collection of scenarios where a reusable toolset would be convenient, and the main components of such a toolset. Then build those components, and refine them incrementally using the feedback from their use in both commercial, community-based, and academic environments. RESULTS: GrimoireLab, an efficient toolset composed of five main components, supporting about 30 different kinds of data sources related to software development. It has been tested in many environments, for performing different kinds of studies, and providing different kinds of services. It features a common API for accessing the retrieved data, facilities for relating items from different data sources, semi-structured storage for easing later analysis and reproduction, and basic facilities for visualization, preliminary analysis and drill-down in the data. It is also modular, making it easy to support new kinds of data sources and analysis. CONCLUSIONS: We present a mature toolset, widely tested in the field, that can help to improve the situation in the area of reusable tools for mining software repositories. We show some scenarios where it has already been used. We expect it will help to reduce the effort for doing studies or providing services in this area, leading to advances in reproducibility and comparison of results.

Case-control study about magnitude of exposure to wood smoke and risk of developing lung cancer.

INTRODUCTION: Exposure to biomass combustion products, particularly firewood, has been considered as a potential carcinogen for developing lung cancer. In this regard, current evidence is widely heterogeneous; besides, in most studies, wood smoke exposure is not appropriately quantified, which further complicates the analysis of wood smoke as a potential carcinogen. The aim of the present study was to estimate the risk of developing lung cancer according to the degree of exposure to wood smoke in patients who use firewood for cooking. MATERIAL AND METHODS: We performed a case-control study that included 482 patients with lung cancer (cases) and 592 hospital controls. Exposure to wood smoke was evaluated as a dichotomous variable (i.e. yes or no); in patients with prior wood smoke exposure, an index of exposure in hours per year was calculated (WSEI). Using bivariate and multivariate logistic regression analyses, the odds ratio (OR) between wood smoke exposure and lung cancer were calculated. RESULTS: The ORs for developing lung cancer (raw and adjusted) for a WSEI > 100 h/year were OR 1.55 [95% confidence interval (CI), 1.06-2.26) and OR 2.26 (95% CI, 1.50-3.40), respectively; the ORs (raw and adjusted) for WSEI >300 h/year were OR 1.76 (95% CI, 1.06-2.91) and OR 3.19 (95% CI, 1.83-5.55), respectively. CONCLUSIONS: Exposure to wood smoke is a risk factor for lung cancer; furthermore, this effect maintains a dose-response relationship which has a multiplicative effect with smoking.

Microbiota intestinal en pediatría / Intestinal microbiota in the pediatric population

La microbiota intestinal es el conjunto de millones de microrganismos vivos ubicados en el tracto gastrointestinal. Es indispensable en múltiples funciones del organismo, regulación de la inmunidad, en aspectos nutricionales y procesos de inflamación sistémica entre otros. La disbiosis es la alteración del equilibrio de la microbiota normal, debido a cambios en la composición, funcionamiento, orden o su distribución; esto puede predisponer al individuo a la adquisición de enfermedades gastrointestinales, alérgicas y metabólicas, entre otras. El objetivo del presente artículo es realizar una revisión narrativa de la literatura sobre los conceptos claves de la microbiota intestinal, sus asociaciones fisiopatológicas con desórdenes gastrointestinales, alérgicos y metabólicos en pediatría.

ntestinal microbiota are the millions of living microbial communities that inhabit the gastrointestinal tract. It is essential for multiple functions of the human organism, such as, immune-regulation, in nutritional aspects, and systemic inflammatory processes, among others. Dysbiosis refers to the alteration of the equilibrium of normal microbiota due to shifts in its composition, functioning, order or distribution; this can predispose the individual to develop gastrointestinal, allergic and metabolic diseases among others. The aim of this article was to conduct a narrative review of the literature on the key concepts of intestinal microbiota, and its pathophysiological associations with gastrointestinal, allergic and metabolic disorders in pediatrics.

Ataque al personal de la salud durante la pandemia de COVID-19 en Latinoamérica / Attacks on healthcare workers during the COVID-19 pandemic in Latin America

Resumen En la actualidad los profesionales de la salud son el recurso más valioso con el que cuenta cada país para combatir la enfermedad COVID-19. Las tasas de contagio intrahospitalario son altas y ligadas al acto de atención sanitaria. Las medidas de protección por parte de los empleadores son fundamentales para el cuidado de los que cuidan. La situación de pánico generada por el temor a contraer o transmitir la enfermedad, siendo primeros respondedores en la línea de combate ante la pandemia, ha sido amplificada por varios factores. Cuestiones como presión psicológica, carga laboral, mediatización, aspectos judiciales, desprotección, falta de descanso, nuevos roles, discriminación y agresiones son algunas de las situaciones a las que se los profesionales se deben enfrentar.(Acta Med Colomb 2020; 45. DOI:https://doi.org/10.36104/amc.2020.1975).

Abstract Today, healthcare professionals are a country's most valuable resource for combating COVID-19. Hospital contagion rates are high and linked to the practice of health care. Employers' protective measures are essential in caring for the caregivers. The panic resulting from a fear of contracting or transmitting the disease, with first responders being at the front line of the battle against the pandemic, has been amplified by various factors. Issues such as psychological pressure, workload, media coverage, legal aspects, lack of protection, lack of rest, new roles, discrimination and assaults are some of the situations faced by these professionals.(Acta Med Colomb 2020; 45. DOI:https://doi.org/10.36104/amc.2020.1975).

Accuracy of closed pleural biopsy in the diagnosis of malignant pleural effusion / Exactitud de la biopsia pleural cerrada para el diagnóstico de derrame pleural maligno

ABSTRACT Objective: Previous studies have demonstrated that closed pleural biopsy (CPB) has a sensitivity of less than 60% for diagnosing malignancy. Therefore, controversy has recently emerged regarding the value of CPB as a diagnostic test. Our objective was to assess the accuracy of CPB in diagnosing malignancy in patients with pleural effusion. Methods: This was a prospective 8-year study of individuals who underwent CPB to establish the etiology of pleural effusion. Information on each patient was obtained from anatomopathological reports and medical records. When CPB findings showed malignancy or tuberculosis, the biopsy was considered diagnostic, and that was the definitive diagnosis. In cases in which biopsy histopathological findings were nonspecific, a definitive diagnosis was established on the basis of other diagnostic procedures, such as thoracoscopy, thoracotomy, fiberoptic bronchoscopy, biochemical and cellular measurements in pleural fluid, and/or microbiological tests. The accuracy of CPB was determined with 2 × 2 contingency tables. Results: A total of 1034 biopsies from patients with pleural effusion were studied. Of those, 171 (16.54%) were excluded from the accuracy analysis either because of inadequate samples or insufficient information. The results of the accuracy analysis were as follows: sensitivity, 77%; specificity, 98%; positive predictive value, 99%; negative predictive value, 66%; positive likelihood ratio, 38.5; negative likelihood ratio, 0.23; pre-test probability, 2.13; and post-test probability, 82. Conclusions: CPB is useful in clinical practice as a diagnostic test, because there is an important change from pre-test to post-test probability.

RESUMEN Objetivo: Estudios previos demuestran que la biopsia pleural cerrada (BPC) para diagnóstico de malignidad tiene una sensibilidad menor al 60%, por lo que recientemente ha despertado controversia su valor como prueba diagnóstica. Nuestro objetivo fue evaluar la exactitud de la BPC para diagnóstico de malignidad en pacientes con derrame pleural. Métodos: Estudio prospectivo de 8 años en individuos que se sometieron a la realización de BPC para establecer la etiología del derrame. La información de cada paciente se tomó de los registros de anatomopatología y del expediente clínico. Cuando el resultado de la BPC demostró malignidad o tuberculosis, esto se tomó como biopsia diagnóstica y quedó éste como diagnóstico definitivo. En los casos en que el resultado del estudio histopatológico de la biopsia resultó inespecífico, el diagnóstico definitivo se estableció en base a otros procedimientos diagnósticos, como toracoscopia, toracotomía, fibrobroncoscopia, estudio bioquímico y celular del líquido pleural y/o pruebas microbiológicas. Mediante una tabla de contingencia de 2 × 2 se midieron los indicadores para una prueba diagnóstica. Resultados: Se estudiaron 1034 biopsias de pacientes con derrame pleural, de las cuales se excluyeron 171 (16.54%) por muestra inadecuada o información insuficiente. El desempeño para malignidad fue: sensibilidad, 77%; especificidad, 98%; valores predictivos positivo y negativo, 99% y 66%, respectivamente; índices de probabilidad positivo y negativo, 38.5 y 0.23, respectivamente; probabilidad antes y después de la prueba, 2.13 y 82, respectivamente. Conclusión: La BPC es útil como prueba diagnóstica en la práctica clínica, debido a que produce un cambio importante de la probabilidad antes de la prueba a la probabilidad después de la prueba.

Assessment of IL-28: rs12979860 and rs8099917 Polymorphisms in a Cohort of Cuban Chronic HCV Genotype 1b Patients.

Hepatitis C virus (HCV) is a significant global public health problem with >185 million infections worldwide. A series of genome-wide association studies (GWAS) has identified IL-28B polymorphisms as a predictor of sustained virologic response (SVR), as well as spontaneous clearance in chronic HCV genotype 1 patients. The objective of this work was to evaluate the prevalence of IL-28B rs12979860 and rs8099917 polymorphisms in Cuban chronic HCV patients. The study cohort included 73 chronic HCV patients treated with concomitant administration of CIGB-230 and nonpegylated IFN-α plus ribavirin (non-pegIFN-α/R) antiviral therapy. The genotype distribution of IL-28B rs12979860CC, -CT, and -TT was 29, 41, and 30%, respectively, and the distribution for rs8099917TT, -TG, and -GG was 63, 31, and 5%, respectively. The allele frequencies for rs12979860C and -T alleles were 51 and 49%, respectively, and for rs8099917G and -T alleles, the values were 21 and 79%, respectively. SVR rates were 55, 42, and 35% for rs12979860CC, -CT, and -TT, respectively, and 52, 30, and 25% for rs8099917TT, -GT, and -GG, respectively. The combined assessment of both single nucleotide polymorphisms (SNPs) resulted in 3 major genotypes (rs12979860CC/rs8099917TT, rs12979860CT/rs8099917TT, and rs12979860CT/rs8099917GG) with a frequency of 30.1, 21.9, and 20.5%, respectively. In patients with heterozygous variant rs12979860CT, the additional genotyping of rs8099917 contributed to increase the SVR rate. It is concluded that in Cuban HCV-infected patients, the responder homogeneous variant rs8099917TT is the most frequent genotype. The simultaneous genotyping of 2 IL-28B SNPs could improve the prediction of SVR contributing to better therapeutic decisions and treatment management.

Accuracy of closed pleural biopsy in the diagnosis of malignant pleural effusion.

OBJECTIVE: Previous studies have demonstrated that closed pleural biopsy (CPB) has a sensitivity of less than 60% for diagnosing malignancy. Therefore, controversy has recently emerged regarding the value of CPB as a diagnostic test. Our objective was to assess the accuracy of CPB in diagnosing malignancy in patients with pleural effusion. METHODS: This was a prospective 8-year study of individuals who underwent CPB to establish the etiology of pleural effusion. Information on each patient was obtained from anatomopathological reports and medical records. When CPB findings showed malignancy or tuberculosis, the biopsy was considered diagnostic, and that was the definitive diagnosis. In cases in which biopsy histopathological findings were nonspecific, a definitive diagnosis was established on the basis of other diagnostic procedures, such as thoracoscopy, thoracotomy, fiberoptic bronchoscopy, biochemical and cellular measurements in pleural fluid, and/or microbiological tests. The accuracy of CPB was determined with 2 × 2 contingency tables. RESULTS: A total of 1034 biopsies from patients with pleural effusion were studied. Of those, 171 (16.54%) were excluded from the accuracy analysis either because of inadequate samples or insufficient information. The results of the accuracy analysis were as follows: sensitivity, 77%; specificity, 98%; positive predictive value, 99%; negative predictive value, 66%; positive likelihood ratio, 38.5; negative likelihood ratio, 0.23; pre-test probability, 2.13; and post-test probability, 82. CONCLUSIONS: CPB is useful in clinical practice as a diagnostic test, because there is an important change from pre-test to post-test probability.

Preparation of plasmid DNA-containing liposomes using a high-pressure homogenization--extrusion technique.

High-pressure homogenization-extrusion (HPHE) is a method that can be used for downsizing large lipid vesicles with commercially available instrumentation (e.g., from Avestin Inc., Canada), which covers a full range of processing capacities from laboratory (0.5-3.5 mL) to large-scale continuous (1-1000 L/h) production. Consequently, the feasibility (at the laboratory scale) of using HPHE for producing DNA-loaded liposomes by the conventional dehydration-rehydration method was explored. HPHE-generated small unilamellar vesicles had a mean size in the range of 27-76 nm depending on the number of processing cycles and lipid (PC:DOPE:DOTAP or PC:DOPE:Ethyl-DOPC, 1:0.5:0.5, mol/mol) formulation. The size could be further regulated by the pore size (50 or 100 nm) of the extrusion membrane. Using plasmids for the V3 loop of HIV-1, and the capsid, E1 and E2 of hepatitis C, entrapment yields of 72-98.2% into dehydrated-rehydrated vesicles (DRV) were obtained over a wide range (0.309-2.5 mg) of DNA quantities. Most of the plasmid DNA was retained by liposomes even in the presence of sodium dodecyl sulfate (from 0.05% to 0.3%) and efficiently protected from nuclease-mediated degradation. Although the encapsulation process slightly decreased (in the range of 42.8-65.7%) the relative abundance of plasmid super coiled isoforms, the transfection efficiency of monkey kidney COS-7 cells with the plasmid DNA extracted from liposomes (9+/-0.4%) was similar to that of the non-treated DNA (8.7+/-0.2%), using the commercial SuperFect(R) Transfection Reagent. Also, it was found that an appreciable loss of lipid mass-either associated with the HPHE or the dehydration-rehydration steps-occurs during the liposome manufacturing process. These results at the bench scale are a useful reference for planning pilot or large-scale manufacture of DNA vaccine-containing liposomes.