RESUMO

A common task in bioinformatics is to compare DNA sequences to identify similarities between organisms at the sequence level. An approach to such comparison is the dot-plots, a 2-dimensional graphical representation to analyze DNA or protein alignments. Dot-plots alignment software existed before the sequencing revolution, and now there is an ongoing limitation when dealing with large-size sequences, resulting in very long execution times. High-Performance Computing (HPC) techniques have been successfully used in many applications to reduce computing times, but so far, very few applications for graphical sequence alignment using HPC have been reported. Here, we present G-SAIP (Graphical Sequence Alignment in Parallel), a software capable of spawning multiple distributed processes on CPUs, over a supercomputing infrastructure to speed up the execution time for dot-plot generation up to 1.68× compared with other current fastest tools, improve the efficiency for comparative structural genomic analysis, phylogenetics because the benefits of pairwise alignments for comparison between genomes, repetitive structure identification, and assembly quality checking.

RESUMO

Las neurociencias constituyen un campo de la ciencia que estudia el sistema nervioso desde el funcionamiento neuronal hasta el comportamiento y cómo sus diferentes elementos interactúan. El Centro de Neurociencias de Cuba es la principal institución de investigación de neurociencia en el país, donde fueron identificadas distintas problemáticas asociadas al lanzamiento y gestión de colas de procesamiento de datasets de neurociencias. El procesamiento que se desarrolla sobre sus bases de datos se realiza de forma manual en sus servidores de HPC (High Performance Computer) debido a dificultades tecnológicas y financieras para acceder a los servicios que ofrecen las plataformas internacionales, por lo que los investigadores se ven obligados a programar instrucciones en consola para ejecutar tareas de procesamiento y análisis. El objetivo de la presente investigación fue desarrollar una herramienta que automatice el proceso de gestión de colas y tareas de procesamiento de neurodatos para la plataforma BrainSSys. Se empleó Python como lenguaje de programación, PyQt5 como marco de trabajo y se utilizó el editor de código Sublime Text 3. Se obtuvo como resultado una herramienta que permite automatizar la gestión de las colas de procesamiento en la plataforma BrainSSys. Las pruebas realizadas determinaron la aceptación y la evaluación funcional de la herramienta, siendo en ambos casos de gran valor para la calidad de la propuesta solución(AU)

Neuroscience is a field of science that studies the nervous system from neural functioning to behavior and how its different elements interact. The Cuban Neuroscience Centre is the main neuroscience research institution in the country, where different problems associated with the launch and management of neuroscience dataset processing queues has been identified. The processing of its databases is carried out manually on their HPC (High Performance Computer) servers due to technological and financial difficulties in accessing the services offered by international platforms, so researchers are forced to program instructions on the console to execute processing and analysis tasks. The aim of this research was to develop a tool that automates the queue management process and neurodata processing tasks for the BrainSSys platform. Python was used as programming language, PyQt5 and Sublime Text 3 as framework and code editor respectively. The result is a tool that automates the management of processing queues on the BrainSSys platform. The tests carried out determined the acceptance and functional evaluation of the tool, being in both cases of great value for the quality of the proposed solution(AU)

Assuntos

RESUMO

Transposable elements (TEs) are non-static genomic units capable of moving indistinctly from one chromosomal location to another. Their insertion polymorphisms may cause beneficial mutations, such as the creation of new gene function, or deleterious in eukaryotes, e.g., different types of cancer in humans. A particular type of TE called LTR-retrotransposons comprises almost 8% of the human genome. Among LTR retrotransposons, human endogenous retroviruses (HERVs) bear structural and functional similarities to retroviruses. Several tools allow the detection of transposon insertion polymorphisms (TIPs) but fail to efficiently analyze large genomes or large datasets. Here, we developed a computational tool, named TIP_finder, able to detect mobile element insertions in very large genomes, through high-performance computing (HPC) and parallel programming, using the inference of discordant read pair analysis. TIP_finder inputs are (i) short pair reads such as those obtained by Illumina, (ii) a chromosome-level reference genome sequence, and (iii) a database of consensus TE sequences. The HPC strategy we propose adds scalability and provides a useful tool to analyze huge genomic datasets in a decent running time. TIP_finder accelerates the detection of transposon insertion polymorphisms (TIPs) by up to 55 times in breast cancer datasets and 46 times in cancer-free datasets compared to the fastest available algorithms. TIP_finder applies a validated strategy to find TIPs, accelerates the process through HPC, and addresses the issues of runtime for large-scale analyses in the post-genomic era. TIP_finder version 1.0 is available at https://github.com/simonorozcoarias/TIP_finder.

RESUMO

Three cases of severe odontogenic infections due to nontuberculous mycobacteria (NTM) in Venezuela that were directly associated with dental procedures and the finding of dental unit waterlines (DUWLs) in dental offices that were colonized with mycobacteria species was the reason for assessing the water quality of DUWLs in dental offices in two capital cities in South America, namely, Quito and Caracas. The main water supplies and the water from 143 DUWLs in both cities were sampled and especially checked for contamination with NTM. To measure the overall bacteriological quality of the water also the presence of heterotrophic bacteria, coliform bacteria, and Pseudomonas was determined. Results showed that respectively 3% and 56% of the DUWLs in Quito and Caracas yielded NTM species (up to 1000 colony-forming units (CFU)/mL). Furthermore, high and unacceptable total viable counts of heterotrophic bacteria and/or coliform bacteria and Pseudomonas were detected in 73% of the samples. We conclude that, in both cities, the water in the majority of DUWLs was contaminated with NTM and other potential pathogens, presenting a risk to human health. The detection of NTM in DUWL water with acceptable heterotrophic bacteria counts shows the need to include NTM in water quality testing. Mycobacteria are more resistant to disinfection procedures than other types of vegetative bacteria, and most testing protocols for DUWLs do not assess mycobacteria and thus do not guarantee risk-free water.

Assuntos

RESUMO

INTRODUCTION: Ischemia-reperfusion (I/R) injury of the liver is a common area of interest to transplant and hepatic surgery. Nevertheless, most of the current knowledge of I/R of the liver derives from the hepatocyte and little is known of what happens to the cholangiocytes. Herein, we assess the sequence of early events involved in the I/R injury of the cholangiocytes. METHODS: Sixty Wistar rats were randomized in a SHAM group and I/R group. Serum biochemistry, histopathology, immunohistochemistry, transmission electron microscopy (TEM) and laser capture microdissection (LCM) were used for group comparison. RESULTS: There was peak of alkaline phosphatase 24 h after IR injury, and an increase of aspartate aminotransferase and alanine aminotransferase after 6 h of reperfusion, followed by a return to normal levels 24 h after injury. The I/R group presented the liver parenchyma with hepatocellular degeneration up to 6 h, followed by hepatocellular necrosis at 24 h. TEM showed cholangiocyte injury, including a progressive nuclear degeneration and cell membrane rupture, beginning at 6 h and peaking at 24 h after reperfusion. Cytokeratin-18 and caspase-3-positive areas were observed in the I/R group, peaking at 24-h reperfusion. Anti-apoptotic genes Bcl-2 and Bcl-xl activity were expressed from 6 through 24 h after reperfusion. BAX expression showed an increase for 24 h. CONCLUSIONS: I/R injury to the cholangiocyte occurs from 6 through 24 h after reperfusion and a combination of TEM, immunohistochemistry and LCM allows a better isolation of the cholangiocyte and a proper investigation of the events related to the I/R injury. Apoptosis is certainly involved in the I/R process, particularly mediated by BAX.

RESUMO

One particular class of Transposable Elements (TEs), called Long Terminal Repeats (LTRs), retrotransposons, comprises the most abundant mobile elements in plant genomes. Their copy number can vary from several hundreds to up to a few million copies per genome, deeply affecting genome organization and function. The detailed classification of LTR retrotransposons is an essential step to precisely understand their effect at the genome level, but remains challenging in large-sized genomes, requiring the use of optimized bioinformatics tools that can take advantage of supercomputers. Here, we propose a new tool: Inpactor, a parallel and scalable pipeline designed to classify LTR retrotransposons, to identify autonomous and non-autonomous elements, to perform RT-based phylogenetic trees and to analyze their insertion times using High Performance Computing (HPC) techniques. Inpactor was tested on the classification and annotation of LTR retrotransposons in pineapple, a recently-sequenced genome. The pineapple genome assembly comprises 44% of transposable elements, of which 23% were classified as LTR retrotransposons. Exceptionally, 16.4% of the pineapple genome assembly corresponded to only one lineage of the Gypsy superfamily: Del, suggesting that this particular lineage has undergone a significant increase in its copy numbers. As demonstrated for the pineapple genome, Inpactor provides comprehensive data of LTR retrotransposons' classification and dynamics, allowing a fine understanding of their contribution to genome structure and evolution. Inpactor is available at https://github.com/simonorozcoarias/Inpactor.

RESUMO

Since the commercial introduction of Ion Mobility coupled with Mass Spectrometry (IM-MS) devices in 2003, a large number of research laboratories have embraced the technique. IM-MS is a fairly rapid experiment used as a molecular separation tool and to obtain structural information. The interpretation of IM-MS data is still challenging and relies heavily on theoretical calculations of the molecule's collision cross section (CCS) against a buffer gas. Here, a new software (HPCCS) is presented, which performs CCS calculations using high perfomance computing techniques. Based on the trajectory method, HPCCS can accurately calculate CCS for a great variety of molecules, ranging from small organic molecules to large protein complexes, using helium or nitrogen as buffer gas with considerable gains in computer time compared to publicly available codes under the same level of theory. HPCCS is available as free software under the Academic Use License at https://github.com/cepid-cces/hpccs. © 2018 Wiley Periodicals, Inc.

RESUMO

Introducción: hoy día el cáncer compite con la cardiopatía isquémica como primera causa de muerte en Cuba, muy por encima incluso de la enfermedad cerebrovascular, los accidentes y la neumonía. En muchos casos, el cáncer se presenta con metástasis y solo se logra identificar el tumor primario en una parte de ellos, mientras que en el resto, se mantiene oculto tras una investigación considerada óptima. Objetivo: determinar la frecuencia con que se identifica en nuestro medio un tumor primario cuando el cáncer se ha presentado con metástasis, la distribución topográfica de los sitios de metástasis y las variantes histológicas en casos de tumor primario oculto. Métodos: estudio transversal, prospectivo y descriptivo realizado en el Servicio de Medicina Interna del Hospital Clinicoquirúrgico Hermanos Ameijeiras en el período comprendido de enero 2010 a enero 2013. ..

Introduction: today cancer competes with ischemic heart disease as the leading cause of death in Cuba, even far above cerebrovascular disease, accidents, and pneumonia. In many cases, cancer has metastasized and only the primary tumor is only identified in a part of them, while in the rest, the tumor remains hidden behind a research considered as optimal . Objective: to determine, in our context, how often a primary tumor is identified when the cancer has metastasized, the topographical distribution of metastasis sites and histological variants in cases of hidden primary. Methods: A cross-sectional, prospective and descriptive study was conducted in the Department of Internal Medicine, at Hermanos Ameijeiras Clinical Hospital from January 2010 to January 2013. The working universe consisted of 100 patients with metastasis with no primary tumor identified as diagnosis of hospitalization, who met the inclusion criteria. ..

Assuntos

RESUMO

INTRODUCCIÓN: hoy día el cáncer compite con la cardiopatía isquémica como primera causa de muerte en Cuba, muy por encima incluso de la enfermedad cerebrovascular, los accidentes y la neumonía. En muchos casos, el cáncer se presenta con metástasis y solo se logra identificar el tumor primario en una parte de ellos, mientras que en el resto, se mantiene "oculto" tras una investigación considerada "óptima". OBJETIVO: determinar la frecuencia con que se identifica en nuestro medio un tumor primario cuando el cáncer se ha presentado con metástasis, la distribución topográfica de los sitios de metástasis y las variantes histológicas en casos de tumor primario "oculto". MÉTODOS: estudio transversal, prospectivo y descriptivo realizado en el Servicio de Medicina Interna del Hospital Clinicoquirúrgico "Hermanos Ameijeiras" en el período comprendido de enero 2010 a enero 2013. El universo de trabajo estuvo constituido por 100 pacientes con metástasis sin primario identificado como diagnóstico de hospitalización, que cumplían los criterios de inclusión. Se utilizaron las variables: localización de tumor primario, sitios de metástasis y variedades histológicas. Se emplearon principalmente métodos de estadística descriptiva, especialmente los aplicables a variables cualitativas (incidencia). RESULTADOS: se logró identificar tumor primario en 50 pacientes. Las localizaciones más frecuentes fueron pulmón (11 %), colon, ovario y próstata (5 % en cada caso). En 50 % de los casos no se identificó tumor primario. El sitio más común de metástasis fue el hígado (56,0 %), seguido por los ganglios (41,0 %) y la pleura pulmón (19,0). En el caso de los pacientes en los que no se logró identificar el tumor primario, la variedad más frecuente fue adenocarcinoma bien diferenciado (42 %) seguida del carcinoma poco diferenciado (34 %) y el carcinoma neuroendocrino (20 %). CONCLUSIONES: en nuestro medio, se logra identificar tumor primario en la mitad de los pacientes que se presentan con metástasis . Ello es independiente del número de metástasis al momento de la presentación. El sitio de afectación metastásica más frecuente es el hígado. La variante histológica predominante entre pacientes con tumor primario "oculto" fue adenocarcinoma.

INTRODUCTION: today cancer competes with ischemic heart disease as the leading cause of death in Cuba, even far above cerebrovascular disease, accidents, and pneumonia. In many cases, cancer has metastasized and only the primary tumor is only identified in a part of them, while in the rest, the tumor remains "hidden" behind a research considered as "optimal". OBJECTIVE: to determine, in our context, how often a primary tumor is identified when the cancer has metastasized, the topographical distribution of metastasis sites and histological variants in cases of "hidden" primary. METHODS: A cross-sectional, prospective and descriptive study was conducted in the Department of Internal Medicine, at Hermanos Ameijeiras Clinical Hospital from January 2010 to January 2013. The working universe consisted of 100 patients with metastasis with no primary tumor identified as diagnosis of hospitalization, who met the inclusion criteria. Location of primary tumor, metastatic sites and histological types were variables used. Descriptive statistics were mainly used, especially those applicable to qualitative variables (incidence). RESULTS: primary tumor was identified in 50 patients. The most common sites were lung (11 %), colon, ovarian and prostate (5 % each). no primary tumor was identified in 50 % of cases. The most common site of metastasis was liver (56.0 %), followed by lymph (41.0 %) lung and pleura (19.0). the most common strain was well-differentiated adenocarcinoma (42 %) in those patients whose primary tumor failed to be identified; followed by the poorly differentiated carcinoma (34 %) and neuroendocrine carcinoma (20 %). CONCLUSIONS: In our context, identifying the primary tumor is achieved in half of the patients with metastases. This is independent of the number of metastases at presentation. Liver is the most common site of metastasis. The predominant histological variant among patients with "hidden" primary was adenocarcinoma.

Assuntos

RESUMO

El cáncer de Próstata (CAP), es una enfermedad compleja de origen multifactorial. Se caracteriza por patrones heterogéneos de crecimiento de tejido neoplásico, que varían ampliamente en su progresión, edad de aparición y respuesta al tratamiento. Se considera la segunda causa más común de muerte por malignidad en hombres y se estima que uno de cada cinco padece de CAP en el curso de su vida. La etiología genética de la transformación neoplásica de las células prostáticas normales aún es desconocida, sin embargo, investigaciones epidemiológicas han demostrado un fuerte componente genético en su desarrollo, y sugieren tanto un patrón de herencia mendeliana como la presencia de loci de susceptibilidad a lo largo del genoma humano. Se ha descrito una región cromosómica relacionada con el CAP denominada como HPC1, en el locus 1q24-25, donde se ubica el gen RNASEL, y las mutaciones en el mismo, se han asociado con la presencia del CAP en múltiples grupos familiares. EL gen RNASEL codifica para una ribonucleasa que degrada ARN viral y celular y que interviene en la apoptosis. Se ha reportado disminución de la actividad enzimática de hasta tres veces en portadores del polimorfismo G1385A de este gen, y la misma se ha asociado frecuentemente con el desarrollo del CAP. Mediante la utilización de una variante de la Reacción en Cadena de la Polimerasa (RCP), una amplificación alelo específica, se estudiaron 103 individuos masculinos con y sin CAP pertenecientes a la población de Maracaibo, Venezuela, evidenciándose ausencia de asociación.

Prostate Cancer (CAP), is a complex disease with a multifactorial origin. It is characterized by heterogenous patterns of growth of neoplasic tissue, varying widely in its progression, age of beginning and therapy response. It is considered as the second most common cause of death by cancer in men and, it has been estimated, that one of five, suffers of CAP through the course of his life. The genetic etiology of neoplasic transformation of normal prostate cells is still not known; nevertheless, investigations in epidemiology have demonstrated a strong genetic component in its development, suggesting so much a pattern of mendelian inheritance as the presence of loci of susceptibility throughout the human genome. It has been described a cromosomic location related to the CAP in locus 1q24-25, denominated HPC1, where the gene RNASEL is located, and the seggregation of its alleles has been associated with the development of CAP in numerous familiar groups. The RNASEL gene codifies for a ribonuclease protein that degrades viral and cellular ARN and takes part in the apoptosis. A decrease of the enzymatic activity up to three times in carriers of the G1385A polymorphism of this gene has been reported, and the same has been associated frequently with the development of CAP. Using a variant of the Polymerase Chain Reaction, Allele specific amplification, this investigation had as objective to determine the association between variant G1385A and CAP, in a sample of 103 masculine individuals with and without CAP, pertaining to the population of Maracaibo, Venezuela, An association between these variants and CAP could not be demonstrated.

Assuntos

RESUMO

The aim of this study was to attain 100 percent drug release of caffeine after 24 h from hydroxypropylcellulose (HPC) tablet matrices and to investigate the effect of co-excipient. Physical properties of the powders were evaluated and suggested for a wet granulation process. The tablet containing caffeine was formulated by different weight ratios of hydrophilic polymers. The results of polymer evaluation confirmed that the increase of HPC level with the same drug content significantly decreased the rate of drug release. The presence of co-polymer excipients carboxymethylcellulose (CMC) and polyvinylpyrrolidone (PVP) in the tablet matrix was also investigated. The release rate was also controlled by low levels of CMC (<10 percent) while PVP did not show any considerably effect. The best fit release rate 100 percent at 24 h was obtained when 10 percent of α-lactose monohydrate was added to the formulation.

O objetivo deste estudo é desenvolver a liberação 100 por cento da droga cafeína em 24 horas em comprimidos matrizes e investigar o uso de hidroxipropilcelulose (HPC) mais os efeitos de co-excipiente. As propriedades físicas dos pós foram avaliadas assim como seu uso no processo de granulação úmida. O comprimido contendo a cafeína foi formulado por diferentes relações de peso dos polímeros hidrofílicos. Os resultados da avaliação do polímero confirmaram que o aumento do nível de HPC com o mesmo índice da droga diminuiu significativamente a taxa de liberação da droga. A presença do co-polímero excipiente carboximetilcelulose (CMC) e do polivinilpirrolidona (PVP) na matriz do comprimido foi também investigado. A taxa de liberação foi controlada principalmente por baixos níveis de CMC (< 10 por cento) enquanto PVP não mostrou efeito diferente considerável. A melhor taxa de liberação de cafeína 100 por cento em 24 horas foi obtida quando 10 por cento da lactose monoidrato foi adicionado na formulação.

RESUMO

Sixty samples of tissue fragments with lesions suggestive of tuberculosis from bovine abattoirs, kept in saturated solution of sodium borate, were subjected to four treatments: 4 percent NaOH (Petroff Method), 12 percent H2SO4 and 1.5 percent HPC (1-Hexadecylpyridinium Chloride) decontamination, and physiological saline solution (control). The HPC method showed the lowest contamination rate (3 percent) when compared to control (88 percent, p<0.001), NaOH (33 percent, p<0.001) and H2SO4 (21.7 percent, p<0.002). Regarding the isolation success, the HPC method was better (40 percent) than the control (3 percent, p<0.001), NaOH (13 percent, p=0.001) and H2SO4 (1.7 percent, p<0.001) methods. These results indicate that HPC is an alternative to the Petroff method.

Sessenta amostras de fragmentos de tecidos com lesões sugestivas de tuberculose provenientes de abatedouros bovinos, conservadas em solução saturada de borato de sódio, foram submetidas a quatro tratamentos: descontaminação através dos métodos NaOH 4 por cento (Método Petroff), H2SO4 12 por cento e HPC (Cloreto de hexadecilpiridínio) 1,5 por cento, e solução salina (controle). O método HPC apresentou a menor proporção de contaminação (3 por cento), em relação ao controle (88 por cento, p<0,001), NaOH (33 por cento, p<0,001) e H2SO4 (21,7 por cento, p=0,002). Em relação ao sucesso no isolamento, o método HPC apresentou o melhor resultado (40 por cento), em relação ao controle (3 por cento, p<0,001), NaOH (13 por cento, p=0,001) e H2SO4 (1,7 por cento, p<0,001). Os resultados indicam que o HPC é uma alternativa à utilização do método Petroff.

Assuntos

RESUMO

SIXTY SAMPLES OF TISSUE FRAGMENTS WITH LESIONS SUGGESTIVE OF TUBERCULOSIS FROM BOVINE ABATTOIRS, KEPT IN SATURATED SOLUTION OF SODIUM BORATE, WERE SUBJECTED TO FOUR TREATMENTS: 4% NaOH (Petroff Method), 12 % H2SO4 and 1.5% HPC (1-Hexadecylpyridinium Chloride) decontamination, and physiological saline solution (control). The HPC method showed the lowest contamination rate (3%) when compared to control (88%, p<0.001), NaOH (33%, p<0.001) and H2SO4 (21.7%, p<0.002). Regarding the isolation success, the HPC method was better (40%) than the control (3%, p<0.001), NaOH (13%, p=0.001) and H2SO4 (1.7%, p<0.001) methods. These results indicate that HPC is an alternative to the Petroff method.

RESUMO

Sixty samples of tissue fragments with lesions suggestive of tuberculosis from bovine abattoirs, kept in saturated solution of sodium borate, were subjected to four treatments: 4% NaOH (Petroff Method), 12 % H2SO4 and 1.5% HPC (1-Hexadecylpyridinium Chloride) decontamination, and physiological saline solution (control). The HPC method showed the lowest contamination rate (3%) when compared to control (88%, p 0.001), NaOH (33%, p 0.001) and H2SO4 (21.7%, p 0.002). Regarding the isolation success, the HPC method was better (40%) than the control (3%, p 0.001), NaOH (13%, p=0.001) and H2SO4 (1.7%, p 0.001) methods. These results indicate that HPC is an alternative to the Petroff method.

Sessenta amostras de fragmentos de tecidos com lesões sugestivas de tuberculose provenientes de abatedouros bovinos, conservadas em solução saturada de borato de sódio, foram submetidas a quatro tratamentos: descontaminação através dos métodos NaOH 4% (Método Petroff), H2SO4 12% e HPC (Cloreto de hexadecilpiridínio) 1,5%, e solução salina (controle). O método HPC apresentou a menor proporção de contaminação (3%), em relação ao controle (88%, p 0,001), NaOH (33%, p 0,001) e H2SO4 (21,7%, p=0,002). Em relação ao sucesso no isolamento, o método HPC apresentou o melhor resultado (40%), em relação ao controle (3%, p 0,001), NaOH (13%, p=0,001) e H2SO4 (1,7%, p 0,001). Os resultados indicam que o HPC é uma alternativa à utilização do método Petroff.