ABPSE: Alineador de ADN Basado en Paralelismo a Nivel de Bit y la Estrategia Siembra y Extiende / ABPSE: DNA Aligner Based on Bit-level Parallelism and the Seed and Extend Strategy

Resumen La alineación de ADN es un proceso clave para la reconstrucción de genomas, a partir de los millones de lecturas cortas producidas por las máquinas de secuenciación paralela masiva. Tal proceso suele realizarse mediante algoritmos con elevada complejidad espacial y temporal, requiriendo varias horas para entregar los resultados, así como decenas de GB de RAM. Esto ha motivado la búsqueda de nuevos algoritmos y/o estrategias que permitan disminuir los tiempos de ejecución, mientras se utilizan recursos mínimos de memoria. En este artículo se presenta ABPSE, un nuevo alineador de ADN que combina el algoritmo de Ferragina y Manzini (o índices de FM) y el algoritmo de Myers, mediante la estrategia siembra y extiende. En la siembra, los índices de FM permiten calcular de manera rápida regiones con alta probabilidad de alineación; mientras que en la extensión, el algoritmo de Myers refina la alineación utilizando operaciones basadas en vectores de bits, calculando simultáneamente varias celdas de la matriz de programación dinámica. Los resultados muestran un 96.1% de lecturas alineadas correctamente, un factor de aceleración de 2.45x en relación a BWA-SW y un uso de memoria de apenas 7.6 GB, cuando se alinea el genoma humano completo.

Abstract DNA alignment is a key process in the assembly of genomes from the millions of short reads that are produced by massive parallel sequencing machines. Such a process is usually done by means of high spatial and temporal complexity algorithms, which takes hours to deliver the results as well as tens of GB of RAM. This has prompted the search for new algorithms and/or strategies that allow shorter runtimes, while using minimal memory footprint. In this article, we present ABPSE, a new DNA aligner that combines the Ferragina and Manzini algorithm (or FM indexes) and the Myers algorithm, by means of the seed and extend strategy. In the seeding, the FM indices allow a rapid calculation of the regions with high probability of alignment. In the extension, the Myers algorithm refines the alignment using operations based on bit vectors. It simultaneously calculates several cells of the dynamic programming matrix. The results show 96.1% of correctly aligned reads, an acceleration factor of 2.45x in relation to BWA-SW and a memory footprint of only 7.6 GB when aligning the entire human genome.

Recomendaciones para el soporte nutricional y metabólico especializado del paciente crítico. Actualización. Consenso SEMICYUC-SENPE: Paciente quemado crítico / Guidelines for specialized nutritional and metabolic support in the critically-ill patient. Update. Consensus of the Spanish Society of Intensive Care Medicine and Coronary Units-Spanish Society of Parenteral and Enteral Nutrition (SEMICYUC-SENPE): Critically- burned patient

La respuesta que se objetiva tras una agresión térmica grave se caracteriza por hipermetabolismo (es el modelo de agresión más hipermetabólica que existe) e hipercatabolismo, con una elevada destrucción de la musculatura esquelética. Los trastornos metabólicos son más evidentes en las 2 primeras semanas tras la quemadura, aunque pueden prolongarse en relación directa con las complicaciones aparecidas. El soporte nutrometabólico forma parte indiscutible del tratamiento de estos pacientes y debe ser precoz, utilizando preferentemente la vía enteral y la nutrición parenteral complementaria. Es dificultoso el cálculo exacto de los requerimientos caloricoproteicos, aun empleando calorimetría indirecta, debido a las elevadas pérdidas cutáneas de proteínas y CO2. Cabe destacar la indicación de farmaconutrientes específicos, de dosis elevadas de micronutrientes y, en algunas situaciones, del empleo de medicaciones o fármacos con efectos anabólicos (AU)

The response to severe burns is characterized by hypermetabolism (the most hypermetabolic existing model of aggression) and hypercatabolism, with a high degree of destruction of the skeletal musculature. Metabolic disorders are most evident in the first two weeks after the burn, although they can be prolonged in direct relation to the complications that these patients develop. Nutritional-metabolic support is an essential part of the treatment of these patients and should be started early, preferentially through the enteral route, with parenteral nutrition as complementary support. Exact calculation of calorie-protein requirements in these patients is dificult, even when indirect calorimetry is used, due to the high loss of proteins and CO2 through the skin. Specific pharmaconutrients are indicated, with a high dose of micronutrients. The use of drugs or medications with anabolic effects is also sometimes indicated (AU)

[Guidelines for specialized nutritional and metabolic support in the critically-ill patient. Update. Consensus of the Spanish Society of Intensive Care Medicine and Coronary Units-Spanish Society of Parenteral and Enteral Nutrition (SEMICYUC-SENPE): critically-burned patient]. / Recomendaciones para el soporte nutricional y metabólico especializado del paciente crítico. Actualización. Consenso SEMICYUC-SENPE: paciente quemado crítico.

The response to severe burns is characterized by hypermetabolism (the most hypermetabolic existing model of aggression) and hypercatabolism, with a high degree of destruction of the skeletal musculature. Metabolic disorders are most evident in the first two weeks after the burn, although they can be prolonged in direct relation to the complications that these patients develop. Nutritional-metabolic support is an essential part of the treatment of these patients and should be started early, preferentially through the enteral route, with parenteral nutrition as complementary support. Exact calculation of calorie-protein requirements in these patients is difficult, even when indirect calorimetry is used, due to the high loss of proteins and CO(2) through the skin. Specific pharmaconutrients are indicated, with a high dose of micronutrients. The use of drugs or medications with anabolic effects is also sometimes indicated.

Análisis de las alternativas a la transfusión en pacientes prequirúrgicos con hemoglobinas bajas / Analysis of the alternatives to transfusion in pre-surgical patients with low hemoglobins

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[Isolation of Campylobacter jejuni ATCC 29428 from inoculated fried pork meat and roasted chicken]. / Recuperación de Campylobacter jejuni ATCC 29428 a partir de carne de cerdo frita y de pollos rostizados inoculados.

The human gastroenteritis caused by Campylobacter jejuni in some industrialized countries is higher than gastroenteritis produced by Salmonella and Shigella. This has induced the development of techniques to demonstrate the presence of the microorganism in different foods using some culture media combinations. There is not a method to isolate C. jejuni from roasted chicken and fried pork meat, which are popular foods in México. The sensitivity of two culture media combinations was compared: Rama broth (RB)-Rama agar (RA) and Preston broth (PB)-Skirrow agar (SA) to isolate C. jejuni from these foods. The RB-RA combination demonstrated to be the best one to isolate C. jejuni.