BLVector: Fast BLAST-Like Algorithm for Manycore CPU With Vectorization

New High-Performance Computing architectures have been recently developed for commercial central processing unit (CPU). Yet, that has not improved the execution time of widely used bioinformatics applications, like BLAST+. This is due to a lack of optimization between the bases of the existing algorithms and the internals of the hardware that allows taking full advantage of the available CPU cores. To optimize the new architectures, algorithms must be revised and redesigned; usually rewritten from scratch. BLVector adapts the high-level concepts of BLAST+ to the x86 architectures with AVX-512, to harness their capabilities. A deep comprehensive study has been carried out to optimize the approach, with a significant reduction in time execution. BLVector reduces the execution time of BLAST+ when aligning up to mid-size protein sequences (∼750 amino acids). The gain in real scenario cases is 3.2-fold. When applied to longer proteins, BLVector consumes more time than BLAST+, but retrieves a much larger set of results. BLVector and BLAST+ are fine-tuned heuristics. Therefore, the relevant results returned by both are the same, although they behave differently specially when performing alignments with low scores. Hence, they can be considered complementary bioinformatics tools.Fil: Gálvez Rojas, Sergio. Universidad de Malaga. Escuela Técnica Superior de Ingeniería Informática. Departamento de Lenguajes y Ciencias de la Computacion.; EspañaFil: Agostini, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Botánica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botánica del Nordeste; ArgentinaFil: Caselli, Javier. Universidad de Malaga. Escuela Técnica Superior de Ingeniería Informática. Departamento de Lenguajes y Ciencias de la Computacion.; EspañaFil: Hernandez, Agustina Pilar. Consejo Superior de Investigaciones Científicas; EspañaFil: Dorado, Gabriel. Universidad de Córdoba; Españ

Agriculture and ritual in the 1000 BP human landscape of the Quebrada de Humahuaca headwaters: Casas Grandes site (Jujuy, Argentina)

Este trabajo presenta los resultados de los estudios arqueológicos llevados a cabo en el sitio Casas Grandes, realizados dentro de un proyecto de investigación regional que abarca las nacientes de la Quebrada de Humahuaca en su intersección con la Puna, ecotono y umbral geo-ambiental que ocurre en este sector de la Provincia de Jujuy, Argentina. Se expone aquí una síntesis del marco general del proyecto, las escalas de análisis (espacial y temporal) así como los lineamientos teórico/metodológicos del mismo. Luego se presentan las características del sitio, su geomorfología, sus sectores y la evidencia arqueológica encontrada en cada uno de ellos. A su vez, se describen los distintos tipos hallazgos realizados y los resultados de sus respectivos análisis, focalizando en el sector bajo del sitio, donde la evidencia hallada aporta excepcional información sobre prácticas económicas y rituales realizadas en torno a los 1000 años antes del presente. En base a estos estudios y a los fechados radiocarbónicos obtenidos se presenta una discusión general sobre la articulación de este sitio con otros estudiados dentro del mismo proyecto, así como su importancia en el contexto de la arqueología de Quebrada y Puna jujeña, a partir de su comparación e integración con la evidencia proveniente de otros sitios con ocupaciones humanas contemporáneas localizados en estos dos geo-ambientes.This paper presents the archeological investigations at the Casas Grandes site, which were carried out as part of a regional research project that encompasses the headwaters of the Quebrada de Humahuaca, where it intersects the Puna. This is an ecotone and environmental threshold that occurs in this part of Jujuy Province, Argentina. It is presented here a synthesis of the project´s general framework, the scales of analysis (spatial and temporal) and the main points of the theoretical and methodological approaches employed. A discussion about the characteristics of the site, its geomorphology, the sectors into which it is divided, and the archaeological evidence recovered is also presented. The different types of findings and their analyses are discussed, focusing on the site´s lower sector, where the evidence recovered provides valuable information about economic and ritual practices from around 1000 BP. On the basis of these studies and the radiocarbon dates obtained, a general discussion about the articulation of this site and others studied within the same project is presented. The relevance of this site within the context of the archaeology of the Quebrada de Humahuaca and the Jujuy Puna is assessed by comparing and integrating the site´s evidence with that from contemporary sites in those two geo-environmental zones.Fil: Hernandez Llosas, Maria Isabel. Universidad de Buenos Aires. Facultad de Filosofía y Letras. Instituto de Arqueología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Leoni, Juan Bautista. Universidad Nacional de Rosario. Facultad de Humanidades y Artes. Escuela de Antropología. Centro de Estudios de Arqueología Historica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; ArgentinaFil: Scaro, Agustina. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Hernández, Anahí. Universidad Nacional de Rosario. Facultad de Humanidades y Artes. Escuela de Antropología. Centro de Estudios de Arqueología Historica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; ArgentinaFil: Fabron, Giorgina. Universidad de Buenos Aires. Facultad de Filosofía y Letras. Instituto de Arqueología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Hesse, Paul. Macquarie University; AustraliaFil: Bosio, Luis Alberto. Equipo Argentino de Antropología Forense; ArgentinaFil: Quinteros, Ramon Alejandro. Universidad de Buenos Aires. Facultad de Filosofía y Letras. Instituto de Arqueología; ArgentinaFil: Castro, Mora del Pilar. Universidad Nacional Arturo Jauretche. Instituto de Cs. de la Salud; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Comparison of seven prognostic tools to identify low-risk pulmonary embolism in patients aged <50 years

publishersversionPeer reviewe

New insights into the genetic etiology of Alzheimer’s disease and related dementias

Characterization of the genetic landscape of Alzheimer’s disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/‘proxy’ AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

New insights into the genetic etiology of Alzheimer’s disease and related dementias

Characterization of the genetic landscape of Alzheimer’s disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/‘proxy’ AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Effects of pre-operative isolation on postoperative pulmonary complications after elective surgery: an international prospective cohort study an international prospective cohort study

We aimed to determine the impact of pre-operative isolation on postoperative pulmonary complications after elective surgery during the global SARS-CoV-2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre-defined sub-group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS-CoV-2 infection. Patients who isolated pre-operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS-CoV-2 incidence and high-income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05–1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre-operative testing; use of COVID-19-free pathways; or community SARS-CoV-2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4–7 days or ≥ 8 days of 1.25 (1.04–1.48), p = 0.015 and 1.31 (1.11–1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care. We aimed to determine the impact of pre-operative isolation on postoperative pulmonary complications after elective surgery during the global SARS-CoV-2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre-defined sub-group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS-CoV-2 infection. Patients who isolated pre-operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS-CoV-2 incidence and high-income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05–1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre-operative testing; use of COVID-19-free pathways; or community SARS-CoV-2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4–7 days or ≥ 8 days of 1.25 (1.04–1.48), p = 0.015 and 1.31 (1.11–1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care