Effect of Conformation Sampling Strategies in Genetic Algorithm for Multiple Protein Docking.

Background Macromolecular protein complexes play important roles in a cell and their tertiary structure can help understand key biological processes of their functions. Multiple protein docking is a valuable computational tool for providing structure information of multimeric protein complexes. In a previous study we developed and implemented an algorithm for this purpose, named Multi-LZerD. This method represents a conformation of a multimeric protein complex as a graph, where nodes denote subunits and each edge connecting nodes denotes a pairwise docking conformation of the two subunits. Multi-LZerD employs a genetic algorithm to sample different topologies of the graph and pairwise transformations between subunits, seeking for the conformation of the optimal (lowest) energy. In this study we explore different configurations of the genetic algorithm, namely, the population size, whether to include a crossover operation, as well as the threshold for structural clustering, to find the optimal experimental setup. Methods Multi-LZerD was executed to predict the structures of three multimeric protein complexes, using different population sizes, clustering thresholds, and configurations of mutation and crossover. We analyzed the impact of varying these parameters on the computational time and the prediction accuracy. Results and conclusions Given that computational resources is a key for handling complexes with a large number of subunits and also for computing a large number of protein complexes in a genome-scale study, finding a proper setting for sampling the conformation space is of the utmost importance. Our results show that an excessive sampling of the conformational space by increasing the population size or by introducing the crossover operation is not necessary for improving accuracy for predicting structures of small complexes. The clustering is effective in reducing redundant pairwise predictions, which leads to successful identification of near-native conformations

Aplicación del taller basado en la técnica de elaboración de ceramios pre-incas de papel para mejorar la identidad histórica en los estudiantes del 1° año de educación secundaria de la I.E. Gastón Vidal Porturas – Nvo. Chimbote 2014

La presente tesis titulada “Aplicación del taller basado en la técnica de elaboración de ceramios pre incas de papel para mejorar la identidad histórica en los estudiantes del 1° año de educación secundaria de la I.E. Gastón Vidal Porturas, 2014” cuyo objetivo será determinar en qué medida la aplicación del taller basado en la técnica de elaboración de ceramios pre-incas de papel, mejora la identidad histórica en el área de Historia, Geografía y Economía; teniendo como variable independiente al taller basado en la técnica de elaboración de ceramios pre-incas y como variable dependiente a la Identidad Histórica. La identidad histórica es el desarrollo de la valoración de nuestros orígenes, la cual mucha veces es ignorada por la sociedad modernizada que erróneamente busca vivir en una constante búsqueda de lo nuevo y novedoso, olvidando la importancia de conocer el pasado con el fin de saber reconocer el respeto por nuestra historia, el instrumento considerado como factor principal de la mejora de la identidad histórica es el taller de elaboración de ceramios pre-incas, lo cual genera el interés por conocer técnicas, formas y significados en cada uno de los ceramios. La investigación es de tipo experimental con un diseño de estudio de dos grupos no equivalentes con pre y post-test; utilizando como muestra a los estudiantes del primer grado A y B del nivel secundario. La hipótesis general de la investigación es: Aplicando el taller basado en la técnica de elaboración de ceramios pre-incas de papel como estrategia didáctica mejoraremos la identidad histórica en los estudiantes del primer año de educación secundaria de la I.E. “Gastón Vidal Porturas” Nvo. Chimbote – 2014. Se logró identificar los niveles de identidad histórica en los estudiantes del primer año de secundaria antes de aplicar la estrategia didáctica planteada, para lo cual se plantearon escalas entre: NO IDENTIFICADO, POCO IDENTIFICADO, IDENTIFICADO y MUY IDENTIFICADO; el resultado obtenido se ubicó en la escala POCO IDENTIFICADO, al ejecutar el taller de elaboración de ceramios de papel como estrategia didáctica, los resultados según el pos-test cambiaron a la escala MUY IDENTIFICADO.Tesi

Exploitation of Mexican agro industrial wastes as raw material for solid-state fermentation processes

Annually, large volumes of wastes are produced by food, agricultural and forestry industries, which if disposed cause serious environmental problems. Therefore, it is of great importance to find alternative ways to reuse them. Due to the composition rich in sugars, which due to their organic nature are easily assimilated by the microorganisms; such wastes could be appropriate for use as raw materials in the production of industrially-relevant compounds under solid-state fermentation (SSF) conditions. However, the physical-chemical and microbiological characteristics of the solid substrate affect the efficiency of the SSF process. In the present study, ten different agro industrial wastes derived from Mexican local regions were evaluated for use as raw material in SSF. The wastes included creosote bush leaves (Larrea tridentata), variegated Caribbean agave (Agave lechuguilla), lemon peel (Citrus aurantifolia), orange peel (Citrus sinensis), apple pomace (Malus domestica), pistachio shell (Pistacia vera), wheat bran (Triticum spp.), coconut husk (Cocos nucífera), pecan nutshell (Carya illinoinensis), and bean residues (Phaseolus vulgaris). All of them were physical-chemically and microbiologically characterized. Physical-chemical tests consisted in the determination of the critical humidity point (CHP) and the water absorption index (WAI), while the microbiological tests were based on the evaluation of Aspergillus niger Aa-20 growth rate in such materials. The study pointed out that coconut husk, apple pomace, lemon and orange peels have great potential to be successfully used as raw material in SSF, since they have low water content linked to the structure (that is ideal to easily adjust the water content according to the process to be used), and allowed good and fast microorganism growth. Their use in SSF would be an interesting alternative to add value to these residues besides to be of great economical advantage and an environmental-friendly way for waste management.info:eu-repo/semantics/publishedVersio

The role of virtual photons in nanoscale photonics

The fundamental theory of processes and properties associated with nanoscale photonics should properly account for the quantum nature of both the matter and the radiation field. A familiar example is the Casimir force, whose significant role in nanoelectromechanical systems is widely recognised; the correct representation invokes the creation of short-lived virtual photons from the vacuum. In fact, there is an extensive range of nanophotonic interactions in which virtual photon exchange plays a vital role, mediating the coupling between particles. This review surveys recent theory and applications, also exhibiting novel insights into key electrodynamic mechanisms. Examples are numerous and include: laser-induced inter-particle forces known as optical binding; non-parametric frequency-conversion processes especially in rare-earth doped materials; light-harvesting polymer materials that involve electronic energy transfer between their constituent chromophores. An assessment of these and the latest prospective applications concludes with a view on future directions of research

Thirty-day outcomes in frail older patients discharged home from the emergency department with acute heart failure: effects of high-risk criteria identified by the DEED FRAIL-AHF trial

Objectives: To study the effect of high-risk criteria on 30-day outcomes in frail older patients with acute heart failure (AHF) discharged from an emergency department (ED) or an ED's observation and short-stay areas. Material and methods: Secondary analysis of discharge records in the Older AHF Key Data registry. We selected frail patients (aged > 70 years) discharged with AHF from EDs. Risk factors were categorized as modifiable or nonmodifiable. The outcomes were a composite endpoint for a cardiovascular event (revisits for AHF, hospitalization for AHF, or cardiovascular death) and the number of days alive out-of-hospital (DAOH) within 30 days of discharge. Results: We included 380 patients with a mean (SD) age of 86 (5.5) years (61.2% women). Modifiable risk factors were identified in 65.1%, nonmodifiable ones in 47.8%, and both types in 81.6%. The 30-day cardiovascular composite endpoint occurred in 83 patients (21.8%). The mean 30-day DAOH observed was 27.6 (6.1) days. Highrisk factors were present more often in patients who developed the cardiovascular event composite endpoint: the rates for patients with modifiable, nonmodifiable, or both types of risk were, respectively, as follows in comparison with patients not at high risk: 25.0% vs 17.2%, P = .092; 27.6% vs 16.7%, P = .010; and 24.7% vs 15.2%, P = .098). The 30-day DAOH outcome was also lower for at-risk patients, according to type of risk factor present: modifiable, 26.9 (7.0) vs 28.4 (4.4) days, P = .011; nonmodifiable, 27.1 (7.0) vs 28.0 (5.0) days, P = .127; and both, 27.1 (6.7) vs 28.8 (3.4) days, P = .005). After multivariate analysis, modifiable risk remained independently associated with fewer days alive (adjusted absolute difference in 30-day DAOH, -1.3 days (95% CI, -2.7 to -0.1 days). Nonmodifiable factors were associated with increased risk for the 30-day cardiovascular composite endpoint (adjusted absolute difference, 10.4%; 95% CI, -2.1% to 18.7%). Conclusion: Risk factors are common in frail elderly patients with AHF discharged home from hospital ED areas. Their presence is associated with a worse 30-day prognosis

Ciencias de la Biología y Agronomía

Este volumen I contiene 17 capítulos arbitrados que se ocupan de estos asuntos en Tópicos Selectos de Ciencias de la Biología y Agronomía, elegidos de entre las contribuciones, reunimos algunos investigadores y estudiantes. Se presenta un Estudio Comparativo de los Recursos Hidrológico-Forestales de la Microcuenca de la Laguna de Epatlan, Pue. (1993 a 2014); la Situación Actual de la Mancha de Asfalto en Maíz (Zea mays L.) en los Municipios de Jiquipilas y Ocozocoautla, Chiapas, México; las poblaciones sobresalientes de maíz de la raza Zapalote Chico, en la Región Istmeña de Oaxaca; Se indica el índice de área foliar de cultivo de Chile Poblano mediante dos métodos en condiciones protegidas; Esquivel, Urzúa y Ramírez exploran el efecto de la biofertilización con Azospirillum en el crecimiento y producción de Jitomate; esbozan su artículo sobre la determinación del nivel de Heterosis en híbridos de Maíz para la Comarca Lagunera; una investigación sobre la estabilización de semilla de Solanum lycopersicum durante el almacenamiento y estimulación de la germinación; acotan sobre el CTAB como una nueva opción para la detección de Huanglongbing en cítricos, plantean su evaluación sobre el aluminio y cómo afecta la vida de florero de Heliconia psittacorum; indican sobre el impacto del H-564C, como un híbrido de maíz con alta calidad de proteina para el trópico húmedo de México; presetan su investigación sobre la producción de Piña Cayena Lisa y MD2 (Ananas comosus L.) en condiciones de Loma Bonita, en Oaxaca; acotan sobre el efecto de coberteras como control biológico por conservación contra áfidos en Nogal Pecanero; esbozan sobre la caracterización de cuatro genotipos de Frijol Negro en Martínez de la Torre, Veracruz, México; presentan una caracterización hidroecológica de la microcuenca de Arroyo Prieto, Yuriría, Gto., y alternativas para su restauración ambiental; presentan su investigación sobre el efecto del hongo Beauveria bassiana sobre solubilización de fosfatos y la disponibilidad de fósforo en el suelo; plantean su investigación sobre la Germinación y regeneración in vitro de Epidendrum falcatum LINDL; esbozan su artículo sobre genotipos de frijol negro y su tolerancia a sequía terminal en Veracruz, México

Hyperdominance in Amazonian Forest Carbon Cycling

While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few ‘hyperdominant’ species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region

Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study

Background Early mobilisation (EM) is an intervention that may improve the outcome of critically ill patients. There is limited data on EM in COVID-19 patients and its use during the first pandemic wave. Methods This is a pre-planned subanalysis of the ESICM UNITE-COVID, an international multicenter observational study involving critically ill COVID-19 patients in the ICU between February 15th and May 15th, 2020. We analysed variables associated with the initiation of EM (within 72 h of ICU admission) and explored the impact of EM on mortality, ICU and hospital length of stay, as well as discharge location. Statistical analyses were done using (generalised) linear mixed-effect models and ANOVAs. Results Mobilisation data from 4190 patients from 280 ICUs in 45 countries were analysed. 1114 (26.6%) of these patients received mobilisation within 72 h after ICU admission; 3076 (73.4%) did not. In our analysis of factors associated with EM, mechanical ventilation at admission (OR 0.29; 95% CI 0.25, 0.35; p = 0.001), higher age (OR 0.99; 95% CI 0.98, 1.00; p ≤ 0.001), pre-existing asthma (OR 0.84; 95% CI 0.73, 0.98; p = 0.028), and pre-existing kidney disease (OR 0.84; 95% CI 0.71, 0.99; p = 0.036) were negatively associated with the initiation of EM. EM was associated with a higher chance of being discharged home (OR 1.31; 95% CI 1.08, 1.58; p = 0.007) but was not associated with length of stay in ICU (adj. difference 0.91 days; 95% CI − 0.47, 1.37, p = 0.34) and hospital (adj. difference 1.4 days; 95% CI − 0.62, 2.35, p = 0.24) or mortality (OR 0.88; 95% CI 0.7, 1.09, p = 0.24) when adjusted for covariates. Conclusions Our findings demonstrate that a quarter of COVID-19 patients received EM. There was no association found between EM in COVID-19 patients' ICU and hospital length of stay or mortality. However, EM in COVID-19 patients was associated with increased odds of being discharged home rather than to a care facility. Trial registration ClinicalTrials.gov: NCT04836065 (retrospectively registered April 8th 2021)

Computational modeling of macromolecular structures

The main purpose of the research in this dissertation is to propose computational methods to create atomic models for macromolecular protein complexes. Protein interactions have been studied extensively, both experimentally and computationally. While traditional high-throughput approaches are useful to create large sets of relationships between proteins, these models do not provide detailed information about the physical mechanisms that proteins use to perform their biological functions. In this study we target three objectives in this domain. First, to develop a method for multiple protein docking. Second, to use multiple protein docking as the basis for Electron Microscopy Fitting. Finally, to create an enhanced probabilistic framework to model macromolecular structures that uses varied feature sources, ranging from Electron Microscopy information to physicochemical properties of interacting proteins. The development of three separate computational methods is explained, each answering the challenges posed by the previous objectives