HPG pore: an efficient and scalable framework for nanopore sequencing data.

BACKGROUND: The use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification. The first nanopore sequencer available, the MinION™ from Oxford Nanopore Technologies, is a USB-connected, portable device that allows real-time DNA analysis. In addition, other new instruments are expected to be released soon, which promise to outperform the current short-read technologies in terms of throughput. Despite the flood of data expected from this technology, the data analysis solutions currently available are only designed to manage small projects and are not scalable. RESULTS: Here we present HPG Pore, a toolkit for exploring and analysing nanopore sequencing data. HPG Pore can run on both individual computers and in the Hadoop distributed computing framework, which allows easy scale-up to manage the large amounts of data expected to result from extensive use of nanopore technologies in the future. CONCLUSIONS: HPG Pore allows for virtually unlimited sequencing data scalability, thus guaranteeing its continued management in near future scenarios. HPG Pore is available in GitHub at http://github.com/opencb/hpg-pore

Lateral Habenula determines long-term storage of aversive memories

The Lateral Habenula (LHb) is a small brain structure that codifies negative motivational value and has been related to major depression. It has been shown recently that LHb activation is sufficient to induce aversive associative learning; however the key question about whether LHb activation is required for an aversive memory to be formed has not been addressed. In this article we studied the function of the LHb in memory formation using the Inhibitory Avoidance task (IA). We found that LHb inactivation during IA training does not disrupt memory when assessed 24 h after, but abolishes it 7 days later, indicating that LHb activity during memory acquisition is not necessary for memory formation, but regulates its temporal stability. These effects suggest that LHb inactivation modifies subjective perception of the training experience.Fil: Tomaiuolo, Micol. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Biología Celular y Neurociencia "Prof. Eduardo de Robertis". Universidad de Buenos Aires. Facultad de Medicina. Instituto de Biología Celular y Neurociencia ; ArgentinaFil: González, María Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Biología Celular y Neurociencia "Prof. Eduardo de Robertis". Universidad de Buenos Aires. Facultad de Medicina. Instituto de Biología Celular y Neurociencia ; ArgentinaFil: Medina, Jorge Horacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Biología Celular y Neurociencia "Prof. Eduardo de Robertis". Universidad de Buenos Aires. Facultad de Medicina. Instituto de Biología Celular y Neurociencia ; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Departamento de Ciencias Fisiológicas; ArgentinaFil: Piriz, Joaquin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Fisiología y Biofísica Bernardo Houssay. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Fisiología y Biofísica Bernardo Houssay; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentin

Práctica de la Gestión de proyectos en la industria de la construcción: un caso en el Estado de México (parte II)

El sector de la construcción contribuye sustancialmente al desarrollo de un país en virtud de que genera la infraestructura requerida por la sociedad para mejorar su calidad de vida. Esto pone de manifiesto la necesidad de diseñar herramientas para que los profesionales del ramo puedan administrar adecuadamente sus proyectos. Los libros y artículos hasta ahora escritos reportan distintas técnicas teóricas, pero son pocos los casos de estudio en los que se ilustra la aplicación de ellas. Esta situación impide que los practicantes tengan ejemplos útiles que les ayuden a implementar nuevas ideas para mejorar los procesos internos de sus compañías. En un esfuerzo por generar conocimiento en este sentido, se ha llevado a cabo un estudio en una empresa del Estado de México, tomando un ejemplo un proyecto sanitario en el cual se aplicaron empíricamente algunas herramientas teóricas de la gestión de proyectos

Epiphytic bryophytes of Quercus forests in Central and North inland Iberian Peninsula

Frontiers of Biogeography 7.1 (2015): 21-28 This Document is Protected by copyright and was first published by Frontiers. All rights reserved. It is reproduced with permissionDiversity patterns are governed by a complex network of interacting factors. Studies directed to disentangle the most important factors affecting diversity have frequently shown divergent results, which has encouraged a rewarding debate about the relative importance of each factor. Scale dependency has been identified as a direct cause of at least part of such divergences. However, studies with spatially-explicit measurements at different scales are costly and therefore they are relatively scarce despite their importance. Here, we present a database to disentangle the cross-scale variation in the importance of factors affecting the diversity of epiphytic bryophyte communities in Quercus dominated forests (Quercus ilex L., Quercus pyrenaica Willd. and Quercus faginea Lam.) in the North-western region of the Iberian Peninsula. We provide species-per-site abundance information with more than 9000 entries and an environmental table containing 20 in situ measured variables at three different scales (forest, stand, and sample). The database will help to advance the research of cross-scale effects of diversity patterns while at the same time providing valuable information on the distribution of a poorly known group of organismsThe fieldwork was funded by the Spanish Government through grants CGL2007-61389, CGL2010-15693 and CGL2011-28857. N.G.M. was supported by a PhD grant from the Spanish Ministry of Education (grant number AP2007-00905

Relationship Between the Plasma Concentration of C-Reactive Protein and Severity of Peripheral Arterial Disease

Objective To determine whether the increase in plasma levels of C-Reactive Protein (CRP), a non-specific reactant in the acute-phase of systemic inflammation, is associated with clinical severity of peripheral arterial disease (PAD). Methods and Results This is a cross-sectional study at a referral hospital center of institutional practice in Madrid, Spain. A stratified random sampling was done over a population of 3370 patients with symptomatic PAD from the outpatient vascular laboratory database in 2007 in the order of their clinical severity: the first group of patients with mild chronological clinical severity who did not require surgical revascularization, the second group consisted of patients with moderate clinical severity who had only undergone only one surgical revascularization procedure and the third group consisted of patients who were severely affected and had undergone two or more surgical revascularization procedures of the lower extremities in different areas or needed late re-interventions. The Neyman affixation was used to calculate the sample size with a fixed relative error of 0.1. A homogeneity analysis between groups and a unifactorial analysis of comparison of medians for CRP was done. The groups were homogeneous for age, smoking status, Arterial Hypertension HTA, diabetes mellitus, dyslipemia, homocysteinemia and specific markers of inflammation. In the unifactorial analysis of multiple comparisons of medians according to Scheffe, it was observed that the median values of CRP plasma levels were increased in association with higher clinical severity of PAD (3.81 mg/L [2.14-5.48] vs. 8.33 [4.38-9.19] vs. 12.83 [9.5-14.16]; p < 0.05) as a unique factor of tested ones. Conclusion Plasma levels of CRP are associated with not only the presence of atherosclerosis but also with its chronological clinical severity

Survey and brain storming studies about machines, constructions, human and environmental risk consideration in the careers of the Universidad Politécnica of Madrid

The Universidad Politécnica of Madrid (UPM) includes schools and faculties that were for engineering degrees, architecture and computer science, that are now in a quick EEES Bolonia Plan metamorphosis getting into degrees, masters and doctorate structures. They are focused towards action in machines, constructions, enterprises, that are subjected to machines, human and environment created risks. These are present in actions such as use loads, wind, snow, waves, flows, earthquakes, forces and effects in machines, vehicles behavior, chemical effects, and other environmental factors including effects of crops, cattle and beasts, forests, and varied essential economic and social disturbances. Emphasis is for authors in this session more about risks of natural origin, such as for hail, winds, snow or waves that are not exactly known a priori, but that are often considered with statistical expected distributions giving extreme values for convenient return periods. These distributions are known from measures in time, statistic of extremes and models about hazard scenarios and about responses of man made constructions or devices. In each engineering field theories were built about hazards scenarios and how to cover for important risks. Engineers must get that the systems they handle, such as vehicles, machines, firms or agro lands or forests, obtain production with enough safety for persons and with decent economic results in spite of risks. For that risks must be considered in planning, in realization and in operation, and safety margins must be taken but at a reasonable cost. That is a small level of risks will often remain, due to limitations in costs or because of due to strange hazards, and maybe they will be covered by insurance in cases such as in transport with cars, ships or aircrafts, in agro for hail, or for fire in houses or in forests. These and other decisions about quality, security for men or about business financial risks are sometimes considered with Decision Theories models, using often tools from Statistics or operational Research. The authors have done and are following field surveys about risk consideration in the careers in UPM, making deep analysis of curricula taking into account the new structures of degrees in the EEES Bolonia Plan, and they have considered the risk structures offered by diverse schools of Decision theories. That gives an aspect of the needs and uses, and recommendations about improving in the teaching about risk, that may include special subjects especially oriented for each career, school or faculty, so as to be recommended to be included into the curricula, including an elaboration and presentation format using a multi-criteria decision model

Análisis de resultados de aprendizaje en programas de ingeniería

Introduction: The present review article is the product of the research “Teaching digital modulation techniques in engineering: experiential learning theory “ developed at the Franciso de Paula Santander University and Pontificia Universidad Javeriana in 2022. Problem: The learning outcomes correspond to the statements related to what the future engineer is expected to be able to do, learn, understand and demonstrate. Objective: Analyze learning outcomes in engineering programs globally. Methodology: A methodology based on analysis stages is used for information selection through search filters and inclusion and exclusion criteria, design for the classification of information by geographic location and area of knowledge, with qualitative results by location and trends by area of knowledge. Results: Divergence was observed towards the way in which learning outcomes are evaluated, and convergence towards the need to involve agents external to the academy in the feedback for the learning outcomes evaluation processes. Conclusion: This allows for the identification of individual and collective strengths and weaknesses, which helps to make informed decisions to improve the quality of education. Originality: Originality is based on the way in which the information is analyzed, considering information by areas of knowledge as well as by continents. Limitations: None given the nature of the literature review.Introducción: El presente artículo de revisión es producto de la investigación “Enseñanza de las técnicas de modulación digital en ingeniería: una mirada desde la teoría del aprendizaje experiencial” desarrollada en la Universidad Francisco de Paula Santander y la Pontificia Universidad Javeriana en 2022. Problema: Los resultados de aprendizaje corresponden a los enunciados relacionados con lo que se espera que el futuro ingeniero sea capaz de hacer, aprender, comprender y demostrar. Objetivo: Analizar los resultados de aprendizaje en los programas de ingeniería a nivel mundial. Metodología: Se utiliza una metodología basada en etapas de análisis para la selección de la información a través de filtros de búsqueda y criterios de inclusión y exclusión, diseño para la clasificación de la información por ubicación geográfica y área de conocimiento, con resultados cualitativos por ubicación y tendencias por área de conocimiento. Resultados: Se observó divergencia hacia la forma de evaluar los resultados de aprendizaje y convergencia hacia la necesidad de involucrar a agentes externos a la academia en la retroalimentación de los procesos de evaluación de resultados de aprendizaje. Conclusiones: Esto permite identificar las fortalezas y debilidades individuales y colectivas, lo que ayuda a tomar decisiones informadas para mejorar la calidad de la educación. Originalidad: La originalidad se basa en la forma de analizar la información, considerando la información por áreas de conocimiento, así como por continentes. Limitaciones: Ninguna dada la naturaleza de la revisión bibliográfica

Identification of Novel Components of the Unfolded Protein Response in Arabidopsis

Unfavorable environmental and developmental conditions may cause disturbances in protein folding in the endoplasmic reticulum (ER) that are recognized and counteracted by components of the Unfolded Protein Response (UPR) signaling pathways. The early cellular responses include transcriptional changes to increase the folding and processing capacity of the ER. In this study, we systematically screened a collection of inducible transgenic Arabidopsis plants expressing a library of transcription factors for resistance toward UPR-inducing chemicals. We identified 23 candidate genes that may function as novel regulators of the UPR and of which only three genes (bZIP10, TBF1, and NF-YB3) were previously associated with the UPR. The putative role of identified candidate genes in the UPR signaling is supported by favorable expression patterns in both developmental and stress transcriptional analyses. We demonstrated that WRKY75 is a genuine regulator of the ER-stress cellular responses as its expression was found to be directly responding to ER stress-inducing chemicals. In addition, transgenic Arabidopsis plants expressing WRKY75 showed resistance toward salt stress, connecting abiotic and ER-stress responses