924 research outputs found

    Protein multi-scale organization through graph partitioning and robustness analysis: Application to the myosin-myosin light chain interaction

    Full text link
    Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the intricate coupling between the different scales. Starting from a physico-chemical atomistic network of interactions that encodes the structure of the protein, we introduce a methodology based on multi-scale graph partitioning that can uncover partitions and levels of organization of proteins that span the whole range of scales, revealing biological features occurring at different levels of organization and tracking their effect across scales. Additionally, we introduce a measure of robustness to quantify the relevance of the partitions through the generation of biochemically-motivated surrogate random graph models. We apply the method to four distinct conformations of myosin tail interacting protein, a protein from the molecular motor of the malaria parasite, and study properties that have been experimentally addressed such as the closing mechanism, the presence of conserved clusters, and the identification through computational mutational analysis of key residues for binding.Comment: 13 pages, 7 Postscript figure

    ICE-NODE: Integration of Clinical Embeddings with Neural Ordinary Differential Equations

    Get PDF
    Early diagnosis of disease can lead to improved health outcomes, including higher survival rates and lower treatment costs. With the massive amount of information available in electronic health records (EHRs), there is great potential to use machine learning (ML) methods to model disease progression aimed at early prediction of disease onset and other outcomes. In this work, we employ recent innovations in neural ODEs combined with rich semantic embeddings of clinical codes to harness the full temporal information of EHRs. We propose ICE-NODE (Integration of Clinical Embeddings with Neural Ordinary Differential Equations), an architecture that temporally integrates embeddings of clinical codes and neural ODEs to learn and predict patient trajectories in EHRs. We apply our method to the publicly available MIMIC-III and MIMIC-IV datasets, and we find improved prediction results compared to state-of-the-art methods, specifically for clinical codes that are not frequently observed in EHRs. We also show that ICE-NODE is more competent at predicting certain medical conditions, like acute renal failure, pulmonary heart disease and birth-related problems, where the full temporal information could provide important information. Furthermore, ICE-NODE is also able to produce patient risk trajectories over time that can be exploited for further detailed predictions of disease evolution

    Distributional extensions of Carollia castanea and Micronycteris minuta from Guatemala, Central America

    Get PDF
    Field expeditions in 2011 that inventoried the terrestrial vertebrate fauna of two wildlife protected areas in the tropical Caribbean of Guatemala have produced the first confirmed records of two bats for the country: the white-bellied big-eared bat, Micronycteris (Schizonycteris) minuta (Gervais 1856) and the Chesnut short-tailed bat Carollia castanea H. Allen, 1890, both of neotropical distribution and with their current northern limit at Lancetilla, Honduras. The record of M. minuta at Sierra de Caral, Guatemala extends the range of this species 137 km to the west, and the record of C. castanea at Cerro San Gil extends its range 147 km to the west

    Some Results of the Educational Experiment APIS (Cervantes Mission on Board ISS)

    Get PDF
    Some results of the analysis of the pictures taken along the performance of the Análisis de Propiedades Inerciales de Sólidos, Analysis of the Inertia Properties of Solid Bodies (APIS) experiment carried out in the Cervantes mission on board ISS, are presented. APIS was an educational experiment devoted to take advantage of the unique conditions of absence of relative gravity forces of a space platform such as ISS, to show some of the characteristics of the free rotational motion of a solid body, which are impossible to carry out on earth. This field of experimental research has application to aerospace engineering science (e.g. attitude control of spacecrafts), to astrophysical sciences (e.g. state of rotation and tumbling motions of asteroids) and to engineering education. To avoid the effect of the ambient atmosphere loads on the motion, the test body is placed inside a sphere, which reduces the effect of the aerodynamic forces to just friction. The drastic reduction of the effect of the surrounding air during the short duration of the experimental sequences allows us to compare the actual motion with the known solutions for the solid body rotation in vacuum. In this paper, some selected, relevant sequences of the sphere enclosing a body with a nominal cylindrical inertia tensor, put into rotation by the astronaut, are shown; the main problems to extract the information concerning the characteristic parameters of the motion are outlined, and some of the results obtained concerning the motion of the test probe are included, which show what seems to be a curious and unexpected solution of the Euler equations for the solid body rotation in vacuum, without energy dissipation, when the angular momentum is almost perpendicular to the axisymmetry axis

    Forage Quality and the Environment

    Get PDF
    The influence of environmental factors on forage quality of temperate and tropical grasses has been reviewed by several authors, who summarized how light, temperature, drought and soil nutrients influence chemical composition, and digestibility of forages grown in contrasting areas of the world. The effects of season of the year on forage growth, grazing behavior and animal performance have also been the subject of numerous papers and reviews. However, there are few recent reviews that summarize how changes in climatic and edaphic factors influence forage quality of legumes with variable levels of condensed tannins (CT), which are important secondary compounds in some temperate and tropical legume species adapted to acid infertile soils. In this paper we summarize properties of CT and their positive and negative effects on forage quality of legumes. We also review published work on the effect of temperature, drought, CO2 concentration, season of the year and soil fertility on the accumulation of CT in temperate and tropical legumes. Results from experiments under controlled conditions indicate that high temperature alone can significantly increase the accumulation of CT in some temperate legume species (i.e. Lotus pedunculatus) but not in others (i.e. L. corniculatus). However, the effect of low or high temperature on accumulation of CT is considerably greater when accompanied with other environmental factors such as drought, high CO2 concentration and soil nutrient deficiencies. Soil nutrient deficiencies can have a major effect on elevation of CT concentration and overall feed value of temperate and tropical legumes, but only when deficiencies are such that they affect plant growth. Soil fertility and climatic conditions affect not only the concentration of CT but also their monomer composition and MW (molecular weight), as was observed in a tropical legume species well adapted to acid infertile soils. The nutritional significance of these findings are not all that well understood, but it would seem that CT in forage legumes are not a uniform chemical entity given that they can change with edaphic and climatic factors. Finally we suggest that there is a need to investigate alternatives to enhance the feed value of legumes with tannins adapted to acid soils through selection of genotypes with less CT and /or through manipulation of environmental factors such as soil fertility. For this we need to better understand how edaphic and climatic factors affect not only accumulation of CT but also their chemical structure and biological activity and relate these changes to forage intake, digestibility, N utilization, and, ultimately, to performance of ruminant animals

    Using network-flow techniques to solve an optimization problem from surface-physics

    Full text link
    The solid-on-solid model provides a commonly used framework for the description of surfaces. In the last years it has been extended in order to investigate the effect of defects in the bulk on the roughness of the surface. The determination of the ground state of this model leads to a combinatorial problem, which is reduced to an uncapacitated, convex minimum-circulation problem. We will show that the successive shortest path algorithm solves the problem in polynomial time.Comment: 8 Pages LaTeX, using Elsevier preprint style (macros included

    Forage quality and the environment

    Get PDF

    Do teams alleviate or exacerbate the extrapolation bias in the stock market?

    Get PDF
    Investigamos la manera en que los equipos influyen en la extrapolación de rentabilidades, un sesgo en la formación de creencias que es generalizado a nivel individual y crucial para los modelos conductuales de valoración de activos. Utilizando una muestra de gestores de fondos de inversión en acciones de EEUU, encontramos que los equipos atenúan el sesgo de extrapolación de sus propios miembros en un 75 %. Esta reducción no se debe al aprendizaje ni a diferencias en la remuneración, la carga de trabajo o los objetivos de inversión entre los fondos administrados individualmente y los administrados en equipo. En cambio, proporcionamos evidencias que apoyan la hipótesis de que la reducción del sesgo proviene de los miembros del equipo que participan en una reflexión cognitiva más profunda.We investigate how teams impact return extrapolation, a bias in belief formation which is pervasive at the individual level and crucial to behavioral asset-pricing models. Using a sample of US equity money managers and a within-subject design, we find that teams attenuate their own members’ extrapolation bias by 75%. This reduction is not due to learning or differences in compensation, workload, or investment objectives between solo-managed and team-managed funds. Rather, we provide supportive evidence that team members engaging in deeper cognitive reflection can explain the bias reduction
    corecore