578 research outputs found
Jmodeltest.org: selection of nucleotide substitution models on the cloud
No full textThis is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record Jose Manuel Santorum, Diego Darriba, Guillermo L. Taboada, David Posada; jmodeltest.org: selection of nucleotide substitution models on the cloud, Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1310–1311, https://doi.org/10.1093/bioinformatics/btu032[Abstract] The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis. Different tools exist to accomplish this task, among which jModelTest 2 (jMT2) is one of the most popular. Still, to deal with large DNA alignments with hundreds or thousands of loci, users of jMT2 need to have access to High Performance Computing clusters, including installation and configuration capabilities, conditions not always met. Here we present jmodeltest.org, a novel web server for the transparent execution of jMT2 across different platforms and for a wide range of users. Its main benefit is straightforward execution, avoiding any configuration/execution issues, and reducing significantly in most cases the time required to complete the analysis.
Availability and implementation:jmodeltest.org is accessible using modern browsers, such as Firefox, Chrome, Opera, Safari and IE from http://jmodeltest.org. User registration is not mandatory, but users wanting to have additional functionalities, like access to previous analyses, have the possibility of opening a user account.European Research Council; 2007-Stg 203161- PHYGENOMMinisterio de Ciencia e Innovación; TIN2010-1673
Dollarization and semi-dollarization in Ecuador
No full textOver the 1980s and 1990s, GDP growth had stagnated because of oil export price volatility and natural disasters, the sacrifice of capital formation to heavy external public debt service, and incomplete and uneven structural reform. The exchange rate depreciation that proved continually necessary to sustain the net-export surplus and limit external debt accumulation induced Ecuadorians to dollarize spontaneously. The 1998 shocks affected real economic activity--hence bank loan portfolios, and widened the fiscal and current acccount deficits. The external imbalance led to exchange rate depreciation. Dollar-denominated bank loans whose borrowers lacked dollar income increasingly turned non-performing. At the same time, the depreciation swelled the locla currency value of dollar deposit liabilities. Many depositors, fearing that banks had become unsafe, withdrew, and over 1999 the Central Bank had to provide banks massive liquidity support. By year's end, the resulting monetary issue ledto the exchange rate collapse and incipient hyperinflation that forced the move to full dollarization. Ecuador's Central Bank will continue operating, using its foreign exchange holdings to carry out limited liquidity management and lender-of-last-resort activities. Ecuador's public accounts and banking system remain vulnerable to commodity-price and natural shocks. Exchange rate adjustment and monetary expansion are no longer available, however, to manage the external accounts, accommodate the public deficit, or assist failing banks. Further structural reform remains essential to assure fiscal discipline and banking system safety.Banks&Banking Reform,Economic Theory&Research,Payment Systems&Infrastructure,Environmental Economics&Policies,Public Sector Economics&Finance,Economic Theory&Research,Banks&Banking Reform,Environmental Economics&Policies,Public Sector Economics&Finance,Financial Intermediation
Ichtiologists of the Argentine: Guillermo Martínez Achenbach.
No full textThis series will include all those people who, by means of their contributions, greatand small, played a part in the consolidation of ichthyology in Argentina.The general plan of this work consists of individual factsheets containing a list ofworks by each author, along with reference bibliography and, whenever possible,personal pictures and additional material.The datasheets will be published primarily in chronological order, although this issubject to change by the availability of materials for successive editions.This work represents another approach for the recovery and revalorization of thosewho set the foundations of Argentine ichthyology while in diverse historicalcircumstances.I expect this to be the beginning of a major work that achieves the description ofsuch a significant part of the history of natural sciences in Argentina. (PDF has 16 pages.)ProBiota: Programa para el estudio y uso sustentable de la biota australLÓPEZ, H. L.; C. A. VIRASORO & J. PONTE GÓMEZ. 2009. Ictiólogos de la Argentina: Guillermo Martínez Achenbach. ProBiota, FCNyM, UNLP, Serie Técnica Didactica, La Plata, Argentina, 14: 1-15. ISSN 1515-9329
Estructura de suelos manejados en siembra directa : efectos sobre la extracción y conversión de agua en el cultivo de soja (Glycine max L. Merril)
No full textEsta tesis tuvo por objetivo avanzar en el entendimiento de los factores que favorecen la compactación de suelos en siembra directa, analizar los mecanismos por los cuales las compactaciones afectan la productividad del agua en soja (Glycine max L. Merril), y analizar la efectividad de intervenciones mecánicas sobre su reversión. Para esto se 6 combinaron: muestreos de suelo a nivel regional, experimentos en invernáculo, un meta7 análisis de publicaciones y experimentos de campo. El muestreo regional mostró que la compactación entre 10-20 cm es un proceso ampliamente extendido, independientemente de la intensidad y aportes de carbono de las rotaciones. Los experimentos controlados mostraron que la compactación genera alteraciones en el crecimiento del sistema de raíces en su conjunto, no sólo en las raíces directamente afectadas. La compactación retrasó la profundización de raíces, y redujo la proliferación de raíces en estratos superficiales y profundos, más allá de 150 cm. Se observaron mecanismos compensatorios a nivel de absorción de agua por unidad de raíz, pero éstos se vieron limitados ante reducciones marcadas en la longitud de raíces. La compactación generó otros efectos que ameritan mayores estudios: redujo la cantidad y actividad de los nódulos directamente e indirectamente afectados. De acuerdo al meta-análisis, la descompactación mecánica permite aliviar las compactaciones y aumentar los rendimientos de soja de la región pampeana (~540 kg.ha-1 en promedio). La descompactación permitió incrementar la captación de agua en el perfil, y su extracción por el cultivo, aunque no la eficiencia de conversión a biomasa. Los efectos no parecen prolongarse más allá de 18-24 meses. Esta tesis permitió una mejor comprensión de los mecanismos por los cuales el deterioro estructural de los suelos en SD, y particularmente la compactación, afecta la utilización de agua y los rendimientos en soja, y en qué medida la descompactación puede aliviar estos efectos
Análisis y Diseño de una Herramienta de Informes de Productividad de Desarrollo Software
No full text[Resumen] A lo largo de este proyecto se analizan y diseñan las posibles soluciones al problema de no haber métricas multiproyecto en los gestores de proyectos, caso concreto del gestor Jira. Este problema es de gran importancia en las organizaciones en las que abundan los proyectos y en las que los empleados están asignados a varios equipos. La relevancia de tener información sobre los proyectos con una visión general es vital para poder obtener la mayor productividad en los mismos y es por ello que se propone este trabajo. Veremos el estado de las herramientas de gestión de proyectos y control de versiones que más popularidad tienen en los entornos de desarrollo software, profundizando en las opciones de Atlassian. Los métodos que tenemos para generar los informes de productividad los analizaremos y diseñaremos, además de hacer pruebas de concepto para ver los resultados posibles.[Abstract] Throughout this project, possible solutions to the problem of not having multi-project
metrics in the project managers, specific case of the Jira manager, are analyzed and designed.
This problem has great importance in organizations that have multiple projects and in which
employees are assigned to several teams. The relevance of having information about projects
with an overview is vital to be able to obtain the highest productivity in projects and that is
why this bachelor thesis is proposed.
We will see the status of the project management and version control tools that are most
popular in software development environments, deepening in Atlassian options. The methods
we have to generate the productivity reports will be analyzed and designed, as well as proof
of concept to see the possible results.Traballo fin de grao (UDC.FIC). Enxeñaría informática. Curso 2019/202
Nonblocking collectives for scalable Java communications
No full textThis is the peer reviewed version of the following article: Ramos, S., Taboada, G. L., Expósito, R. R., & Touriño, J. (2015). Nonblocking collectives for scalable Java communications. Concurrency and Computation: Practice and Experience, 27(5), 1169-1187, which has been published in final form at https://doi.org/10.1002/cpe.3279. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.[Abstract] This paper presents a Java implementation of the recently published MPI 3.0 nonblocking message passing collectives in order to analyze and assess the feasibility of taking advantage of these operations in shared memory systems using Java. Nonblocking collectives aim to exploit the overlapping between computation and communication for collective operations to increase scalability of message passing codes, as it has been carried out for nonblocking point‐to‐point primitives. This scalability has become crucial not only for clusters but also for shared memory systems because of the current trend of increasing the number of cores per chip, which is leading to the generalization of multi‐core and many‐core processors. Message passing libraries based on remote direct memory access, thread‐based progression, or implementing pure multi‐threading shared memory support could potentially benefit from the lack of imposed synchronization by nonblocking collectives. But, although the distributed memory scenario has been well studied, the shared memory one has not been tackled yet. Hence, nonblocking collectives support has been included in FastMPJ, a Message Passing in Java (MPJ) implementation, and evaluated on a representative shared memory system, obtaining significant improvements because of overlapping and lack of implicit synchronization, and with barely any overhead imposed over common blocking operations.Ministerio de Ciencia e Innovación; TIN2010-16735Xunta de Galicia; CN2012/211Xunta de Galicia; GRC2013/05
Common variants of NFE2L2 gene predisposes to acute respiratory distress syndrome in patients with severe sepsis
No full textThis work was funded by the Instituto de Salud Carlos III (CB06/06/1088, PI10/00393, PI14/00844, FI11/00074) and by the European Regional Development Funds “A way of making Europe.” MPY was supported by a post-doctoral fellowship from Fundación Ramón Areces, Madrid, Spain.Acosta-Herrera, M., Pino-Yanes, M., Blanco, J., Ballesteros, J.C., Ambrós, A., Corrales, A., Gandía, F., Subirá, C., Domínguez, D., Baluja, A., Añón, J.M., Adalia, R., Pérez-Méndez, L., Flores, C., Villar, J., Fernández, L.R., Espinosa, E., Campo, R.D., Fernández, R., Rodríguez, J.A., álvarez, J., González, E., Hernández, O., Solano, R., Pérez-Crespo, J., Arellano, P., Zavala, E., Martínez, J., Torres, A., Badia, J., Alba, F., Corpas, R., Muriel, A., Sagredo, V., Taboada, F., Albaiceta, G.M., Bobillo, F., Tamayo, L., Labattut, A.G., Carriedo, D., Collado, J., Diaz, F.J., Valledor, M., Antuña, M., de Frutos, M., López, M.J., Cortina, J.J., Saldaña, T., Caballero, A., álvarez, T., álvarez, B., Sandoval, J
Low‐latency Java communication devices on RDMA‐enabled networks
No full textThis is the peer reviewed version of the following article: Expósito, R. R., Taboada, G. L., Ramos, S., Touriño, J., & Doallo, R. (2015). Low‐latency Java communication devices on RDMA‐enabled networks. Concurrency and Computation: Practice and Experience, 27(17), 4852-4879., which has been published in final form at https://doi.org/10.1002/cpe.3473. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.[Abstract] Providing high‐performance inter‐node communication is a key capability for running high performance computing applications efficiently on parallel architectures. In fact, current systems deployments are aggregating a significant number of cores interconnected via advanced networking hardware with Remote Direct Memory Access (RDMA) mechanisms, that enable zero‐copy and kernel‐bypass features. The use of Java for parallel programming is becoming more promising thanks to some useful characteristics of this language, particularly its built‐in multithreading support, portability, easy‐to‐learn properties, and high productivity, along with the continuous increase in the performance of the Java virtual machine. However, current parallel Java applications generally suffer from inefficient communication middleware, mainly based on protocols with high communication overhead that do not take full advantage of RDMA‐enabled networks. This paper presents efficient low‐level Java communication devices that overcome these constraints by fully exploiting the underlying RDMA hardware, providing low‐latency and high‐bandwidth communications for parallel Java applications. The performance evaluation conducted on representative RDMA networks and parallel systems has shown significant point‐to‐point performance increases compared with previous Java communication middleware, allowing to obtain up to 40% improvement in application‐level performance on 4096 cores of a Cray XE6 supercomputer.Ministerio de Economía y Competitividad; TIN2013-42148-PXunta de Galicia; GRC2013/055Ministerio de Educación y Ciencia; AP2010-434
El racionalismo metapoético de Guillermo Carnero (1971-1977): más allá de las tesis bousoñianas
No full textGuillermo Carnero’s metapoetry has been interpreted in different ways; one of the most important has followed Carlos Bousoño’s prologue to Ensayo de una teoría de la visión (Poesía 1966-1977). It is proposed to rethink the Bousoñian idea that the Valencian metapoetry manifests itself as an «incapacity of rationalist reason to know reality» (1979, 25). Through the analysis of three poems by the author published between 1971 and 1977, the existence of a metapoetic project of rationalist knowledge of reality is suggested. It is also argued that Carnero’s metapoetry operates as a new rationalist reason that combines epistemological search and demystifying irony, recovering aspects of Neoclassicism of 18th century, ideas of Wittgenstein, linguistics of Saussure and from some poststructuralist schools.La metapoesía de Guillermo Carnero se ha interpretado de distintas maneras; una de las más importantes ha seguido el prólogo de Carlos Bousoño a Ensayo de una teoría de la visión (Poesía 1966-1977). Se propone repensar la idea bousoñiana de que la metapoesía del valenciano se manifiesta como una «incapacidad de la razón racionalista para conocer la realidad» (1979, 25). Mediante el análisis de tres poemas del autor publicados entre 1971 y 1977 se sugiere la existencia de un proyecto metapoético de conocimiento racionalista de la realidad. También se plantea que la metapoesía de Carnero opera como una nueva razón racionalista que aúna búsqueda epistemológica e ironía desmitificadora, recuperando aspectos del Neoclasicismo del s. XVIII, de las ideas de Wittgenstein, de la lingüística de Saussure y de algunas escuelas posestructuralistas
Exploratory Data Analysis and Data Envelopment Analysis of Urban Rail Transit
No full text[Abstract]
This paper deals with the efficiency and sustainability of urban rail transit (URT) using exploratory data analytics (EDA) and data envelopment analysis (DEA). The first stage of the proposed methodology is EDA with already available indicators (e.g., the number of stations and passengers), and suggested indicators (e.g., weekly frequencies, link occupancy rates, and CO2 footprint per journey) to directly characterize the efficiency and sustainability of this transport mode. The second stage is to assess the efficiency of URT with two original models, based on a thorough selection of input and output variables, which is one of the key contributions of EDA to this methodology. The first model compares URT against other urban transport modes, applicable to route personalization, and the second scores the efficiency of URT lines. The main outcome of this paper is the proposed methodology, which has been experimentally validated using open data from the Transport for London (TfL) URT network and additional sources.Ministerio de Economía, Industria y Competitividad; TIN2016-75845-PAgencia Estatal de Investigación; SNEO-20161147Xunta de Galicia; ED431G2019/01Xunta de Galicia; ED431C 2017/04Xunta de Galicia; ED431G2019/0
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