OpenCLIPER: an OpenCL-based C++ Framework for Overhead-Reduced Medical Image Processing and Reconstruction on Heterogeneous Devices

Medical image processing is often limited by the computational cost of the involved algorithms. Whereas dedicated computing devices (GPUs in particular) exist and do provide significant efficiency boosts, they have an extra cost of use in terms of housekeeping tasks (device selection and initialization, data streaming, synchronization with the CPU and others), which may hinder developers from using them. This paper describes an OpenCL-based framework that is capable of handling dedicated computing devices seamlessly and that allows the developer to concentrate on image processing tasks. The framework handles automatically device discovery and initialization, data transfers to and from the device and the file system and kernel loading and compiling. Data structures need to be defined only once independently of the computing device; code is unique, consequently, for every device, including the host CPU. Pinned memory/buffer mapping is used to achieve maximum performance in data transfers. Code fragments included in the paper show how the computing device is almost immediately and effortlessly available to the users algorithms, so they can focus on productive work. Code required for device selection and initialization, data loading and streaming and kernel compilation is minimal and systematic. Algorithms can be thought of as mathematical operators (called processes), with input, output and parameters, and they may be chained one after another easily and efficiently. Also for efficiency, processes can have their initialization work split from their core workload, so process chains and loops do not incur in performance penalties. Algorithm code is independent of the device type targeted

Exploring Twitter by Combining Structured and Unstructured Information

En este artículo mostramos cómo es posible sacar partido de la información estructurada que proporciona la red social Twitter. Los textos escritos en Twitter son cortos y de baja calidad, lo que dificulta la aplicación de técnicas y herramientas que tradicionalmente se han venido usando para procesar textos en lenguaje natural. Sin embargo, Twitter ofrece mucho más que los 140 caracteres de sus mensajes para trabajar. En el ecosistema Twitter hay muchos objetos (tweets, hashtags, usuarios, palabras, ...) y relaciones entre ellos (co-ocurrencia, menciones, re-tuiteos, ...) que ofrecen innumerables posiblidades de procesado alternativo a las técnicas clásicas de PLN. En este trabajo hemos puesto nuestra atención en la tarea de clasificación de tweets. Sólo usando la información de la relación Follow hemos conseguido un clasificador que iguala los resultados de un clasificador basado en bolsas de palabras. Cuando usamos las features de los dos modelos, el resultado de la clasificación mejora en más de 13 puntos porcentuales con respecto a los modelos originales lo que demuestra que ambos clasificadores aportan informaciones complementarias. También hemos aplicado la misma filosofía a la tarea de recopilación del corpus con el que hemos trabajado, usando una técnica de recuperación dinámica basada en relaciones entre entidades Twitter que nos ha permitido construir una colección de tweets más representativa.In this paper we show how it is possible to extract useful knowledge from Twitter structured information that can improve the results of a NLP task. Tweets are short and low quality and this makes it difficult to apply classical NLP techniques to this kind of texts. However, Twitter offers more than 140 characters in their messages to work with. In Twitter ecosystem there are many objects (tweets, hashtags, users, words, ...) and relationships between them (co-occurrence, mentions, re-tweets, ...) that allow us to experiment with alternative processing techniques. In this paper we have worked with a tweet classification task. If we only use knowledge extracted from the relationship Follow we achieve similar results to those of a classifier based on bags of words. When we combine the knowledge from both sources we improve the results in more than 13 percentual points with respect to the original models. This shows that structured information is not only a good source of knowledge but is also complementary to the content of the messages. We also have applied the same philosophy to the task of collecting the corpus for our classification task. In this case we have use a dynamic retrieval technique based on relationships between Twitter entities that allows us to build a collection of more representative tweets.Este trabajo ha sido financiado a través de los proyectos ATTOS-ACOGEUS (TIN2012-38536-C03-02) y AORESCU (P11-TIC-7684 MO)

A modular approach for lexical normalization applied to Spanish tweets

Twitter is a social media platform with widespread success where millions of people continuously express ideas and opinions about a myriad of topics. It is a huge and interesting source of data but most of these texts are usually written hastily and very abbreviated, rendering them unsuitable for traditional Natural Language Processing (NLP). The two main contributions of this work are: the characterization of the textual error phenomena in Twitter and the proposal of a modular normalization system that improves the textual quality of tweets. Instead of focusing on a single technique, we propose an extensible normalization system that relies on the combination of several independent ‘‘expert modules’’, each one addressing an very specific error phenomenon in its own way, thus increasing module accuracy and lowering the module building costs. Broadly speaking, the system resembles to an ‘‘expert board’’: modules independently propose correction candidates for each Out of Vocabulary (OOV) word, rank the candidates and the best one is selected. In order to evaluate our proposal, we perform several experiments using texts from Twitter written in Spanish about a specific topic. The flexibility of defining resources at different language levels (core language, domain, genre) combined with the modular architecture lead to lower costs and a good performance: requiring a minimal effort for building the resources and achieving more than 82% of accuracy compared to the 31% yielded by the baseline.Ministerio de Economía y Competitividad TIN2012-38536-C03-02Junta de Andalucía P11-TIC-7684 M

Planktonic cyanobacteria from the Abreus Reservoir, Cienfuegos, Cuba

The study of the cyanobacteria that make up the phytoplankton community of reservoirs is very important due to the production of toxins by some phytoplankton taxa. The composition and abundance of cyanobacteria and their relationship to physicochemical variables was determined during six months (March, April, June, September, November and December) in 2018 at five stations in the Abreus Reservoir, which is located in the south center of the Cienfuegos province (Cuba). Eleven new taxa were observed in the reservoir grouped into seven families, 14 genera, and 34 species. The toxigenic genera Microcystis and Raphidiopsis were observed at all collection points throughout the year, presenting a potentially persistent toxicity threat in this reservoir. Semi-accumulative blooms were reported in September. Microcystis sp. and Raphidiopsis sp. were the most abundant genera during observed blooms. The abundance of some cyanobacterial genera, including Microcystis, Aphanocapsa, Raphidiopsis and Dolichospermum, were strongly correlated with water temperature and transparency. Microcystin values are reported for the first time in Abreus Reservoir

Perfil laboral, formativo e investigador del profesional de español como lengua extranjera o segunda (ELE/EL2): datos cuantitativos y cualitativos

El presente estudio responde a la necesidad de obtener datos a escala global sobre los profesionales del español como lengua extranjera (ELE) o segunda (EL2), ante la escasez de información de carácter empírico sobre la profesión. Para ello, se dan a conocer las respuestas de 1675 informantes de 84 países obtenidas mediante un cuestionario en línea estructurado en tres bloques temáticos: a) perfil laboral y docente, b) perfil formativo, y c) perfil investigador. A partir del análisis cuantitativo y cualitativo de las respuestas, ofrecemos perspectivas actuales sobre los profesionales del español en el mundo y sobre los diversos ámbitos en los que se desenvuelven. El cotejo de los resultados permite dilucidar algunos de los retos y desafíos inmediatos a los que se enfrentan los profesionales del idioma. El estudio concluye con unas líneas de actuación concretas para cada perfil analizado. Esta es la primera investigación empírica que ofrece datos sobre la profesión desde tres puntos de vista distintos pero complementarios.This study fills the gap in the availability of empirical data on L2 Spanish language professionals around the world. We surveyed 1,675 individuals from 84 countries through an online questionnaire divided into three thematic sections: a) professional profile, b) educational profile, and c) research profile. The analysis of this unique set of quantitative and qualitative data enables us to offer current and novel perspectives on L2 Spanish language professionals worldwide and on the different environments in which they work, as well as to analyse the main challenges and opportunities that L2 Spanish language professionals face. Based on these data, the study concludes with concrete recommended lines of action for each of the three areas. This is the first empirical study to offer data on the profession from three different, but complementary, angles.La publicación de este artículo se enmarca en la beca otorgada a Javier Muñoz-Basols como investigador visitante de la Universidad de Salamanca en el Programa “CEI 15-11 USAL en red” asociado al Centro Internacional del Español. La información aquí presentada pertenece también a los proyectos I+D+i “Identidades y culturas digitales en la educación lingüística” (EDU2014-57677-C2-1-R) y “Género, humor e identidad: desarrollo, consolidación y aplicabilidad de mecanismos lingüísticos en español” (FFI2015-64540-C2-1-P), del programa estatal de investigación, desarrollo e innovación orientado a los retos de la sociedad, del Ministerio de Economía y Competitividad de España. Asimismo, la elaboración del estudio y su publicación han sido posibles gracias al proyecto I+D+i concedido a Alberto Rodríguez-Lifante, “Competencia existencial en el profesorado de español como lengua extranjera en Grecia” (ACIE16-8)

Temperature- and salinity-decoupled overproduction of hydroxyectoine by chromohalobacter salexigens

Hydroxyectoine overproduction by the natural producer Chromohalobacter salexigens is presented in this study. Genetically engineered strains were constructed that at low salinity coexpressed, in a vector derived from a native plasmid, the ectoine (ectABC) and hydroxyectoine (ectD) genes under the control of the ectA promoter, in a temperature-independent manner. Hy- droxyectoine production was further improved by increasing the copies of ectD and using a C. salexigens genetic background unable to synthesize ectoines

Integración de la bicicleta en el sistema de transporte público de la Comunidad de Madrid

[ES] La integración de la bicicleta como parte del sistema de transporte público es un desafío y, a la vez, una oportunidad histórica para favorecer un modelo de transporte más sostenible. La bicicleta ha de ser tomada como aliada y complementaria a otros modos de transporte en una estrategia global de movilidad. En el caso de la Comunidad de Madrid, desde hace muchos años no ha existido una gran tradición de ciclismo urbano aunque el ciclismo deportivo sí que ha mantenido una amplia base social cimentada sobre todo en el boom de la bicicleta de montaña. Una serie de prejuicios, como la célebre afirmación de que “Madrid no es una ciudad para la bicicleta” están siendo afortunadamente superados y no hay más que salir a nuestras calles para constatarlo. Tanto en la capital como en el resto de la región madrileña, la visibilidad de la bicicleta es cada día mayor.Delgado Ruiz, MÁ.; Criado Fernández, L.; Rodríguez Ranz, J.; Moya Porras, J. (2016). Integración de la bicicleta en el sistema de transporte público de la Comunidad de Madrid. En XII Congreso de ingeniería del transporte. 7, 8 y 9 de Junio, Valencia (España). Editorial Universitat Politècnica de València. 139-142. https://doi.org/10.4995/CIT2016.2016.4271OCS13914

Involvement of EupR, a response regulator of the NarL/FixJ family, in the control of the uptake of the compatible solutes ectoines by the halophilic bacterium Chromohalobacter salexigens

de Lucena DK, Pühler A, Weidner S. The role of sigma factor RpoH1 in the pH stress response of Sinorhizobium meliloti. BMC Microbiology. 2010;10(1): 256.Background: Environmental pH stress constitutes a limiting factor for S. meliloti survival and development. The response to acidic pH stress in S. meliloti is versatile and characterized by the differential expression of genes associated with various cellular functions. The purpose of this study was to gain detailed insight into the participation of sigma factors in the complex stress response system of S. meliloti 1021 using pH stress as an effector. Results: In vitro assessment of S meliloti wild type and sigma factor mutants provided first evidence that the sigma factor RpoH1 plays a major role in the pH stress response. Differential expression of genes related to rhizobactin biosynthesis was observed in microarray analyses performed with the rpoH1 mutant at pH 7.0. The involvement of the sigma factor RpoH1 in the regulation of S. meliloti genes upon pH stress was analyzed by comparing timecourse experiments of the wild type and the rpoH1 mutant. Three classes of S. meliloti genes could be identified, which were transcriptionally regulated in an RpoH1-independent, an RpoH1-dependent or in a complex manner. The first class of S. meliloti genes, regulated in an RpoH1-independent manner, comprises the group of the exopolysaccharide I biosynthesis genes and also the group of genes involved in motility and flagellar biosynthesis. The second class of S. meliloti genes, regulated in an RpoH1-dependent manner, is composed of genes known from heat shock studies, like ibpA, grpE and groEL5, as well as genes involved in translation like tufA and rplC. Finally, the third class of S. meliloti genes was regulated in a complex manner, which indicates that besides sigma factor RpoH1, further regulation takes place. This was found to be the case for the genes dctA, ndvA and smc01505. Conclusions: Clustering of time-course microarray data of S. meliloti wild type and sigma factor rpoH1 mutant allowed for the identification of gene clusters, each with a unique time-dependent expression pattern, as well as for the classification of genes according to their dependence on RpoH1 expression and regulation. This study provided clear evidence that the sigma factor RpoH1 plays a major role in pH stress response

Unravelling the adaptation responses to osmotic and temperature stress in Chromohalobacter salexigens, a bacterium with broad salinity tolerance

Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. Osmoprotection is achieved by the accumulation of compatible solutes either by transport (betaine, choline) or synthesis (mainly ectoine and hydroxyectoine). Ectoines can play additional roles as nutrients and, in the case of hydroxyectoine, in thermotolerance. A supplementary solute, trehalose, not present in cells grown at 37°C, is accumulated at higher temperatures, suggesting its involvement in the response to heat stress. Trehalose is also accumulated at 37°C in ectoine-deficient mutants, indicating that ectoines suppress trehalose synthesis in the wild-type strain. The genes for ectoine (ectABC) and hydroxyectoine (ectD, ectE) production are arranged in three different clusters within the C. salexigens chromosome. In order to cope with changing environment, C. salexigens regulates its cytoplasmic pool of ectoines by a number of mechanisms that we have started to elucidate. This is a highly complex process because (i) hydroxyectoine can be synthesized by other enzymes different to EctD (ii) ectoines can be catabolized to serve as nutrients, (iii) the involvement of several transcriptional regulators (σS, σ32, Fur, EctR) and hence different signal transduction pathways, and (iv) the existence of post-trancriptional control mechanisms. In this review we summarize our present knowledge on the physiology and genetics of the processes allowing C. salexigens to cope with osmotic stress and high temperature, with emphasis on the transcriptional regulation

Antiparasitic Tannin-Rich Plants from the South of Europe for Grazing Livestock: A Review

Internal parasites are one of the main causes of health threats in livestock production, especially in extensive livestock farming. Despite the environmental toxic effects (loss of dung beetles, biodiversity, and other issues) and resistance phenomenon derived from their prolonged use, anti-parasitic chemical pharmaceuticals are frequently used, even in organic farming. Such a situation within the context of climate change requires urgent exploration of alternative compounds to solve these problems and apparent conflicts between organic farming objectives regarding the environment, public health, and animal health. This review is focused on some plants (Artemisia spp., Cichorium intybus L., Ericaceae family, Hedysarum coronarium L., Lotus spp., Onobrychis viciifolia Scop.) that are well known for their antiparasitic effect, are voluntarily grazed and ingested, and can be spontaneously found or cultivated in southern Europe and other regions with a Mediterranean climate. The differences found between effectiveness, parasite species affected, in vitro/in vivo experiments, and active compounds are explored. A total of 87 papers where antiparasitic activity of those plants have been studied are included in this review; 75% studied the effect on ruminant parasites, where gastrointestinal nematodes were the parasite group most studied (70%), and these included natural (31%) and experimental (37%) infections