ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

Background: Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results: We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion: ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.

Visualization of flow fields in the web platform

Visualization of vector fields plays an important role in research activities nowadays -- Web applications allow a fast, multi-platform and multi-device access to data, which results in the need of optimized applications to be implemented in both high-performance and low-performance devices -- Point trajectory calculation procedures usually perform repeated calculations due to the fact that several points might lie over the same trajectory -- This paper presents a new methodology to calculate point trajectories over highly-dense and uniformly-distributed grid of points in which the trajectories are forced to lie over the points in the grid -- Its advantages rely on a highly parallel computing architecture implementation and in the reduction of the computational effort to calculate the stream paths since unnecessary calculations are avoided, reusing data through iterations -- As case study, the visualization of oceanic currents through in the web platform is presented and analyzed, using WebGL as the parallel computing architecture and the rendering Application Programming Interface

Characterization of the susceptibility of the vineyard of Château Margaux to the main fungal-like and diseases

Mestrado Vinifera Euromaster - Instituto Superior de Agronomia - UL

A reflective characterization of occasional user

This work revisits established user classifications and aims to characterise a historically unspecified user category, the Occasional User (OU). Three user categories, novice, intermediate and expert, have dominated the work of user interface (UI) designers, researchers and educators for decades. These categories were created to conceptualise user's needs, strategies and goals around the 80s. Since then, UI paradigm shifts, such as direct manipulation and touch, along with other advances in technology, gave new access to people with little computer knowledge. This fact produced a diversification of the existing user categories not observed in the literature review of traditional classification of users. The findings of this work include a new characterisation of the occasional user, distinguished by user's uncertainty of repetitive use of an interface and little knowledge about its functioning. In addition, the specification of the OU, together with principles and recommendations will help UI community to informatively design for users without requiring a prospective use and previous knowledge of the UI. The OU is an essential type of user to apply user-centred design approach to understand the interaction with technology as universal, accessible and transparent for the user, independently of accumulated experience and technological era that users live in.

Integrating a web-enhanced study module into the accounting classroom: student perceptions and academic results.

Student engagement in a course is an important precursor of academic success. Within the discipline of accounting, successful completion of the self-study component of the course is a critical aspect of student engagement and success. Web-enhanced learning offers an apportunity to provide a structured learning environment with improved access to learning tools and immediate feedback that can improve completion rates of self-study activities. This study evaluated student perceptions and academic results relating to the implementation of a web-enhanced study module in an introductory accounting course in Business Administration department at John Abbott College. The results of this study indicate both a strongly favourable student perception of the web-enhanced study module as well as improved homework completion rates and academic results, particularly among students that had previously performed poorly within a tradional, non web-enhanced seelf study environment.||Résumé : L'engagement des élèves dans un cours est un précurseur important de la réussite scolaire. Dans la discipline de la comptabilité, la réussite de la composante d'auto-apprentissage du cours est un aspect critique de l'engagement et la réussite des élèves. Amélioration de l'apprentissage par Internet offre la possibilité de fournir un environnement d'apprentissage structuré avec un meilleur accès aux outils d'apprentissage et la rétroaction immédiate qui peuvent améliorer les taux d'achèvement des activités d'auto-apprentissage. Cette étude a évalué les perceptions des élèves et les résultats scolaires relatives à la mise en oeuvre d'un module d'étude avec accès Internet à un cours d'introduction à la comptabiblilté dans le département d'administration des affaires au Cégep John Abbott. Les résultats de cette étude indiquent à la fois une perception des étudiants fortement favorable du module d'étude avec accès Internet ansi que l'amélioration des taux d'achèvement des devoirs et des résultats scolaires en particulier chez les élèves qui avaient de mauvais résultats dans un cadre traditionnel, l'environnement d'étude non accès Internet.

Caracterización sociodemográfica de las enfermedades huérfanas en Colombia

Las enfermedades huérfanas en Colombia, se definen como aquellas crónicamente debilitantes, que amenazan la vida, de baja prevalencia (menor 1/5000) y alta complejidad. Se estima que a nivel mundial existen entre 6000 a 8000 enfermedades raras diferentes(1). Varios países a nivel mundial individual o colectivamente, en los últimos años han creado políticas e incentivos para la investigación y protección de los pacientes con enfermedades raras. Sin embargo, a pesar del creciente número de publicaciones; la información sobre su etiología, fisiología, historia natural y datos epidemiológicos persiste escasa o ausente. Los registros de pacientes, son una valiosa herramienta para la caracterización de las enfermedades, su manejo y desenlaces con o sin tratamiento. Permiten mejorar políticas de salud pública y cuidado del paciente, contribuyendo a mejorar desenlaces sociales, económicos y de calidad de vida. En Colombia, bajo el decreto 1954 de 2012 y las resoluciones 3681 de 2013 y 0430 de 2013 se creó el fundamento legal para la creación de un registro nacional de enfermedades huérfanas. El presente estudio busca determinar la caracterización socio-demográfica y la prevalencia de las enfermedades huérfanas en Colombia en el periodo 2013. Métodos: Se realizó un estudio observacional de corte transversal de fuente secundaria sobre pacientes con enfermedades huérfanas en el territorio nacional; basándose en el registro nacional de enfermedades huérfanas obtenido por el Ministerio de Salud y Protección Social en el periodo 2013 bajo la normativa del decreto 1954 de 2012 y las resoluciones 3681 de 2013 y 0430 de 2013. Las bases de datos obtenidas fueron re-categorizadas en Excel versión 15.17 para la extracción de datos y su análisis estadístico posterior, fue realizado en el paquete estadístico para las ciencias sociales (SPSS v.20, Chicago, IL). Resultados: Se encontraron un total de 13173 pacientes con enfermedades huérfanas para el 2013. De estos, el 53.96% (7132) eran de género femenino y el 46.03% (6083) masculino; la mediana de la edad fue de 28 años con un rango inter-cuartil de 39 años, el 9% de los pacientes presentaron discapacidad. El registro contenía un total de 653 enfermedades huérfanas; el 34% del total de las enfermedades listadas en nuestro país (2). Las patologías más frecuentes fueron el Déficit Congénito del Factor VIII, Miastenia Grave, Enfermedad de Von Willebrand, Estatura Baja por Anomalía de Hormona de Crecimiento y Displasia Broncopulmonar. Discusión: Se estimó que aproximadamente 3.3 millones de colombianos debían tener una enfermedad huérfana para el 2013. El registro nacional logró recolectar datos de 13173 (0.4%). Este bajo número de pacientes, marca un importante sub-registro que se debe al uso de los códigos CIE-10, desconocimiento del personal de salud frente a las enfermedades huérfanas y clasificación errónea de los pacientes. Se encontraron un total de 653 enfermedades, un 34% de las enfermedades reportadas en el listado nacional de enfermedades huérfanas (2) y un 7% del total de enfermedades reportadas en ORPHANET para el periodo 2013 (3). Conclusiones: La recolección de datos y la sensibilización sobre las enfermedades huérfanas al personal de salud, es una estrategia de vital importancia para el diagnóstico temprano, medidas específicas de control e intervenciones de los pacientes. El identificar apropiadamente a los pacientes con este tipo de patologías, permite su ingreso en el registro y por ende mejora el sub-registro de datos. Sin embargo, cabe aclarar que el panorama ideal sería, el uso de un sistema de recolección diferente al CIE-10 y que abarque en mayor medida la totalidad de las enfermedades huérfanas.

VALORACIÓN ECONÓMICA DE LOS RECURSOS HÍDRICOS EN LAS CUENCAS DE LOS RÍOS BANANO Y BANANITO

Entre los meses de marzo y setiembre del 2004, el Centro Internacional en Política Económica para el Desarrollo Sostenible de la Universidad Nacional (CINPE-UNA) elaboró el estudio Valoración económica de los recursos hI’dricos en las cuencas de los rfos Banano y Bananito3 . El objetivo general de éste responde a “estimar el valor del recurso hídrico en las cuencas de los ríos Banano y Bananito, en función de los usos prioritarios, para la recomendación de mecanismos efectivos para la sostenibilidad de un sistema de compensación por los servicios hidrológicos”. Para cumplir con este objetivo se plantean los siguientes objetivos específicos: (1) identificar el método de valoración económica para el recurso hídrico más apropiado dadas las condiciones de la zona, (2) cuantificar los servicios hidrológicos en las cuencas de los ríos Banano y Bananito en función de los principales usos, y (3) recomendar un mecanismo de pago voluntario por el servicio ambiental hídrico, basado en los resultados del estudio, que provea al Área de Conservación La Amistad Caribe (ACLA-C) los elementos para el desarrollo de una experiencia concreta.Producto de una exhaustiva revisión bibliográfica y dados los objetivos del estudio se seleccionó el Análisis de Múltiples Criterios (AMC), como la metodología marco para la valoración económica. Esto implica la aplicación de un método no tradicional, que permite combinar variables cuantitativas y cualitativas. A este respecto, el uso de una metodología participativa y multisectorial hizo posible la participación de los principales grupos de actores usuarios del agua. que se clasificaron en cinco grupos: (1) Asociaciones Administradoras de Acueductos Rurales (ASADAS) y acueductos rurales, (2) ONG’s y organizaciones comunales, (3) sociedad civil, (4) empresa privada y (5) sector público.Luego de sistematizar la información recabada durante las 23 sesiones de consulta participativa. se procede al análisis de los datos, que sirven de insumos para realizar la valoración económica y, finalmente, el diseño de la propuesta de mecanismos de cobro por grupo de usuarios para el pago por servicios ambientales. Los resultados finales se presentan mediante el uso de matrices y gráficos de telaraña.Este informe presenta los avances correspondientes al primer objetivo específico. Asimismo, incluye los comentarios y las sugerencias realizadas durante y posterior al taller de discusión con representantes de PROARCA-APM, TNC y ACLA-C. El documento contiene la caracterización económica y social del área en estudio, una revisión de estudios de valoración, y métodos, así como el método de valoración seleccionado y su forma de aplicación.A bstract:Between March and September 2004, the International Center of Economic Policy for Sustainable Development of the National University (CINPE.IJNA) elaborated the study Economic Valuation of ihe Water Resources in ihe Basins of ihe rivers Banano and Bananito4. The general objcctive of it answers to “estimate the value of the water resource in the basin of the rivers Banano and Bananito, depending on the prior uses, for the recommendation of effective mechanisms for the sustainability of a system of compensation for the hydrological serv ices”.The following specific objectives appear to reach the general objective: (1) To identify the most appropriate method of economic valuation for water resource given (he conditions of the zone. (2) To quantify the hydrological services in the basins of the rivers Banano and Bananito depending on (he principal uses. And (3) to recommend a mechanism of voluntary payment for the environmental water service based on the results of the study, which provides to La Amistad Caribe Conservation Area (ACLA-C), the elements for the development of a concrete experience.Product and given of an exhaustive bibliographical review, the Analysis of Multiple Criteria (AMC) is selected as (he methodology for the economic valuation. It implies (he application of a not traditional method, which allows combining quantitative and qualitative variables. In this regard, the use of a participatory methodoiogy there made possible the participation of the principal groups of actors users of the water, who quatified ¡n five groups to knowing, (1) administrative associations of rural aqueducts (ASADAS), (2) ONG and communal organizations, (3) civil society, (4) private sector and (5) public sector.After systematizing the information obtained during 23 meetings of participatory consultation. one proceeds to the analysis of the information, which use as ¡nputs to realize the economic valuation. Finally, the design of the offer of collection mechanisms for user group for the payment for environmental services is presented. The final results appear by means of the use of counterfoils and spider web graphs.This repon includes the commentaries and suggestions realized during and later to ihe workshop of discussion with representatives of PROARCA-APM, TNC and ACLA-C. The document also contains the economic and social characterization of the area under study, a review of studies of valuation, and methods. as well as the method of valuation selected and its form of application.

EL ANÁLISIS MULTICRITERIO, UN CASO ESPECÍFICO: PROYECTO PROLAND

La técnica del análisis multicriterio se aplicó en la evaluación de técnicas de manejo alternativo para áreas de pendiente deforestadas usadas en la agricultura en Costa Rica y Guatemala. Se identificaron objetivos de evalua­ción entre los actores locales, con la ayuda de diferentes herramientas; pudién­dose identificar la pérdida de suelo, el ingreso de la finca, los insumes agrícolas, el lavado de nitrógeno, protección de la biodiversidad y necesidades nutricionales. Luego mediante algoritmos y fórmulas matemáticas, fueron caracteriza­dos todos los objetivos. Este modelo se utilizó como base para la construcción de una herramienta para apoyar la toma de decisiones que hace posible el cálculo del valor de cada objetivo bajo diferentes escenarios de producción y protección. ABSTRACT The multimedia analysis approach was applied to the evaluation of alternative management practices in deforested sloping áreas used for farming in Central American countries (Guatemala, Costa Rica). A major number of major evaluation objectives were identified, with the help of workshop ,whit local actors, including soil loss, farm income, agricultural inputs, nitrogen leaching, protection of biodiversity, and local nutrition needs. Then, appropriate algorithms and other mathematical formulas were put together for the quantitative characterization of all these objectives. This model was used as the basis for the construction of a user-friendly decision support tool, making possible the calculation of the values of the objectives for each scenario.

WEB RÁDIO: AS REDES DE FORMAÇÃO E A PERSPECTIVA GEOGRÁFICA NA COMUNICAÇÃO DO CIBERESPAÇO

Paulatinamente o mundo se transforma e as maneiras de se comunicar com ele também. Os avanços tecnológicos, principalmente na área da comunicação, têm implicado no surgimento de novas técnicas e novas estratégias para a educação e para o ensino da Geografia. Contudo, buscamos avaliar em nossa pesquisa a maneira pela qual nos inserir como geógrafos no ciberespaço, atuando de forma a produzir conteúdo geográfico na grande rede da WAN[1], e ainda utilizando-se dessa ferramenta, participar do processo de construção e colaboração das TIC’S, voltadas para a educação e difundi-las através da grande rede. Desta maneira propondo meios alternativos que contribuam para a formação a docência e seja alicerce da formação básica. Nesta perspectiva, avaliamos o local e as condições das quais partimos, em uma pesquisa de caráter inicial, ocasionando implicações positivas referentes ao alcance de escalas maiores, alianças comunitárias que fortaleçam os espaços de resistência e refletem a práxis geográfica. Neste sentido, a pesquisa é fomentada pelo Laboratório Áudio Visual Cinema Paraíso e permeará rasamente buscando linear o contexto em que nos inserimos.

DINÁMICA TERRITORIAL ASOCIADA A LA ACTIVIDAD AGROPECUARIA EN EL CANTÓN DE POÁS, ALAJUELA

Este artículo presenta la dinámica y articulación de las actividades agrícolas del cantón de Poás.Considera además los rasgos sobresalientes de dichas actividades a saber: café, caña de azúcar, fresas, plantas ornamentales, ganadería de leche y hortalizas. Asimismo, relaciona la dinámica de inserción de la población en este sector productivo, justificando las actividades agrícolas como relevantes en el desarrollo económico del cantón. La caracterización efectuada permitió identificar las tendencias de los sistemas agrícolas tradicionales, no tradicionales y las actividades agrícolas emergentes. La metodología involucra la revisión de datos secundarios de diversas fuentes, estadísticas y censales, enriquecidas con levantamiento de campo, visitas y entrevistas de campo a  productores. Este trabajo se enmarca dentro del plan regulador del cantón de Poás, realizado por la Escuela de Ciencias Geográficas de la Universidad Nacional. ABSTRACT This article presents the dynamics and articulation of agricultural activities in the canton of Poás. Also considered are the salient features of such activities, namely, coffee, sugar cane, strawberries, rnamental plants, dairy and vegetables. At the same time, the article relates the dynamics of inclusion of the population in the productive sector, justifying agricultural activities as relevant to the economic  evelopment of the canton. This characterization made it possible to identify trends in traditional farming systems as well as non-traditional and emerging agricultural activities. The methodology involves a review of secondary data from various sources, statistics and census, supplemented with field surveys, field visits and interviews about producer experiences. This work is part of the Poás regulatory plan onducted by the School of Geographical Sciences at Universidad Nacional, Costa Rica.

Enabling 5G and beyond: millimeter wave propagation and cloud RAN evolution

In the last few years, mobile wireless technology has gone through a revolutionary change. Web-enabled devices have evolved into essential tools for communication, information, and entertainment. The fifth generation (5G) of mobile communication networks is envisioned to be a key enabler of the next upcoming wireless revolution. Millimeter wave (mmWave) spectrum and the evolution of Cloud Radio Access Networks (C-RANs) are two of the main technological innovations of 5G wireless systems and beyond. Because of the current spectrum-shortage condition, mmWaves have been proposed for the next generation systems, providing larger bandwidths and higher data rates. Consequently, new radio channel models are being developed. Recently, deterministic ray-based models such as Ray-Tracing (RT) are getting more attractive thanks to their frequency-agility and reliable predictions. A modern RT software has been calibrated and used to analyze the mmWave channel. Knowledge of the electromagnetic properties of materials is therefore essential. Hence, an item-level electromagnetic characterization of common construction materials has been successfully achieved to obtain information about their complex relative permittivity. A complete tuning of the RT tool has been performed against indoor and outdoor measurement campaigns at 27 and 38 GHz, setting the basis for the future development of advanced beamforming techniques which rely on deterministic propagation models (as RT). C-RAN is a novel mobile network architecture which can address a number of challenges that network operators are facing in order to meet the continuous customers’ demands. C-RANs have already been adopted in advanced 4G deployments; however, there are still some issues to deal with, especially considering the bandwidth requirements set by the forthcoming 5G systems. Open RAN specifications have been proposed to overcome the new 5G challenges set on C-RAN architectures, including synchronization aspects. In this work it is described an FPGA implementation of the Synchronization Plane for an O-RAN-compliant radio system.

Nanomechanical characterization of soft bioelectronic interfaces via modeling-informed atomic force microscopy

The field of bioelectronics involves the use of electrodes to exchange electrical signals with biological systems for diagnostic and therapeutic purposes in biomedical devices and healthcare applications. However, the mechanical compatibility of implantable devices with the human body has been a challenge, particularly with long-term implantation into target organs. Current rigid bioelectronics can trigger inflammatory responses and cause unstable device functions due to the mechanical mismatch with the surrounding soft tissue. Recent advances in flexible and stretchable electronics have shown promise in making bioelectronic interfaces more biocompatible. To fully achieve this goal, material science and engineering of soft electronic devices must be combined with quantitative characterization and modeling tools to understand the mechanical issues at the interface between electronic technology and biological tissue. Local mechanical characterization is crucial to understand the activation of failure mechanisms and optimizing the devices. Experimental techniques for testing mechanical properties at the nanoscale are emerging, and the Atomic Force Microscope (AFM) is a good candidate for in situ local mechanical characterization of soft bioelectronic interfaces. In this work, in situ experimental techniques with solely AFM supported by interpretive models for the characterization of planar and three-dimensional devices suitable for in vivo and in vitro biomedical experimentations are reported. The combination of the proposed models and experimental techniques provides access to the local mechanical properties of soft bioelectronic interfaces. The study investigates the nanomechanics of hard thin gold films on soft polymeric substrates (Poly(dimethylsiloxane) PDMS) and 3D inkjet-printed micropillars under different deformation states. The proposed characterization methods provide a rapid and precise determination of mechanical properties, thus giving the possibility to parametrize the microfabrication steps and investigate their impact on the final device.

Power converters in WBG device technology for automotive applications and characterization setups for GaN power transistors

This PhD dissertation envisages the design of innovative power converters exploiting WBG devices to get state-of-the-art performance in products intended for industrial applications of automotive field. The collaborations with different specialized companies, provided the opportunity to access commercially-available state-of-the-art SiC and GaN technologies and the possibility to realize innovative converter prototypes. Concerning SiC technology, the complete design of a $350kW$ Battery Emulator instrument in collaboration with a company leader in the automotive testing sector, was carried out from scratch exploiting state-of-the-art SiC power-modules, planar magnetics and top-notch MCU technologies. Discrete high-voltage GaN switches were exploited in the Power Supplies design for automotive charger application to target improved performances compared to the market state-of-the-art. Specifically, two high-efficiency prototypes, an AC/DC converter and a DC/DC converter of $7.5kW$, have been realized for this purpose. To further investigate the characteristics of state-of-the-art GaN power devices two measurement set-ups have been designed. In particular, the trapping phenomenon causing the collapse of drain current during ON-state with a consequent degradation of ON-resistance has been analyzed.

Molecular And Biochemical Characterization Of Caffeine Synthase And Purine Alkaloid Concentration In Guarana Fruit.

Guarana seeds have the highest caffeine concentration among plants accumulating purine alkaloids, but in contrast with coffee and tea, practically nothing is known about caffeine metabolism in this Amazonian plant. In this study, the levels of purine alkaloids in tissues of five guarana cultivars were determined. Theobromine was the main alkaloid that accumulated in leaves, stems, inflorescences and pericarps of fruit, while caffeine accumulated in the seeds and reached levels from 3.3% to 5.8%. In all tissues analysed, the alkaloid concentration, whether theobromine or caffeine, was higher in young/immature tissues, then decreasing with plant development/maturation. Caffeine synthase activity was highest in seeds of immature fruit. A nucleotide sequence (PcCS) was assembled with sequences retrieved from the EST database REALGENE using sequences of caffeine synthase from coffee and tea, whose expression was also highest in seeds from immature fruit. The PcCS has 1083bp and the protein sequence has greater similarity and identity with the caffeine synthase from cocoa (BTS1) and tea (TCS1). A recombinant PcCS allowed functional characterization of the enzyme as a bifunctional CS, able to catalyse the methylation of 7-methylxanthine to theobromine (3,7-dimethylxanthine), and theobromine to caffeine (1,3,7-trimethylxanthine), respectively. Among several substrates tested, PcCS showed higher affinity for theobromine, differing from all other caffeine synthases described so far, which have higher affinity for paraxanthine. When compared to previous knowledge on the protein structure of coffee caffeine synthase, the unique substrate affinity of PcCS is probably explained by the amino acid residues found in the active site of the predicted protein.

Characterization Of Microsatellite Markers Developed From Prosopis Rubriflora And Prosopis Ruscifolia (leguminosae - Mimosoideae), Legume Species That Are Used As Models For Genetic Diversity Studies In Chaquenian Areas Under Anthropization In South America.

Prosopis rubriflora and Prosopis ruscifolia are important species in the Chaquenian regions of Brazil. Because of the restriction and frequency of their physiognomy, they are excellent models for conservation genetics studies. The use of microsatellite markers (Simple Sequence Repeats, SSRs) has become increasingly important in recent years and has proven to be a powerful tool for both ecological and molecular studies. In this study, we present the development and characterization of 10 new markers for P. rubriflora and 13 new markers for P. ruscifolia. The genotyping was performed using 40 P. rubriflora samples and 48 P. ruscifolia samples from the Chaquenian remnants in Brazil. The polymorphism information content (PIC) of the P. rubriflora markers ranged from 0.073 to 0.791, and no null alleles or deviation from Hardy-Weinberg equilibrium (HW) were detected. The PIC values for the P. ruscifolia markers ranged from 0.289 to 0.883, but a departure from HW and null alleles were detected for certain loci; however, this departure may have resulted from anthropic activities, such as the presence of livestock, which is very common in the remnant areas. In this study, we describe novel SSR polymorphic markers that may be helpful in future genetic studies of P. rubriflora and P. ruscifolia.