Pipeline for macro- and microarray analyses

The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA.

Association between independence in daily activities and social roles in older adults with stroke

La réadaptation des personnes âgées ayant subi un accident vasculaire cérébral vise à améliorer les capacités et l’indépendance dans les activités de la vie courante. Les personnes âgées reprennent leurs rôles sociaux lorsqu’elles retournent vivre dans la communauté. L’objectif de ce mémoire est de clarifier la relation entre l’indépendance dans les activités de la vie courante au congé de la réadaptation intensive et la reprise des rôles sociaux six mois plus tard. L’échantillon se compose de 111 participants recrutés au congé et réévalués 6 mois plus tard. L’indépendance dans les activités de la vie courante est mesurée avec les sections pertinentes du Système de Mesure de l’Autonomie Fonctionnelle (SMAF). Les rôles sociaux sont mesurés avec la Mesure des Habitudes de Vie (MHAVIE); un score total ainsi que 4 sous-scores pour les responsabilités civiles, la vie communautaire, les relations interpersonnelles et les loisirs sont générés. Des analyses de régression hiérarchique sont utilisées pour vérifier l’association entre les activités de la vie courantes (variable indépendante) et les rôles sociaux (variables dépendante) tout en contrôlant pour les capacités (variables de contrôle). Les résultats suggèrent des associations significatives (p < .001) entre les activités de la vie courante et les rôles sociaux (score total de la MHAVIE), les sous scores des responsabilités civiles et de la vie communautaire, mais aucune association avec les relations interpersonnelles et les loisirs. Les scores les plus faibles sont obtenus pour les loisirs. Une deuxième phase de réadaptation après le retour à domicile pourrait permettre le développement des loisirs.

Downscaling and Modeling the Effects of Climate Change on Hydrology and Water Resources in the Upper Blue Nile River Basin, Ethiopia

The Upper Blue Nile River Basin (UBNRB) located in the western part of Ethiopia, between 7° 45’ and 12° 45’N and 34° 05’ and 39° 45’E has a total area of 174962 km2 . More than 80% of the population in the basin is engaged in agricultural activities. Because of the particularly dry climate in the basin, likewise to most other regions of Ethiopia, the agricultural productivity depends to a very large extent on the occurrence of the seasonal rains. This situation makes agriculture highly vulnerable to the impact of potential climate hazards which are about to inflict Africa as a whole and Ethiopia in particular. To analyze these possible impacts of future climate change on the water resources in the UBNRB, in the first part of the thesis climate projection for precipitation, minimum and maximum temperatures in the basin, using downscaled predictors from three GCMs (ECHAM5, GFDL21 and CSIRO-MK3) under SRES scenarios A1B and A2 have been carried out. The two statistical downscaling models used are SDSM and LARS-WG, whereby SDSM is used to downscale ECHAM5-predictors alone and LARS-WG is applied in both mono-model mode with predictors from ECHAM5 and in multi-model mode with combined predictors from ECHAM5, GFDL21 and CSIRO-MK3. For the calibration/validation of the downscaled models, observed as well as NCEP climate data in the 1970 - 2000 reference period is used. The future projections are made for two time periods; 2046-2065 (2050s) and 2081-2100 (2090s). For the 2050s future time period the downscaled climate predictions indicate rise of 0.6°C to 2.7°C for the seasonal maximum temperatures Tmax, and of 0.5°C to 2.44°C for the minimum temperatures Tmin. Similarly, during the 2090s the seasonal Tmax increases by 0.9°C to 4.63°C and Tmin by 1°C to 4.6°C, whereby these increases are generally higher for the A2 than for the A1B scenario. For most sub-basins of the UBNRB, the predicted changes of Tmin are larger than those of Tmax. Meanwhile, for the precipitation, both downscaling tools predict large changes which, depending on the GCM employed, are such that the spring and summer seasons will be experiencing decreases between -36% to 1% and the autumn and winter seasons an increase of -8% to 126% for the two future time periods, regardless of the SRES scenario used. In the second part of the thesis the semi-distributed, physically based hydrologic model, SWAT (Soil Water Assessment Tool), is used to evaluate the impacts of the above-predicted future climate change on the hydrology and water resources of the UBNRB. Hereby the downscaled future predictors are used as input in the SWAT model to predict streamflow of the Upper Blue Nile as well as other relevant water resources parameter in the basin. Calibration and validation of the streamflow model is done again on 1970-2000 measured discharge at the outlet gage station Eldiem, whereby the most sensitive out the numerous “tuneable” calibration parameters in SWAT have been selected by means of a sophisticated sensitivity analysis. Consequently, a good calibration/validation model performance with a high NSE-coefficient of 0.89 is obtained. The results of the future simulations of streamflow in the basin, using both SDSM- and LARS-WG downscaled output in SWAT reveal a decline of -10% to -61% of the future Blue Nile streamflow, And, expectedly, these obviously adverse effects on the future UBNRB-water availibiliy are more exacerbated for the 2090’s than for the 2050’s, regardless of the SRES.

Data-Driven Text Generation using Neural Networks & Provenance is Complicated and Boring — Is there a solution?

Title: Data-Driven Text Generation using Neural Networks Speaker: Pavlos Vougiouklis, University of Southampton Abstract: Recent work on neural networks shows their great potential at tackling a wide variety of Natural Language Processing (NLP) tasks. This talk will focus on the Natural Language Generation (NLG) problem and, more specifically, on the extend to which neural network language models could be employed for context-sensitive and data-driven text generation. In addition, a neural network architecture for response generation in social media along with the training methods that enable it to capture contextual information and effectively participate in public conversations will be discussed. Speaker Bio: Pavlos Vougiouklis obtained his 5-year Diploma in Electrical and Computer Engineering from the Aristotle University of Thessaloniki in 2013. He was awarded an MSc degree in Software Engineering from the University of Southampton in 2014. In 2015, he joined the Web and Internet Science (WAIS) research group of the University of Southampton and he is currently working towards the acquisition of his PhD degree in the field of Neural Network Approaches for Natural Language Processing. Title: Provenance is Complicated and Boring — Is there a solution? Speaker: Darren Richardson, University of Southampton Abstract: Paper trails, auditing, and accountability — arguably not the sexiest terms in computer science. But then you discover that you've possibly been eating horse-meat, and the importance of provenance becomes almost palpable. Having accepted that we should be creating provenance-enabled systems, the challenge of then communicating that provenance to casual users is not trivial: users should not have to have a detailed working knowledge of your system, and they certainly shouldn't be expected to understand the data model. So how, then, do you give users an insight into the provenance, without having to build a bespoke system for each and every different provenance installation? Speaker Bio: Darren is a final year Computer Science PhD student. He completed his undergraduate degree in Electronic Engineering at Southampton in 2012.

Dificultades de comprensión lingüística oral, propuesta de mejora utilizando las nuevas tecnologías : diálogo hombre-máquina mediante instrucciones expresadas en lenguaje natural.

Responder cómo se procesa el lenguaje, cómo funcionan todos los elementos que intervienen en la comprensión y en qué orden se produce el procesamiento lingüístico. Alumnos de ESO, que no presentan discapacidad auditiva. El grupo experimental lo compone 31 chicos y 12 niñas que presentan dificultades en Lengua, algunos de ellos también tienen problemas de aprendizaje en Matemáticas y Lengua inglesa. Se realizan dos pruebas. La primera trata de comprensión oral. Reciben un cuadernillo cada uno. Disponen de 25 minutos. Los datos personales es lo último que deben escribir. Si no escuchan bien, lo indican en el cuadernillo y así se controla la falta de comprensión por deficiencias de sonido. Se les pone una grabación tres veces. Durante las grabaciones se controlan las diferencias acústicas entre los que están en la primera fila y la última. Los alumnos contestan a las preguntas. A los que presentan problemas con las definiciones se les pide que rellenen la última hoja para comprobar si conocen el significado, no su capacidad de expresión. El segundo cuadernillo lo reciben al acabar todo el grupo. Disponen de tiempo ilimitado. Si no conocen una palabra se les explica el significado. Finalmente se les pasa una prueba de memoria auditiva inmediata . Se pretende controlar la variable 'memoria' y estudiar su incidencia en la prueba. La segunda prueba consiste en originar un modelo de lenguaje utilizando el mismo texto presentado a los estudiantes. También se pretende conocer lo que pasa si se introducen oraciones incompletas para rellenar por los alumnos. La única información que dispone el ordenador es la señal vocal y con ella realiza el modelo de lenguaje. Grabadora mono portátil, cinta de casete, cuadernillo de respuesta de comprensión oral, cuadernillo de respuesta de estrategias de comprensión utilizada, cuaderno de respuestas de estrategias de procedimiento de comprensión, hoja de respuestas para la prueba de memoria, programa SPSS y Excel para análisis de datos. Para la segunda prueba los materiales son: la grabadora mono portátil Panasonic, cinta casete, reconocedor Via Voice 98, Pentium III, tarjeta de sonido, C.M.U. Statistical Language Modeling Tool Kit, Programa tex2wfreq, text2idngram, idngram21m,evallm. Para la primera prueba se confecciona un diseño experimental multivariado; las variables fueron: memoria, comprensión auditiva y estrategias utilizadas para comprender. Las variables contaminadoras: experimentador, material, condiciones acústicas, centro educativo, nivel socioeconómico y edad. Éstas se controlan por igualación. Las variables organísmicas y el sexo se controlan aleatoriamente. La memoria auditiva tuvo que ser controlada a través de un análisis de covarianza. En la segunda prueba, la variable fue la comprensión lingüística oral, para después establecer una comparación. Los resultados de la primera prueba revelan que las correlaciones que se obtienen entre las variables analizadas son independientes y arrojan diferencias entre el grupo experimental y el de control. Se encuentran puntuaciones más altas en los sujetos sin dificultades en memoria y comprensión. No hay diferencias entre los dos grupos en estrategias de comprensión. Los resultados obtenidos en la fase de evaluación de la segunda prueba indican que ninguna respuesta resulta elegida correctamente por lo que no se puede realizar ninguna comparación . Parece que la muestra utiliza el mismo modelo para comprender, todos utilizan las mismas estrategias, las diferencias son cuantitativas y debidas a variables organísmicas, entre ellas, la memoria. La falta de vocabulario es la primera dificultad en el grupo con dificultades, la falta de memoria impide corregir palabras mal pronunciadas, buscar conocimientos previos y relacionar ideas en su memoria a largo plazo. Son también incapaces de encontrar la idea principal. La comprensión es tan lenta que no pueden procesar. Se demuestra que los programas informáticos imitan al hombre a niveles elementales, en Tecnología del Habla se utilizan prioritariamente modelos semánticos.

Estimates of hourly diffuse radiation on tilted surfaces in southeast of brazil

The global radiation incident on a tilted surfaces consists of components direct, diffuse and reflected from the ground. On a hourly database, the direct radiation can be calculated by geometric projections (ratio of the incidence angle to the solar zenith angle). The reflected radiation has a small effect on calculations and may be calculated with an isotropic model. Both components presents dependence of measures in incidence or horizontal surface. The great difficulty is to evaluate the diffuse radiation by variations of circumsolar, brightness horizontal, isotropic and anisotropic subcomponents. This study evaluated twenty models to estimate hourly diffuse radiation incident on tilted surfaces at 12.85° (latitude - 10°), 22.85° (latitude) and 32.85° (latitude + 10°) facing to North, under different cloudiness sky conditions, in Botucatu, São Paulo State, Brazil (22°53' S, 48°26' W and 786 m above the mean sea level). In contrast, models for estimating the diffuse component show major differences, which justify the validation for local calibrations. There is a decrease of the maximum total radiation scattered with increasing atmospheric transmissivity and inclination angle. The best results are obtained by anisotropic models: Ma and Iqbal, Hay, Reindl et al. and Willmott; isotropic: Badescu and Koronakis, and the Circumsolar model. The increase of the inclination angle allows for a reduction in the performance of statistical parametric models for estimating the hourly diffuse radiation.

Uso de modelos estatísticos para dados de escore de crédito de uma instituição financeira

Pós-graduação em Engenharia de Produção - FEB

An empirical analysis of technology absorption capacity of the Brazilian industry

Includes bibliography.

Anisotropia da irradiância solar difusa medida pelo método de sombreamento Melo-Escobedo: fatores de correção anisotrópicos e modelos de estimativa

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Um software de reconhecimento de voz para português brasileiro

Descreve a implementação de um software de reconhecimento de voz para o Português Brasileiro. Dentre os objetivos do trabalho tem-se a construção de um sistema de voz contínua para grandes vocabulários, apto a ser usado em aplicações em tempo-real. São apresentados os principais conceitos e características de tais sistemas, além de todos os passos necessários para construção. Como parte desse trabalho foram produzidos e disponibilizados vários recursos: modelos acústicos e de linguagem, novos corpora de voz e texto. O corpus de texto vem sendo construído através da extração e formatação automática de textos de jornais na Internet. Além disso, foram produzidos dois corpora de voz, um baseado em audiobooks e outro produzido especificamente para simular testes em tempo-real. O trabalho também propõe a utilização de técnicas de adaptação de locutor para resolução de problemas de descasamento acústico entre corpora de voz. Por último, é apresentada uma interface de programação de aplicativos que busca facilitar a utilização do decodificador Julius. Testes de desempenho são apresentados, comparando os sistemas desenvolvidos e um software comercial.

Trajetória teórico-metodológica da geografia agrária brasileira: a produção em periódicos científicos de 1939-2009

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Análise matemática e estatística da produtividade de lavouras cafeeiras agroquímica e orgânica na região da alta paulista

Studies with organic systems have shown the feasibility and ecological and social sustainability of these agroecosystems, unlike the systems agrochemicals (conventional) production. Some studies have concluded that for the model agrochemical exists less interaction between the flow of internal energy, basically the crop receives all inputs to production with no increase in "energy quality" within the system, while in the organic model of production has increased interaction between different resources in the system. The current economic and ecological crisis, exposed no sustainability of the production pattern of industrialized agriculture developed in a way, showing the dependence of developed countries on imports of agricultural commodities produced in the third world, among there coffee. Given these facts, developed a survey to identify problems in the Alta Paulista region, west of São Paulo State, in relation to coffee production systems. Actually, the fundamental problem, according to the research, farmers in this region, is to choose a viable production system correctly (environmental, social and economic); agrochemical or organic. The objectives of this study were to analyze the yield of production systems and agro-chemical and organic coffee in the period from 2003 to 2007, in 30 producing properties, located in this region, in order to point the production system to produce the highest yield. According to the methodology of CONAB, data collected were recorded on spreadsheets to be used as variables in statistical analysis models and mathematics. We performed a descriptive analysis of productivity data and were used for statistical analysis tests for parametric and nonparametric analysis of variance. The mathematical analyses of the curves were prepared with Origin for Windows 6.0 software, which uses numerical methods to fit the data supplied to a function of variable parameters. Unlike conventional systems of production, the organic system showed greater viability of the production model. Furthermore, with the quantitative modeling proposal, it is possible to perform the evaluation of these types of investments, providing more security to the farmer at the time of decision.

Determination of Pelvic Orientation from Ultrasound Images Using Patch-SSMs and a Hierarchical Speed of Sound Compensation Strategy

In the field of computer assisted orthopedic surgery (CAOS) the anterior pelvic plane (APP) is a common concept to determine the pelvic orientation by digitizing distinct pelvic landmarks. As percutaneous palpation is - especially for obese patients - known to be error-prone, B-mode ultrasound (US) imaging could provide an alternative means. Several concepts of using ultrasound imaging to determine the APP landmarks have been introduced. In this paper we present a novel technique, which uses local patch statistical shape models (SSMs) and a hierarchical speed of sound compensation strategy for an accurate determination of the APP. These patches are independently matched and instantiated with respect to associated point clouds derived from the acquired ultrasound images. Potential inaccuracies due to the assumption of a constant speed of sound are compensated by an extended reconstruction scheme. We validated our method with in-vitro studies using a plastic bone covered with a soft-tissue simulation phantom and with a preliminary cadaver trial.

A chrysophyte stomatocyst-based reconstruction of cold-season air temperature from Alpine Lake Silvaplana (AD 1500–2003); methods and concepts for quantitative inferences

Relatively little is known about past cold-season temperature variability in high-Alpine regions because of a lack of natural cold-season temperature proxies as well as under-representation of high-altitude sites in meteorological, early-instrumental and documentary data sources. Recent studies have shown that chrysophyte stomatocysts, or simply cysts (sub-fossil algal remains of Chrysophyceae and Synurophyceae), are among the very few natural proxies that can be used to reconstruct cold-season temperatures. This study presents a quantitative, high-resolution (5-year), cold-season (Oct–May) temperature reconstruction based on sub-fossil chrysophyte stomatocysts in the annually laminated (varved) sediments of high-Alpine Lake Silvaplana, SE Switzerland (1,789 m a.s.l.), since AD 1500. We first explore the method used to translate an ecologically meaningful variable based on a biological proxy into a simple climate variable. A transfer function was applied to reconstruct the ‘date of spring mixing’ from cyst assemblages. Next, statistical regression models were tested to convert the reconstructed ‘dates of spring mixing’ into cold-season surface air temperatures with associated errors. The strengths and weaknesses of this approach are thoroughly tested. One much-debated, basic assumption for reconstructions (‘stationarity’), which states that only the environmental variable of interest has influenced cyst assemblages and the influence of confounding variables is negligible over time, is addressed in detail. Our inferences show that past cold-season air-temperature fluctuations were substantial and larger than those of other temperature reconstructions for Europe and the Alpine region. Interestingly, in this study, recent cold-season temperatures only just exceed those of previous, multi-decadal warm phases since AD 1500. These findings highlight the importance of local studies to assess natural climate variability at high altitudes.

The Virtual Skeleton Database: An Open Access Repository for Biomedical Research and Collaboration

Background: Statistical shape models are widely used in biomedical research. They are routinely implemented for automatic image segmentation or object identification in medical images. In these fields, however, the acquisition of the large training datasets, required to develop these models, is usually a time-consuming process. Even after this effort, the collections of datasets are often lost or mishandled resulting in replication of work. Objective: To solve these problems, the Virtual Skeleton Database (VSD) is proposed as a centralized storage system where the data necessary to build statistical shape models can be stored and shared. Methods: The VSD provides an online repository system tailored to the needs of the medical research community. The processing of the most common image file types, a statistical shape model framework, and an ontology-based search provide the generic tools to store, exchange, and retrieve digital medical datasets. The hosted data are accessible to the community, and collaborative research catalyzes their productivity. Results: To illustrate the need for an online repository for medical research, three exemplary projects of the VSD are presented: (1) an international collaboration to achieve improvement in cochlear surgery and implant optimization, (2) a population-based analysis of femoral fracture risk between genders, and (3) an online application developed for the evaluation and comparison of the segmentation of brain tumors. Conclusions: The VSD is a novel system for scientific collaboration for the medical image community with a data-centric concept and semantically driven search option for anatomical structures. The repository has been proven to be a useful tool for collaborative model building, as a resource for biomechanical population studies, or to enhance segmentation algorithms.