Linked Data based Health Information Representation, Visualization and Retrieval System on the Semantic Web

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Tbx1 and Bmp2 in the development of the ear, neural crest and pharyngeal system in mice

Dissertation presented to obtain the Ph.D degree in Biology

A semi-automatic approach to code smells detection

Eradication of code smells is often pointed out as a way to improve readability, extensibility and design in existing software. However, code smell detection remains time consuming and error-prone, partly due to the inherent subjectivity of the detection processes presently available. In view of mitigating the subjectivity problem, this dissertation presents a tool that automates a technique for the detection and assessment of code smells in Java source code, developed as an Eclipse plugin. The technique is based upon a Binary Logistic Regression model that uses complexity metrics as independent variables and is calibrated by expert‟s knowledge. An overview of the technique is provided, the tool is described and validated by an example case study.

Detection and molecular analysis of Toxoplasma gondii and Neospora caninum from dogs with neurological disorders

INTRODUCTION: Toxoplasma gondii and Neospora caninum are related Apicomplexa parasites responsible for systemic diseases in many species of animals, including dogs. METHODS: This study aimed to determine the occurrence of T. gondii and N. caninum infections in 50 dogs with neurological signs that were admitted to the Veterinary Hospital of Universidade Estadual Paulista, City of Botucatu, Brazil. All animals were screened for antibodies using an immunofluorescent antibody test for both parasites. Tissues of positive animals were bioassayed in mice (T. gondii) and gerbils (N. caninum), and DNA was analyzed using the polymerase chain reaction (PCR). Positive samples for T. gondii by PCR were typed using restriction fragment length polymorphism-PCR for 11 markers: SAG1, SAG2 (5′-3′-SAG2 and alt.SAG2), SAG3, Btub, GRA6, L358, c22-8, c29-6, PK1 and Apico, and CS3 marker for virulence analysis. RESULTS: Specific antibodies were detected in 11/50 (22%; 95% confidence interval (CI95%), 12.8-35.3%) animals for T. gondii and 7/50 (14%; CI95%, 7.02-26.3%) for N. caninum. In the bioassay and PCR, 7/11 (63.6%; CI95%, 34.9-84.8%) samples were positive for T. gondii and 3/7 (42.9%; CI95%I, 15.7-75.5%) samples were positive for N. caninum. Three different genotypes were identified, but only 1 was unique. CONCLUSIONS: These data confirm the presence of T. gondii and N. caninum in dogs from Brazil, indicating the importance of this host as a sentinel of T. gondii for human beings, and the genotypic variation of this parasite in Brazil.

Emotional and behavioral problems in preschoolers: risk factors and assessment Issues

Tese de Doutoramento em Psicologia Aplicada.

Caracterización genética de la cepa Sinorhizobium meliloti 3DOh13 y evaluación de la capacidad fijadora de nitrógeno en alfalfa. Genetic characterization of the strain Sinorhizobium meliloti 3DOh13 and assessment of the capacity to fix nitrogen in alfalfa.

La provincia de Córdoba participa con aproximadamente el 23 por ciento del área total sembrada anualmente con alfalfa en nuestro país y, en los últimos años, se ha incrementado levemente, en contraste con las provincias de Buenos Aires, Santa Fe y Entre Ríos, donde ha decrecido. La inoculación de este cultivo con cepas del género Sinorhizobium ha permitido mejorar su rendimiento en los suelos de la región semiárida. La utilización para la siembra de semillas preinoculadas con microorganismos de origen extranjero, cuya eficiencia y adaptación a las condiciones locales no siempre se conocen, y con escasa capacidad de competencia ante las cepas naturalizadas, trae como consecuencia un bajo establecimiento de la nodulación y por consiguiente una escasa reposición del nitrógeno removido del suelo. Aún cuando la inoculación está relativamente difundida, en la actualidad no se ha determinado la proporción relativa de nitrógeno fijado por las cepas introducidas respecto de las nativas o naturalizadas, ni la competencia que se genera en el suelo por la ocupación de los sitios potenciales para la formación de nódulos. Nuestra hipótesis de trabajo es: "la inoculación con cepas de Sinorhizobium meliloti debidamente caracterizadas y eficientes en la fijación del nitrógeno atmosférico mejorará el rendimiento de alfalfa en la región centro-sur de Córdoba". Los objetivos de este estudio son caracterizar fenotípica y genotípica el aislamiento Sinorhizobium meliloti 3DOh13 y evaluar su eficiencia simbiótica en el cultivo de alfalfa, mediante ensayos de infectividad, eficiencia y competencia con cepas nativas. La evaluación de la infectividad de la cepa comprende estudios de cinética de la nodulación, número total de nódulos y ubicación de los mismos en experiencias donde las plantas crecen en condiciones de invernáculo sobre un soporte de tierra:arena:perlita (2:1:1). Se realizarán ensayos de competitividad, coinoculando semillas con la cepa DOh13 y otras nativas, en bolsas plásticas con medio mineral en los que se desafiarán los distintos aislamientos. Se inoculan las plantas con sólo dos aislamientos y los nódulos de la raíz principal serán extraídos a fin de aislar los microorganismos ocupantes, los que serán diferenciados por marca de resistencia a antibioticos. La eficiencia en la fijación de nitrógeno será cuantificada por las técnicas de reducción del acetileno en el nódulo y, en caso de ser necesario, se usará el método de Kjeldahl (N total) para la raíz, tejido aéreo o planta entera. La caracterización genotípica de S. meliloti 3DOh13 incluirá métodos de fingerprint de ADN por técnicas de PCR y secuenciamiento del ADNr 16S. Esta investigación permitirá obtener información precisa sobre la respuesta de alfalfa a la inoculación con la cepa de referencia. El producto que se espera obtener es un nuevo inoculante, formulado con una cepa efectiva en la fijación de nitrógeno, debidamente caracterizada y con probada capacidad de adaptación a los suelos de la región

Forearm surface EMG signals recognition and muscoloskeletal system dynamics identification using intelligent computational methods

Biosignals processing, Biological Nonlinear and time-varying systems identification, Electomyograph signals recognition, Pattern classification, Fuzzy logic and neural networks methods

Socio-economic impacts and assessment biological invasions

Biological invasions have been object of ecological research for years. As one objective, natural scientists investigate the effects of invasive species on ecosystems and their functioning (Levine et al. 2003). However, impacts on ecosystems are also of relevance for society. Changes in ecosystems affect humans in so far as ecosystems provide goods and services, such as fresh water, food and fibbers or recreation, which might be altered due to invasive species. Therefore impacts of biological invasions should be an object of socio-economic interest, which is also demanded by the Convention on Biological Diversity

The Discrimination of Colored Acrylic, Cotton, and Wool Textile Fibers Using Micro-Raman Spectroscopy. Part 1 : In Situ Detection and Characterization of Dyes

Raman spectroscopy has been applied to characterize fiber dyes and determine the discriminating ability of the method. Black, blue, and red acrylic, cotton, and wool samples were analyzed. Four excitation sources were used to obtain complementary responses in the case of fluorescent samples. Fibers that did not provide informative spectra using a given laser were usually detected using another wavelength. For any colored acrylic, the 633-nm laser did not provide Raman information. The 514-nm laser provided the highest discrimination for blue and black cotton, but half of the blue cottons produced noninformative spectra. The 830-nm laser exhibited the highest discrimination for red cotton. Both visible lasers provided the highest discrimination for black and blue wool, and NIR lasers produced remarkable separation for red and black wool. This study shows that the discriminating ability of Raman spectroscopy depends on the fiber type, color, and the laser wavelength.

Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation.

The introduction of culture-independent molecular screening techniques, especially based on 16S rRNA gene sequences, has allowed microbiologists to examine a facet of microbial diversity not necessarily reflected by the results of culturing studies. The bacterial community structure was studied for a pesticide-contaminated site that was subsequently remediated using an efficient degradative strain Arthrobacter protophormiae RKJ100. The efficiency of the bioremediation process was assessed by monitoring the depletion of the pollutant, and the effect of addition of an exogenous strain on the existing soil community structure was determined using molecular techniques. The 16S rRNA gene pool amplified from the soil metagenome was cloned and restriction fragment length polymorphism studies revealed 46 different phylotypes on the basis of similar banding patterns. Sequencing of representative clones of each phylotype showed that the community structure of the pesticide-contaminated soil was mainly constituted by Proteobacteria and Actinomycetes. Terminal restriction fragment length polymorphism analysis showed only nonsignificant changes in community structure during the process of bioremediation. Immobilized cells of strain RKJ100 enhanced pollutant degradation but seemed to have no detectable effects on the existing bacterial community structure.

Visceral leishmaniasis in Teresina, state of Piauí, Brazil: preliminary observations on the detection and transmissibility of canine and sandfly infections

A Leishmania donovani-complex specific DNA probe was usedto confirm the widespread dissemination of amastigotes in apparently normal skinof dogs with canine visceral leishmaniasis. When Lutzomyia longipalpis were fed on abnormal skin of five naturally infected dogs 57 of 163 (35 per cent) fliesbecame infected: four of 65 flies (6 per cent) became infected when fed on apparently normal skin. The bite of a single sandfly that had fed seven days previouslyon a naturally infected dog transmitted the infection to a young dog from a non-endemic area. Within 22 days a lesion had developed at the site of the infectivebite (inner ear): 98 days after infection organisms had not disseminated throughout the skin, bone marrow, spleen or liver and the animal was still serologically negative by indirect immunofluorescence and dot-enzyme-linked immunosorbent assay. When fed Lu. longipalpis were captured from a kennel with a sick dog known to be infected, 33 out of 49 (67 per cent) of flies contained promastigotes. In contrast only two infections were detected among more than 200 sandflies captured in houses. These observations confirm the ease of transmissibility of L.chagasi from dog to sandfly to dog in Teresina. It is likely that canine VL is the major source of human VL by the transmission route dog-sandfly-human. the Lmet2 DNA probe was a useful epidemiological tool for detecting L. chagasi in sandflies.