So called discrete models have been successfully used in engineering and computational systems biology. This thesis discusses algebraic methods for modeling and analysis of gene regulatory networks within the discrete modeling context. The first chapter gives a background for discrete models and put in context some of the main research problems that have been pursued in this field for the last fifty years. It also outlines the content of each subsequent chapter. The second chapter focuses on the problem of inferring dynamics from the structure (topology) of the network. It also discusses the characterization of the attractor structure of a network when a particular class of functions control the nodes of the network. Chapters~3 and 4 focus on the study of multi-state nested canalyzing functions as biologically inspired functions and the characterization of their dynamics. Chapter 5 focuses on stochastic methods, specifically on the development of a stochastic modeling framework for discrete models. Stochastic discrete modeling is an alternative approach from the well-known mathematical formalizations such as stochastic differential equations and Gillespie algorithm simulations. Within the discrete setting, a framework that incorporates propensity probabilities for activation and degradation is presented. This approach allows a finer analysis of discrete models and provides a natural setup for cell population simulations. Finally, Chapter 6 discusses future research directions inspired by the work presented here. / Ph. D.

Cryptosporidium is a parasite that causes gastrointestinal issues such as diarrhoea and stomach pain. The main transmission routes are through contaminated water or food, between humans and from animal to humans. Cryptosporidium infects through oocysts which contain four sporozoites that releases when entering a host and can continue to breed inside the body. Cryptosporidium can cause massive outbreaks if established in a water source used for drinking water. To prevent and detect an outbreak it´s important to trace the transmission back to the source. The GP60-gene is used to identify and subtype Cryptosporidium and is a very useful tool during contact tracing. The purpose of this study was to identify species and subtype of Cryptosporidium using nanopore sequencing. In this study the GP60-gene was amplified using a Nested PCR protocol and then sequenced using nanopore sequencing. The sequences acquired where then used to make a search in BLAST to identify the species. The GP60 subtyping method uses the hypervariable region on the GP60-gene. A series of tandem repeats are used to identify the subtype. In this study seven positive Cryptosporidium faeces samples were amplified and sequenced. Nanopore sequencing was possible for five of the seven samples with C. parvum identified in four of these samples. Targeting the GP60-gene to determine species and subtype works well for the most common human pathogen species of Cryptosporidium. Further optimization is required before the method can be implemented för diagnostic use.

Made available in DSpace on 2016-01-26T12:51:36Z (GMT). No. of bitstreams: 1 adrianafurini_dissert.pdf: 2158923 bytes, checksum: d683b1dc320b2c811cfcf58d6d1c21ac (MD5) Previous issue date: 2010-11-18 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Introduction. The diagnosis of paucibacillary forms of tuberculosis (TB), which mostly affects children, immunocompromised patients, transplanted and extra-pulmonary forms is limited by phenotypic techniques of smear and culture. Moreover, the diagnosis of mycobacteriosis, also has committed itself by the phenotypic methods. The polymerase chain reaction (PCR) and its variations, such as Nested-PCR (NPCR), has been described as promising techniques for rapid diagnosis of tuberculosis and mycobacteriosis. Objective. Evaluation of a NPCR protocol for detection of Mycobacterium tuberculosis in pulmonary and extrapulmonary anatomic sites of patients with clinical suspicion of TB. Subjects and Methods. Were included, prospectively, 24 pulmonary samples of 85 extrapulmonary, collected from 49 individuals HIV-seropositive and 28 HIV-seronegative and submitted to the gold standard method and NPCR targeting the transposon IS6110. Results. Tuberculosis was diagnosed in 11 patients (14,3%), with 54,5% of extrapulmonary forms and 45,5% pulmonary. The NPCR was positive in all, while the culture was positive in only seven of them. Smear positivity among the clinical specimens was 9,2%. The culture allowed the isolation of seven strains of M. tuberculosis and two M. avium complex (8,25%). The molecular positivity was described in 23,85% of samples. NPCR's performance against the culture, for pulmonary (n=22) and extrapulmonary samples (n = 83) was similar (100% sensitivity and specificity of approximately 83%). Positivity by NPCR was significantly greater than the isolation by culture among the extrapulmonary samples (p = 0,0042). Conclusions. The results suggest to perform further studies to corroborate the potential of NPCR-IS6110 for detection of mycobacterial genome in extrapulmonary TB, especially among immunocompromised. Furthermore, the detection of mycobacteria remains as diagnostic confirmation and the opportunity of investigation of the sensitivity profile, promoting effective treatment for any age and immune status. / Introdução. O diagnóstico das formas paucibacilares da tuberculose (TB), que acomete principalmente crianças, imunocomprometidos, transplantados e formas extrapulmonares é limitado pelas técnicas fenotípicas de baciloscopia e cultura. Ademais, o diagnóstico das micobacterioses, também apresenta-se comprometido pelos métodos fenotípicos. A reação da polymerase em cadeia (PCR) e suas variações, tais como a Nested-PCR (NPCR), tem sido descritas como técnicas promissoras para o rápido diagnóstico da tuberculose e micobacterioses. Objetivos. Avaliação de um protocolo de NPCR para detecção do complexo Mycobacterium tuberculosis em sítios anatômicos pulmonares e extrapulmonares de indivíduos com suspeita clínica de TB. Casuística e Método. Foram incluídas, prospectivamente, 24 amostras de sítios pulmonares e 85 extrapulmonares, coletadas a partir de 49 indivíduos soropositivos para o HIV e 28 soronegativos e submetidas ao método gold standard e a NPCR tendo como alvo o transposon IS6110. Resultados. A tuberculose foi diagnosticada em 11 pacientes (14,3%), com 54,5% de formas extrapulmonares e 45,5% pulmonares. A NPCR foi positiva em todos, enquanto a cultura em apenas cinco deles. A positividade da baciloscopia entre os espécimes clínicos foi de 9.2%. A cultura permitiu o isolamento de sete cepas de M. tuberculosis e duas do Complexo M. avium (8,25%). A positividade molecular foi descrita em 23,85% das amostras. O desempenho da NPCR frente a cultura, para amostras pulmonares (n=22) e extrapulmonares (n=83) foi similar (100% de sensibilidade e aproximadamente 83% de especificidade). A positividade pela NPCR foi significantemente maior que o isolamento por cultura entre as amostras extrapulmonares (p=0.0042). Conclusões. Os resultados obtidos sugerem a realização de estudos mais amplos que corroborem o potencial da NPCR-IS6110 para a detecção do genoma micobacteriano na TB extrapulmonar, em especial entre imunocomprometidos. Ademais, a detecção da micobactéria permanece como confirmação diagnóstica e a oportunidade de investigação do perfil de sensibilidade, favorecendo o tratamento efetivo para qualquer faixa etária e status imunológico.

Image segmentation is a critical step in building a computer vision algorithm that is able to distinguish between separate objects in an image scene. Image segmentation is based on two fundamentally intertwined components: pixel comparison and pixel grouping. In the pixel comparison step, pixels are determined to be similar or different from each other. In pixel grouping, those pixels which are similar are grouped together to form meaningful regions which can later be processed. This thesis makes original contributions to both of those areas. First, given a Markov Random Field framework, a Stochastic Nested Aggregation (SNA) framework for pixel and region grouping is presented and thoroughly analyzed using a Potts model. This framework is applicable in general to graph partitioning and discrete estimation problems where pairwise energy models are used. Nested aggregation reduces the computational complexity of stochastic algorithms such as Simulated Annealing to order O(N) while at the same time allowing local deterministic approaches such as Iterated Conditional Modes to escape most local minima in order to become a global deterministic optimization method. SNA is further enhanced by the introduction of a Graduated Models strategy which allows an optimization algorithm to converge to the model via several intermediary models. A well-known special case of Graduated Models is the Highest Confidence First algorithm which merges pixels or regions that give the highest global energy decrease. Finally, SNA allows us to use different models at different levels of coarseness. For coarser levels, a mean-based Potts model is introduced in order to compute region-to-region gradients based on the region mean and not edge gradients. Second, we develop a probabilistic framework based on hypothesis testing in order to achieve color constancy in image segmentation. We develop three new shading invariant semi-metrics based on the Dichromatic Reflection Model. An RGB image is transformed into an R'G'B' highlight invariant space to remove any highlight components, and only the component representing color hue is preserved to remove shading effects. This transformation is applied successfully to one of the proposed distance measures. The probabilistic semi-metrics show similar performance to vector angle on images without saturated highlight pixels; however, for saturated regions, as well as very low intensity pixels, the probabilistic distance measures outperform vector angle. Third, for interferometric Synthetic Aperture Radar image processing we apply the Potts model using SNA to the phase unwrapping problem. We devise a new distance measure for identifying phase discontinuities based on the minimum coherence of two adjacent pixels and their phase difference. As a comparison we use the probabilistic cost function of Carballo as a distance measure for our experiments.

Image segmentation is a critical step in building a computer vision algorithm that is able to distinguish between separate objects in an image scene. Image segmentation is based on two fundamentally intertwined components: pixel comparison and pixel grouping. In the pixel comparison step, pixels are determined to be similar or different from each other. In pixel grouping, those pixels which are similar are grouped together to form meaningful regions which can later be processed. This thesis makes original contributions to both of those areas. First, given a Markov Random Field framework, a Stochastic Nested Aggregation (SNA) framework for pixel and region grouping is presented and thoroughly analyzed using a Potts model. This framework is applicable in general to graph partitioning and discrete estimation problems where pairwise energy models are used. Nested aggregation reduces the computational complexity of stochastic algorithms such as Simulated Annealing to order O(N) while at the same time allowing local deterministic approaches such as Iterated Conditional Modes to escape most local minima in order to become a global deterministic optimization method. SNA is further enhanced by the introduction of a Graduated Models strategy which allows an optimization algorithm to converge to the model via several intermediary models. A well-known special case of Graduated Models is the Highest Confidence First algorithm which merges pixels or regions that give the highest global energy decrease. Finally, SNA allows us to use different models at different levels of coarseness. For coarser levels, a mean-based Potts model is introduced in order to compute region-to-region gradients based on the region mean and not edge gradients. Second, we develop a probabilistic framework based on hypothesis testing in order to achieve color constancy in image segmentation. We develop three new shading invariant semi-metrics based on the Dichromatic Reflection Model. An RGB image is transformed into an R'G'B' highlight invariant space to remove any highlight components, and only the component representing color hue is preserved to remove shading effects. This transformation is applied successfully to one of the proposed distance measures. The probabilistic semi-metrics show similar performance to vector angle on images without saturated highlight pixels; however, for saturated regions, as well as very low intensity pixels, the probabilistic distance measures outperform vector angle. Third, for interferometric Synthetic Aperture Radar image processing we apply the Potts model using SNA to the phase unwrapping problem. We devise a new distance measure for identifying phase discontinuities based on the minimum coherence of two adjacent pixels and their phase difference. As a comparison we use the probabilistic cost function of Carballo as a distance measure for our experiments.

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Made available in DSpace on 2016-12-08T16:24:06Z (GMT). No. of bitstreams: 1 PGCA10MA046.pdf: 2836538 bytes, checksum: df03fbb548e05bbfeb41e5f0f1ba5a4f (MD5) Previous issue date: 2010-05-13 / Porcine parvovirosis is a disease that causes reproductive failure and its causative agent is the Porcine Parvovirus Type 1 (PPV1). This disease, with high prevalence and worldwide distribution, affects mostly non-immune nulliparous sows. Clinically, it is observed return to estrus, delayed parturition date, birth of unviable piglets, weak, stillborn and particularly mummified fetuses in different sizes. These reproductive problems lead economic losses demonstrated by low productivity. This study aimed to implement and validate techniques for laboratory diagnosis PPV1 in natural infections in pig herds with reproductive problems and perform the characterization of these isolates. More specifically, it aimed to diagnose through nested-PCR, and characterize, through phylogenetic analysis, PPV1 isolates from tissue samples and stomach fluid from fetuses and reproductive tract from culled sows. The objectives were to further evaluate histologically the tissues that were positive by nested-PCR; to standardize an internal amplification control (IAC) for PVS1 nested-PCR; to standardize immunohistochemistry technique (IHC) in fetal tissues and to standardize PCR for Porcine Parvovirus Type 4 (PPV4). A total of 27 pig herds were studied, where 230 fetuses stillborn, mummified, aborted and unviable piglets were necropsied to harvest organs and stomach fluid. PPPV1 viral DNA was detected by nested-PCR in organs of six (2.61%) out of 230 fetuses analyzed, the cerebellum and spinal cord were the organs where the virus was detected more frequently (50%). Stomach fluids of three (2.75%) fetuses were positive by nested-PCR, out of 109 examined. In addition, samples of reproductive organs from 83 culled sows were collected also ovarian follicular fluid from 71 of them. The genetic material of PPV1 was diagnosed in six organs from sows (7.23%) and follicular fluid of three (4.22%) of them. Histological lesions were observed in four of 19 PPV1 positive organs of fetuses. Also, six ovaries and six uteri of six culled sows were PPV1 positive by nested-PCR. Exams showed that five of those ovaries were cycling, one was in anestrous and four uterus had some degree of endometritis. The IAC developed for nested-PCR was amplified in all reactions, as expected. In the IHC test the virus presence was confirmed in fetal tissue. The PCR for PPV4 was standardized and tested in fetal organs and reproductive organs from culled sows. Some samples from sow s reproductive organs were positive for this new porcine parvovirus. The results from this study show a low detection of PPV1 in herds analyzed, as well as from the reproductive organs of culled sows, considering the reduced PPV1 involvement in reproductive failure. Moreover, standardized techniques can be incorporated into routine diagnostic of PPV1 and PPV4 / A parvovirose suína é uma doença causadora de falhas reprodutivas e seu agente etiológico é o Parvovírus Suíno Tipo 1 (PVS1). Essa enfermidade, de alta prevalência e distribuição mundial, afeta principalmente porcas nulíparas não imunes. Clinicamente observa-se retorno ao cio, atraso na data de parição, nascimento de leitões inviáveis, fracos, natimortos e, principalmente, mumificados em diferentes tamanhos. Estes problemas reprodutivos acarretam prejuízos econômicos demonstrados pelos baixos índices produtivos. O presente trabalho objetivou implantar e validar técnicas de diagnóstico laboratorial para detecção de PVS1 em infecções naturais em rebanhos suínos que apresentam problemas reprodutivos e realizar caracterização desses isolados. Mais especificamente, objetivou-se diagnosticar, através de nested-PCR, e caracterizar, através de análise filogenética, isolados de PVS1 em amostras de tecidos e líquido estomacal de fetos e em aparelho reprodutivo de porcas descartadas. Objetivou-se ainda avaliar histologicamente os tecidos que resultaram positivos na nested-PCR; padronizar um controle interno de amplificação (CIA) para a nested-PCR de PVS1; padronizar técnica de imunohistoquímica (IHQ) em tecidos fetais e padronizar PCR para Parvovírus Suíno Tipo 4 (PVS4). De 27 rebanhos de suínos, foram colhidos 230 fetos entre natimortos, mumificados e abortados, os quais foram necropsiados para colheita de órgãos e líquido estomacal. O DNA viral foi detectado por nested-PCR em órgãos de seis (2,61%) fetos dos 230 analisados, sendo o cerebelo e a medula os órgãos onde o vírus foi detectado com maior frequência (50%). Líquido estomacal de três (2,75%) fetos foram positivos por nested-PCR, de 109 analisados. Além disso, amostras de órgãos reprodutivos de 83 porcas descartadas foram colhidas e também fluido folicular ovariano de 71 delas. O material genético do PVS1 foi diagnosticado em órgãos de seis porcas (7,23%) e em fluido folicular de três (4,22%) delas. De 19 órgãos positivos de fetos na nested-PCR, quatro tiveram lesão histológica. De seis ovários e seis úteros das seis fêmeas suínas descartadas positivas na nested-PCR, cinco ovários estavam ciclando, um estava em anestro e quatro úteros tinham algum grau de endometrite. O CIA desenvolvido para a nested-PCR foi amplificado em todas as reações, conforme o esperado. Nos testes de IHQ a presença do vírus foi confirmada em tecido fetal. A PCR para o PVS4 foi padronizada e testada em órgãos fetais e de porcas descartadas. Algumas amostras de porcas foram positivas para este novo parvovírus suíno. Os resultados obtidos no estudo evidenciam baixa freqüência do PVS1 nos rebanhos analisados, bem como nos órgãos reprodutivos de porcas descartadas, considerando baixo o envolvimento do PVS1 nas falhas reprodutivas. Além disso, as técnicas padronizadas podem ser incorporadas na rotina de diagnóstico de PVS1 e PVS4

[pt] Os recentes avanços em tecnologias de reconhecimento, como fala, toque e gesto, deram origem a uma nova classe de interfaces de usuário que não apenas explora múltiplas modalidades de interação, mas também permite múltiplos usuários interagindo. O desenvolvimento de aplicativos com interações multimodais e multiusuários trazem desafios para a sua especificação e execução. A especificação de uma aplicação multimodal é comumente o foco das pesquisas em interação multimodal, enquanto a especificação de sincronismos audiovisuais geralmente é o foco das pesquisas em multimídia. Nesta tese, com o objetivo de auxiliar a especificação de tais aplicações, buscamos integrar conceitos dessas duas pesquisas e propomos estender linguagens multimídia com entidades de primeira classe para suportar recursos multiusuário e multimodais. Essas entidades foram instanciadas nas linguagens NCL e HTML. Para avaliar nossa abordagem, realizamos uma avaliação com desenvolvedores NCL e HTML para capturar indícios de aceitação das entidades propostas e suas sintaxes nessas linguagens. / [en] Recent advances in recognition technologies, such as speech, touch and gesture, have given rise to a new class of user interfaces that does not only explore multiple modalities but also allows for multiple interacting users. The development of applications with both multimodal and multiuser interactions arise new specification and execution issues. The specification of multimodal application is commonly the focus of multimodal interaction research, while the specification of the synchronization of audiovisual media is usually the focus of multimedia research. In this thesis, aiming to assist the specification of such applications, we propose to integrate concepts from those two research areas and to extend multimedia languages with first-class entities to support multiuser and multimodal features. Those entities were instantiated in NCL and HTML. To evaluate our approach, we performed an evaluation with NCL and HTML developers to capture evidences of their acceptance of the proposed entities and instantiations in those languages.

Den här studien syftade till att undersöka om mental arbetsbelastning kan påverka benägenhetenatt begå konjunktionsfelet vid sannolikhetsbedömningar, trots att man fått ledtrådarsom synliggjort konjunktionsregeln. Detta undersöktes med en experimentell mellangruppsdesign.I studien deltog 57 deltagare, varav 27 i experimentgruppen och 30 i kontrollgruppen.Deltagarna var i huvudsak studenter på universitetsnivå. Grupperna hade en jämn könsfördelning.Vad gäller ålder så var medelvärdet i kontrollgruppen 24.8 och medelvärdet i experimentgruppenvar 30.7. Samtliga deltagare fick utföra ett datorbaserat test. Båda gruppernastest bestod av sannolikhetsbedömningsuppgifter, felstavningsuppgifter, samt en tilläggsuppgiftdär deltagarna ombads ange om ett visst ord förekommit i tidigare fråga eller ej. Experimentbetingelseninnehöll dessutom en visuospatial arbetsminnesuppgift. Resultatet visade attmental arbetsbelastning inte ökade antalet konjunktionsfel vid sannolikhetsbedömningar dådeltagarna fått ledtrådar som synliggjort konjunktionsregeln. Slutsatsen visar att det inte behövervara mer resurskrävande för arbetsminnet att göra normativa bedömningar och att tillgodogörandetav konjunktionsregeln är robust mot mental arbetsbelastning. Framtida forskningskulle kunna undersöka vilken betydelse ett visst antal ledtrådar har för om tillgodogörandetav konjunktionsregeln påverkas av mental arbetsbelastning. / The aim of this study was to investigate whether mental workload can affect the tendency tocommit the conjunction fallacy in probability assessments, despite having read clues that exposethe conjunction rule. This was investigated with an experimental between-group design.In total, the study had 57 participants, whereof 27 in the experiment group and 30 in the controlgroup. The groups were equally balanced concerning sex. The average age in the controlgroup was 24.8 years compared to 30.7 years in the experiment group. All participants performeda computer-based test. Both groups’ test consisted of tasks with probability assessments,discovering misspelled words and an additional task about estimating whether a certainword had occurred during the previous task. The experimental condition also consisted ofa visuo-spatial working memory task. The result indicated that mental workload did not increasethe number of conjunction fallacies committed in probability assessments, given thatthe participants had read clues that expose the conjunction rule. From this result, the conclusionis drawn that normative judgments are not necessarily more demanding for the workingmemory, also that the utilization of the conjunction rule is resistant to mental workload. Futureresearch might investigate what impact a certain number of clues has for whether theutilization of the conjunction rule is affected by mental work load.

In an open economy economic agents distribute their spending between domestic and various import goods and they may reconsider their choice whenever relative international prices change. Armington elasticities quantify these reallocations in demand for goods produced in different countries. Recent analytical frameworks allow to further differentiate between a macro elasticity of substitution between domestic and import goods and a micro elasticity between different import sources. Despite the relevance of Armington elasticities for evaluating trade policy there has been no systematic study on whether micro and macro elasticities significantly differ for highly integrated economies within a free trade area and whether there is a common pattern. Using highly disaggregated data, this paper estimates Armington elasticities for a panel of 15 EMU Member States. Empirical results indicate a significant difference between micro and macro elasticities for up to one half of the consistent product groups considered, implying preferences across EMU countries are not perfectly aligned with non-discriminatory tariffs. I conclude that both the absolute and relative macro elasticities are informative and that heterogeneous preference patterns link to current trade imbalances. (author's abstract) / Series: Department of Economics Working Paper Series