Object recognition is imperfect; often incomplete processing or deprived information yield misperceptions (i.e., misidentification) of objects. While quickly rectified and typically benign, instances of such errors can produce dangerous consequences (e.g., police shootings). Through a series of experiments, this study examined the competitive process of multiple object interpretations (candidates) during the earlier stages of object recognition process using a lexical decision task paradigm. Participants encountered low-pass filtered objects that were previously demonstrated to evoke multiple responses: a highly frequented interpretation (“primary candidates”) and a lesser frequented interpretation (“secondary candidates”). When objects were presented without context, no facilitative effects were observed for primary candidates. However, secondary candidates demonstrated evidence for being actively suppressed. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2017. / FAU Electronic Theses and Dissertations Collection

A manutenção da infecção latente pelo M. tuberculosis (TBIL) pode ser atribuída à sua capacidade de sobreviver durante anos no organismo humano em um estado não replicativo (dormente). A proteína HspX do M. tuberculosis, induzida sob condições de hipóxia, está fortemente associada com a manutenção da viabilidade do bacilo na TBIL. O presente estudo tem como objetivo, verificar se a superexpressão da proteína HspX altera a expressão de genes envolvidos com a síntese de componentes da parede celular, replicação do DNA e divisão celular de bacilos, assim como, na expressão de genes envolvidos com a resposta imune inata em macrófagos infectados com esses bacilos. O gene hspX foi amplificado pela PCR a partir do DNA do M. tuberculosis H37Rv, clonado no vetor de expressão pFPCA1GFP, e a proteína HspX expressa em M. smegmatis mc2155. As bactérias, nas quais, a presença da proteína recombinante foi confirmada por Western Blot, foram utilizadas, para a análise de expressão gênica tanto em bactérias quanto em macrófagos infectados. O estudo de expressão gênica foi realizado utilizando a RT-qPCR. Quando comparado aos controles, as bactérias que expressavam a proteína HspX apresentaram uma redução na expressão de genes de replicação do DNA e divisão celular, que foi acompanhado por uma tendência a filamentação das células e uma redução no tamanho das colônias. Além disso, nos macrófagos infectados com a bactéria expressando a proteína HspX, houve um aumento tanto da expressão do mRNA quanto da secreção de IL-1b, citocina importante para estabilização do granuloma, e uma redução na expressão de IRGM, gene relacionado com o processo autofágico, importante mecanismo de defesa do hospedeiro contra bactérias intracelulares. Portanto, em conjunto, essas alterações de expressão gênica, em consequência da presença da proteína HspX sugerem uma contribuição, direta ou indireta, dessa proteína para a adaptação morfológica e metabólica da bactéria dormente durante a TBIL, e consequentemente, para a resposta imune inata dos macrófagos infectados favorecendo a viabilidade intracelular dessas bactérias. / The maintenance of Mycobacterium tuberculosis infection latent (TBIL) may be attributed to its ability to persist for years in the host in a non-replicative state (dormant). The HspX protein from M. tuberculosis, induced under hypoxic, is strongly associated with maintaining the bacillus viability in TBIL. This study aims to determine if HspX overexpression chances the expression of genes involved in the synthesis of cell wall components, DNA replication and cell division of bacilli, as well as, the expression of genes involved in innate immune response of macrophages infected. The gene hspX was amplified by PCR from DNA of M. tuberculosis H37Rv, and cloned into the expression vector pFPCA1GFP. The HspX was expressed in M. smegmatis mc2155 and the recombinant protein was confirmed by Western blot. The bacterias expressing HspX were used for gene expression analysis both in bacteria and in infected macrophages by RT-PCRq. In bacterias expressing HspX, it was observed a reduction in expression of genes involved in DNA replication and cell division, and with cells more filamentous and smaller colonies, compared with controls. In addition, in macrophages infected with bacillus expressing HspX, there was an increase in both mRNA expression and secretion of IL-1b, an important cytokine for granuloma stability, and a reduction in expression of IRGM, an autophagic gene, important for host defense mechanism against intracellular bacteria. Together, these results suggest a direct or indirect contribution of HspX protein for metabolic and morphological adaptation of dormant bacteria in TBIL, and for the innate immune response in infected macrophages, improving the bacteria intracellular viability.

Introdução: A terapêutica da psoríase foi modificada pela introdução dos imunobiológicos, que permitem melhor controle da doença e melhor qualidade de vida aos pacientes, mas promovem aumento do risco de tuberculose latente, exigindo diagnóstico antecedendo seu início. Objetivo: Avaliar o desempenho do teste T-SPOT.TB no diagnóstico de infecção tuberculosa latente em pacientes com psoríase. Métodos: Em estudo experimental, prospectivo, analítico, com comparação de grupos,de prevenção primária, para validade de teste diagnóstico, 33 pacientes com psoríase (grupo psoríase) e 30 pacientes com outras doenças dermatológicas (grupo base), atendidos nos Ambulatório de Dermatologia Geral ou de Psoríase do Centro de Estudos Dermatológicos do Recife, da Santa Casa de Misericórdia, entre fevereiro e novembro de 2009, foram submetidos aos testes do PPD e T-SPOT.TB. Para ambos os grupos, admitiu-se inclusão com idade mínima de 18 anos e critérios de exclusão doenças ou condições fisiológicas que comprometessem a competência imunológica, exceto psoríase, para o grupo psoríase. Adotou-se a técnica de Mantoux para o teste do PPD e uma variante simplificada da técnica Enzyme-Linked Immunospot para a determinação de células T efetoras, secretoras de IFN-g em resposta à estimulação pelos antígenos específicos do M. tuberculosis para o teste T-SPOT.TB. As variáveis dependentes foram os resultados do teste T-SPOT.TB contra antígenos ESAT-6, CFP-10, e os resultados do teste do PPD, considerando enduração de 0-4 mm: não reator; 5-9 mm: reator fraco; ≥ 10 mm: reator forte. As variáveis independentes foram: idade, sexo, cor da pele, tempo de evolução da psoríase, ocupação, história de contato intradomiciliar e renda, alcoolismo e gravidade da doença. Foram submetidos a teste Qui quadrado ou exato de Fisher, em nível de significância de 0, 05, assim como ao teste de Mantel-Haenszel, três modelos comparando o teste T-SPOT.TB com teste do PPD, contato intradomiciliar e associação teste do PPD e contato intradomiciliar. A pesquisa foi aprovada pelos Comitês de Ética da Universidade Federal de Pernambuco e Universidade de São Paulo. Resultados: O grupo psoríase diferiu do grupo base quanto a razão de sexo com predomino do masculino (razão=0,7:1; p=0,047); maior idade média 42,1±1,9 anos (contra 34,1±1,4 anos no grupo base, p=0,023); fototipos I e II (p=0,020); menor nível de instrução e renda média mensal e contato intradomiciliar com tuberculose menos freqüente (p=0,001). Os grupos também diferiram quanto à positividade do teste do PPD (maior no grupo base; p=0,001). O teste T-SPOT.TB apresentou sensibilidade e especificidade de 9,1% e 95,5%, no modelo 1, 27,3% e 60%, no modelo 2, e valores de 60% e 53,3%, respectivamente no modelo 3. Foi no modelo 1 do grupo psoríase que o teste TSPOT. TB mostrou a maior concordância e o maior valor de Odds Ratio ponderado pelo teste de Mantel-Haenszel, tendo esses dois parâmetros significância estatística, quando comparados aos outros dois modelos. Conclusões: O teste T-SPOT.TB apresentou maior capacidade de diagnosticar casos negativos para tuberculose latente, constituindo-se numa opção para triagem de pacientes na instituição de terapêutica com imunobiológicos. / Introduction: The therapy for psoriasis was modified by the introduction of immunebiological products that allow better disease control and better quality of life for patients, but promotes increased risk forf latent tuberculosis, requiring diagnosis shortly before its establishment. Purpose: To assess the performance of T-SPOT.TB test for the diagnosis of latent tuberculosis infection in patients with psoriasis. Methods: Within a experimental, prospective, analytic, clinical assay type study, with comparison of groups, to validate a diagnostic test, 33 patients with psoriasis (psoriasis group) and 30 patients with other dermatological diseases (basis group), attempted at General Dermatology and Psoriasis Out-patients Departments of Recife\'s Dermatological Studies Center of Santa Casa de Misericórdia, from February to November 2009, were submitted to PPD and TSPOT. TB tests. For both groups, we admitted 18 years as minimal age for inclusion. The exclusion criteria included disease ou physiological conditions that compromised immunological competence, except psoriasis to psoriasis group. We used Mantoux technique for PPD test and a simplified variant of Enzyme-Linked Immunospot technique to determine effector T cells, secretors of IFN-g in response to M. tuberculosis specific antigens, to T-SPOT.TB test. Dependent variables were the results of T-SPOT.TB test against ESAT-6 and CPF-10 antigens, and the results to PPD test, considering enduration of 0-4 mm as non reactor; 5-10 mm weak reactor and ≥ 10 mm, strong reactor. Independent variables were age, sex, skin color, psoriasis evolution time, occupation, history of intradomiciliar contact and income, alcoolism and disease grade. Three models, comparing T-SPOT.TB test to PPD test, intradomiciliar contact and both, were submitted to Qui Squared test or Exact Fisher Test, at significance level of 0.05, as well as to Mantel- Haenszel test. The research has been approved by Ethics Committee of Universidade Federal de Pernambuco e Universidade de São Paulo. Results: Psoriasis group differed from base group on sex ratio with predominance of male gender (rate=0.7:1; p=0,047), major mean age (42,1 ± 1.9 years against 34,1 ± 1.4 years in basic group, p = 0,023) phototypes I and II (p = 0,020); lower scholarship, income and less frequent intradomiciliar contact with tuberculosis (p = 0,001). The groups also differed on the positivity of PPD test (greater in base group; p = 0,001). T-SPOT.TB test had sensibility and specificity of 9,1% and 95.5%, in model 1; 27,3% and 60%, in model 2, and values of 60% and 53,3% respectively in model 3. Model 1 showed greater concordance and highest value of Odds Ratio test weighted by Mantel-Haenszel test, having these two parameters statistical significance when compared to the other two models. Conclusions: T-SPOT.TB test had great ability to diagnose negative cases for latent tuberculosis, and constitutes an option for screening patients to immunobiological therapy administration.

This thesis deals with the reporting of criminal offenses both in terms of individual and procedural criminal law, and from the point of view of the importance of this issue in criminology. The thesis is divided into ten chapters. The first chapter describes the role of reporting criminal offenses in criminal proceedings. In particular, it deals with the status of the procedure for initiating criminal prosecution in criminal proceedings. It then deals with the very aspects of the procedure for filing a crime report, in particular with crime reporting, its formalities, options in filing a criminal complaint, and procedures following the filing of a criminal complaint, while it points out the issue of imposing the act of closed file. Chapter two highlights the rights of the complainant, the injured and the victim in connection with the reported crime. This chapter addresses issues with informing the injured person or victim at the point of crime reporting. Furthermore, this chapter deals with the right of the complainant to an effective investigation. Chapter three deals with the benefits of crime reporting by its perpetrator as encompassed in the Criminal Code. Chapter four addresses the issue of misuse of the criminal reporting system, especially the possible ways of system abuse and the responsibility for...

Introdução: A tuberculose é uma doença de repercussão mundial que desafia os serviços de saúde (SS). Estima-se que um terço da população mundial apresenta a forma latente da doença. Os profissionais da saúde (PAS) inseridos na assistência direta podem ter maior probabilidade de contágio; entretanto, os índices de ocorrência da doença nesta população não foram, até o momento, reconhecidos de forma sistemática. Objetivo: Estimar a prevalência e a incidência de tuberculose ocupacional nos serviços de saúde. Método: Trata-se de uma revisão sistemática de literatura segundo protocolo do Joanna Briggs Institute, que buscou responder quais os índices de tuberculose ocupacional nos SS. Foram considerados estudos primários que incluíssem dados de incidência e prevalência de tuberculose ocupacional ou de viragem tuberculínica em PAS. Foram definidos como PAS indivíduos em formação ou formados em cursos na área da saúde e que atuam na assistência direta. Quanto a SS, foram consideradas instituições de atendimento em qualquer um dos níveis assistenciais e que realizam atendimento direto a pacientes suspeitos ou portadores de tuberculose em suas fases transmissíveis, de forma a manter a homogeneidade da investigação. Foram excluídos os relatos de surtos e as ações dirigidas a populações em geral. Resultados: Foram identificadas 2.081 citações potencialmente relevantes em dez bases de dados, sem limites de tempo e idioma, a seleção final levou a 17 estudos. Em todos os artigos selecionados o desfecho estudado foi tuberculose latente. Não foram identificados estudos com dados com relação à tuberculose doença. O teste tuberculínico foi utilizado em 88,2% dos estudos. A prevalência de tuberculose latente (TL) variou entre 0,1% e 59,7% e a taxa de incidência anual variou de 3,3% a 26%. Um estudo identificou a densidade de incidência de 547/100.000 pessoas/ano. Conclusão: As evidências demonstram que a tuberculose é um importante agravo entre os PAS nos Serviços de Saúde, com importantes variações de acordo com o contexto. Os resultados indicam que a despeito da relevância do fenômeno, ainda há lacunas de informação sobre a incidência e a prevalência da tuberculose doença em PAS. / Introduction: Tuberculosis is a disease of worldwide repercussion that defies health care services (HS). It is estimated that one-third of the world population has a latent form of the disease. Healthcare workers (HCW) dealing with direct patient assistance may have higher contagion probability. However, the rates of the disease occurrence in this population have not been established in a systematic way yet. Objective: To estimate the global prevalence and incidence of occupational tuberculosis in HS by means of the literature review. Method: This is a systematic literature review according to the Joanna Briggs Institute, which sought to identify the rates of occupational tuberculosis in HCW. Primary studies were considered to include data on the incidence and prevalence of occupational tuberculosis or tuberculin skin test reaction in HCW. Reports of outbreaks and actions addressed to the community in general were excluded. Results: Out of ten cross-referenced databases, 2,081 potentially relevant studies were identified, without time and language limits, and the final selection was 17 studies. In all the articles selected, the outcome was latent tuberculosis. No studies with data regarding the tuberculosis disease were identified. The tuberculin skin test was used in 88.2% of the studies. The prevalence of latent tuberculosis ranged from 0.1 % to 59.7%. The annual incidence rate varied from 3.3% to 26%. As the risk and occupational exposure the absence of vaccination prior, the duration of care and performance in tuberculosis specific services were shown as relevant factors. One study identified the density of incidence of 547/100,000 people per year. Conclusion: Evidence indicates that tuberculosis is a relevant disease with the HCW and has important rates variations according to the context. The results demonstrate that despite the relevance of the phenomenon, there are still gaps in information on the incidence and prevalence of the tuberculosis disease in HCW.

In cluster analysis interest lies in probabilistically capturing partitions of individuals, items or observations into groups, such that those belonging to the same group share similar attributes or relational profiles. Bayesian posterior samples for the latent allocation variables can be effectively obtained in a wide range of clustering models, including finite mixtures, infinite mixtures, hidden Markov models and block models for networks. However, due to the categorical nature of the clustering variables and the lack of scalable algorithms, summary tools that can interpret such samples are not available. We adopt a Bayesian decision theoretical approach to define an optimality criterion for clusterings and propose a fast and context-independent greedy algorithm to find the best allocations. One important facet of our approach is that the optimal number of groups is automatically selected, thereby solving the clustering and the model-choice problems at the same time. We consider several loss functions to compare partitions and show that our approach can accommodate a wide range of cases. Finally, we illustrate our approach on both artificial and real datasets for three different clustering models: Gaussian mixtures, stochastic block models and latent block models for networks.

The eCommerce industry introduced new business principles, as well as new strategies for achieving these principles, and as a result some traditional measures of success are no longer valid. We classified and ranked the performance of twenty business-to-consumer eCommerce companies by developing critical benchmarks using the Balanced scorecard methodology. We applied a Latent class model, a statistical model along the Bayesian framework, to facilitate the determination of the best and worst performing companies. An eCommerce site's greatest asset is its customers, which is why some of the most valued and sophisticated metrics used today evolve around customer behavior. The results from our classification and ranking procedure showed that companies that ranked high overall also ranked comparatively well in the customer analysis ranking, For example, Amazon.com, one of the highest rated eCommerce companies with a large customer base ranked second in the critical benchmark developed towards measuring customer analysis. The results from our simulation also showed that the Latent class model is a good fit for the classification procedure, and it has a high classification rate for the worst and best performing companies. The resulting work offers a practical tool with the ability to identify profitable investment opportunities for financial managers and analysts.

Intratumoural heterogeneity complicates the molecular interpretation of biopsies, as multiple distinct tumour genomes are sampled and analysed at once. Ignoring the presence of these populations can lead to erroneous conclusions, and so a correct analysis must account for the clonal structure of the sample. Several methods to reconstruct tumour clonality from sequencing data have been proposed, spanning methods that either do not consider phylogenetic constraints or posit a perfect phylogeny. Models of the first type are typically latent feature models that can describe the observed data flexibly, but whose results may not be reconcilable with a phylogeny. The second type, instead, generally comprises non-parametric mixture models, with strict assumptions on the tumour’s evolutionary process. The focus of this dissertation is on the development of a phylogenetic latent feature model that can bridge the advantages of these two approaches, allowing deviations from a perfect phylogeny. The work is recounted by three statistical models of increasing complexity. First, I present a non-parametric model based on the Indian Buffet Process prior, and highlight the need for phylogenetic constraints. Second, I develop a finite, phylogenetic extension of the previous model, and show that it can outperform competing methods. Third, I generalise the phylogenetic model to arbitrary copy-number states. Markov chain Monte Carlo algorithms are presented to perform inference. The models are tested on datasets that include synthetic data, controlled biological data, and clinical data. In particular, the copy-number generalisation is applied to longitudinal circulating tumour DNA samples. Liquid biopsies that leverage circulating tumour DNA require sensitive techniques in order to detect mutations at low allele fractions. One method that allows sensitive mutation calling is the amplicon sequencing strategy TAm-Seq. I present bioinformatic tools to improve both the development of TAm-Seq amplicon panels and the analysis of its sequencing data. Finally, an enhancement of this method is presented and shown to detect mutations de novo and in a multiplexed manner at allele fractions less than 0.1%.

Human cytomegalovirus (HCMV) is a betaherpesvirus which establishes a lifelong persistent infection, underpinned by its ability to establish latent infection in early myeloid lineage cells, in the infected host. Although well controlled by a healthy immune system, HCMV causes pathological and life threatening disease in individuals with a compromised or immature immune response, which can come from primary HCMV infection or reactivation of latent infection. Although progress is being made in understanding the mechanisms by which HCMV maintains latency and reactivates, a better understanding is essential towards the aim of targeting and killing latently infected cells. In this thesis, I will present evidence that the HCMV-encoded chemokine receptor homologue US28, which is expressed during latent infection of CD14+ monocytes, is necessary for maintaining HCMV latency in these monocytes and, in the absence of US28 protein expression, HCMV undergoes lytic infection. US28 expression was found to attenuate cellular signalling pathways in latently infected cells; in particular, MAP kinase and NFκB. Interestingly, deletion of the US28 gene or inhibition of the US28 protein resulted in the expression of lytic antigens which allowed detection of infected monocytes by the immune system. This observation may lead to a potential new immunotherapeutic strategy against latent HCMV. Having demonstrated that US28 protein is expressed on the surface of latently infected monocytes, I tested whether a new fusion-toxin protein, called F49A-FTP, which binds US28 protein, could be used to target and kill latently infected cells. I developed a protocol for treating latently infected monocytes with F49A-FTP which resulted in a significant reduction in virus reactivation after monocyte differentiation to dendritic cells. I was also able to show that this treatment kills CD34+ progenitor cells, which were experimentally latently infected with HCMV, as well as latently infected monocytes from a healthy, seropositive blood donor. Finally, during my investigations into the role of US28 during HCMV latency, a mass spectrometry screen was performed to measure changes in cellular protein expression when US28 protein is expressed in isolation, in THP-1 monocyte-like cell line. This identified CTCF, a transcription factor which appears to be modified by US28 in THP-1 cells. I showed that CTCF has a repressive effect on the HCMV MIEP, and that CTCF likely plays a role in HCMV latency. In summary, this work provides insights into the role of US28 during HCMV latency, and proposes potential novel therapeutic strategies to kill latently infected cells.

Resumo: Considerando a importância da compreensão da dinâmica espaço temporal dos componentes do balanço de energia (BE) em escala regional para o gerenciamento de recursos hídrico e o manejo agrícola, o objetivo principal desta tese foi construir e analisar uma série temporal dos componentes do BE adequada às condições de clima subtropical úmido do Estado do Rio Grande do Sul. Para tanto, inicialmente foi avaliada a adequação de modelos de estimativa de BE para o Estado. Nesta etapa foram utilizados produtos MODIS e dados de referência medidos em uma torre micrometeorológica instalada em Cruz Alta – RS, usando valores instantâneos para um período de estudo de 2009 a 2011. Na sequência foi avaliada a adequação dos modelos em representar a variabilidade espacial dos componentes do BE. Nesta etapa foram usados produtos MODIS, dados de reanálise ERA Interim, dados de referência da torre micrometeorológica e dados de estações meteorológicas do INMET, para o mesmo período de estudo. Na última etapa do trabalho foi construída a série temporal dos componentes do BE usando o modelo METRIC, a qual abrangeu um período de 14 anos, de 2002 a 2016. Os resultados demonstraram que os três modelos analisados apresentam coerência com as medidas de referência, sendo as maiores limitações apresentadas pelo modelo SEBAL, as quais se atribui principalmente às condições ecoclimáticas do Estado e a baixa resolução espacial das imagens. Na análise da variabilidade espacial, o modelo METRIC apresentou maior consistência nos resultados e proporcionou maior número de dias com resultados válidos, sendo assim apontado como o mais apto para realização do restante do estudo. A série temporal construída possibilitou a compreensão dos padrões de distribuição espaço temporal dos componentes do BE no estado do Rio Grande do Sul. Há uma marcada sazonalidade nos componentes do BE, com maiores valores no verão e menores no inverno. G (fluxo de calor no solo) é o componente de menor magnitude e sua distribuição espacial e temporal é determinada pela distribuição de Rn (saldo de radiação). Já os componentes LE (fluxo de calor latente) e H (fluxo de calor sensível), são os que mostram magnitude maior e apresentam padrões de distribuição espacial e temporal coerentes com as condições climáticas e com os tipos de uso e cobertura na área de estudo. Observase um padrão inverso, com um gradiente de LE no sentido noroeste para sudeste e para o componente H, no sentido sudeste para noroeste. Sendo estas informações de grande importância para gerenciamento de recursos hídricos em escala regional, para estudos de zoneamento agrícola. / Abstract: Given the importance of understanding the temporal and spatial dynamics of of the energy balance (EB) components in a regional scale for the management of water resources and agricultural, the main objective of this thesis was to construct and analyze a time series of the components of BE appropriate to the subtropical humid climate conditions of the State of Rio Grande do Sul. In order to reach the objective initially, the adequacy of the models for the humid climate conditions was evaluated, in this step we used MODIS data and reference data measured in a micrometeorological tower installed in Cruz Alta - RS. The analyzes performed with instantaneous values and the study period was from 2009 to 2011. The next step evaluate the spatial variability of the BE components, the data used were the MODIS products, ERA Interim reanalysis data, reference data of the micrometeorological tower and INMET meteorological stations, for the same study period. In the last stage the time series of the BE components was constructed from the METRIC model. The period series was 14 years from 2002 to 2016.The results showed that the three models analyzed were consistent with the reference measurements, with the greatest limitations presented by the SEBAL model, which are mainly attributed to the state's eco-climatic conditions and the low spatial resolution of the images In the analysis of the spatial variability, the METRIC model presented greater consistency in the results and provided greater number of days with valid results, this model thus indicated as the most suitable for the rest of the study. The time series constructed allowed us to understand the temporal distribution patterns of BE components in the state of Rio Grande do Sul. There is a marked seasonality in the BE components, with higher values in summer and lower in winter. G is the smallest magnitude component and its spatial and temporal distribution is determined by the Rn distribution. On the other hand, the LE and H components are those that show higher magnitude and present spatial and temporal distribution patterns consistent with the climatic conditions and the types of use and coverage in the study area. An inverse pattern is observed, with a LE gradient from north-west to south-east and for H-component, from southeast to northwest.