Pine cone beetles (Conophthorus sp.) are serious pests of many forest ecosystems since they burrow into pine cone tissues for egg deposition, causing the death of the seeds. Management of these beetles in natural and commercial stands of pines has been problematic due to lack of understanding about species limits and distribution. This study was conducted to investigate the phylogeography and phylogenetics of the genus. Several species represented by disjunct populations appear to be monophyletic including Conophthorus edulis, C. mexicanus, C. coniperda, and C. conicollens, whereas C. ponderosae is polyphyletic with many distinct clades isolated by geography. This study explored whether host use or geography has played a greater role in the diversification of this genus, focusing on the polyphyletic C. ponderosae and the monophyletic C. edulis. In the first study, 751bp of the mtDNA CO1 gene were sequenced to reconstruct a phylogeny of the genus, and the distribution and host use were compared to investigate whether these factors were significantly associated. The second study addressed population structure and possible historical influences on the C. edulis and C. ponderosae populations using a nested clade analysis of the mtDNA haplotypes. Despite potential limitations due to sampling, several conclusions could be drawn. Three separate haplotype networks were found for the C. ponderosae haplotypes, indicating that there have been at least three lineages that have associated with P. ponderosa. Geography was significantly associated with the phylogeny at greater distances (>900km), but host use was not significant. At the species level, association with geography is variable. Population structure for C. ponderosae at the species level is minimal, and suggests that there has not been much time for lineage sorting of the haplotypes based on the nested clade analysis as compared to C. edulis.

Submitted by Programa de Pós-graduação em Biotecnologia (mebiotec.ufba@gmail.com) on 2017-09-12T13:18:14Z No. of bitstreams: 1 DISSERTAÇÃO Final - Madina Lyve.pdf: 1838310 bytes, checksum: 0edc784fb4493f69c9c8d82247d22030 (MD5) / Approved for entry into archive by Edvaldo Souza (edvaldosouza@ufba.br) on 2017-09-19T18:53:06Z (GMT) No. of bitstreams: 1 DISSERTAÇÃO Final - Madina Lyve.pdf: 1838310 bytes, checksum: 0edc784fb4493f69c9c8d82247d22030 (MD5) / Made available in DSpace on 2017-09-19T18:53:06Z (GMT). No. of bitstreams: 1 DISSERTAÇÃO Final - Madina Lyve.pdf: 1838310 bytes, checksum: 0edc784fb4493f69c9c8d82247d22030 (MD5) / FAPESB / A gastroenterite aguda é considerada uma importante causa de morbidade e mortalidade entre crianças em todo o mundo, especialmente nos primeiros anos de vida. Tal doença pode ser provocada por infecções causadas por bactérias, fungos, protozoários e, principalmente, vírus. Dentre as infecções virais, destacam-se: Norovírus (NoV), Rotavírus (HRV), Adenovírus (AdV) e, mais recentemente identificado, o Bocavírus Humano (HBoV). O HBoV possui DNA de fita simples, não envelopado e pertencente à família Parvoviridae, gênero Bocavírus. Apresenta quatro proteínas, sendo estas VP1 e VP2, proteínas estruturais, NS1, proteína não estrutural e a nucleoproteína NP1 com função desconhecida. Com o intuito de verificar a existência e determinar as espécies circulantes do HBoV em Salvador-Bahia, no período de Janeiro a Julho de 2012, o presente estudo analisou 105 amostras fecais de crianças menores de 5 anos de idade que deram entrada na emergência de uma Unidade Hospitalar com quadro clínico de gastroenterite aguda. Através da extração do DNA e posterior reação do nested-PCR foi possível observar que o HBoV estava presente em 42% das amostras testadas, percentual de positividade considerado alto quando comparado a outros estudos onde a frequência do vírus havia sido menor. Além disso, testes imunoenzimáticos também foram realizados nessas amostras para verificar a presença de viroses entéricas (NoV, HRV e AdV), revelando que 27% das amostras positivas para HBoV estavam co-infectadas com NoV e AdV, enquanto a maior parte tratava-se de infecção apenas por HBoV. O sequenciamento e análise filogenética das sequências virais mostraram que estas pertencem as espécies HBoV-1 e HBoV-2A, sendo esta última, até o momento, nunca relatada no Brasil. Por fim, o presente trabalho busca, de forma inovadora e pioneira no estado da Bahia, direcionar as pesquisas para este novo agente etiológico que vem sendo identificado em pacientes com sintomas de gastroenterite aguda em todo o mundo e que agora também foi detectado na população de Salvador.

Doctor of Philosophy / Department of Agronomy / Geoffrey Morris / Climate change has been anticipated to affect agriculture, with most the profound effect in regions where low input agriculture is being practiced. Understanding of how plants evolved in adaptation to diverse climatic conditions in the presence of local stressors (biotic and abiotic) can be beneficial for improved crop adaptation and yield to ensure food security. Great genetic diversity exists for agroclimatic adaptation in sorghum (Sorghum bicolor L. Moench) but much of it has not been characterized. Thus, limiting its utilization in crop improvement. The application of next-generation sequencing has opened the plant genome for analysis to identify patterns of genome-wide nucleotide variations underlying agroclimatic adaptation. To understand the genetic basis of adaptive traits in sorghum, the genetic architecture of sorghum inflorescence traits was characterized in the first study. Phenotypic data were obtained from multi-environment experiments and used to perform joint linkage and genome-wide association mapping. Mapping results identified previously mapped and novel genetic loci underlying inflorescence morphology in sorghum. Inflorescence traits were found to be under the control of a few large and many moderate and minor effect loci. To demonstrate how our understanding of the genetic basis of adaptive traits can facilitate genomic enabled breeding, genomic prediction analysis was performed with results showing high prediction accuracies for inflorescence traits. In the second study, the sorghum-nested association mapping (NAM) population was used to characterize the genetic architecture of leaf erectness, leaf width, and stem diameter. About 2200 recombinant inbred lines were phenotyped in multiple environments. The obtained phenotypic data was used to perform joint linkage mapping using ~93,000 markers. The proportion of phenotypic variation explained by QTL and their allele frequencies were estimated. Common and moderate effects QTL were found to underlie marker-trait associations. Furthermore, identified QTL co-localized with genes involved in both vegetative and inflorescence development. Our results provide insights into the genetic basis of leaf erectness and stem diameter in sorghum. The identified QTL will also facilitate the development of genomic-enable breeding tools for crop improvement and molecular characterization of the underlying genes Finally, in a third study, 607 Nigerian accessions were genotyped and the resulting genomic data [about 190,000 single nucleotide polymorphisms (SNPs)] was used for downstream analysis. Genome-wide scans of selection and genome-wide association studies (GWAS) were performed and alongside estimates of levels of genetic differentiation and genetic diversity. Results showed that phenotypic variation in the diverse germplasm had been shaped by local adaptation across climatic gradient and can provide plant genetic resources for crop improvement.

Submitted by Amanda Silva (amanda.osilva2@ufpe.br) on 2015-03-13T15:17:34Z No. of bitstreams: 2 DISSERTAÇÃO Nayara Evaristo Pontes.pdf: 1260344 bytes, checksum: 91a47c546488e8c96e02bf7cbc6d3631 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-03-13T15:17:34Z (GMT). No. of bitstreams: 2 DISSERTAÇÃO Nayara Evaristo Pontes.pdf: 1260344 bytes, checksum: 91a47c546488e8c96e02bf7cbc6d3631 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2014 / CNPq; CAPES / O Circovírus suíno tipo 2 (PCV2) é um vírus sem envelope e contém um DNA fita simples circular com 1,7 kb de tamanho. O vírus pertence ao gênero Circovírus da família Circoviridae. O PCV2 é o agente etiológico da Síndrome Multissistêmica do Definhamento dos Suínos (PMWS), doença que causa grande impacto econômico na suinocultura mundial. O objetivo deste trabalho foi desenvolver a técnica de STNPCR para detecção do Circovírus suíno tipo 2 (PCV2) bem como avaliar a presença de diferentes variantes virais em Pernambuco. Foram utilizados controles positivos, negativos, e 55 amostras de tecidos de animais clinicamente normais obtidas em abatedouro. Para o desenvolvimento da STNPCR foram avaliadas diferentes temperaturas de anelamento para os primers externos e internos. A atuação de ambos os pares de primers foi realizada de forma independente, sendo que o segundo par de primers foi imobilizado na parte interna da tampa do microtubo e após a primeira etapa de amplificação os primers foram eluídos por inversão do microtubo. Além disso, foi realizada a análise de achado técnico buscando encontrar os genótipos do PCV2 já descritos no Brasil e mundialmente, os subtipos PCV2a e PCV2b. Na aplicação clínica, a STNPCR foi comparada com a NPCR e resultaram em reações positivas para o PCV2 em 100% (55/55) das amostras analisadas, revelando igual sensibilidade e especificidade, porém, com menor risco de contaminação cruzada. Na análise de achado técnico (sequências da ORF2 do PCV2), foi possível identificar os genótipos PCV2a e PCV2b. A técnica molecular STNPCR demonstrou ser eficaz para detecção do DNA viral e pode ser aplicada em estudos epidemiológicos para o PCV2 e auxiliar no diagnóstico laboratorial da PMWS.

Made available in DSpace on 2014-06-12T17:21:58Z (GMT). No. of bitstreams: 2 arquivo6593_1.pdf: 1372457 bytes, checksum: 7d328b5860db2137060c9694c0610e5c (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2011 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Essa dissertação é dividida em dois ensaios. O primeiro objetiva caracterizar a demanda por medicamentos no Brasil. Para isso é feita uma revisão da literatura sobre o tema e expostas suas particularidades para o caso brasileiro por meio dos microdados da POF 2002-2003. Com isso são estimadas as probabilidades de gastos por categoria de medicamento. Conforme os resultados, em geral, essas probabilidades são crescentes com a renda e o grau de instrução do chefe da família. Contudo, outras características como raça, região e idade possuem relevantes efeitos sobre essas probabilidades, onde isso dependerá também do medicamento adquirido. O segundo ensaio visa apresentar como se dá o acesso aos medicamentos pelos brasileiros. Para tanto são aplicados modelos de Escolha discreta, para em seguida, com os dados da PNAD-Saúde 2009, a partir de estimações por Multinomial Logit e Nested Logit, realizar inferências sobre a tomada de decisão de consumo dos indivíduos. Os resultados sugerem que a renda, o grau de instrução e o tipo de doenças infringidas são fatores relevantes. Onde a presença deste último fator afeta diretamente a tomada de decisão de consumo dos brasileiros, principalmente, no caso das doenças mais danosas à saúde

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Research on engineering design is a core area of concern within engineering education, and a fundamental understanding of how engineering students approach and undertake design is necessary in order to develop effective design models and pedagogies. This dissertation contributes to scholarship on engineering design by addressing a critical, but as yet underexplored, problem: how does the context in which students design shape their design practices? Using a qualitative study comprising of video data of design sessions, focus group interviews with students, and archives of their design work, this research explored how design decisions and actions are shaped by context, specifically the context of higher education. To develop a theoretical explanation for observed behavior, this study used the "nested structuration" framework proposed by Perlow, Gittell, & Katz (2004). This framework explicated how teamwork is shaped by mutually reinforcing relationships at the individual, organizational, and institutional levels. I appropriated this framework to look specifically at how engineering students working on a course-related design project identify constraints that guide their design and how these constraints emerge as students interact while working on the project. I first identified and characterized the parameters associated with the design project from the student perspective and then, through multi-case studies of four design teams, I looked at the role these parameters play in student design practices. This qualitative investigation of first-year engineering student design teams revealed mutual and interconnected relationships between students and the organizations and institutions that they are a part of. In addition to contributing to research on engineering design, this work provides guidelines and practices to help design educators develop more effective design projects by incorporating constraints that enable effective design and learning. Moreover, I found that when appropriated in the context of higher education, multiple sublevels existed within nested structuration's organizational context and included course-level and project-level factors. The implications of this research can be used to improve the design of engineering course projects as well as the design of research efforts related to design in engineering education. / Ph. D.

Distributed Transactional Memory (DTM) is an emerging, alternative concurrency control model that aims to overcome the challenges of distributed-lock based synchronization. DTM employs transactions in order to guarantee consistency in a concurrent execution. When two or more transactions conflict, all but one need to be delayed or rolled back. Transactional Memory supports code composability by nesting transactions. Nesting how- ever can be used as a strategy to improve performance. The closed nesting model enables partial rollback by allowing a sub-transaction to abort without aborting its parent, thus reducing the amount of work that needs to be retried. In the open nesting model, sub- transactions can commit to the shared state independently of their parents. This reduces isolation and increases concurrency. Our first main contribution in this dissertation are two extensions to the existing Transac- tional Forwarding Algorithm (TFA). Our extensions are N-TFA and TFA-ON, and support closed nesting and open nesting, respectively. We additionally extend the existing SCORe algorithm with support for open nesting (we call the result SCORe-ON). We implement these algorithms in a Java DTM framework and evaluate them. This represents the first study of transaction nesting in the context of DTM, and contributes the first DTM implementation which supports closed nesting or open nesting. Closed nesting through our N-TFA implementation proved insufficient for any significant throughput improvements. It ran on average 2% faster than flat nesting, while performance for individual tests varied between 42% slowdown and 84% speedup. The workloads that benefit most from closed nesting are characterized by short transactions, with between two and five sub-transactions. Open nesting, as exemplified by our TFA-ON and SCORe-ON implementations, showed promising results. We determined performance improvement to be a trade-off between the overhead of additional commits and the fundamental conflict rate. For write-intensive, high- conflict workloads, open nesting may not be appropriate, and we observed a maximum speedup of 30%. On the other hand, for lower fundamental-conflict workloads, open nesting enabled speedups of up to 167% in our tests. In addition to the two nesting algorithms, we also develop Hyflow2, a high-performance DTM framework for the Java Virtual Machine, written in Scala. It has a clean Scala API and a compatibility Java API. Hyflow2 was on average two times faster than Hyflow on high-contention workloads, and up to 16 times faster in low-contention workloads. Our second main contribution for improving DTM performance is automated data partition- ing. Modern transactional processing systems need to be fast and scalable, but this means many such systems settled for weak consistency models. It is however possible to achieve all of strong consistency, high scalability and high performance, by using fine-grained partitions and light-weight concurrency control that avoids superfluous synchronization and other over- heads such as lock management. Independent transactions are one such mechanism, that rely on good partitions and appropriately defined transactions. On the downside, it is not usually straightforward to determine optimal partitioning schemes, especially when dealing with non-trivial amounts of data. Our work attempts to solve this problem by automating the partitioning process, choosing the correct transactional primitive, and routing transactions appropriately. Our third main contribution is Alvin, a system for managing concurrently running trans- actions on a geographically replicated data-store. Alvin supports general-purpose transactions, and guarantees strong consistency criteria. Through a novel partial order broadcast protocol, Alvin maximizes the parallelism of ordering and local transaction processing, resulting in low client-perceived latency. Alvin can process read-only transactions either lo- cally or globally, according to the desired consistency criterion. Conflicting transactions are ordered across all sites. We built Alvin in the Go programming language. We conducted our evaluation study on Amazon EC2 infrastructure and compared against Paxos- and EPaxos- based state machine replication protocols. Our results reveal that Alvin provides significant speed-up for read-dominated TPC-C workloads: as much as 4.8x when compared to EPaxos on 7 datacenters, and up to 26% in write-intensive workloads. Our fourth and final contribution is M2Paxos, a multi-leader implementation of Generalized Consensus. Single leader-based consensus protocols are known to stop scaling once the leader reaches its saturation point. Ordering commands based on conflicts is appealing due to the potentially higher parallelism, but is imperfect due to the higher quorum sizes required for fast decisions and the need to compare commands and track their dependencies. M2Paxos on the other hand exploits fast decisions (i.e., delivery of a command in two communication delays) by leveraging a classic quorum size, matching a majority of nodes deployed. M2Paxos does not establish command dependencies based on conflicts, but it binds accessed objects to nodes, making sure commands operating on the same object will be ordered by the same node. Our evaluation study of M2Paxos (also built in Go) confirms the effectiveness of this approach, getting up to 7⨉ improvements in performance over state- of-the-art consensus and generalized consensus algorithms. / Ph. D.

Yes / The research presented in this paper addresses the challenge of developing functional models for complex systems that have multiple modes of operation or use cases. An industrial case study of an electric vehicle is used to illustrate the proposed methodology, which is based on a systematic modelling of functions through nested systems using the system state flow diagram (SSFD) method. The paper discusses the use of SSFD parameter based state definition to identify physical and logical conditions for joining function models, and the use of heuristics to construct complex function models.

Made available in DSpace on 2015-04-11T13:38:41Z (GMT). No. of bitstreams: 1 Dissertacao-Janaina Roriz Hipolito.pdf: 4312682 bytes, checksum: ecb7ef268b16e006660e9770d5f663b4 (MD5) Previous issue date: 2006-07-28 / Fundação de Amparo à Pesquisa do Estado do Amazonas / A malária é um problema de saúde pública na região Amazônica, mais de 200 mil casos dessa doença ocorrem anualmente no Amazonas, sendo 80% deles causados pelo P. vivax, que vem apresentando índices crescentes de morbidade, principalmente associados à diminuição da sensibilidade aos antimaláricos. Dentre as estratégias para combate e controle da doença, a identificação rápida e precisa da espécie é ferramenta indispensável para um tratamento apropriado, diminuição do risco de transmissão e melhor entendimento da epidemiologia desses parasitas. A técnica microscópica da gota espessa é a principal para diagnóstico da malária, entretanto, outros métodos vêm sendo testados, principalmente os moleculares que tem se mostrado mais sensíveis e específicos para detectar e diferenciar as espécies em baixas parasitemias. Avanços desse método, como a PCR em tempo real, permitem que o resultado do teste seja detectado simultaneamente a amplificação, diminuindo o tempo gasto para a realização do diagnóstico. Com o intuito de detectar molecularmente a malária, verificando a presença de plasmódios, o diagnóstico molecular foi realizado através das técnicas de PCR em tempo real e nested-PCR, para se fazer uma comparação desses dois métodos com o diagnóstico microscópico da gota espessa em 300 amostras criopreservadas, 200 coletadas no dia inicial do tratamento (D0), das quais 88% (176/200) eram provenientes de pacientes de Manaus, as 24 amostras restantes (12%) eram provenientes de localidades do interior do Amazonas: São Gabriel da Cachoeira (09), Tefé (08), Humaitá (04) e Careiro (03). Apenas 9% dessas amostras tinham diagnóstico microscópico de monoinfecção por P. falciparum e 91% (182/200) por P. vivax, não havia nenhuma amostra mista pelo diagnóstico microscópico. O diagnóstico molecular por nested-PCR confirmou a presença de DNA de plasmódio em 100% das amostras monoinfectadas. Adicionalmente, foram observadas infecções mistas, co-infecção de P. falciparum e P. vivax, em 19% (38/200) destas amostras. O diagnóstico molecular por PCR em tempo real (Lightcycler, Roche®) foi realizado em apenas 17% (34/200) dessas amostras. A co-positividade (sensibilidade) dos testes para P. vivax foi em média 71% e a co-negatividade (especificidade) 92%, para P. falciparum a co-positividade foi 91% e a conegatividade 79%. A concordância entre os testes foi regular. As 100 amostras restantes haviam sido coletadas no sétimo dia (D7) de tratamento e eram negativas pela microscopia. O diagnóstico molecular demonstrou 21% de positividade. Este estudo mostrou que muitas infecções mistas vêm sendo subestimadas para fins de avaliação epidemiológica, demonstrando que a sensibilidade e especificidade do diagnóstico molecular são superiores a do teste microscópico. O diagnóstico molecular seria então mais indicado como teste complementar no diagnóstico de pacientes com baixas parasitemias, na análise da quantidade de portadores assintomáticos, em estudo de infecções criptônicas e na avaliação da negativação da parasitemia para monitoramento terapêutico, e em estudos que visem a diminuição da transmissão pela existência de prováveis gametócitos persistentes após o tratamento. Entretanto, esse método não é indicado para rotina de diagnóstico de malária, uma vez que os resultados positivos por essa técnica não significam necessariamente que o paciente desenvolva a doença.