abstract: Micro-electro-mechanical systems (MEMS) film bulk acoustic resonator (FBAR) demonstrates label-free biosensing capabilities and is considered to be a promising alternative of quartz crystal microbalance (QCM). FBARs achieve great success in vacuum, or in the air, but find limited applications in liquid media because squeeze damping significantly degrades quality factor (Q) and results in poor frequency resolution. A transmission-line model shows that by confining the liquid in a thickness comparable to the acoustic wavelength of the resonator, Q can be considerably improved. The devices exhibit damped oscillatory patterns of Q as the liquid thickness varies. Q assumes its maxima and minima when the channel thickness is an odd and even multiple of the quarter-wavelength of the resonance, respectively. Microfluidic channels are integrated with longitudinal-mode FBARs (L-FBARs) to realize this design; a tenfold improvement of Q over fully-immersed devices is experimentally verified. Microfluidic integrated FBAR sensors have been demonstrated for detecting protein binding in liquid and monitoring the Vroman effect (the competitive protein adsorption behavior), showing their potential as a promising bio-analytical tool. A contour-mode FBAR (C-FBAR) is developed to further improve Q and to alleviate the need for complex integration of microfluidic channels. The C-FBAR consists of a suspended piezoelectric ring made of aluminum nitride and is excited in the fundamental radial-extensional mode. By replacing the squeeze damping with shear damping, high Qs (189 in water and 77 in human whole blood) are obtained in semi-infinite depth liquids. The C-FBAR sensors are characterized by aptamer - thrombin binding pairs and aqueous glycerine solutions for mass and viscosity sensing schemes, respectively. The C-FBAR sensor demonstrates accurate viscosity measurement from 1 to 10 centipoise, and can be deployed to monitor in-vitro blood coagulation processes in real time. Results show that its resonant frequency decreases as the viscosity of the blood increases during the fibrin generation process after the coagulation cascade. The coagulation time and the start/end of the fibrin generation are quantitatively determined, showing the C-FBAR can be a low-cost, portable yet reliable tool for hemostasis diagnostics. / Dissertation/Thesis / Ph.D. Electrical Engineering 2011

Synaptic vesicle (SV) recycling in the presynapse is essential for the maintenance of neurotransmission. During mild stimulation clathrin-mediated endocytosis (CME) dominates, however during intense stimulation activity-dependent bulk endocytosis (ADBE) is the dominant form of membrane retrieval. The aim of this thesis was to determine how the signalling molecule GSK3 controlled ADBE, with the hypothesis that this enzyme was required at multiple stages of this endocytosis mode. I also hoped to identify a specific cargo for ADBE. I found that during intense action potential stimulation, a localised calcium increase is necessary for the activation of Akt, which inhibited GSK3. This activation was mediated via a phosphatidylinositol 3-kinase (PI3K)-dependent mechanism. Furthermore, I found that phosphatidylinositol 4-kinaseIIα (PI4KIIα), a molecule whose abundance is regulated by GSK3, had a key role in ADBE. Specifically, I found that the absence of PI4KIIα accelerated CME but inhibited ADBE and that PI4KIIα controls CME and ADBE via distinct mechanisms. The PI4KIIα study revealed potential cross-talk between CME and ADBE. To determine whether modulation of either endocytosis mode impacts on the other, the retrieval of genetically-encoded reporters of SV cargo was monitored during intense stimulation during inhibition of either CME or ADBE. The recovery of almost all SV cargo was unaffected by ADBE inhibition but was arrested by abolishing CME. In contrast, VAMP4-pHluorin retrieval was perturbed by inhibiting ADBE and not by blocking CME. Knockdown of VAMP4 also arrested ADBE, indicating that in addition to being the first identified ADBE cargo, it is also essential for this endocytosis mode to proceed.

A theory is developed to explain the dependence of carrier transport in a thin semiconducting film on film thickness, magnetic field strength, and the dominant bulk scattering mechanism. This theory is based on the solution of the linearized Boltzmann equation in relaxation time form. The semiconductor is assumed to be bounded and nondegenerate with spherical energy surfaces and a scalar effective mass, It is also assumed to be flat banded with totally diffuse scattering at the surface. Classical Boltzmann statistics are used for equilibrium. The dependence of the relaxation time on the carrier energy is approximated by a power law equation. The principle improvement over similar theories is the treatment of the dependence of the relaxation time on carrier energy. The power law approximation for this dependence is valid for randomizing and elastic scattering mechanisms.

Les approches de parallélisme structuré sont un compromis entre la parallélisation automatique et la programmation concurrentes et réparties telle qu'offerte par MPI ou les Pthreads. Le parallélisme à squelettes est l'une de ces approches. Un squelette algorithmique peut être vu comme une fonction d'ordre supérieur qui capture un algorithme parallèle classique tel qu'un pipeline ou une réduction parallèle. Souvent la sémantique des squelettes est simple et correspondant à celle de fonctions d'ordre supérieur similaire dans les langages de programmation fonctionnels. L'utilisation combine les squelettes disponibles pour construire son application parallèle. Lorsqu'un programme parallèle est conçu, les performances sont bien sûr importantes. Il est ainsi très intéressant pour le programmeur de disposer d'un modèle de performance, simple mais réaliste. Le parallélisme quasi-synchrone (BSP) offre un tel modèle. Le parallélisme étant présent maintenant dans toutes les machines, du téléphone au super-calculateur, il est important que les modèles de programmation s'appuient sur des sémantiques formelles pour permettre la vérification de programmes. Les travaux menés on conduit à la conception et au développement de la bibliothèque Orléans Skeleton Library ou OSL. OSL fournit un ensemble de squelettes algorithmiques data-parallèles quasi-synchrones. OSL est une bibliothèque pour le langage C++ et utilise des techniques de programmation avancées pour atteindre une bonne efficacité. Les communications se basent sur la bibliothèque MPI. OSL étant basée sur le modèle BSP, il est possible non seulement de prévoir les performances des programmes OSL mais également de fournir une portabilité des performances. Le modèle de programmation d'OSL a été formalisé dans l'assistant de preuve Coq. L'utilisation de cette sémantique pour la preuve de programmes est illustrée par un exemple. / Structured parallelism approaches are a trade-off between automatic parallelisation and concurrent and distributed programming such as Pthreads and MPI. Skeletal parallelism is one of the structured approaches. An algorithmic skeleton can be seen as higher-order function that captures a pattern of a parallel algorithm such as a pipeline, a parallel reduction, etc. Often the sequential semantics of the skeleton is quite simple and corresponds to the usual semantics of similar higher-order functions in functional programming languages. The user constructs a parallel program by combined calls to the available skeletons. When one is designing a parallel program, the parallel performance is of course important. It is thus very interesting for the programmer to rely on a simple yet realistic parallel performance model. Bulk Synchronous Parallelism (BSP) offers such a model. As the parallelism can now be found everywhere from smart-phones to the super computers, it becomes critical for the parallel programming models to support the proof of correctness of the programs developed with them. . The outcome of this work is the Orléans Skeleton Library or OSL. OSL provides a set of data parallel skeletons which follow the BSP model of parallel computation. OSL is a library for C++ currently implemented on top of MPI and using advanced C++ techniques to offer good efficiency. With OSL being based over the BSP performance model, it is possible not only to predict the performances of the application but also provides the portability of performance. The programming model of OSL is formalized using the big-step semantics in the Coq proof assistant. Based on this formal model the correctness of an OSL example is proved.

The aim of this work was to evaluate the quality of raw cow's milk during the year depending on the breed. In two agricultural companies, respectively in three farms there were monitored total bacteria count (TBC), somatic cell count (SCC), residues of inhibitory substances (RIS), freezing point, protein content and fat content in 2015. Limits of TBC given by European Union (100,000/ml) were kept in all farms. Limits set for SCC (400,000/ml) were exceeded in 25% samples in breeding I and the average value was significantly increased (p <0.001) in comparison to breeding II and III. These results suggest a possible occurrence of subclinical mastitis. For the company it means a significant economic loss. RIS has not been found in any sample. Average protein content of monitored breeding was not too different (3.69; 3.70; 3.67%). Fat content in breeding I (3.84%) was statistically significantly decreased (p <0.001) in comparison to breeding II and III (4.18 4.12%).

Silos metálicos para armazenagem de diferentes tipos de produto são muito empregados no Brasil, isso faz com que compreender melhor o funcionamento deste tipo de sistemas estrutural possa levar a soluções mais inteligentes e econômicas. Com esse intuito no presente trabalho estudam-se as colunas de sustentação de um tipo de silo metálico para armazenagem de ração animal. Neste estudo as colunas foram analisadas seguindo as determinações da norma brasileira de dimensionamento de perfis conformados a frio e com modelos numéricos de diferentes níveis de complexidade. Primeiramente se estudou o perfil conformado a frio utilizado nas colunas dos silos através do método das faixas finitas e obtiveram-se as forças axiais de flambagem local e distorcional elástica. Estes valores foram utilizados no método da resistência direta para obtenção dos índices de esbeltez associados a estes modos de flambagem. Foram definidas as forças axiais de colapso, seguindo as metodologias da norma ABNT NBR 14762:2010 (método das larguras efetivas, seção efetiva e resistência direta) para diversos comprimentos do perfil. Foi desenvolvido um modelo numérico para cálculo via método dos elementos finitos, considerando não linearidades materiais e geométricas e imperfeições geométricas iniciais. Os resultados obtidos através deste modelo numérico foram comparados com os obtidos através da norma ABNT NBR 14762:2010. Após ajuste do modelo numérico se realizou um estudo paramétrico para conhecer a influência da rigidez de fixação, entre a coluna de sustentação e o corpo silo, na força de colapso do perfil. São aplicadas diversas condições de contorno com o objetivo de aproximar o modelo numérico das condições reais de fixação da coluna. Finalmente os resultados obtidos são utilizados para determinar a relação entre a força resistente do perfil e a força solicitante na coluna do silo segundo as condições usuais de segurança referentes aos estados-limites últimos determinados pela ABNT NBR 14762:2010. / Tubular steel silos for storage of different product types are widely used in Brazil. The knowledge of these structural systems can result to smarter and economic solutions. In this work is studied the structural columns of some bulk feed tanks with the national standard design code and numeric models with several complexity level. First were studied the cold-formed steel member used in the silo’s columns with the finite strip methods, and were obtained the elastic local/distorcional buckling axial forces. These values were used with the Direct Strength Method to find out slenderness ratios associated with these modes of buckling. The axial collapse forces were defined following the conception of standard ABNT NBR 14762:2010(using the methods of effective width, effective section and direct resistance) for several members’ lengths. A numeric model was development to calculate with finite elements method, considering materials and geometrics nonlinearities with initial geometric imperfections. The results obtained by this numeric model were compared with those obtained by the standard ABNT NBR 14762:2010. After the numeric model adjust, a parametric study was made to know the influences of the connection stiffness between the column and the silo’s cylindrical wall, in the member’s allowable axial strength. Several boundary conditions were applied with the main purpose to approximate the numeric model with the actual columns' end conditions. Finally the obtained results were used to determine the ration between the axial allowable strength and the required load on the silo’s columns by the usual safety conditions using the ultimate limit state determined by the ABNT NBR 14762:2010.

A tecnologia do concreto compactado com rolo tem se desenvolvido e transformado o cenário das construções de barragens, modernizando os conceitos sobre os processos construtivos, além de se mostrar uma técnica competitiva em comparação com os métodos já consagrados de construção de Barragens de terra, enrocamento e enrocamento com face de concreto. Até a década de 70 era usual o lançamento de um elemento de ligação entre camadas de concreto. Nesta época, estudos realizados pelo U.S. Bureau of Reclamation e U.S. Army Corps of Engineers mostraram que a sua utilização era desnecessária, desde que as juntas fossem cuidadosa e adequadamente preparadas. A construção da barragem de Willow Creek, com CCR sem nenhuma especificação de um elemento de ligação entre as camadas de concretagem, acabou resultando num alto nível de percolação de água. Devido a este fato, os grandes projetistas de estruturas hidráulicas e de barragens passaram a adotar um concreto de berço, lançado entre as camadas de CCR, abrangendo entre 30 % da seção superficial da junta, a partir do paramento de montante, até toda a camada. Neste projeto de pesquisa foi proposta a execução de maciços experimentais em laboratório, os quais simulam uma pequena fatia de uma barragem de CCR. Para simular o lançamento e adensamento do concreto destes maciços utilizou-se um equipamento existente no Laboratório de Concreto de FURNAS Centrais Elétricas S.A., localizado em Goiânia-GO. Foram confeccionados 11 maciços experimentais, nos quais foram realizadas avaliações referentes ao intervalo de lançamento entre camadas de concreto compactado com rolo, variando-se o tempo de exposição, a temperatura ambiente de lançamento, o tipo de tratamento da junta e a utilização de argamassa de ligação, ou seja, procurou-se avaliar o grau de maturidade das juntas, a partir do qual são necessárias providências para promover uma adequada aderência entre camadas e mostrar a importância da confecção prévia de maciços experimentais em laboratório para auxiliar a tomada de decisão durante a elaboração do projeto. / The roller compacted concrete technology has been increasable developed and, consequently, modified the dam constructions procedures, leading to improved concepts about the construction processes, besides presenting technical competitively when compared to earth, rockfill and concrete faced rockfill gravity dams construction methodology. The use of a bonding element (concrete or mortar), between concrete layers was common in the 70´s. At that time, studies conducted by the U.S. Bureau of Reclamation and the U.S. Army Corps of Engineers showed that this technique was unnecessary in traditional dam constructions for the cases of well and strictly prepared joints. The Willow Creek dam construction, using RCC without any specification about bonding element between layers, presented a high level of percolation. Since that, great hydraulic structures designers adopted a bed of small aggregate concrete, placed between RCC layers in about 30% of the superficial section of joint from the upstream face. To the herein research it was proposed the execution of experimental laboratory bulks simulating a small part of a RCC dam. For the simulation of placing and compaction of concrete it was used the equipment owned by FURNAS CENTRAIS ELETRICAS S.A., at the laboratory of Goiania, Brazil. Eleven experimental bulks were produced, in which were assessed the exposure of RCC layers in different time delays and temperatures, varying the layer concrete surface treatment and the use of mortar between layers in order to evaluate the maturity degree of joints and to define the procedures to a suitable bonding between layers. The studies show the importance of laboratory test fills during the design phases, as useful tools to help the technical decision processes.

Neste trabalho foi elaborado um microcontrolador 8051 tolerante à radiação, usando para isso técnicas de recomputação de instruções. A base para este trabalho foi a descrição VHDL desse microcontrolador, sendo proposto o uso de sensores de radiação, Bulk-BICS, e códigos de proteção de erros para os elementos de memória, como forma de suporte à técnica apresentada. Inicialmente serão abordados sucintamente a origem e os efeitos prejudiciais da radiação nos dispositivos eletrônicos, motivando a realização deste trabalho. Serão mostrados em detalhes os passos para implementar a técnica de recomputação, que consiste em monitorar os sensores e, ao ser detectado um pulso transiente, fazer o processador reler a última instrução e executá-la novamente, a fim de mitigar o efeito do SET (Single Event Transient). Para isso a manipulação do contador de programa (PC) e o apontador de pilha (SP) são fundamentais. Durante esse processo também deve ser garantido que nenhum dado, potencialmente corrompido, seja armazenado na memória. Contra SEUs (Single Event Upsets) é pressuposto que todos os elementos de memória do microcontrolador estão protegidos através de algum código de correção de erros, assunto já pesquisado por outros autores. Na seqüência serão apresentadas várias simulações realizadas, onde é possível ver o processo de recomputação sendo iniciado a partir da incidência de partículas geradas através de um testbench. Por fim será feita uma comparação entre o 8051 original e o protegido, mostrando dados de área, freqüência de operação e potência de cada um. / This work presents a radiation hard 8051 microcontroller, designed using instruction recomputation techniques. The basis for this work was the VHDL description of the microcontroller. To make the microcontroller radiation hard, built in radiation sensors, called Bulk-BICS, were use to protect the combinational logic blocks. Codes for error detection and correction were used to protect the memory elements. Initially, this work discusses the sources of ionizing radiation and its harmful effects on digital integrated circuits, showing the motivation for this work. Next, the details of the implemented instruction re-computation technique are shown. It consists in monitoring the radiation sensors and, if the incidence of ionizing radiation is detected, the processor reads the last instruction and executes it again, in order to mitigate the effect of a single event transient (SET). In order to implement this re-computation, the manipulation of the program counter (PC) and stack pointer (SP) is essential. During this process it must be guaranteed that any data, potentially corrupted, will not be stored in memory. Regarding radiation effects on memory elements (Single Event Upsets-SEUs), it is assumed that all memory elements of the microcontroller are protected by some error detection and correction code, a topic previously studied by other authors. Finally, several simulations will be shown, where it is possible to see the evolution of the re-computation process, from the detection of the incidence of ionizing radiation (incidence generated by a testbench) to the full re-computation of the instruction. Finally, a comparison is made between the performance of the original 8051 and the radiation hardened version, showing overheads of area, frequency of operation and power.

O vírus da diarreia viral bovina (BVDV) causa uma das doenças mais importantes de bovinos em termos de custos econômicos e sociais, uma vez que é largamente disseminado na população de gado leiteiro. Os objetivos do trabalho foram estimar a prevalência em nível de rebanho e investigar fatores associados aos níveis de anticorpos em leite de tanque através de um estudo transversal, bem como discutir e comparar diferentes técnicas de modelagem, as tradicionais como regressão e as menos usuais para este fim, como as de Machine learning (ML) como Random Forest. O estudo transversal foi realizado no estado do Rio Grande do Sul para a estimação da prevalência de doenças reprodutivas baseados em amostras de tanque de leite, partindo de uma população total de 81.307 rebanhos. Foram coletadas 388 amostras de tanque de leite, e nas propriedades selecionadas foi aplicado um questionário epidemiológico. Como resultados se identificou uma prevalência de 23,9% (IC95% = 19,8 - 28,1) de propriedades positivas. Através de análise de regressão de Poisson se identificou como fatores associados o BVDV: o exame retal como rotina para o diagnóstico de prenhes, Razão de Prevalência [PR] = 2,73 (IC 95%: 1.87-3.98), contato direto entre animais (contato via cerca de propriedades lindeiras) (PR=1,63, IC 95%: 1.13-2.95) e propriedades que não utilizavam inseminação artificial (PR=2.07, IC 95%: 1.38-3.09) Na técnica de Random Forest pôde-se identificar uma dependência na ocorrência de BVDV devido a: inseminação artificial quando realizada pelo proprietário da propriedade ou capataz, o número de vizinhos que também possuem criação de bovinos, e em concordância com os resultados da regressão quanto a dependência da ocorrência de BVDV devido a palpação retal. Como resultado, pôde-se perceber que o BVDV está distribuído no estado do RS e caso seja de interesse do poder público, o desenvolvimento de um programa de controle da doença pode ser baseado nos resultados encontrados. Por outro lado, a contribuição deste estudo vai além das tradicionais análises realizadas em epidemiologia veterinária, principalmente devido os bons resultados obtidos com a abordagem por ML neste estudo transversal. Por fim, a utilização de técnicas estatísticas mais avançadas contribuiu para elucidar melhor os fatores possivelmente envolvidos com a ocorrência de BVDV no rebanho leiteiro gaúcho. / The bovine viral diarrhea virus (BVDV) causes one of the most important disease of cattle in terms of economic and social costs, since it is widely disseminated in dairy cattle population. The objectives were to estimate the herd level prevalence at and investigate factors associated with antibody levels in bulk tank milk through a cross sectional study, discuss and compare different modeling techniques such as the traditional regression with the ones less used for this approach machine learning (ML). The cross sectional study was conducted in Rio Grande do Sul state to estimate the prevalence of reproductive diseases based on bulk tank milk samples, from a total population of 81,307 herds. Milk samples from 388 bulk tank were sampled, and an epidemiological questionnaire was applied in each farm. The prevalence was 23.9% (95% CI 19.8 - 28.1). Through the Poisson regression analysis, the following factors associated with BVDV were found: routine use of rectal examination for pregnancy (Prevalence Ratio [PR] = 2.73 (IC 95%: 1.87-3.98), direct contact between/among animals (contact over the fence of neighboring farms) (PR = 1.63, IC 95%: 1.13-2.95) and properties that did not use artificial insemination (PR = 2.07, IC 95%: 1.38-3.09). On the other hand, using ML techniques, it was identify a dependency upon the occurrence of BVDV due to: artificial insemination when carried out by the owner of the property or foreman; the number of neighbors who also have cattle, and in accordance with the regression results as the dependence of the occurrence of BVDV due to routine use of rectal examination for pregnancy. BVDV is spread across the State and if the government's interest to launch a disease control program measures should be focusing mainly on better conditions and care in reproduction. On the other hand, the contribution of this study goes beyond traditional analyzes in veterinary epidemiology, mainly due to the good results obtained with the approach by ML in this cross-sectional study. Finally, the use of advances statistics techniques it has been made progress to better elucidate the factors possibly involved in the occurrence of BVDV in state dairy herds.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv & Cons Biol) / Fire as a form of disturbance is unique in the way it impacts upon the environment, acting like a herbivore with a ubiquitous appetite. Consuming both dead and living material, converting complex organic molecules into organic and mineral products, which return to the soil. The role of disturbance has long been considered a driver of diversity within Mediterranean type ecosystems. Recently the interest in soil microbes has been piqued, as the importance thereof has been emphasised, particularly their role in nutrient cycling and the chelation of essential plant nutrients. The occurrence of fire results in several environmental and ecological impacts on soil, as well as the dynamics of the microbial populations present. This study explores the impact of fire as a disturbance on the plant and bulk soil microbial communities of the Succulent Karoo. This was achieved through two sub-studies, in which three different states were studied: unburnt, 7-year and 2-year post-fire. Today microbial profiles are also used as indicators of disturbance, thus many techniques exploring microbial community composition are available.