The real time multitasking systems are becoming increasingly popular for control and monitoring functions typically encountered in industry as well as day to day life. They have to manage adequately many concurrent processes or tasks, each of which is sequential in nature. The concurrency is achieved by running asynchronous tasks at different speeds and providing for communication and synchronization. In order to fully exploit the power and capabilities of today's sophisticated microprocessors and to provide a programming methodology for structuring real time applications a real time multitasking operating system becomes critical. / Master of Science

This thesis presents two proactive resource allocation algorithms, RBA* and OBA, for asynchronous real-time distributed systems. The algorithms consider an application model where timeliness requirements are expressed using Jensen's benefit functions and propose adaptation functions to describe anticipated workload for future time intervals. Furthermore, an adaptation model is considered where processes are replicated for sharing workload increases. A real-time Ethernet system model is considered where message collisions are resolved. Given such models, the objective is to maximize aggregate application benefit and minimize aggregate missed deadline ratio. Since determining the optimal allocation is computationally intractable, the algorithms heuristically compute the allocation so that it is as "close" as possible to the optimal allocation. While RBA* analyzes process response times to determine the allocation, OBA analyzes processor overloads to compute the decision in a much faster way. RBA* incurs a quadratic amortized complexity in terms of subtask arrivals for the most computationally intensive component when DASA is used as the underlying process-scheduling algorithm, whereas OBA incurs a logarithmic amortized complexity for the corresponding component. To study how different process-scheduling and message-scheduling algorithms affect the performance of the algorithms and to compare their performances, benchmark-driven experiments were conducted. The experimental results reveal that RBA* produces higher aggregate benefit and lower missed deadline ratio when DASA is used for process scheduling and message scheduling. Furthermore, it is observed that RBA* produces higher aggregate benefit and lower missed deadline ratio than OBA, confirming the intuition that accurate response time analysis can lead to better results. / Master of Science

Nutrient transporters in the small intestine are responsible for dietary nutrient assimilation and therefore the expression of these transporters can influence the overall nutrient status as well as the growth and development of the animal. This thesis examined correlated responses to selection in the developmental gene expression of the peptide transporter PepT1, the glutamate/aspartate transporter EAAT3, the sodium-dependent glucose transporter SGLT1, and the fructose transporter GLUT5 in the small intestine of chickens from lines divergently selected for high (HH) or low (LL) eight-week body weight and their reciprocal crosses, (HL and LH). Chicks were weighed and killed on embryonic day 20 (E20), day of hatch (DOH with no access to feed), and days 3 (D3), 7(D7), and 14 (D14) post hatch. Duodenum, jejunum, ileum and liver were collected. DNA extracted from liver was used to sex birds by PCR. RNA was extracted from the intestinal segments of four males and four females from each mating combination (MC) and time point except E20 HL males (n = 3) and D7 LL females (n = 2). Expression of nutrient transporters was assayed by real-time PCR using the relative quantification method. In comparing HH and LL males and females there was a line by segment interaction in PepT1 gene expression, with no segment difference in HH and greatest expression in the ileum of the LL (P < 0.05). There was also a MC by age by sex interaction for PepT1 gene expression (P < 0.0001) with peak gene expression occurring on DOH for LL females, on D7 for HH females, on D7 for LL males and D14 for HH males. Overall, females had greater EAAT3 expression (P < 0.03). Gene expression of EAAT3 was greatest in the ileum, intermediate in the jejunum, and least in the duodenum (P < 0.0007). There was an age by segment interaction for EAAT3 expression (P = 0.0002) and a MC by segment interaction (P < 0.02), with LL having greater expression than HH in the ileum. Females had greater SGLT1 expression than males (P < 0.0001). There was a sex by age interaction for the expression of SGLT1 (P < 0.0001). Females induced SGLT1 expression on DOH and maintained this level through D14, while males gradually increased expression through D7 and decreased expression by D14. These results indicate that expression of PepT1, EAAT3, SGLT1 are differentially expressed in male and female chickens regardless of selection for high or low juvenile body weight. These results also show a sexual dimorphism in the capacity to absorb peptides, anionic amino acids, and glucose from the intestine, which has implications for the poultry industry with regard to diet formulations for straight-run and sex-separate grow-out operations. In comparing male HH, HL, LH, and LL chicks, overall LL had the greatest level of expression (P <0.06), HH had the least level of expression (P < 0.006) and HL and LH had intermediate levels of expression (P < 0.06). Greatest PepT1 gene was expression in the ileum (P < 0.0003) and there was a MC by segment interaction with expression increasing from duodenum to ileum in LL, but there was no segment difference in any other MC (P < 0.08). Within each intestinal segment there was a MC difference (P < 0.02). There was an effect of sire for PepT1 expression, with progeny from low weight selected sires (LWS) having greater expression than progeny from high weight selected (HWS) sires (P = 0.0008). There was no difference between intestinal segments in progeny from HWS sires, however, greatest PepT1 gene expression was seen in the ileum of progeny from LWS sires (P < 0.0001). Overall, expression of EAAT3 was greatest in the ileum, intermediate in the jejunum and least in the ileum (P < 0.0001) and there was a segment by age interaction for EAAT3 expression (P < 0.0001). In all MCs except HH, EAAT3 gene expression increased from duodenum to ileum (P < 0.08). Within the ileum, the LL had greatest EAAT3 gene expression, LH and HL had intermediate gene expression, and HH had least expression (P < 0.08). Expression of SGLT1 gradually increased through D7 and decreased by D14 (P < 0.0001) and overall, was greatest in the distal small intestine (P < 0.0001). There was a MC by segment interaction, with SGLT1 gene expression being greatest in the distal small intestine in LL, LH, and HL, but greatest in the jejunum of HH (P < 0.04). Within the ileum, LL had greater SGLT1 gene expression than HH (P < 0.06). Overall, greatest GLUT5 expression was in the distal small intestine (P < 0.0001) and there was a MC by segment interaction, with expression being greatest in the distal small intestine in LL and HL (P < 0.02), greatest in the ileum of LH (P < 0.08), and greatest in the jejunum of HH (P < 0.09). Within the ileum there was a MC difference (P < 0.07). These results indicate that selection for high or low juvenile body weight may have influenced the gene expression pattern of these nutrient transporters in the small intestine, which may contribute to the overall differences in the growth and development of these lines of chickens. / Master of Science

Members of the alphavirus genus pose a serious or potential threat to public health in many areas of the world. Nearly all alphaviruses are maintained in nature by transmission cycles that involve alternating replication in a susceptible vertebrate and invertebrate host. The maintenance of this transmission cycle depends on the establishment of a life-long persistent infection in the invertebrate vector host. Although alphavirus replication has been extensively studied in vertebrate models, the strand-specific replication kinetics of alphaviruses during persistent infections of the invertebrate host have not been reported. We investigated the strand-specific replication of different alphavirus genotypes in invertebrate cells. By comparing different detection strategies and chemistries, we identified an optimal ssqPCR assay design for strand-specific quantification of viral RNAs in infected cells and tissues. We found that primer sets incorporating the use of a non-target tag sequence were able to avoid real-time PCR detection of amplicons that were falsely-primed during reverse-transcription. We also determined that DNA hydrolysis probes increased the sensitivity of ssqPCR assays when compared to a double-stranded DNA-specific dye, SYBR Green. Using this information, we determined the replication kinetics of two different genotypes of o'nyong nyong virus (ONNV) and chikungunya virus (CHIKV) in infected mosquito cells. We found that (-) strand viral RNAs persisted in invertebrate cells for up to 21 days after infection. We also found that significantly less (-) strand RNA was present in cells infected with opal variants of both ONNV and CHIKV than sense variants at several time points post infection, suggesting that the opal codon has a functional role in (-) strand RNA regulation. We also report the development of an ONNV replicon expression system. In total, the tools we developed for this report will facilitate future replication studies in the mosquito that may shed light on questions regarding the regulatory role of the opal codon and the persistence of (-) strand RNAs during long-term infections. The strand-specific replication kinetics of ONNV and CHIKV genotypes reported here will serve as a foundation for such investigations. / Master of Science in Life Sciences

This thesis investigates a new architecture for modeling and simulating complex distributed real-time systems. Modeling adequately a large distributed real time system may involve, due to its complexity, several different theoretical vehicles such as queuing theory, finite state machines, and others. Currently there are no software tools, which would offer combining such heterogeneous features into a single comprehensive simulation environment. This study involves integrating 3 tools, SES/workbench, an offline simulator using queuing theory as its modeling discipline, ObjecTime as a real-time simulator based on finite state machines as its modeling discipline, and VxWorks real-time kernel used for free modeling in the VMEbus environment. We developed an architecture, which connects all 3 simulators into an integrated system, in which parameters and simulation results can be freely exchanged between tools. In addition, the system is enhanced by a web-based interface, which can be used to provide input and obtain output of the entire system and help in distributing the simulation over the Internet. The new architecture was extensively tested and applied to a large-scale distributed embedded simulation in a military environment.

No description available.

With ever increasing contents (safety, driver assistance, infotainment, etc.) in today's automotive systems that rely on electronics and software, the supporting architecture is integrated by a complex set of heterogeneous data networks. A modern automobile contains up to 100 ECUs and several heterogeneous communication buses (such as CAN, FlexRay, etc.), exchanging thousands of signals. The automotive Original Equipment Manufacturers (OEMs) and suppliers face a number of challenges such as reliability, safety and cost to incorporate the growing functionalities in vehicles. Additionally, reliability, safety and cost are major concerns for the industry. One of the important challenges in automotive design is the efficient and reliable transmission of signals over communication networks such as CAN and CAN-FD. With the growing features in automotives, the OEMs already face the challenge of saturation of bus bandwidth hindering the reliability of communication and the inclusion of additional features. In this dissertation, we study the problem of optimization of bandwidth utilization (BU) over CAN-FD networks. Signals are transmitted over the CAN/CAN-FD bus in entities called frames. The signal-to-frame-packing has been studied in the literature and it is compared to the bin packing problem which is known to be NP-hard. By carefully optimizing signal-to-frame packing, the CAN-FD BU can be reduced. In Chapter 3, we propose a method for offset assignment to signals and show its importance in improving BU. One of our contributions for an industrial setting is a modest improvement in BU of about 2.3%. Even with this modest improvement, the architecture's lifetime could potentially be extended by several product cycles, which may translate to saving millions of dollars for the OEM. Therefore, the optimization of signal-to-frame packing in CAN-FD is the major focus of this dissertation. Another challenge addressed in this dissertation is the reliable mapping of a task model onto a given architecture, such that the end-to-end latency requirements are satisfied. This avoids costly redesign and redevelopment due to system design errors. / Ph. D. / Automobiles today are equipped with a variety of advanced features, such as adaptive cruise control, lane departure warning systems, information and entertainment systems, etc. These advanced features rely on electronics and software. A modern automobile consists of up to 100 computer systems that are interconnected by several buses (in-vehicle communication networks), exchanging thousands of signals (which are data entities such as sensor data, control commands, etc.). The addition of new functionalities means additional complexity and more demand of existing resources such as bus bandwidth. The automotive companies face a number of challenges such as reliability, safety and cost to incorporate the growing features in vehicles with the limited resources. In this dissertation, we study the problem of optimization of bandwidth utilization (BU) over a communication bus used in automotives. In Chapter 3, we show that for an automobile company even a modest improvement in BU of about 2.3% could potentially extend the bus architecture’s lifetime by several product cycles. This may translate to saving millions of dollars for the company. Therefore, the optimization of bandwidth utilization over a communication bus is the major focus of this dissertation. Another problem addressed in this dissertation is the reliable mapping of a software model onto a given architecture (for an automotive system), such that the timing requirements are satisfied. This avoids costly redesign and redevelopment due to system design errors.

Passive acoustic systems composed of hydrophone array have been shown useful for underwater acoustic source detection and tracking. The work presented here demonstrates use of a passive acoustic system for an Autonomous Underwater Vehicle (AUV) composed of a 2D hydrophone array along with a post processing algorithm for real time detection and tracking of surface vessels. Important design decisions for development of the hydrophone array are taken based on different factors such as the frequency range of broadband surface vessel noise, review of literature, financial as well as structural constraints of the AUV. The post-processing algorithm, developed using a phased array principle called acoustic beamforming, outputs real-time heading angles of the target surface vessels. Initial measurements conducted at Claytor Lake with the developed passive acoustic system to locate a white noise acoustic source showed better performance with functional beamforming technique among others. Various hydrophone array configurations are tested during these measurements to determine the optimal hydrophone placement. Furthermore, field tests are conducted at Norfolk Bay area to assess the performance of the developed system to real time detect and track surface vessels of different sizes in mission relevant environment. Cross-spectral matrix subtraction approach to subtract AUV's self noise is investigated to improve signal range and thus the detection range of these different surface vessels. This approach showed improvement in detection range of up to 350%. Another set of measurements again at Claytor Lake demonstrates real time detection and tracking of a small boat using an AUV integrated with the developed passive acoustic system operating at different propeller conditions. Results showed that low signal to noise ratio at higher AUV propeller rpm makes the detection and tracking difficult limiting the operating AUV propeller rpm up to 1500. This work also explores custom build hydrophones based on piezoelectric material of different shapes and sized to replace the expensive industry purchased hydrophones to lower the cost of developed system. / Master of Science / In field of underwater acoustic, hydrophone arrays have gained popularity for the detection and tracking of sound sources by just listening to them. This study presents design, development and testing of such hydrophone array attached to an AUV for real time detection and tracking of surface vessels. Multiple hydrophones in an array collect the underwater noise radiated by the target surface vessel which are essentially the unsteady pressure fluctuations. The phase difference between signals acquired by different hydrophones is then used to predict the direction of arrival of a sound wave from the target ship. Such a phased array principle called acoustic beamforming is used to develop a post processing algorithm which takes hydrophone array signals as input and outputs the heading angle of the target ship. This work first demonstrates capability of the developed hydrophone array and the algorithm to detect a white noise acoustic source (speaker) placed inside water at Claytor Lake. These measurements investigated performance of different acoustic beamforming techniques as well as different hydrophone array configurations. Furthermore, measurements conducted with actual surface vessel at Norfolk Bay area proved capability of the developed hydrophone array and the algorithm to detect and track ships in real time. The performance of the hydrophone array is characterized in terms of detection range and was observed to improve by 350% when the AUV's self noise is removed from the acquired hydrophone signals. Combined single unit of AUV and developed hydrophone array system also demonstrated real time detection and tracking of a small boat at Claytor Lake for different AUV operating conditions. Moreover, custom build hydrophones manufactured using piezoelectric material are found to be a feasible replacement for the expensive industry purchased hydrophones in order to reduce cost of the array.

<p>Many products are built from more or less independently developed subsystems. For instance, a car consists of subsystems for transmission, braking, suspension, etc. These subsystems are frequently controlled by an embedded computer system. In the automotive industry, as well as in other application domains, there is currently a trend from an approach where subsystems have dedicated computer hardware and other resources (a federated approach) to an approach where subsystems share hardware and other resources (an integrated approach). This is motivated by a strong pressure to reduce product cost, at the same time as an increasing number of subsystems are being introduced.</p><p>When integrating subsystems, it is desirable that guarantees valid before integration are also valid after integration, since this would eliminate the need for costly reverifications. The computer network is a resource that is typically shared among all subsystems. Hence, a central issue when integrating subsystems is to provide an efficient scheduling of message transmissions on the network. There are essentially three families of schedulers that can be used: priority-driven schedulers that assign priorities to messages, time-driven schedulers that assign specific time-slots for transmission of specific messages, and share-driven schedulers that assign shares of the available network capacity to groups of messages.</p><p>This thesis presents a framework for share-driven scheduling, to be implemented and used in embedded networks, with the aim to facilitate subsystem integration by reducing the risk of interference between subsystems. The framework is applied in the automotive domain.</p><p>The initial parts of the thesis give an overview of systems, subsystems and network technologies found and used in the automotive domain. Then, the share-driven scheduling framework is presented, analytically investigated and proven, as well as evaluated in a simulation study. Finally it is shown how the framework is to be configured and used in the context of subsystem integration. The results show that the framework allows for flexible and efficient scheduling of messages with real-time constraints, facilitating integration of subsystems from a network point of view.</p>

A toxoplasmose é uma zoonose de ampla distribuição mundial afetando homens e diversas espécies animais. Levantamentos sorológicos indicam elevados índices de infecção, porém relatos de doença severa é rara. A infecção pelo T. gondii induz uma intensa resposta imune mediada pelo interferon-&#947; (IFN-&#947;) que rapidamente controla a multiplicação parasitária. Com o objetivo de explorar a resistência da espécie suína à toxoplasmose como modelo de estudo para a compreensão dos mecanismos de defesa a infecção, foram realizadas infecções orais com 4,5 x 105; oocistos (cepa VEG) e colheitas de amostras de linfonodo hepato-esplênico (LN HS), mesentérico (LN M) e íleo-cólico (LN IC), fígado, sangue, íleo, jejuno, baço e timo aos 2, 4, 7 e 14 dias pós-infecção (DPI). Analisou-se a expressão de 69 genes ligados a resposta de defesa às infecções pela Real-Time RT-PCR*. LN M, LN HS e fígado foram as amostras que apresentaram a maior quantidade de genes e maior intensidade de ativação enquanto que células mononucleares de sangue periférico (CMSP) e timo apresentaram reduzida resposta à infecção. A expressão e a produção de IFNG foram mais altas nas amostras de LN M e LN HS comparadas às amostras de LN traqueo-bronquial e CMSP, indicando diferentes níveis de resposta local. Intensa indução de resposta inata e inflamatória foi observada em vários tecidos, envolvendo os genes IL1B, IL6, IFNA1, TNF, ORM1, MYD88, TLR2, TLR4; estimulação de resposta Th1, mediada por IFNG incluiu os genes IRF1, IL23A, IL18, STAT1, SOCS1, SOCS3, ICSBP1, TBX21; balanceada pela expressão de citocinas regulatórias IL10, TGFB1 e TGFB3. Uma proeminente indução de ARG1, INDO and SLC11A1 indica ativação de mecanismos de proteção do hospedeiro envolvendo metabolismo de aminoácidos (arginina, triptofano) e ferro. A presença de parasitas foi detectada no LN M aos 2DPI pela Real-Time PCR e pela imunohistoquímica. Aumento do número de parasitas no 4DPI foi seguida de intensa resposta inflamatória, edema e necrose tecidual no 7DPI principalmente no fígado e no LN M. Elevados níveis de AST sérico no 7DPI confirmam a lesão de hepatócitos. A diminuição da inflamação e da quantidade de parasitas no 14DPI sugerem controle da proliferação parasitária. Elevados níveis de haptoglobina e óxido nítrico séricos detectados aos 4DPI (&#945;=0,05) indicam respectivamente a ativação de proteínas de fase aguda e de macrófagos. A análise de citometria de fluxo mostra elevação da porcentagem de células CD2/CD16 DP sugerindo envolvimento de células NK e não foram observadas alterações na porcentagem de células CD4+/CD8+, CD3+/CD25+. A estimulação na expressão gênica, a produção de IFN-&#947;, as determinações séricas e lesões histológicas apresentam padrão similar, com início de resposta no 2DPI, elevação no 4DPI e 7DPI e diminuição no 14DPI. A análise da expressão de mRNA nos tecidos revelou alguns dos mecanismos de defesa do hospedeiro ativados durante a infecção pelo T. gondii. Observou-se uma equilibrada ativação de citocinas pró- e anti-inflamatórias envolvendo uma intrincada rede de mecanismos co-estimulatórios e regulatórios coordenando a resposta do tipo Th1. *Siglas dos genes segundo o Human Gene Nomenclature Committee (HGNC) / Toxoplasmosis is a widespread zoonosis affecting humans and large range of animal species worldwide. Serological surveillance indicates high infection rates, but rarely is associated to severe disease. T. gondii (Tg) infection induces a strong IFN-&#947; dominated immune response that rapidly controls parasite replication. Pig resistance to toxoplasmosis was explored as an experimental model to evaluate host defense mechanisms. Pigs were fed 4.5 x 105 oocysts (VEG strain) and hepato-splenic (HS LN), mesenteric (MLN) and ileal lymph nodes (I LN), liver, blood, ileum, jejunum, spleen and thymus samples were collected at 2, 4, 7 and 14 days after infection (DAI). Gene expression analysis for a panel of 69 immune related genes were performed by Real-Time RT-PCR*. Most intense response were detected in MLN, HS LN and liver samples, whereas low changes were observed in periferic blood monocytes (PBMC) and thymus. IFNG mRNA expression and protein production were higher in MLN and HSLN cells than in tracheo-bronchial LN and PBMC, suggesting different levels of local response. Intense innate and inflammatory induction were observed in most of the tissues involving IL1B, IL6, IFNA1, TNF, ORM1, MYD88, TLR2, TLR4; stimulation of IFNG dominated Th1 response included IRF1, IL23A, IL18, STAT1, SOCS1, SOCS3, ICSBP1, TBX21; balanced by expression of regulatory cytokines IL10, TGFB1 and TGFB3. Prominent ARG1, INDO and SLC11A1 upregulation indicate activation of host amino acid (arginine and tryptophan) and iron protective mechanisms. Tg parasites were detected by Real-Time PCR and immunohistochemistry in MLN as early as 2DAI. Increase of parasite burden at 4DPI was followed by an intense inflammatory response, edema and tissue necrosis in liver and LNM at 7DPI. Increased serum AST levels at 7DPI confirmed liver damage. Reduced parasite numbers and inflammatory response suggest control of parasite replication at 14 DPI. High serum haptoglobin and nitric oxide at 4DAI (&#945;=0.05) indicate acute phase protein and macrophage activation, respectively. Flow citometry analysis showed increased percentage of CD2/CD16 DP suggesting involvement of NK cells, whereas no changes were observed at CD4+/CD8+, CD3+/CD25+ cells. Gene expression stimulation, IFN-&#947; production, serum determinations and histological lesions showed similar pattern, of induction at 2DPI, increasing at 4DPI and 7DPI and decreasing at 14DPI. Tissue mRNA expression analysis revealed some of the host defense mechanisms activated during T. gondii infection. A balance of pro- and anti-inflammatory cytokine activation, involving an intricated co-stimulatory and regulatory mechanisms that coordinates Th1 response was observed.*Gene names according to Human Gene Nomenclature Committee (HGNC)