System-on-a-Chip (SoC) based hardware acceleration in Register Transfer Level (RTL) design

Today, modern System-on-a-Chip (SoC) systems have grown rapidly due to the increased processing power, while maintaining the size of the hardware circuit. The number of transistors on a chip continues to increase, but current SoC designs may not be able to exploit the potential performance, especially with energy consumption and chip area becoming two major concerns. Traditional SoC designs usually separate software and hardware. Thus, the process of improving the system performance is a complicated task for both software and hardware designers. The aim of this research is to develop hardware acceleration workflow for software applications. Thus, system performance can be improved with constraints of energy consumption and on-chip resource costs. The characteristics of software applications can be identified by using profiling tools. Hardware acceleration can have significant performance improvement for highly mathematical calculations or repeated functions. The performance of SoC systems can then be improved, if the hardware acceleration method is used to accelerate the element that incurs performance overheads. The concepts mentioned in this study can be easily applied to a variety of sophisticated software applications. The contributions of SoC-based hardware acceleration in the hardware-software co-design platform include the following: (1) Software profiling methods are applied to H.264 Coder-Decoder (CODEC) core. The hotspot function of aimed application is identified by using critical attributes such as cycles per loop, loop rounds, etc. (2) Hardware acceleration method based on Field-Programmable Gate Array (FPGA) is used to resolve system bottlenecks and improve system performance. The identified hotspot function is then converted to a hardware accelerator and mapped onto the hardware platform. Two types of hardware acceleration methods – central bus design and co-processor design, are implemented for comparison in the proposed architecture. (3) System specifications, such as performance, energy consumption, and resource costs, are measured and analyzed. The trade-off of these three factors is compared and balanced. Different hardware accelerators are implemented and evaluated based on system requirements. 4) The system verification platform is designed based on Integrated Circuit (IC) workflow. Hardware optimization techniques are used for higher performance and less resource costs. Experimental results show that the proposed hardware acceleration workflow for software applications is an efficient technique. The system can reach 2.8X performance improvements and save 31.84% energy consumption by applying the Bus-IP design. The Co-processor design can have 7.9X performance and save 75.85% energy consumption.

System-on-a-Chip (SoC) based Hardware Acceleration in Register Transfer Level (RTL) Design

Today, modern System-on-a-Chip (SoC) systems have grown rapidly due to the increased processing power, while maintaining the size of the hardware circuit. The number of transistors on a chip continues to increase, but current SoC designs may not be able to exploit the potential performance, especially with energy consumption and chip area becoming two major concerns. Traditional SoC designs usually separate software and hardware. Thus, the process of improving the system performance is a complicated task for both software and hardware designers. The aim of this research is to develop hardware acceleration workflow for software applications. Thus, system performance can be improved with constraints of energy consumption and on-chip resource costs. The characteristics of software applications can be identified by using profiling tools. Hardware acceleration can have significant performance improvement for highly mathematical calculations or repeated functions. The performance of SoC systems can then be improved, if the hardware acceleration method is used to accelerate the element that incurs performance overheads. The concepts mentioned in this study can be easily applied to a variety of sophisticated software applications. The contributions of SoC-based hardware acceleration in the hardware-software co-design platform include the following: (1) Software profiling methods are applied to H.264 Coder-Decoder (CODEC) core. The hotspot function of aimed application is identified by using critical attributes such as cycles per loop, loop rounds, etc. (2) Hardware acceleration method based on Field-Programmable Gate Array (FPGA) is used to resolve system bottlenecks and improve system performance. The identified hotspot function is then converted to a hardware accelerator and mapped onto the hardware platform. Two types of hardware acceleration methods – central bus design and co-processor design, are implemented for comparison in the proposed architecture. (3) System specifications, such as performance, energy consumption, and resource costs, are measured and analyzed. The trade-off of these three factors is compared and balanced. Different hardware accelerators are implemented and evaluated based on system requirements. 4) The system verification platform is designed based on Integrated Circuit (IC) workflow. Hardware optimization techniques are used for higher performance and less resource costs. Experimental results show that the proposed hardware acceleration workflow for software applications is an efficient technique. The system can reach 2.8X performance improvements and save 31.84% energy consumption by applying the Bus-IP design. The Co-processor design can have 7.9X performance and save 75.85% energy consumption.

Design and evaluation of a consulting system for database design

Database design is a difficult problem for non-expert designers. It is desirable to assist such designers during the problem solving process by means of a knowledge based (KB) system. A number of prototype KB systems have been proposed, however there are many shortcomings. Few have incorporated sufficient expertise in modeling relationships, particularly higher order relationships. There has been no empirical study that experimentally tested the effectiveness of any of these KB tools. Problem solving behavior of non-experts, whom the systems were intended to assist, has not been one of the bases for system design. In this project a consulting system for conceptual database design that addresses the above short comings was developed and empirically validated.^ The system incorporates (a) findings on why non-experts commit errors and (b) heuristics for modeling relationships. Two approaches to knowledge base implementation--system restrictiveness and decisional guidance--were used and compared in this project. The Restrictive approach is proscriptive and limits the designer's choices at various design phases by forcing him/her to follow a specific design path. The Guidance system approach which is less restrictive, provides context specific, informative and suggestive guidance throughout the design process. The main objectives of the study are to evaluate (1) whether the knowledge-based system is more effective than a system without the knowledge-base and (2) which knowledge implementation--restrictive or guidance--strategy is more effective. To evaluate the effectiveness of the knowledge base itself, the two systems were compared with a system that does not incorporate the expertise (Control).^ The experimental procedure involved the student subjects solving a task without using the system (pre-treatment task) and another task using one of the three systems (experimental task). The experimental task scores of those subjects who performed satisfactorily in the pre-treatment task were analyzed. Results are (1) The knowledge based approach to database design support lead to more accurate solutions than the control system; (2) No significant difference between the two KB approaches; (3) Guidance approach led to best performance; and (4) The subjects perceived the Restrictive system easier to use than the Guidance system. ^

Diversity of Hymenoptera, cultivated plants and management practices in home garden agroecosystems, Kyrgyz Republic

Pollination-dependent fruit trees grown in home gardens play an important role in the agricultural based economy of Central Asian countries, yet little is known about the status of pollinator communities, the cultivated plant composition or the factors that influence management practices in Kyrgyz home garden agroecosystems. As agricultural systems are human created and managed, a logical approach to their study blends anthropological and ecological methods, an ethnoecological approach. Over three years, I investigated how species richness and abundance of Hymenoptera, cultivated plants, and home garden management were related using quantitative and qualitative methods in the Issyk-kul Man and Biosphere reserve. Structured surveys were undertaken with heads of households using a random sample stratified by village. Gardens were then mapped with participation of household members to inventory edible species in gardens, most of which are pollinator-dependent, and to compare home garden diversity as reported by respondents during interviews. Apple diversity was studied to the variety level to understand respondents’ classification system in the context of in situ agrobiodiversity conservation. Household members identified 52 edible plant species when mapping the garden, compared with 32 reported when interviewed. The proportion of plant species received from others through exchange and the number of plots cultivated significantly explained the variation in edible plant diversity among gardens. Insects were sampled in gardens and orchards to determine potential pollinator community composition and the effect of different management practices on Hymenoptera richness and abundance. I collected 756 Hymenoptera individuals (56 bee; 12 wasp species); 12 species were new records for Kyrgyzstan or within Kyrgyzstan. Economic pressures to intensify cultivation could impact management practices that currently promote diversity. A home garden development initiative was undertaken to study management practice improvement. Participants in the initiative had higher adoption rates than controls of management practices that improve long-term yield, ecological sustainability and stability of home gardens. Home gardens, as currently managed, support abundant and diverse pollinator communities and have high cultivated plant diversity with few differences in community composition between garden management types.

Structural Health Monitoring using Index Based Reasoning for Unmanned Aerial Vehicles

Unmanned Aerial Vehicles (UAVs) may develop cracks, erosion, delamination or other damages due to aging, fatigue or extreme loads. Identifying these damages is critical for the safe and reliable operation of the systems. ^ Structural Health Monitoring (SHM) is capable of determining the conditions of systems automatically and continually through processing and interpreting the data collected from a network of sensors embedded into the systems. With the desired awareness of the systems’ health conditions, SHM can greatly reduce operational cost and speed up maintenance processes. ^ The purpose of this study is to develop an effective, low-cost, flexible and fault tolerant structural health monitoring system. The proposed Index Based Reasoning (IBR) system started as a simple look-up-table based diagnostic system. Later, Fast Fourier Transformation analysis and neural network diagnosis with self-learning capabilities were added. The current version is capable of classifying different health conditions with the learned characteristic patterns, after training with the sensory data acquired from the operating system under different status. ^ The proposed IBR systems are hierarchy and distributed networks deployed into systems to monitor their health conditions. Each IBR node processes the sensory data to extract the features of the signal. Classifying tools are then used to evaluate the local conditions with health index (HI) values. The HI values will be carried to other IBR nodes in the next level of the structured network. The overall health condition of the system can be obtained by evaluating all the local health conditions. ^ The performance of IBR systems has been evaluated by both simulation and experimental studies. The IBR system has been proven successful on simulated cases of a turbojet engine, a high displacement actuator, and a quad rotor helicopter. For its application on experimental data of a four rotor helicopter, IBR also performed acceptably accurate. The proposed IBR system is a perfect fit for the low-cost UAVs to be the onboard structural health management system. It can also be a backup system for aircraft and advanced Space Utility Vehicles. ^

Analysis of Heterokaryon Formation in Fusarium oxysporum f. sp. cubense.

Fusarium oxysporum forma specialis cubense is a soilborne phytopathogen that infects banana. The true evolutionary identity of this so called species, Fusarium oxysporum, is still unknown. Many techniques have been applied in order to gain insight for the observed genetic diversity of this species. The current classification system is based on vegetative compatibility groups (VCG's). Vegetative compatibility is a self non-self recognition system in which only those belonging to a VCG can form stable heterokaryons, cells containing two distinct nuclei. Heterokaryons in turn, are formed from hypha! anastomosis, the fusion of two hyphae. Furthermore, subsequent to heterokaryon formation potential mechanisms exist which may generate genetic variability. One is through viral transfer upon hyphal anastomosis. The other mechanism is a form of mitotic recombination referred to as the parasexual cycle. Very little research has been performed to directly obser.ve the cellular events; hypha! anastomosis, heterokaryon formation, and the parasexual cycle in Fusarium oxysporum f. sp. cubense. The purpose of this research was to design and use methods which would allow for the detection of hypha! anastomosis and heterokaryon formation, as well as any characteristics surrounding this event, within and between VCG's in Foe. First, some general growth properties were recorded: the number of nuclei per hypha, the size ofthe hyphal tip cell, the size of the cell adjacent to the hypha! tip (pre-tip) cell, and the number of cells to the first branch point. Second, four methods were designed in order to assay hyphal anastomosis and heterokaryon formation: 1) pairings on membrane: phase or brightfield microscopy, 2) pairings on membrane: fluorescence microscopy, 3) spore crosses: fluorescence microscopy, and 4) double picks in fractionated MMA. All of these methods were promtsmg.

Localized surface plasmon resonance biosensors for real-time biomolecular binding study

Surface Plasmon Resonance (SPR) and localized surface plasmon resonance (LSPR) biosensors have brought a revolutionary change to in vitro study of biological and biochemical processes due to its ability to measure extremely small changes in surface refractive index (RI), binding equilibrium and kinetics. Strategies based on LSPR have been employed to enhance the sensitivity for a variety of applications, such as diagnosis of diseases, environmental analysis, food safety, and chemical threat detection. In LSPR spectroscopy, absorption and scattering of light are greatly enhanced at frequencies that excite the LSPR, resulting in a characteristic extinction spectrum that depends on the RI of the surrounding medium. Compositional and conformational change within the surrounding medium near the sensing surface could therefore be detected as shifts in the extinction spectrum. This dissertation specifically focuses on the development and evaluation of highly sensitive LSPR biosensors for in situ study of biomolecular binding process by incorporating nanotechnology. Compared to traditional methods for biomolecular binding studies, LSPR-based biosensors offer real-time, label free detection. First, we modified the gold sensing surface of LSPR-based biosensors using nanomaterials such as gold nanoparticles (AuNPs) and polymer to enhance surface absorption and sensitivity. The performance of this type of biosensors was evaluated on the application of small heavy metal molecule binding affinity study. This biosensor exhibited ∼7 fold sensitivity enhancement and binding kinetics measurement capability comparing to traditional biosensors. Second, a miniaturized cell culture system was integrated into the LSPR-based biosensor system for the purpose of real-time biomarker signaling pathway studies and drug efficacy studies with living cells. To the best of our knowledge, this is the first LSPR-based sensing platform with the capability of living cell studies. We demonstrated the living cell measurement ability by studying the VEGF signaling pathway in living SKOV-3 cells. Results have shown that the VEGF secretion level from SKOV-3 cells is 0.0137 ± 0.0012 pg per cell. Moreover, we have demonstrated bevacizumab drug regulation to the VEGF signaling pathway using this biosensor. This sensing platform could potentially help studying biomolecular binding kinetics which elucidates the underlying mechanisms of biotransportation and drug delivery.

Fuzzy Modeling and Control Based Virtual Machine Resource Management

Virtual machines (VMs) are powerful platforms for building agile datacenters and emerging cloud systems. However, resource management for a VM-based system is still a challenging task. First, the complexity of application workloads as well as the interference among competing workloads makes it difficult to understand their VMs’ resource demands for meeting their Quality of Service (QoS) targets; Second, the dynamics in the applications and system makes it also difficult to maintain the desired QoS target while the environment changes; Third, the transparency of virtualization presents a hurdle for guest-layer application and host-layer VM scheduler to cooperate and improve application QoS and system efficiency. This dissertation proposes to address the above challenges through fuzzy modeling and control theory based VM resource management. First, a fuzzy-logic-based nonlinear modeling approach is proposed to accurately capture a VM’s complex demands of multiple types of resources automatically online based on the observed workload and resource usages. Second, to enable fast adaption for resource management, the fuzzy modeling approach is integrated with a predictive-control-based controller to form a new Fuzzy Modeling Predictive Control (FMPC) approach which can quickly track the applications’ QoS targets and optimize the resource allocations under dynamic changes in the system. Finally, to address the limitations of black-box-based resource management solutions, a cross-layer optimization approach is proposed to enable cooperation between a VM’s host and guest layers and further improve the application QoS and resource usage efficiency. The above proposed approaches are prototyped and evaluated on a Xen-based virtualized system and evaluated with representative benchmarks including TPC-H, RUBiS, and TerraFly. The results demonstrate that the fuzzy-modeling-based approach improves the accuracy in resource prediction by up to 31.4% compared to conventional regression approaches. The FMPC approach substantially outperforms the traditional linear-model-based predictive control approach in meeting application QoS targets for an oversubscribed system. It is able to manage dynamic VM resource allocations and migrations for over 100 concurrent VMs across multiple hosts with good efficiency. Finally, the cross-layer optimization approach further improves the performance of a virtualized application by up to 40% when the resources are contended by dynamic workloads.

Diversity of Hymenoptera, Cultivated Plants and Management Practices in Home Garden Agroecosystems, Kyrgyz Republic

Pollination-dependent fruit trees grown in home gardens play an important role in the agricultural based economy of Central Asian countries, yet little is known about the status of pollinator communities, the cultivated plant composition or the factors that influence management practices in Kyrgyz home garden agroecosystems. As agricultural systems are human created and managed, a logical approach to their study blends anthropological and ecological methods, an ethnoecological approach. Over three years, I investigated how species richness and abundance of Hymenoptera, cultivated plants, and home garden management were related using quantitative and qualitative methods in the Issyk-kul Man and Biosphere reserve. Structured surveys were undertaken with heads of households using a random sample stratified by village. Gardens were then mapped with participation of household members to inventory edible species in gardens, most of which are pollinator-dependent, and to compare home garden diversity as reported by respondents during interviews. Apple diversity was studied to the variety level to understand respondents’ classification system in the context of in situ agrobiodiversity conservation. Household members identified 52 edible plant species when mapping the garden, compared with 32 reported when interviewed. The proportion of plant species received from others through exchange and the number of plots cultivated significantly explained the variation in edible plant diversity among gardens. Insects were sampled in gardens and orchards to determine potential pollinator community composition and the effect of different management practices on Hymenoptera richness and abundance. I collected 756 Hymenoptera individuals (56 bee; 12 wasp species); 12 species were new records for Kyrgyzstan or within Kyrgyzstan. Economic pressures to intensify cultivation could impact management practices that currently promote diversity. A home garden development initiative was undertaken to study management practice improvement. Participants in the initiative had higher adoption rates than controls of management practices that improve long-term yield, ecological sustainability and stability of home gardens. Home gardens, as currently managed, support abundant and diverse pollinator communities and have high cultivated plant diversity with few differences in community composition between garden management types.

Design and evaluation of a consulting system for database design

Database design is a difficult problem for non-expert designers. It is desirable to assist such designers during the problem solving process by means of a knowledge based (KB) system. Although a number of prototype KB systems have been proposed, there are many shortcomings. Firstly, few have incorporated sufficient expertise in modeling relationships, particularly higher order relationships. Secondly, there does not seem to be any published empirical study that experimentally tested the effectiveness of any of these KB tools. Thirdly, problem solving behavior of non-experts, whom the systems were intended to assist, has not been one of the bases for system design. In this project, a consulting system, called CODA, for conceptual database design that addresses the above short comings was developed and empirically validated. More specifically, the CODA system incorporates (a) findings on why non-experts commit errors and (b) heuristics for modeling relationships. Two approaches to knowledge base implementation were used and compared in this project, namely system restrictiveness and decisional guidance (Silver 1990). The Restrictive system uses a proscriptive approach and limits the designer's choices at various design phases by forcing him/her to follow a specific design path. The Guidance system approach, which is less restrictive, involves providing context specific, informative and suggestive guidance throughout the design process. Both the approaches would prevent erroneous design decisions. The main objectives of the study are to evaluate (1) whether the knowledge-based system is more effective than the system without a knowledge-base and (2) which approach to knowledge implementation - whether Restrictive or Guidance - is more effective. To evaluate the effectiveness of the knowledge base itself, the systems were compared with a system that does not incorporate the expertise (Control). An experimental procedure using student subjects was used to test the effectiveness of the systems. The subjects solved a task without using the system (pre-treatment task) and another task using one of the three systems, viz. Control, Guidance or Restrictive (experimental task). Analysis of experimental task scores of those subjects who performed satisfactorily in the pre-treatment task revealed that the knowledge based approach to database design support lead to more accurate solutions than the control system. Among the two KB approaches, Guidance approach was found to lead to better performance when compared to the Control system. It was found that the subjects perceived the Restrictive system easier to use than the Guidance system.

Localized Surface Plasmon Resonance Biosensors for Real-Time Biomolecular Binding Study

Surface Plasmon Resonance (SPR) and localized surface plasmon resonance (LSPR) biosensors have brought a revolutionary change to in vitro study of biological and biochemical processes due to its ability to measure extremely small changes in surface refractive index (RI), binding equilibrium and kinetics. Strategies based on LSPR have been employed to enhance the sensitivity for a variety of applications, such as diagnosis of diseases, environmental analysis, food safety, and chemical threat detection. In LSPR spectroscopy, absorption and scattering of light are greatly enhanced at frequencies that excite the LSPR, resulting in a characteristic extinction spectrum that depends on the RI of the surrounding medium. Compositional and conformational change within the surrounding medium near the sensing surface could therefore be detected as shifts in the extinction spectrum. This dissertation specifically focuses on the development and evaluation of highly sensitive LSPR biosensors for in situ study of biomolecular binding process by incorporating nanotechnology. Compared to traditional methods for biomolecular binding studies, LSPR-based biosensors offer real-time, label free detection. First, we modified the gold sensing surface of LSPR-based biosensors using nanomaterials such as gold nanoparticles (AuNPs) and polymer to enhance surface absorption and sensitivity. The performance of this type of biosensors was evaluated on the application of small heavy metal molecule binding affinity study. This biosensor exhibited ~7 fold sensitivity enhancement and binding kinetics measurement capability comparing to traditional biosensors. Second, a miniaturized cell culture system was integrated into the LSPR-based biosensor system for the purpose of real-time biomarker signaling pathway studies and drug efficacy studies with living cells. To the best of our knowledge, this is the first LSPR-based sensing platform with the capability of living cell studies. We demonstrated the living cell measurement ability by studying the VEGF signaling pathway in living SKOV-3 cells. Results have shown that the VEGF secretion level from SKOV-3 cells is 0.0137 ± 0.0012 pg per cell. Moreover, we have demonstrated bevacizumab drug regulation to the VEGF signaling pathway using this biosensor. This sensing platform could potentially help studying biomolecular binding kinetics which elucidates the underlying mechanisms of biotransportation and drug delivery.