Algorithm and Architecture Co-design for High-performance Digital Signal Processing.

CMOS scaling has been the driving force behind the revolution of digital signal processing (DSP) systems, but scaling is slowing down and the CMOS device is approaching its fundamental scaling limit. At the same time, DSP algorithms are continuing to evolve, so there is a growing gap between the increasing complexities of the algorithms and what is practically implementable. The gap can be bridged by exploring the synergy between algorithm and hardware design, using the so-called co-design techniques. In this thesis, algorithm and architecture co-design techniques are applied to X-ray computed tomography (CT) image reconstruction. Analysis of fixed-point quantization and CT geometry identifies an optimal word length and a mismatch between the object and projection grids. A water-filling buffer is designed to resolve the grid mismatch, and is combined with parallel fixed-point arithmetic units to improve the throughput. The analysis eventually leads to an out-of-order scheduling architecture that reduces the off-chip memory access by three orders of magnitude. The co-design techniques are further applied to the design of neural networks for sparse coding. Analysis of the neuron spiking dynamics leads to the optimal tuning of network size, spiking rate, and update step size to keep the spiking sparse. The resulting sparsity enables a bus-ring architecture to achieve both high throughput and scalability. A 65nm CMOS chip implementing the architecture demonstrates feature extraction at a throughput of 1.24G pixel/s at 1.0V and 310MHz. The error tolerance of sparse coding can be exploited to enhance the energy efficiency. As a natural next step after the sparse coding chip, a neural-inspired inference module (IM) is designed for object recognition. The object recognition chip consists of an IM based on sparse coding and an event-driven classifier. A learning co-processor is integrated on chip to enable on-chip learning. The throughput and energy efficiency are further improved using architectural techniques including sub-dividing the IM and classifier into modules and optimal pipelining. The result is a 65nm CMOS chip that performs sparse coding at 10.16G pixel/s at 1.0V and 635MHz. The co-design techniques can be applied to the design of other advanced DSP algorithms for emerging applications.PhDElectrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113344/1/jungkook_1.pd

Estimating the malaria transmission of Plasmodium vivax based on serodiagnosis

Background: Plasmodium vivax re-emerged in 1993 and has now become a major public health problem during the summer season in South Korea. The aim of this study was to interpret and understand the meaning of seroepidemiological studies for developing the best malaria control programme in South Korea. Methods: Blood samples were collected in Gimpo city, Paju city, Yeoncheon County, Cheorwon County and Goseong County of high risk area in South Korea. Microscopy was performed to identify patients infected with P. vivax. Antibody detection for P. vivax was performed using indirect fluorescent antibody test (IFAT). Results: A total of 1,574 blood samples was collected from participants in the study areas and evaluated against three parameters: IFAT positive rate, annual antibody positive index (AAPI), and annual parasite index (API). The IFAT positive rate was 7.24% (n = 114). Of the five study areas, Gimpo had the highest IFAT positive rate (13.68%) and AAPI (4.63). Yeongcheon had the highest API in 2005 (2.06) while Gimpo had the highest API in 2006 (5.00). No correlation was observed between any of the three parameters and study sites' distance from the demilitarized zone (DMZ). Conclusions: These results showed that P. vivax antibody levels could provide useful information about the prevalence of malaria in endemic areas. Furthermore, AAPI results for each year showed a closer relationship to API the following year than the API of the same year and thus could be helpful in predicting malaria transmission risks

Genetic polymorphism of merozoite surface protein-1 and merozoite surface protein-2 in Plasmodium falciparum field isolates from Myanmar

<p>Abstract</p> <p>Background</p> <p>Merozoite surface protein-1 (MSP-1) and MSP-2 of <it>Plasmodium falciparum </it>are potential vaccine candidate antigens for malaria vaccine development. However, extensive genetic polymorphism of the antigens in field isolates of <it>P. falciparum </it>represents a major obstacle for the development of an effective vaccine. In this study, genetic polymorphism of MSP-1 and MSP-2 among <it>P. falciparum </it>field isolates from Myanmar was analysed.</p> <p>Methods</p> <p>A total of 63 <it>P. falciparum </it>infected blood samples, which were collected from patients attending a regional hospital in Mandalay Division, Myanmar, were used in this study. The regions flanking the highly polymorphic characters, block 2 for MSP-1 and block 3 for MSP-2, were genotyped by allele-specific nested-PCR to analyse the population diversity of the parasite. Sequence analysis of the polymorphic regions of MSP-1 and MSP-2 was also conducted to identify allelic diversity in the parasite population.</p> <p>Results</p> <p>Diverse allelic polymorphism of MSP-1 and MSP-2 was identified in <it>P. falciparum </it>isolates from Myanmar and most of the infections were determined to be mixed infections. Sequence analysis of MSP-1 block 2 revealed that 14 different alleles for MSP-1 (5 for K1 type and 9 for MAD20 type) were identified. For MSP-2 block 3, a total of 22 alleles (7 for FC27 type and 15 for 3D7 type) were identified.</p> <p>Conclusion</p> <p>Extensive genetic polymorphism with diverse allele types was identified in MSP-1 and MSP-2 in <it>P. falciparum </it>field isolates from Myanmar. A high level of mixed infections was also observed, as was a high degree of multiplicity of infection.</p

Erratum: Nation-Wide Korean Breast Cancer Data from 2008 Using the Breast Cancer Registration Program

nation-wide breast cancer data and analyzed the data using their online registration program biannually. The purpose of this study was to evaluate the characteristics of Korean breast cancer from 2008 and examine chronological based patterns. Methods: Data were collected from 38 medical schools (67 hospitals), 20 general hospitals, and 10 private clinics. The data on the total number, gender, and age distribution were collected through a questionnaire as well as other detailed data analyzed via the online registration program. Results: In 2008, there were 13,908 patients who were newly diagnosed with breast cancer. The crude incidence rate of female breast cancer was 57.3 among 100,000 and the median age was 49 years. The age distribution had not changed since the initial survey; however the proportion of postmenopausal patients had increased and median age was older than the past. In staging distribution, the proportion of early breast cancer (stage 0, I) was 47.2 % with, breast-conserving surgery performed in 58 % and mastectomy in 39.5%. Conclusion: Compared to past data, the incidence of breast cancer in Korea continues to rise. Furthermore, the proportion of those detected by screening and breast conservation surgery has increased remarkably. To understand the patterns of Korean breast cancer, the nation-wide data should continuously investigated

Effects of laser polarizations on shock generation and shock ion acceleration in overdense plasmas

The effects of laser-pulse polarization on the generation of an electrostatic shock in an overdense plasma were investigated using particle-in-cell simulations. We found, from one-dimensional simulations, that total and average energies of reflected ions from a circular polarization- (CP) driven shock front are a few times higher than those from a linear polarization- (LP) driven one for a given pulse energy. Moreover, it was discovered that the pulse transmittance is the single dominant factor for determining the CP-shock formation, while the LP shock is affected by the plasma scale length as well as the transmittance. In two-dimensional simulations, it is observed that the transverse instability, such as Weibel-like instability, can be suppressed more efficiently by CP pulses.clos

Quantitative measurements of C-reactive protein using silicon nanowire arrays

A silicon nanowire-based sensor for biological application showed highly desirable electrical responses to either pH changes or receptor-ligand interactions such as protein disease markers, viruses, and DNA hybridization. Furthermore, because the silicon nanowire can display results in real-time, it may possess superior characteristics for biosensing than those demonstrated in previously studied methods. However, despite its promising potential and advantages, certain process-related limitations of the device, due to its size and material characteristics, need to be addressed. In this article, we suggest possible solutions. We fabricated silicon nanowire using a top-down and low cost micromachining method, and evaluate the sensing of molecules after transfer and surface modifications. Our newly designed method can be used to attach highly ordered nanowires to various substrates, to form a nanowire array device, which needs to follow a series of repetitive steps in conventional fabrication technology based on a vapor-liquid-solid (VLS) method. For evaluation, we demonstrated that our newly fabricated silicon nanowire arrays could detect pH changes as well as streptavidin-biotin binding events. As well as the initial proof-of-principle studies, C-reactive protein binding was measured: electrical signals were changed in a linear fashion with the concentration (1 fM to 1 nM) in PBS containing 1.37 mM of salts. Finally, to address the effects of Debye length, silicon nanowires coupled with antigen proteins underwent electrical signal changes as the salt concentration changed