Functional Characterization of Pectin Methylesterase Inhibitors in Rice (Oryza sativa)

Nguyen Thi Hong Phuong 경희대학교 대학원 2016 국내박사

Pectin, an enriched component in primary cell walls and middle lamellae, is an essential polysaccharide in all higher plants. Homogalacturonan (HG), a major form of pectin, is synthesized and methyl-esterified by enzymes localized in the Golgi apparatus and transported into the cell wall. Depending on cell type, the degree and pattern of pectin methyl-esterification are strictly regulated by cell wall-localized pectin methylesterases (PMEs) which are governed by multiple pectin methylesterase inhibitors (PMEIs) in vivo. Pectin methylesterases (PMEs, EC 3.1.1.11), belonging to carbohydrate esterase family 8, cleave the ester bond between a galacturonic acid and a methyl group, resulting change in pectin methyl-esterification status which clearly impacts diverse plant developmental processes and stress responses. PMEs play major roles in modification of pectin properties, such as the stiffening by forming Ca2+-pectate cross-link complexes or loosening by triggering CWDEs to break out cell wall components including pectins and its interactions with other cell wall components. By inhibition of PME activity, the action of PMEIs results in opposite consequences on pectin properties, leading to contrary phenotypes between the actions of each individual in PME-PMEI pairs. Optimal pectin methyl-esterification status in each cell type is determined by the balance between PME activity and post-translational PME inhibition by PME inhibitors (PMEIs). The detail information is explained in Chapter1 in which the PMEs and PMEIs were introduced from the structures to biological functions or biotechnological applications with an update knowledge, suggesting ideal for the further studies on models of PMEs and PMEIs and trying to answer opening questions from the previous researches, finally, to put an overview of PMEs and PMEIs functioning as a whole pathway in biology. Despite the importance of the PMEs and PMEIs in plant developments, environmental responses and biotechnology applications, there are only a few genes of these large families characterized in dicot plants and little is known about the physiological functions of pectins and its properties controlled by pectin methyl-esterification status in rice (Oryza sativa), an essential staple crop utilized by human being. Cultivation of this crop is now facing a big challenge when coping with diverse abiotic and/or biotic stresses and the increasing demands due to population growth. Thus, study of pectin methyl-esterification status in rice (Oryza sativa) can contribute precious genetic information to improve agronomic traits, sustaining food safety. Gene redundancy and the complicated regulation mechanisms in the OsPME family are the big challenges for the study of pectin methyl-esterification status in rice (Oryza sativa) by using the knockout approach due to the recovery of PME activity by other isoforms. Therefore, employing the overexpression of the inhibitor OsPMEIs, the endogenous OsPME activity is reduced by which phenotypes related to modification of pectin methyl-esterification status in rice can be observed and elucidated. Following this ideal, my research started with the elucidation of functional pectin in rice and pectin modification by de-methyl-esterification via PME activity. These works were done and reported in the Chapter2. The presence of pectin in rice cell walls was substantiated by uronic acid quantification and immunodetection of JIM7 monoclonal antibodies. PME activity assays were performed with cell wall proteins isolated from different rice tissues. In accordance with data from Arabidopsis, the highest activity was observed in germinating tissues, young culm, and spikelets. Transcriptional profiling of OsPMEs, containing 43 different isoforms, by real-time PCR and meta-analysis indicated that PMEs exhibit spatial- and stress-specific expression patterns during rice developments. Based on in silico analysis, subcellular compartments, isoelectric point, and cleavage sites of OsPMEs were identified. Taken together, these findings provided an important tool for further studies seeking to unravel the functional importance of pectin modification during plant development and abiotic and biotic responses in grass plants. In the Chapter3, OsPMEIs were functional characterized by biochemical approaches and further analyzed the potential inhibitory on local PME activity using subcellular localization and transcriptional analysis employing the quantitative real-time PCR (qRT-PCR) method. There were 49 PMEI members found in PMEI family in the rice genome. Analysis of their transcript levels by qRT-PCR and meta-expression analysis showed that they were regulated spatially and temporally, as well as in response to diverse stresses. Quantification of cell wall bound methyl-esters indicated that the degree of pectin methyl-esterification was developmentally regulated; in particular, higher PMEI activities were detected in cell wall proteins prepared from young leaves. Furthermore, an activity assay demonstrated that two recombinant OsPMEI proteins (OsPMEI8 and 12) were able to inhibit the enzymatic activity of a commercial PME protein. Subcellular localization showed that OsPMEI8 was targeted to the middle lamella and OsPMEI12 was localized in the plasma membrane, suggesting the involvement of OsPMEI8 in cell adhesion and OsPMEI12 in inhibitory activity of PMEs working on the walls closely located at the plasma membrane such as secondary cell walls. In sum, these results were the first molecular and biochemical evidences of functional characterization of PMEIs in rice growth and development. Rice contains 49 PMEIs and none of them are functionally characterized. Genomic sequence analysis led to the identification of rice PMEI28 (OsPMEI28). In the chapter4, the phenotype of overexpression of OsPMEI28 was introduced as the first evidence of OsPMEIs function in plant morphology, particularly, the phenotype related to modification of pectin methyl-esterification status in rice (Oryza sativa). Overexpression of OsPMEI28 in rice resulted in an increased level of cell-wall-bound methyl-ester groups and differential changes in the composition of cell wall neutral monosaccharides and lignin content in culm tissues. Consequently, transgenic plants overexpressing OsPMEI28 exhibited dwarf phenotypes and reduced culm diameter. Recombinant OsPMEI28 exhibited inhibitory activity against commercial PME protein with the highest activities detected at pH 8.5, suggesting OsPMEI28 was a typical PMEI working on inhibition of endogenous OsPME activity in vivo. The dwarf phenotype was a result of inhibited activity of an OsPME functioning in cell wall loosening in rice culm tissues, resulting cell extension. In summary, OsPMEI28 functioned as a critical structural modulator by regulating the degree of pectin methyl-esterification by which physiochemical properties of the cell wall components were affected, leading to abnormal cell extensibility in rice culm tissues. In conclusion, in rice the modification of pectin methyl-esterification also affects the plant morphology as observed on the overexpression of OsPMEI28 resulted in dwarf phenotype. However, the cognate PME or PMEs which specifically inhibited by OsPMEI28 has/have not been elucidated in my study. It seems like the PME(s) maybe interact with BR signaling to control plant height as in AtPMEI5 overexpression (Wolf et al. 2012) or it (they) can act as the cell loosening factors by their own ways, de-methyl-esterification of pectin. The de-esterified pectin will be the substrate of cell-wall-degrading enzymes (CWDEs), resulting in loosening the cell wall, thus, facilitating cell extension. The number of candidate PMEs will be narrowed down by in silico analysis of tissue specific expression of both OsPMEI28 and candidate PMEs, and, finally, experimentally performed co-expression analysis using reporter genes in transplant tissues. These are the further studies not only for OsPMEI28 and its PME partner but also for other OsPMEs and OsPMEIs in the big families which showed dynamic expressions during plant development and in response to diverse stresses, promising multi-functions of these families in plant biology, specially, in rice researches. The contents of this thesis are being prepared / have been published in the following papers: Chapter 1: Hong Phuong Nguyen, and Chanhui Lee*, “A review of Pectin Methylesterase (PME) and Pectin Methylesterase Inhibitor (PMEI): Roles of PMEs and PMEIs in plant physiology and biotechnological applications” (in preparation) Chapter 2: Ho Young Jeong§, Hong Phuong Nguyen§, and Chanhui Lee*, “Genome-wide identification and expression analysis of rice pectin methylesterases: Implication of functional roles of pectin modification in rice physiology”, Journal of plant physiology. 2015, 183:23-29 (§: equal contribuition) Chapter 3: Hong Phuong Nguyen, Ho Young Jeong, Hun Kim, Young Chang Kim, and Chanhui Lee*, “Molecular and biochemical characterization of rice pectin methylesterase inhibitors (OsPMEIs)”, Plant Physiology and Biochemistry. 2016, 101: 105-112 Chapter 4: Hong Phuong Nguyen, Ho Young Jeong and Chanhui Lee*, “Rice Pectin Methylesterase Inhibitor28 (OsPMEI28) encodes a functional PMEI and its overexpression results in a dwarf phenotype through reduced pectin methylesterfication levels” (submitted)

Investigation of Copper-containing photocathode for enhanced solar hydrogen production via photoelectrochemical water splitting

Nguyen Hoang Lam 영남대학교 대학원 2023 국내박사

최근 몇 년간, 환경 친화적이고 오염물질이 없는 수소 생산 방법으로써 광촉매 물분해에 대한 관심이 증가하고 있습니다. 이 분야에서의 주요 과제 중 하나는 태양광을 이용하여 효율적으로 물을 분해할 수 있는 시스템을 저렴하고 비독성인 재료를 사용하여 개발하는 것입니다. PEC(광전기화학) 수분해 시스템에 사용되는 광전극에서는 상업 생산에 사용될 수 있는 특정 속성을 갖는 반도체가 이상적입니다. 그러나 이러한 물질들의 보고된 효율은 때때로 이론적 최대값보다 낮습니다. 따라서 광촉매 활성을 향상시키기 위해서는 광전극의 효율을 제한하는 요인들에 대한 명확한 이해가 필요합니다. 본 논문의 4, 5, 6 장에는 실험에 대한 구체적인 내용이 수록되어 있습니다. 4장에는 XRD, SEM 및 TEM 기술을 사용하여 분석된 구리 기반 분말 NPs (Cu/Cu2O 나노복합상)의 결정 구조에 초점을 맞추었으며, W-H, N-R, Rietveld 정제 등의 몇 가지 방법을 사용하여 PNCs의 결정 구조를 심도있게 분석하기 위해 노력했습니다. 용액 합성 방법 중 다양한 합성 조건에서 PNC의 결정 구조 변화를 관찰하기 위해 두 가지 실험을 진행하였습니다. 해당 실험을 통해 결정 구조의 철저한 분석과 비교를 하였습니다. 5장에서는 CuO 박막의 구조적 및 광학적 특성 및 PEC 성능에 초점을 맞추었습니다. 브로콜리 모양을 가진 이 박막은 물분해 응용을 위한 광전극으로 사용하기 위해 수열법을 사용하여 제조하였습니다. XRD, SEM, XPS, PL 및 UV-Vis와 같은 다양한 기술을 사용하여 박막의 형태학적, 구조적 및 광학적 특성을 측정하였습니다. 또한 이러한 박막의 PEC 성능은 삼전극 시스템에서 평가되었습니다. 6장에서는 CuO 박막의 성능 향상 방법에 대해 설명합니다. PEC 물분해 응용에서 CuO의 단점을 해결하기 위해 수열법, 스핀 코팅 및 열처리를 통해 FTO 기판 상에 CuO와 CuBi2O4를 합성하여 이종접합 광전극을 제작했습니다 (FTO/CuO/CuBi2O4). 각 샘플의 특성(합성 방법, 구조, 구성, 형태 등)은 다양한 합성 조건에서 철저히 논의하였습니다. CuBi2O4를 CuO와 접합함으로써 두 개의 반도체가 밀접하게 결합되어 광전극의 PEC 효율이 향상되었습니다. 또한 CuO 층은 전자 생성 층으로 작용하고, CuBi2O4 층은 광부식을 방지하고 전자를 전극/전해질 접합부로 운반하여 HER을 용이하게 합니다 In recent years, there has been a growing interest in using photocatalytic water splitting as a way to produce hydrogen that is both environmentally friendly and free of pollutants. One of the primary challenges in this field is developing systems that can efficiently dissociate water using sunlight, while also relying on inexpensive and non-toxic materials. For photocathodes used in PEC water splitting systems, it is ideal to have semiconductors with specific properties that can be used in commercial production. However, the reported efficiencies for these materials are often below their theoretical maximum values. Therefore, it is important to have a clear understanding of the factors limiting the efficiency of these photocathodes if the photocatalytic activity is to be improved. The experiments in this dissertation are structured into three sections. The fourth chapter of this dissertation focused on the crystalline structure of copper-based powder NPs (Cu/Cu2O nanocomposite phase), which was analyzed using XRD, SEM, and TEM techniques. There are some methods such as W-H, N-R, and Rietveld refinement were used to deeply analyze the crystalline structure of PNCs. Two experiments were conducted to observe the changes in the crystalline structure of PNC under different synthesis conditions in the colloidal solution method. A thorough analysis and comparison of the crystalline structure were performed. In the fifth chapter, the focus is on the structural, and optical properties of CuO thin films, as well as their PEC performance. These thin films, which exhibit a broccoli-like structure, were prepared using a hydrothermal method to serve as a photocathode for water splitting applications. Various techniques, including XRD, SEM, XPS, PL, and UV-Vis, were used to measure and characterize the morphological, structural, and optical properties of the thin films. Additionally, the PEC performance of these thin films was evaluated in a three-electrode system. In the sixth chapter, a method for enhancing the performance of CuO thin films is described. To address the drawbacks of CuO in PEC water splitting applications, a heterojunction photocathode was produced by synthesizing CuO and CuBi2O4 on an FTO substrate (FTO/CuO/CuBi2O4) through hydrothermal methods, spin coating, and annealing. The characteristics of each sample under various synthesis conditions, including synthesis method, structure, composition, and morphology are thoroughly discussed. The integration of CuBi2O4 with CuO resulted in the two semiconductors being closely bonded, enhancing the PEC efficiency of the photocathode. Additionally, the layer of CuO acted as the electron-generating layer, while the CuBi2O4 layer prevented photo-corrosion and aided in the transportation of carriers to the electrode/electrolyte interface to facilitate HER

Development of Machine Learning Algorithms for Low-Resolution MIMO Signal Processing

Nguyen, Van Ly ProQuest Dissertations & Theses University of Cali 2022 해외박사(DDOD)

Due to the proliferation of mobile devices and services, the scale of multiple-input-multiple-output (MIMO) communication systems is getting larger and larger and can be massive in future wireless networks. This results in significant increases in hardware cost and power consumption. Recently, low-resolution analog-to-digital converters (ADCs) have been considered as a practical solution for reducing hardware cost and power consumption in MIMO systems. This is because low-resolution ADCs have simple hardware architectures as well as very low power consumption. However, the severe nonlinearity of low-resolution ADCs causes significant distortions in the received signals and therefore makes signal processing tasks such as channel estimation and data detection much more challenging compared to those in high-resolution systems. Motivated by the fact that machine learning is very powerful in solving non-linear problems, this dissertation exploits machine learning to develop low-complexity yet efficient and robust algorithms for channel estimation and data detection in MIMO systems with low-resolution ADCs.

Synegistic Anti-proliferation Effects of All -trans Retinoic Acid with Paclitaxel on Autosomal Polycystic Kidney Disease Cell Line

NGUYEN THANH THANH QUE Graduate School Gachon University 2020 국내석사

ABSTRACT Synergistic anti-proliferation effects of all-trans retinoic acid with paclitaxel on autosomal polycystic kidney disease cell line. Que Thanh Thanh Nguyen Supervisor: Prof. Jae Young Kim Department of Life Science Graduate School of Gachon University Autosomal dominant polycystic kidney disease (ADPKD) has been well-known as a monogenic inherited disorder and characterized by cyst development in the kidney. In recent years, the mechanism in autosomal dominant polycystic kidney disease (ADPKD) associated to genetic factors and non-genetic factors have been widely studied to get deep knowledge about ADPKD. In renal tubules, renal epithelial cells over-growth due to lower intracellular calcium level and the mitogenic effect of cAMP (cyclic adenosine monophosphate), is one of the hallmark features that originated cystogenesis. In this study, for the first time, we investigated the synergistic effects of combinatory treatment between all-trans retinoic acid (ATRA), an active form of vitamin A, and paclitaxel, a high effective anticancer drug, on the autosomal dominant polycystic kidney cell line. Cells were treated with a combination of ATRA with paclitaxel for 48 h and then analyzed by cell viability assay. In combinatory treatment groups, our data indicated that the percentage of cell viability was significantly decreased in the comparison with DMSO (control) and ATRA/paclitaxel (alone) treatment. Cell cycle arrest showed that the combinatory treatment of ATRA with paclitaxel induce ADPKD cell line arrest at the G2/M phase. Furthermore, apoptotic cells were detected in our study by Annexin V/PI staining. The up-regulation of p53 protein expression and caspase activation could be involved in apoptosis signal and cell cycle arrest. We revealed that the intra-calcium level was sharply increased by combined treatment of ATRA and paclitaxel after 72 h of treatment and this enhance was blocked by RARα/RXRα antagonist or calcium channel blockers. Besides, ADPKD cell proliferation was controlled through the ERK signaling pathway by in phosphorylated ERK. Our result suggested the function of combinatorial treatment of ATRA with paclitaxel which expresses synergistic anti-proliferation effect on ADPKD cell proliferation by inducing cell cycle arresting, apoptosis and suppressing the ERK signaling pathway. Keywords: Autosomal polycystic kidney disease (ADPKD), ATRA, paclitaxel, cell cycle arrest, apoptosis, intracellular calcium, phosphorylated ERK1/2.

Welcome to the Family!: Hospitality, Kinship, and Mourning in Vietnamese Diasporic Literature

Nguyen, Catherine Hong ProQuest Dissertations & Theses University of Cali 2018 해외박사(DDOD)

Welcome to the Family!: Hospitality, Kinship, and Mourning in Vietnamese Diasporic Literature is a comparative study of Vietnamese immigration that focuses on the representation of adoption and sponsorship through the respective figures of the w.

Qualitative Theory of Dynamical Systems induced by Differential Equations

NGUYEN 忠南大學校 大學院 2022 국내박사

본 논문에서는, 미분방정식(differential equations)에 의한 동력계(dynamical systems)의 질적 이론 연구하였다. 1장에서는, 미분방정식(differential equations)에 의해 유도된 Nemytskii operators와 dynamical systems의 규칙성(regularity)에 대해 연구하였다. 2장에서는, C1 perturbation에서 Robin 경계 조건을 갖는 reaction diffusion equations의 안정성을 연구하였다. 3장에서는, Lipschitz perturbation에서 Robin 경계 조건을 갖는 reaction diffusion equations의 안정성을 연구하였다. In this thesis, the qualitative theory of dynamical systems by differential equations was studied. In Chapter 1, Nemytskii operators derived from differential equations and the regularity of dynamical systems were studied. In Chapter 2, the stability of reaction diffusion equations with Robin boundary conditions in C1 perturbation was studied. In Chapter 3, the stability of reaction diffusion equations with Robin boundary conditions in Lipschitz perturbation is studied.

Sum-Rate Maximization for Device-to-device Communications in Multicarrier Cellular Networks

Thanh-Huy Nguyen 인제대학교 대학원 2016 국내석사

ABSTRACT Sum-rate Maximization for Device-to-device Communications in Multicarrier Cellular Networks Thanh-Huy Nguyen (Advisor: Prof. Won-Joo Hwang) Department of Information and Communication System Graduate School, Inje University With the diversity of high-rate nearby applications, device-to-device (D2D) communications have become a mainstream in the current research trend as a future technology candidate. Optimization in D2D communication usually focuses on mitigating interference or maximizing the primary cellular network throughput while keeping D2D communications data rate above the requirements. Although the quality of service (QoS) requirements of both cellular users (CUs) and D2D users are guaranteed, D2D communication performance is still limited. From the high demand of stable connectivity, large capacity for serving many D2D devices, D2D communication performance should be taken into account. In this thesis, we formulate the sum-rate maximization problem in the aim of enhancing spectral efficiency for multiple D2D users in multicarrier systems (i.e OFDMA). On the other hand, increasing spectral efficiency, which is measured in bits/s/Hz, is one of important issues in wireless systems. Since the optimization problem has non-convex structure due to the mutual interference among D2D pairs, it is more challenging to solve the problem with high complexity. Exploiting the concept of time-sharing condition, the duality gap of the multiuser spectrum optimization in multicarrier systems tends to zero when the number of subcarriers is sufficiently large regardless the convexity of the primal problem. By utilizing dual optimization theory, the solution simply finds the set of optimal values that maximize the Lagrangian function while the Lagrangian multipliers are obtained using iterative subgradient method. In this thesis, we firstly investigate the D2D communication performance through the optimal resource allocation algorithm which is developed to make a full framework for CUs and D2D users. Then the resource allocation algorithm is proposed to efficiently allocate transmit power of D2D users. Due to the impacts of CUs achievable data rate, the algorithm is divided into two schemes: fixed power and dynamic power. Numerical results are provided to demonstrate the convergence of our methods and the comparison of the two proposed algorithms. The effectiveness of our methods is also evaluated through comparing with other methods.

Hydroxyl-Presenting Metal-Organic Frameworks as Support Platforms for Vanadium- and Titanium-Based Oxidation Catalysts

Nguyen, Huong Giang Thai Northwestern University 2015 해외박사(DDOD)

Heterogeneous catalysts such as supported vanadium oxides have great potential to be developed into economically viable oxidation catalysts if they can exhibit greater selectivity; however, their current syntheses often yield a mixture of species, rendering the analysis of structure-activity relationships for each possible vanadium oxide species difficult and, thus, frustrating efforts to improve catalyst activity and selectivity. To address this issue, two metal-organic framework (MOF) systems possessing well-defined and single-site catecholate supports for monomeric vanadyl species were synthesized and their catalytic activities were tested. Through post-synthesis grafting of catechol-presenting dopamine to the unsaturated Cr centers of MIL-101, followed by metallation with vanadyl ion, vanadyl monocatecholate-functionalized V(dop)-MIL-101 was obtained. V(dop)-MIL-101 can efficiently catalyze the oxidation of an organic sulfide and exhibited tunable selectivity for the sulfoxide product. In an alternative strategy, a series PG-CatBrO (PG = protecting group) paddlewheel MOFs were constructed from ZnII ions, tetracarboxylate struts, and protected catecholate dipyridyl struts, which could be deprotected and subsequently metallated with vanadyl ions to give V-CatBrO MOF. This MOF can catalyze the benzylic oxidation of tetralin to tetralol and tetralone. To demonstrate that MOF-based catalysts are viable for gas-phase reactions, a thermally stable hydroxyl-presenting MOF, UiO-66, was explored as a MOF-based support. V-UiO-66 proved to be an effective analogue of hydroxyl-presenting solid supports for VV species in gas-phase oxidation reactions, catalyzing the oxidative dehydrogenation of cyclohexene to benzene at high temperatures (350 °C). Generalization of the metallation of the hydroxyl-presenting nodes of UiO-66 to other redox-active metals, such as titanium, has also allowed other chemical oxidations to be accessed.

Construction of Mesh-type Phantoms of reference korean adults and their potential applications

Nguyen, Tat Thang 한양대학교 대학원 2018 국내박사

Over 50 years, the computational human phantoms have been used in computational dosimetry for purposes of radiation protection, nuclear medicine, and radiation therapy. Earlier versions of the computational phantoms however have some deficiencies in their fidelity presenting details of complicated anatomy of the human body, particularly of thin layers of tissue volume. In addition, they are rather fixed objects so as to have limited flexibility for application to different geometry settings. The mesh-type phantom, represented by polygonal mesh (PM) or tetrahedral mesh (TM), is considered as a good alternative model to overcome such deficiencies. Acknowledging the advantages of the mesh-type phantom, the International Commission on Radiological Protection (ICRP) has recently developed a set of mesh-type reference computational phantoms (MRCPs) for adult male and female, and considers them as a potential candidate to replace the adult male and female voxel-type reference computational phantoms (VRCPs) described in ICRP Publication 110. In the present study, considering the advantages of the mesh geometry model, we have developed a set of new mesh-type reference Korean phantoms (MRKPs), male and female, representing Korean adults, of which quality is equivalent to that of the MRCPs. For the development of the phantoms, a comprehensive dataset of Korean reference anatomical values was first established. Most of organs and tissues of the phantoms were constructed using information from high-quality 3-D models and images for Korean adults provided by Korean governmental agencies. Some complex organs including eye lens, lymphatic nodes, muscle, and blood vessels of the phantoms were constructed using the same approaches used in the development of the MRCPs. Finally, all other target and source regions specifically needed for effective dose calculations (such as the micron-thick target and source regions of the skin and alimentary and respiratory track systems) were defined following the assumptions set in the current dosimetry models. The developed MRKPs were then implemented in the Geant4 Monte Carlo simulation code for illustrative calculations of the internal and external dose coefficients for photons and electrons, and the calculated dose coefficients were compared with the values given in ICRP Publications 116 and 133, which are based on the VRCPs, and the values calculated with the MRCPs. The comparison showed that the dose coefficients calculated with MRKPs were generally well close to those calculated with the MRCPs and the ICRP reference values. For electron exposures, however, the dose coefficients show partly significant differences from those of the MRCPs and ICRP values due to the nature of electron dose distribution highly affected by the distances to the target volume. The MRKPs developed in the present study, due to many advantages they offer, are expected to be excellent subjects for further studies including creation of database of dose coefficients for Korean workers and members of the public, development of body-shape and posture dependent phantoms for Korean adults, installation of detailed organ models of interest in medical applications, and development of Korean reference physical phantoms in the future. 지난 50여 년 동안 인체 전산팬텀은 몬테칼로 전산모사 기법과 함께 인체 내 장기선량 및 유효선량을 계산하기 위한 핵심도구로서 방사선방호, 핵의학, 방사선치료 등 다양한 분야에서 활용되어 왔다. 대표적인 전산팬텀인 복셀형 전산팬텀은 일반적으로 CT 영상이나 MRI 영상과 같은 의료영상을 기반으로 제작되어 인체의 해부학적 구조를 비교적 사실적으로 묘사하고 있지만, 복셀의 해상도 및 구조적인 한계로 인해 작거나 얇은 장기들의 세부 구조를 표현할 수 없고 자세나 체형의 변형이 어렵다는 문제점을 지니고 있다. 이에 따라, 전 세계의 많은 연구자들은 복셀형 전산팬텀의 문제점들을 극복하기 위한 노력의 일환으로 새로운 형태인 메시 기반의 전산팬텀을 개발하는 연구를 수행하고 있다. 최근 국제방사선방호위원회(International Commission on Radiological Protection, ICRP)의 제 2분과 위원회에서도 기존의 복셀형 표준 성인남녀 전산팬텀 한 쌍을 메시 형태로 변환하는 연구를 수행하였으며, 변환된 메시형 전산팬텀을 차세대 표준 성인남녀 전산팬텀으로 채택한 바 있다. 본 연구에서는 이러한 최신 연구 동향에 따라 한국인에 대한 선량 평가의 정확성과 신뢰성을 제고하기 위하여 다양한 문헌 및 데이터를 분석하여 한국인에 대한 표준 인체치수 및 장기 데이터를 확립하고, 메시형 ICRP 표준 전산팬텀과 동일한 수준의 표준 한국인 성인남녀 전산팬텀을 개발하였다. 전산팬텀은 국내 여러 정부출연 연구기관에서 제공하는 한국인에 대한 모델들(연속절단면 컬러해부영상, 골격 평균화 모델, 표준체형 모델)을 바탕으로 제작되어, 한국인의 해부학적 특징을 매우 정밀하게 표현하고 있다. 뿐만 아니라, 메시형 표준 한국인 전산팬텀은 ICRP 표준 전산팬텀과 동일하게 유효선량 계산에 필요한 호흡기 및 소화기 계통의 방사선 민감층 및 선원 영역을 모두 포함하고 있다. 본 연구에서는 개발된 전산팬텀을 Geant4 몬테칼로 전산모사 코드에 입력하여 외부피폭 및 내부피폭에 대한 선량계수를 산출하고, 이를 메시형 ICRP 표준 전산팬텀을 이용하여 계산한 결과 및 ICRP 보고서에서 제공하는 표준 값과 비교하였다. 비교 결과, 메시형 한국인 전산팬텀의 결과는 일반적으로 메시형 ICRP 표준 전산팬텀의 결과 및 ICRP 표준 값과 매우 유사한 선량을 제공하는 것을 확인하였다. 그러나 투과력이 낮은 전자 선원의 경우 메시형 ICRP 표준 전산팬텀의 결과 및 ICRP 표준 값과 크게 다른 것을 확인하였는데, 이는 인종 간 해부학적 구조의 차이로 인해 인체 내 전자의 선량 분포가 다르게 형성되었기 때문이다. 본 연구에서 개발된 전산팬텀은 메시형 ICRP 표준 전산팬텀과 동급인 세계 최고 수준의 전산팬텀으로서, 국내 방사선작업종사자 및 일반인의 피폭선량을 정확하게 산출할 수 있도록 하여 국내 방사선방호 및 안전규제를 보다 합리적으로 이행하는데 사용될 수 있을 것으로 기대된다. 또한, 개발된 전산팬텀은 변형이 용이하여 피폭자의 특성에 맞게 자세 및 체형을 변형하는데 사용될 수 있으며, 의료 방사선방호에 중요한 상세 장기 모델을 설치할 수 있는 플랫폼으로서 사용될 수 있다. 이 외에도 전파와 인체와의 상호작용, 자동차 충격 전산모사, 가상공간 수술 등의 비방사선 분야에도 활용될 수 있을 것으로 기대된다.

Improving software quality with programming patterns

Nguyen, Tung Thanh Iowa State University 2013 해외박사(DDOD)

Software systems and services are increasingly important, involving and improving the work and lives of billions people. However, software development is still human-intensive and error-prone. Established studies report that software failures cost the global economy $312 billion annually and software vendors often spend 50-75% of the total development cost for finding and fixing bugs, i.e. subtle programming errors that cause software failures. People rarely develop software from scratch, but frequently reuse existing software artifacts. In this dissertation, we focus on programming patterns, i.e. frequently occurring code resulted from reuse, and explore their potential for improving software quality. Specially, we develop techniques for recovering programming patterns and using them to find, fix, and prevent bugs more effectively. This dissertation has two main contributions. One is Graph-based Object Usage Model (GROUM), a graph-based representation of source code. A GROUM abstracts a fragment of code as a graph representing its object usages. In a GROUM, nodes correspond to the function calls and control structures while edges capture control and data relationships between them. Based on GROUM, we developed a graph mining technique that could recover programming patterns of API usage and use them for detecting bugs. GROUM is also used to find similar bugs and recommend similar bug fixes. The other main contribution of this dissertation is SLAMC, a Statistical Semantic LAnguage Model for Source Code. SLAMC represents code as sequences of code elements of different roles, e.g. data types, variables, or functions and annotate those elements with sememes, a text-based annotation of their semantic information. SLAMC models the regularities over the sememe sequences code-based factors like local code context, global concerns, and pair-wise associations, thus, implicitly captures programming idioms and patterns as sequences with high probabilities. Based on SLAMC, we developed a technique for recommending most likely next code sequences, which could improve programming productivity and might reduce the odds of programming errors. Empirical evaluation shows that our approaches can detect meaningful programming patterns and anomalies that might cause bugs or maintenance issues, thus could improve software quality. In addition, our models have been successfully used for several other problems, from library adaptation, code migration, to bug fix generation. They also have several other potential applications, which we will explore in the future work.