THE NATURAL AND ORTHOGONAL INTERACTION (NOIA) MODELS FOR QUANTITATIVE TRAITS (QTs) AND COMPLEX DISEASES

My dissertation focuses on developing methods for gene-gene/environment interactions and imprinting effect detections for human complex diseases and quantitative traits. It includes three sections: (1) generalizing the Natural and Orthogonal interaction (NOIA) model for the coding technique originally developed for gene-gene (GxG) interaction and also to reduced models; (2) developing a novel statistical approach that allows for modeling gene-environment (GxE) interactions influencing disease risk, and (3) developing a statistical approach for modeling genetic variants displaying parent-of-origin effects (POEs), such as imprinting. In the past decade, genetic researchers have identified a large number of causal variants for human genetic diseases and traits by single-locus analysis, and interaction has now become a hot topic in the effort to search for the complex network between multiple genes or environmental exposures contributing to the outcome. Epistasis, also known as gene-gene interaction is the departure from additive genetic effects from several genes to a trait, which means that the same alleles of one gene could display different genetic effects under different genetic backgrounds. In this study, we propose to implement the NOIA model for association studies along with interaction for human complex traits and diseases. We compare the performance of the new statistical models we developed and the usual functional model by both simulation study and real data analysis. Both simulation and real data analysis revealed higher power of the NOIA GxG interaction model for detecting both main genetic effects and interaction effects. Through application on a melanoma dataset, we confirmed the previously identified significant regions for melanoma risk at 15q13.1, 16q24.3 and 9p21.3. We also identified potential interactions with these significant regions that contribute to melanoma risk. Based on the NOIA model, we developed a novel statistical approach that allows us to model effects from a genetic factor and binary environmental exposure that are jointly influencing disease risk. Both simulation and real data analyses revealed higher power of the NOIA model for detecting both main genetic effects and interaction effects for both quantitative and binary traits. We also found that estimates of the parameters from logistic regression for binary traits are no longer statistically uncorrelated under the alternative model when there is an association. Applying our novel approach to a lung cancer dataset, we confirmed four SNPs in 5p15 and 15q25 region to be significantly associated with lung cancer risk in Caucasians population: rs2736100, rs402710, rs16969968 and rs8034191. We also validated that rs16969968 and rs8034191 in 15q25 region are significantly interacting with smoking in Caucasian population. Our approach identified the potential interactions of SNP rs2256543 in 6p21 with smoking on contributing to lung cancer risk. Genetic imprinting is the most well-known cause for parent-of-origin effect (POE) whereby a gene is differentially expressed depending on the parental origin of the same alleles. Genetic imprinting affects several human disorders, including diabetes, breast cancer, alcoholism, and obesity. This phenomenon has been shown to be important for normal embryonic development in mammals. Traditional association approaches ignore this important genetic phenomenon. In this study, we propose a NOIA framework for a single locus association study that estimates both main allelic effects and POEs. We develop statistical (Stat-POE) and functional (Func-POE) models, and demonstrate conditions for orthogonality of the Stat-POE model. We conducted simulations for both quantitative and qualitative traits to evaluate the performance of the statistical and functional models with different levels of POEs. Our results showed that the newly proposed Stat-POE model, which ensures orthogonality of variance components if Hardy-Weinberg Equilibrium (HWE) or equal minor and major allele frequencies is satisfied, had greater power for detecting the main allelic additive effect than a Func-POE model, which codes according to allelic substitutions, for both quantitative and qualitative traits. The power for detecting the POE was the same for the Stat-POE and Func-POE models under HWE for quantitative traits.

Design, Synthesis and Development of Transporter Targeting Agents for Image-guided Therapy and Drug Delivery

The purpose of this study was to design, synthesize and develop novel transporter targeting agents for image-guided therapy and drug delivery. Two novel agents, N4-guanine (N4amG) and glycopeptide (GP) were synthesized for tumor cell proliferation assessment and cancer theranostic platform, respectively. N4amG and GP were synthesized and radiolabeled with 99mTc and 68Ga. The chemical and radiochemical purities as well as radiochemical stabilities of radiolabeled N4amG and GP were tested. In vitro stability assessment showed both 99mTc-N4amG and 99mTc-GP were stable up to 6 hours, whereas 68Ga-GP was stable up to 2 hours. Cell culture studies confirmed radiolabeled N4amG and GP could penetrate the cell membrane through nucleoside transporters and amino acid transporters, respectively. Up to 40% of intracellular 99mTc-N4amG and 99mTc-GP was found within cell nucleus following 2 hours of incubation. Flow cytometry analysis revealed 99mTc-N4amG was a cell cycle S phase-specific agent. There was a significant difference of the uptake of 99mTc-GP between pre- and post- paclitaxel-treated cells, which suggests that 99mTc-GP may be useful in chemotherapy treatment monitoring. Moreover, radiolabeled N4amG and GP were tested in vivo using tumor-bearing animal models. 99mTc-N4amG showed an increase in tumor-to-muscle count density ratios up to 5 at 4 hour imaging. Both 99mTc-labeled agents showed decreased tumor uptake after paclitaxel treatment. Immunohistochemistry analysis demonstrated that the uptake of 99mTc-N4amG was correlated with Ki-67 expression. Both 99mTc-N4amG and 99mTc-GP could differentiate between tumor and inflammation in animal studies. Furthermore, 68Ga-GP was compared to 18F-FDG in rabbit PET imaging studies. 68Ga-GP had lower tumor standardized uptake values (SUV), but similar uptake dynamics, and different biodistribution compared with 18F-FDG. Finally, to demonstrate that GP can be a potential drug carrier for cancer theranostics, several drugs, including doxorubicin, were selected to be conjugated to GP. Imaging studies demonstrated that tumor uptake of GP-drug conjugates was increased as a function of time. GP-doxorubicin (GP-DOX) showed a slow-release pattern in in vitro cytotoxicity assay and exhibited anti-cancer efficacy with reduced toxicity in in vivo tumor growth delay study. In conclusion, both N4amG and GP are transporter-based targeting agents. Radiolabeled N4amG can be used for tumor cell proliferation assessment. GP is a potential agent for image-guided therapy and drug delivery.

Development and Characterization of an in vitro Four-species Anaerobic Dental Biofilm Model

Dental caries is the most common chronic disease worldwide. It is characterized by the demineralization of tooth enamel caused by acid produced by cariogenic dental bacteria growing on tooth surfaces, termed bacterial biofilms. Cariogenesis is a complex biological process that is influence by multiple factors and is not attributed to a sole causative agent. Instead, caries is associated with multispecies microbial biofilm communities composed of some bacterial species that directly influence the development of a caries lesion and other species that are seemingly benign but must contribute to the community in an uncharacterized way. Clinical analysis of dental caries and its microbial populations is challenging due to many factors including low sensitivity of clinical measurement tools, variability in saliva chemistry, and variation in the microbiota. Our laboratory has developed an in vitro anaerobic biofilm model for dental carries to facilitate both clinical and basic research-based analyses of the multispecies dynamics and individual factors that contribute to cariogenicity. The rational for development of this system was to improve upon the current models that lack key elements. This model places an emphasis on physiological relevance and ease of maintenance and reproducibility. The uniqueness of the model is based on integrating four critical elements: 1) a biofilm community composed of four distinct and representative species typically associated with dental caries, 2) a semi-defined synthetic growth medium designed to mimic saliva, 3) physiologically relevant biofilm growth substrates, and 4) a novel biofilm reactor device designed to facilitate the maintenance and analysis. Specifically, human tooth sections or hydroxyapatite discs embedded into poly(methyl methacrylate) (PMMA) discs are incubated for an initial 24 hr in a static inverted removable substrate (SIRS) biofilm reactor at 37°C under anaerobic conditions in artificial saliva (CAMM) without sucrose in the presence of 1 X 106 cells/ml of each Actinomyces odontolyticus, Fusobacterium nucleatum, Streptococcus mutans, and Veillonella dispar. During days 2 and 3 the samples are maintained continually in CAMM with various exposures to 0.2% sucrose; all of the discs are transferred into fresh medium every 24 hr. To validate that this model is an appropriate in vitro representation of a caries-associated multispecies biofilm, research aims were designed to test the following overarching hypothesis: an in vitro anaerobic biofilm composed of four species (S. mutans, V. dispar, A. odontolyticus, and F. nucleatum) will form a stable biofilm with a community profile that changes in response to environmental conditions and exhibits a cariogenic potential. For these experiments the biofilms as described above were exposed on days 2 and 3 to either CAMM lacking sucrose (no sucrose), CAMM with 0.2% sucrose (constant sucrose), or were transferred twice a day for 1 hr each time into 0.2% sucrose (intermittent sucrose). Four types of analysis were performed: 1) fluorescence microscopy of biofilms stained with Syto 9 and hexidium idodine to determine the biofilm architecture, 2) quantitative PCR (qPCR) to determine the cell number of each species per cm2, 3) vertical scanning interferometry (VSI) to determine the cariogenic potential of the biofilms, and 4) tomographic pH imaging using radiometric fluorescence microscopy after exposure to pH sensitive nanoparticles to measure the micro-environmental pH. The qualitative and quantitative results reveal the expected dynamics of the community profile when exposed to different sucrose conditions and the cariogenic potential of this in vitro four-species anaerobic biofilm model, thus confirming its usefulness for future analysis of primary and secondary dental caries.

Experimental models for p53, hepatitis B and aflatoxin hepatocarcinogenesis

The major risk factors for liver cancer in Southeast Asia: HBV infection, aflatoxin exposure and p53 expression/mutation, were examined in experimental models. Four groups were examined for development of hepatocellular carcinoma (HCC) with and without neonatal exposure to aflatoxin (AFB$\sb1)$: (Group I.) Transgenic HBsAg mice with one p53 allele. (Group II) Transgenic HBsAg mice with two p53 alleles. (Group III) Non-transgenic litter mates with one p53 allele. (Group IV) Non-transgenic litter mates with two p53 alleles. HCC developed in Group I animals exposed to aflatoxin at an earlier time and were of a higher grade than those seen later in other groups. These results provide an explanation for as to why p53 is a target for deletion and/or mutation in human HCC especially when found in high risk areas where HBV infection and Aflatoxin B1 food contamination is high, and nicely illustrates a synergistic interaction among these three factors. None of the tumors analyzed had loss or mutation in the p53 gene.^ To determine the significance of the specific p53ser249 mutation found in HBV/aflatoxin associated human hepatomas in an in-vivo experimental model using transgenic mice, a two-nucleotide change in the mouse p53 gene at amino acid position 246, which is equivalent to that of 249 in human p53, was introduced. Transgenic mice with mutant p53 controlled by the albumin promoter were generated and shown to express the p53ser246 mutant RNA and protein specifically in liver. Three groups were examined for development of HCC with and without neonatal exposure to aflatoxin: (Group V) Transgenic p53ser246 mice with two p53 alleles. (Group VI) Transgenic p53ser246 mice with one p53 allele. (Group VII) Double transgenic for p53ser246 and HBsAg with two p53 alleles. One hundred percent of male mice with the three risk factors injected with aflatoxin developed high grade liver tumors, compared to 66.6% from group VI and only 14.2% of group V suggesting synergistic interaction between HBsAg and this particular ser246 p53 mutation.^ In order to examine the growth properties of hepatocytes and correlation with p53 loss and/or mutation, cell proliferation and ploidy analysis of liver from normal heterozyous, homozygous null mice and from transgenic mutant p53ser246, mice were studied. Loss of wild-type p53 increased G1/G0 ratios of cells as well as proliferation and decreased cell ploidy. The mutant p53ser246 did not show a significant effect on cell ploidy or proliferation. However a striking 5-10X increase in G1/G0 ratio suggests that this specific mutation specifically induces G0 to G1 transition, which in turn further predisposes hepatocytes to the damaging effect of Aflatoxin. (Abstract shortened by UMI.) ^

Age models, color measurements, and calculated sea surface temperatures of sediment cores from the Bering Sea and the Sea of Okhotsk

Past changes in North Pacific sea surface temperatures and sea-ice conditions are proposed to play a crucial role in deglacial climate development and ocean circulation but are less well known than from the North Atlantic. Here, we present new alkenone-based sea surface temperature records from the subarctic northwest Pacific and its marginal seas (Bering Sea and Sea of Okhotsk) for the time interval of the last 15 kyr, indicating millennial-scale sea surface temperature fluctuations similar to short-term deglacial climate oscillations known from Greenland ice-core records. Past changes in sea-ice distribution are derived from relative percentage of specific diatom groups and qualitative assessment of the IP25 biomarker related to sea-ice diatoms. The deglacial variability in sea-ice extent matches the sea surface temperature fluctuations. These fluctuations suggest a linkage to deglacial variations in Atlantic meridional overturning circulation and a close atmospheric coupling between the North Pacific and North Atlantic. During the Holocene the subarctic North Pacific is marked by complex sea surface temperature trends, which do not support the hypothesis of a Holocene seesaw in temperature development between the North Atlantic and the North Pacific.

Helium isotope ratios and sedimentation rate models of ODP holes

A continuous age model for the brief climate excursion at the Paleocene-Eocene boundary has been constructed by assuming a constant flux of extraterrestrial 3He (3He[ET]) to the seafloor. 3He[ET] measurements from ODP Site 690 provide quantitative evidence for the rapid onset (models indicating extremely rapid release of isotopically light carbon, possibly from seafloor methane hydrate, as the proximal cause of the event. However, the 3He[ET] technique indicates a previously unrecognized and extreme increase in sedimentation rate coincident with the return of climate proxies to pre-event values. The 3He[ET]-based age model thus suggests a far more rapid recovery from the climatic perturbation than previously proposed or predicted on the basis of the modern carbon cycle, and so may indicate additional or accelerated mechanisms of carbon removal from the ocean-atmosphere system during this period. 3He[ET] was also measured at ODP Site 1051 to test the validity of the Site 690 chronology. Comparison of these data sets seems to require removal of several tens of kyr of sediment within the climatic excursion at Site 1051, an observation consistent with sediment structures and previous age modeling efforts. The Site 1051 age model shows a ~30 kyr period in which climate proxies return toward pre-event values, after which they remain invariant for ~80 kyr. If this rise represents the recovery interval identified at Site 690, then the 3HeET-based age models of the two sites are in good agreement. However, alternative interpretations are possible, and work on less disrupted sites is required to evaluate the reliability of the proposed new chronology of the climate excursion. Regardless of these details, this work shows that the 3HeET technique can provide useful independent evidence for the development and testing of astronomically calibrated age models.

Gridded climate data from 5 Global Climate Models (GCM) of the Last Glacial Maximum (LGM) downscaled to 30 arc seconds for Europe, with links to NetCDF files

Studies on the impact of historical, current and future global change require very high-resolution climate data (less or equal 1km) as a basis for modelled responses, meaning that data from digital climate models generally require substantial rescaling. Another shortcoming of available datasets on past climate is that the effects of sea level rise and fall are not considered. Without such information, the study of glacial refugia or early Holocene plant and animal migration are incomplete if not impossible. Sea level at the last glacial maximum (LGM) was approximately 125m lower, creating substantial additional terrestrial area for which no current baseline data exist. Here, we introduce the development of a novel, gridded climate dataset for LGM that is both very high resolution (1km) and extends to the LGM sea and land mask. We developed two methods to extend current terrestrial precipitation and temperature data to areas between the current and LGM coastlines. The absolute interpolation error is less than 1°C and 0.5 °C for 98.9% and 87.8% of all pixels for the first two 1 arc degree distance zones. We use the change factor method with these newly assembled baseline data to downscale five global circulation models of LGM climate to a resolution of 1km for Europe. As additional variables we calculate 19 'bioclimatic' variables, which are often used in climate change impact studies on biological diversity. The new LGM climate maps are well suited for analysing refugia and migration during Holocene warming following the LGM.

Age models and summer sea surface temperature and winter sea ice concentration for the EPILOG-LGM time slice in the Pacific Southern Ocean

Sea surface temperatures and sea-ice extent are the most critical variables to evaluate the Southern Ocean paleoceanographic evolution in relation to the development of the global carbon cycle, atmospheric CO2 variability and ocean-atmosphere circulation. In contrast to the Atlantic and the Indian sectors, the Pacific sector of the Southern Ocean has been insufficiently investigated so far. To cover this gap of information we present diatom-based estimates of summer sea surface temperature (SSST) and winter sea-ice concentration (WSI) from 17 sites in the polar South Pacific to study the Last Glacial Maximum (LGM) at the EPILOG time slice (19,000-23,000 cal. years BP). Applied statistical methods are the Imbrie and Kipp Method (IKM) and the Modern Analog Technique (MAT) to estimate temperature and sea-ice concentration, respectively. Our data display a distinct LGM east-west differentiation in SSST and WSI with steeper latitudinal temperature gradients and a winter sea-ice edge located consistently north of the Pacific-Antarctic Ridge in the Ross sea sector. In the eastern sector of our study area, which is governed by the Amundsen Abyssal Plain, the estimates yield weaker latitudinal SSST gradients together with a variable extended winter sea-ice field. In this sector, sea-ice extent may have reached sporadically the area of the present Subantarctic Front at its maximum LGM expansion. This pattern points to topographic forcing as major controller of the frontal system location and sea-ice extent in the western Pacific sector whereas atmospheric conditions like the Southern Annular Mode and the ENSO affected the oceanographic conditions in the eastern Pacific sector. Although it is difficult to depict the location and the physical nature of frontal systems separating the glacial Southern Ocean water masses into different zones, we found a distinct temperature gradient in latitudes straddled by the modern Southern Subtropical Front. Considering that the glacial temperatures north of this zone are similar to the modern, we suggest that this represents the Glacial Southern Subtropical Front (GSSTF), which delimits the zone of strongest glacial SSST cooling (>4K) to its North. The southern boundary of the zone of maximum cooling is close to the glacial 4°C isotherm. This isotherm, which is in the range of SSST at the modern Antarctic Polar Front (APF), represents a circum-Antarctic feature and marks the northern edge of the glacial Antarctic Circumpolar Current (ACC). We also assume that a glacial front was established at the northern average winter sea ice edge, comparable with the modern Southern Antarctic Circumpolar Current Front (SACCF). During the glacial, this front would be located in the area of the modern APF. The northward deflection of colder than modern surface waters along the South American continent leads to a significant cooling of the glacial Humboldt Current surface waters (4-8K), which affects the temperature regimes as far north as into tropical latitudes. The glacial reduction of ACC temperatures may also result in the significant cooling in the Atlantic and Indian Southern Ocean, thus may enhance thermal differentiation of the Southern Ocean and Antarctic continental cooling. Comparison with temperature and sea ice simulations for the last glacial based on numerical simulations show that the majority of modern models overestimate summer and winter sea ice cover and that there exists few models that reproduce our temperature data rather well.

A multimodal tablet-based interface for designing and reviewing 3D engineering models

The ability to view and interact with 3D models has been happening for a long time. However, vision-based 3D modeling has only seen limited success in applications, as it faces many technical challenges. Hand-held mobile devices have changed the way we interact with virtual reality environments. Their high mobility and technical features, such as inertial sensors, cameras and fast processors, are especially attractive for advancing the state of the art in virtual reality systems. Also, their ubiquity and fast Internet connection open a path to distributed and collaborative development. However, such path has not been fully explored in many domains. VR systems for real world engineering contexts are still difficult to use, especially when geographically dispersed engineering teams need to collaboratively visualize and review 3D CAD models. Another challenge is the ability to rendering these environments at the required interactive rates and with high fidelity. In this document it is presented a virtual reality system mobile for visualization, navigation and reviewing large scale 3D CAD models, held under the CEDAR (Collaborative Engineering Design and Review) project. It’s focused on interaction using different navigation modes. The system uses the mobile device's inertial sensors and camera to allow users to navigate through large scale models. IT professionals, architects, civil engineers and oil industry experts were involved in a qualitative assessment of the CEDAR system, in the form of direct user interaction with the prototypes and audio-recorded interviews about the prototypes. The lessons learned are valuable and are presented on this document. Subsequently it was prepared a quantitative study on the different navigation modes to analyze the best mode to use it in a given situation.

Theoretical Models Based on a Flowchart Approach to Industrial Cluster Policy

This article examined the issue of whether or not the currency exchange rate, country risk, and cooperate tax rate affect decisions of multinational firms to invest in industrial clusters. First, if the exchange rate between a multinational company in an industry of diminishing returns to scale and a developing country is appreciated, then production in the developing country should increase. Second, if the investment period becomes longer, the currency exchange rate of a multinational company's country should be revalued more in order for it to further invest in the developing country. Third, if the investment period becomes longer, the developing country's risk should become less. Fourth, compensation for the developing country's high risk can be made by lowering its corporate tax rate.

Transport Development and the Evolution of Economic Geography

In this paper, based on the recent advances in the new economic geography (e.g., Fujita, Krugman and Venables [12]), we analyze impacts of transport costs on the spatial patterns of economic agglomeration. We first identify prototypes from the existing models, and explain the mechanism of how transport costs influence the balance between economic forces of agglomeration and dispersion. We then investigate the transformation of the agglomeration/dispersion patterns given gradually decreasing transport costs for different goods.

On the Evolution of the Spatial Economy with Multi-unit/Multi-plant Firms: The Impact of IT Development

This paper examines how the decline of communication costs between management and production facilities within firms and the decrease in trade costs of manufactured goods affect the spatial organization of a two-region economy with multi-unit/multi-plant firms. The development of information technology decreases the costs of communication and trade costs. Thus, the fragmentation of firms is promoted. Our result indicates that, with decreasing communication costs, firms producing low trade-cost products (such as consumer electronics) tend to concentrate their manufacturing plants in low wage countries. In contrast, firms producing high trade-cost products (such as automobiles) tend to have multiple plants serving to segmented markets, even in the absence of wage differentials.

Infrastructure (Rural Road) Development and Poverty Alleviation in Lao PDR

Rural road in Lao PDR defined as connecting road from village to main road, where it will lead them to market and access to other economic and social service facilities. However, due to mostly rural people accustom with subsistence farming, connecting road seems less important for rural people as their main farming produce is for own consumption rather than markets. After the introduction and implementation of New Economic Mechanism (NEM) since 1986, many rural villages have gradually developed and integrated into market system where people have significantly changed their livelihood with a better system. This progress has significantly contributed in improving income earning of people, better living standard and reduce poverty. The paper aims to illustrate the significant of rural road as connecting road from village to markets or a market access approach of farm produces. It also demonstrates through which approach, rural farmers/people could improve their income earning, develop their farming system, living standard and reduce poverty.

Input-Output Based Economic Impact Evaluation System for Small City Development: A Case Study on Saemangeum's Flux City Design

The paper aims to develop a quasi-dynamic interregional input-output model for evaluating the macro-economic impacts of small city development. The features of the model are summarized as follows: (1) the consumption expenditure of households is regarded as an endogenous variable, (2) the technological change is determined by the change of industrial Location Quotient caused by firm's investment activities. (3) a strong feedback function between the city design and the economic analysis is provided. For checking the performance of the model, Saemangeum's Flux City Design Plan is used as the simulation target in our paper.