STATISTICAL METHODS FOR RARE AND COMMON VARIANT ASSOCIATION STUDIES

Complex human diseases are a major challenge for biological research. The goal of my research is to develop effective methods for biostatistics in order to create more opportunities for the prevention and cure of human diseases. This dissertation proposes statistical technologies that have the ability of being adapted to sequencing data in family-based designs, and that account for joint effects as well as gene-gene and gene-environment interactions in the GWA studies. The framework includes statistical methods for rare and common variant association studies. Although next-generation DNA sequencing technologies have made rare variant association studies feasible, the development of powerful statistical methods for rare variant association studies is still underway. Chapter 2 demonstrates two adaptive weighting methods for rare variant association studies based on family data for quantitative traits. The results show that both proposed methods are robust to population stratification, robust to the direction and magnitude of the effects of causal variants, and more powerful than the methods using weights suggested by Madsen and Browning [2009]. In Chapter 3, I extended the previously proposed test for Testing the effect of an Optimally Weighted combination of variants (TOW) [Sha et al., 2012] for unrelated individuals to TOW &ndash F, TOW for Family &ndash based design. Simulation results show that TOW &ndash F can control for population stratification in wide range of population structures including spatially structured populations, is robust to the directions of effect of causal variants, and is relatively robust to percentage of neutral variants. In GWA studies, this dissertation consists of a two &ndash locus joint effect analysis and a two-stage approach accounting for gene &ndash gene and gene &ndash environment interaction. Chapter 4 proposes a novel two &ndash stage approach, which is promising to identify joint effects, especially for monotonic models. The proposed approach outperforms a single &ndash marker method and a regular two &ndash stage analysis based on the two &ndash locus genotypic test. In Chapter 5, I proposed a gene &ndash based two &ndash stage approach to identify gene &ndash gene and gene &ndash environment interactions in GWA studies which can include rare variants. The two &ndash stage approach is applied to the GAW 17 dataset to identify the interaction between KDR gene and smoking status.

A NATURALISTIC COMPUTATIONAL MODEL OF HUMAN BEHAVIOR IN NAVIGATION AND SEARCH TASKS

Planning, navigation, and search are fundamental human cognitive abilities central to spatial problem solving in search and rescue, law enforcement, and military operations. Despite a wealth of literature concerning naturalistic spatial problem solving in animals, literature on naturalistic spatial problem solving in humans is comparatively lacking and generally conducted by separate camps among which there is little crosstalk. Addressing this deficiency will allow us to predict spatial decision making in operational environments, and understand the factors leading to those decisions. The present dissertation is comprised of two related efforts, (1) a set of empirical research studies intended to identify characteristics of planning, execution, and memory in naturalistic spatial problem solving tasks, and (2) a computational modeling effort to develop a model of naturalistic spatial problem solving. The results of the behavioral studies indicate that problem space hierarchical representations are linear in shape, and that human solutions are produced according to multiple optimization criteria. The Mixed Criteria Model presented in this dissertation accounts for global and local human performance in a traditional and naturalistic Traveling Salesman Problem. The results of the empirical and modeling efforts hold implications for basic and applied science in domains such as problem solving, operations research, human-computer interaction, and artificial intelligence.

Understanding "Just Enough" Computer Users: Motivation Style and Proficiency

Among daily computer users who are proficient, some are flexible at accomplishing unfamiliar tasks on their own and others have difficulty. Software designers and evaluators involved with Human Computer Interaction (HCI) should account for any group of proficient daily users that are shown to stumble over unfamiliar tasks. We define "Just Enough" (JE) users as proficient daily computer users with predominantly extrinsic motivation style who know just enough to get what they want or need from the computer. We hypothesize that JE users have difficulty with unfamiliar computer tasks and skill transfer, whereas intrinsically motivated daily users accomplish unfamiliar tasks readily. Intrinsic motivation can be characterized by interest, enjoyment, and choice and extrinsic motivation is externally regulated. In our study we identified users by motivation style and then did ethnographic observations. Our results confirm that JE users do have difficulty accomplishing unfamiliar tasks on their own but had fewer problems with near skill transfer. In contrast, intrinsically motivated users had no trouble with unfamiliar tasks nor with near skill transfer. This supports our assertion that JE users know enough to get routine tasks done and can transfer that knowledge, but become unproductive when faced with unfamiliar tasks. This study combines quantitative and qualitative methods. We identified 66 daily users by motivation style using an inventory adapted from Deci and Ryan (Ryan and Deci 2000) and from Guay, Vallerand, and Blanchard (Guay et al. 2000). We used qualitative ethnographic methods with a think aloud protocol to observe nine extrinsic users and seven intrinsic users. Observation sessions had three customized phases where the researcher directed the participant to: 1) confirm the participant's proficiency; 2) test the participant accomplishing unfamiliar tasks; and 3) test transfer of existing skills to unfamiliar software.

Driver Safety in Far-side and Far-oblique Crashes: A Study of Patrol Vehicles in the United States of America

The dissertation titled "Driver Safety in Far-side and Far-oblique Crashes" presents a novel approach to assessing vehicle cockpit safety by integrating Human Factors and Applied Mechanics. The methodology of this approach is aimed at improving safety in compact mobile workspaces such as patrol vehicle cockpits. A statistical analysis performed using Michigan state's traffic crash data to assess various contributing factors that affect the risk of severe driver injuries showed that the risk was greater for unrestrained drivers (OR=3.38, p<0.0001) and for incidents involving front and far-side crashes without seatbelts (OR=8.0 and 23.0 respectively, p<0.005). Statistics also showed that near-side and far-side crashes pose similar threat to driver injury severity. A Human Factor survey was conducted to assess various Human-Machine/Human-Computer Interaction aspects in patrol vehicle cockpits. Results showed that tasks requiring manual operation, especially the usage of laptop, would require more attention and potentially cause more distraction. A vehicle survey conducted to evaluate ergonomics-related issues revealed that some of the equipment was in airbag deployment zones. In addition, experiments were conducted to assess the effects on driver distraction caused by changing the position of in-car accessories. A driving simulator study was conducted to mimic HMI/HCI in a patrol vehicle cockpit (20 subjects, average driving experience = 5.35 years, s.d. = 1.8). It was found that the mounting locations of manual tasks did not result in a significant change in response times. Visual displays resulted in response times less than 1.5sec. It can also be concluded that the manual task was equally distracting regardless of mounting positions (average response time was 15 secs). Average speeds and lane deviations did not show any significant results. Data from 13 full-scale sled tests conducted to simulate far-side impacts at 70 PDOF and 40 PDOF was used to analyze head injuries and HIC/AIS values. It was found that accelerations generated by the vehicle deceleration alone were high enough to cause AIS 3 - AIS 6 injuries. Pretensioners could mitigated injuries only in 40 PDOF (oblique) impacts but are useless in 70 PDOF impacts. Seat belts were ineffective in protecting the driver's head from injuries. Head would come in contact with the laptop during a far-oblique (40 PDOF) crash and far-side door for an angle-type crash (70 PDOF). Finite Element analysis head-laptop impact interaction showed that the contact velocity was the most crucial factor in causing a severe (and potentially fatal) head injury. Results indicate that no equipment may be mounted in driver trajectory envelopes. A very narrow band of space is left in patrol vehicles for installation of manual-task equipment to be both safe and ergonomic. In case of a contact, the material stiffness and damping properties play a very significant role in determining the injury outcome. Future work may be done on improving the interiors' material properties to better absorb and dissipate kinetic energy of the head. The design of seat belts and pretensioners may also be seen as an essential aspect to be further improved.

An Experience-Driven Pedagogy for the Instruction of Software Testing in Computer Science

In the realm of computer programming, the experience of writing a program is used to reinforce concepts and evaluate ability. This research uses three case studies to evaluate the introduction of testing through Kolb's Experiential Learning Model (ELM). We then analyze the impact of those testing experiences to determine methods for improving future courses. The first testing experience that students encounter are unit test reports in their early courses. This course demonstrates that automating and improving feedback can provide more ELM iterations. The JUnit Generation (JUG) tool also provided a positive experience for the instructor by reducing the overall workload. Later, undergraduate and graduate students have the opportunity to work together in a multi-role Human-Computer Interaction (HCI) course. The interactions use usability analysis techniques with graduate students as usability experts and undergraduate students as design engineers. Students get experience testing the user experience of their product prototypes using methods varying from heuristic analysis to user testing. From this course, we learned the importance of the instructors role in the ELM. As more roles were added to the HCI course, a desire arose to provide more complete, quality assured software. This inspired the addition of unit testing experiences to the course. However, we learned that significant preparations must be made to apply the ELM when students are resistant. The research presented through these courses was driven by the recognition of a need for testing in a Computer Science curriculum. Our understanding of the ELM suggests the need for student experience when being introduced to testing concepts. We learned that experiential learning, when appropriately implemented, can provide benefits to the Computer Science classroom. When examined together, these course-based research projects provided insight into building strong testing practices into a curriculum.

VISUAL-INERTIAL INTEGRATION FOR HUMAN MOTION TRACKING AND NAVIGATION IN FREE-LIVING ENVIRONMENTS

The aging population has become a burning issue for all modern societies around the world recently. There are two important issues existing now to be solved. One is how to continuously monitor the movements of those people having suffered a stroke in natural living environment for providing more valuable feedback to guide clinical interventions. The other one is how to guide those old people effectively when they are at home or inside other buildings and to make their life easier and convenient. Therefore, human motion tracking and navigation have been active research fields with the increasing number of elderly people. However, motion capture has been extremely challenging to go beyond laboratory environments and obtain accurate measurements of human physical activity especially in free-living environments, and navigation in free-living environments also poses some problems such as the denied GPS signal and the moving objects commonly presented in free-living environments. This thesis seeks to develop new technologies to enable accurate motion tracking and positioning in free-living environments. This thesis comprises three specific goals using our developed IMU board and the camera from the imaging source company: (1) to develop a robust and real-time orientation algorithm using only the measurements from IMU; (2) to develop a robust distance estimation in static free-living environments to estimate people’s position and navigate people in static free-living environments and simultaneously the scale ambiguity problem, usually appearing in the monocular camera tracking, is solved by integrating the data from the visual and inertial sensors; (3) in case of moving objects viewed by the camera existing in free-living environments, to firstly design a robust scene segmentation algorithm and then respectively estimate the motion of the vIMU system and moving objects. To achieve real-time orientation tracking, an Adaptive-Gain Orientation Filter (AGOF) is proposed in this thesis based on the basic theory of deterministic approach and frequency-based approach using only measurements from the newly developed MARG (Magnet, Angular Rate, and Gravity) sensors. To further obtain robust positioning, an adaptive frame-rate vision-aided IMU system is proposed to develop and implement fast vIMU ego-motion estimation algorithms, where the orientation is estimated in real time from MARG sensors in the first step and then used to estimate the position based on the data from visual and inertial sensors. In case of the moving objects viewed by the camera existing in free-living environments, a robust scene segmentation algorithm is firstly proposed to obtain position estimation and simultaneously the 3D motion of moving objects. Finally, corresponding simulations and experiments have been carried out.