A Study Of Computational Problems In Computational Biology And Social Networks: Cancer Informatics And Cascade Modelling

It is undoubtedly that everything in this world is related and nothing independently exists. Entities interact together to form groups, resulting in many complex networks. Examples involve functional regulation models of proteins in biology, communities of people within social network. Since complex networks are ubiquitous in daily life, network learning had been gaining momentum in a variety of discipline like computer science, economics and biology. This call for new technique in exploring the structure as well as the interactions of network since it provides insight in understanding how the network works and deepening our knowledge of the subject in hand. For example, uncovering proteins modules helps us understand what causes lead to certain disease and how protein co-regulate each others. Therefore, my dissertation takes on problems in computational biology and social network: cancer informatics and cascade model-ling. In cancer informatics, identifying specific genes that cause cancer (driver genes) is crucial in cancer research. The more drivers identified, the more options to treat the cancer with a drug to act on that gene. However, identifying driver gene is not easy. Cancer cells are undergoing rapid mutation and are compromised in regards to the body\u27s normally DNA repair mechanisms. I employed Markov chain, Bayesian network and graphical model to identify cancer drivers. I utilize heterogeneous sources of information to discover cancer drivers and unlocking the mechanism behind cancer. Above all, I encode various pieces of biological information to form a multi-graph and trigger various Markov chains in it and rank the genes in the aftermath. We also leverage probabilistic mixed graphical model to learn the complex and uncertain relationships among various bio-medical data. On the other hand, diffusion of information over the network had drawn up great interest in research community. For example, epidemiologists observe that a person becomes ill but they can neither determine who infected the patient nor the infection rate of each individual. Therefore, it is critical to decipher the mechanism underlying the process since it validates efforts for preventing from virus infections. We come up with a new modeling to model cascade data in three different scenario

Creating Online Lessons: A Faculty Development Seminar Series

The World Wide Web is being used increasingly to deliver instruction in medical education. Consequently, there is a need to train faculty in developing and implementing online instruction. We developed and implemented a seminar series to teach faculty to create educationally sound, well designed online instruction. Instruction was delivered to 15 participants via a six session seminar on developing web based lessons, supplemented with web-based instruction. First, the participants learned the basics of instructional design via a web based module. They then completed content outlines for their online lessons prior to the first seminar. Lesson development, web site development and the use of a web based instructional shell to implement the online lessons were each taught in two two hour sessions. Eight participants developed online lessons and four actually implemented them. Feedback was mostly positive, with suggestions for improvement. All eight participants who completed the series said they would recommend it to their colleagues. Because a longitudinal workshop type of seminar series requires a large amount of participant time outside of class, a six month seminar series may be too long. It is important at the beginning of the series to help participants select topics suitable for online instruction and to help them narrow their topics. We may change the attendance guidelines so faculty would attend only the session on instructional design and have their staff attend the technical sessions on web site design, HTML editing and online course delivery systems. This would better match the actual practice of faculty designing the instruction and staff developing it

MULTIPLE-OBJECTIVE DECISION MAKING FOR AGROECOSYSTEM MANAGEMENT

Multiple-objective decision making (MODEM) provides an effective framework for integrated resource assessment of agroecosystems. Two elements of integrated assessment are discussed and illustrated: (1) adding noneconomic objectives as constraints in an optimization problem; and (2) evaluating tradeoffs among competing objectives using the efficiency frontier for objectives. These elements are illustrated for a crop farm and watershed in northern Missouri. An interactive, spatial decision support system (ISDSS) makes the MODEM framework accessible to unsophisticated users. A conceptual ISDSS is presented that assesses the socioeconomic, environmental, and ecological consequences of alternative management plans for reducing soil erosion and nonpoint source pollution in agroecosystems. A watershed decision support system based on the ISDSS is discussed.Agribusiness,

The peculiar velocity field: constraining the tilt of the Universe

A large bulk flow, which is in tension with the Lambda Cold Dark Matter ($\Lambda$CDM) cosmological model, has been observed. In this paper, we provide a physically plausible explanation of this bulk flow, based on the assumption that some fraction of the observed dipole in the cosmic microwave background is due to an intrinsic fluctuation, so that the subtraction of the observed dipole leads to a mismatch between the cosmic microwave background (CMB) defined rest frame and the matter rest frame. We investigate a model that takes into account the relative velocity (hereafter the tilted velocity) between the two frames, and develop a Bayesian statistic to explore the likelihood of this tilted velocity. By studying various independent peculiar velocity catalogs, we find that: (1) the magnitude of the tilted velocity $u$ is around 400 km/s, and its direction is close to what is found from previous bulk flow analyses; for most catalogs analysed, u=0 is excluded at about the $2.5 \sigma$ level;(2) constraints on the magnitude of the tilted velocity can result in constraints on the duration of inflation, due to the fact that inflation can neither be too long (no dipole effect) nor too short (very large dipole effect); (3) Under the assumption of a super-horizon isocurvature fluctuation, the constraints on the tilted velocity require that inflation lasts at least 6 e-folds longer (at the 95% confidence interval) than that required to solve the horizon problem. This opens a new window for testing inflation and models of the early Universe from observations of large scale structure.Comment: 7 pages, 7 figures, match the published version in Phys.Rev.

The Struggle for the Supremacy of the Coast : Baseball and Identity in Boothbay Harbor, Maine

During the summer months of the first decade of the twentieth century, the Boothbay Harbor region was invigorated with baseball fever. By 1900, Americans had come to understand baseball as its national game, and Boothbay Harbor discovered and nourished the game in the final decades of the nineteenth century. But as the twentieth century began, baseball became more than a game: it was a business, a spectacle, and an opportunity for inhabitants of the region to define themselves based upon the team they supported

Analysis, Modeling, and Simulation (AMS) Case Studies of Connected and Automated Vehicle (CAV) Implementations Specific to the South Central Region

Connected and automated vehicles (CAVs) offer potentially transformative and far-reaching impacts to the transportation system. However, realized benefits will be directly tied to how well agencies prepare for these technologies. This report documents efforts that support CAV preparatory actions in Louisiana and includes: (1) conducting a stakeholder survey to inform engagement activities to develop strategic partnerships in CAV deployment and (2) conducting crash analyses for deployment scenarios of CAV-based queue warning systems (QWSs). An electronic survey was developed and disseminated to 273 Louisiana organizations. The purpose of the survey was to engage these organizations under the context of CAV planning and gauge their awareness, perception, and viewed importance of planning for CAV technologies. Survey results were clustered in three main groups: Group A—those uninformed of CAV technologies and do not believe they will impact their organization, Group B—those more informed but also do not believe their organization will be impacted, and Group C—those aware, positively perceive, and believe it is important to prepare. Results indicate a strong correlation between the level of awareness and perception of CAV technologies. Low awareness and perception by economic development, freight, and transit groups indicate areas of concern. Survey results were further analyzed utilizing a CAV-specific capability maturity framework, and recommendations were developed to engage stakeholders in planning efforts. A crash analysis was conducted at four proposed locations across Louisiana to determine QWS suitability. The analysis utilized five-year historical crash data and focused on crash rate, severity level, manner of collision, and level of service of safety. Due to overrepresented rear-end crashes, QWSs may be suitable at the Jefferson Parish and West Baton Rouge Parish locations. Each effort was prepared to be general and beneficial to transportation agencies involved in similar CAV activities

Sustainable Entrepreneurship and the Effects of Climate Change

Sustainable entrepreneurship is a field that explores opportunities to exploit market failures in a sustainable manner, particularly when environmental challenges like climate change arise. Entrepreneurship researchers primarily focus on opportunities to mitigate climate change, not opportunities to exploit the effects of climate change. To address this gap, we present a camping case to study the effects of climate change on daily tent and RV sales from January 2007 to October 2016 at a for-profit campsite in the central United States. Findings demonstrate that daily weather and extreme weather (i.e., the operationalization of the effects of climate change) are significantly related to campsite sales dependent on meteorological season and camping type (i.e., tent or RV). There is also a strong weekend effect on sales. Based on our findings, we assert that camping businesses are capable of sustainably (i.e., without increasing camping capacity) exploit improving weather conditions in the focal study region