Towards the prediction of mutations in genomic sequences

Bio-systems are inherently complex information processing systems. Furthermore, physiological complexities of biological systems limit the formation of a hypothesis in terms of behavior and the ability to test hypothesis. More importantly the identification and classification of mutation in patients are centric topics in today's cancer research. Next generation sequencing (NGS) technologies can provide genome-wide coverage at a single nucleotide resolution and at reasonable speed and cost. The unprecedented molecular characterization provided by NGS offers the potential for an individualized approach to treatment. These advances in cancer genomics have enabled scientists to interrogate cancer-specific genomic variants and compare them with the normal variants in the same patient. Analysis of this data provides a catalog of somatic variants, present in tumor genome but not in the normal tissue DNA. In this dissertation, we present a new computational framework to the problem of predicting the number of mutations on a chromosome for a certain patient, which is a fundamental problem in clinical and research fields. We begin this dissertation with the development of a framework system that is capable of utilizing published data from a longitudinal study of patients with acute myeloid leukemia (AML), who's DNA from both normal as well as malignant tissues was subjected to NGS analysis at various points in time. By processing the sequencing data at the time of cancer diagnosis using the components of our framework, we tested it by predicting the genomic regions to be mutated at the time of relapse and, later, by comparing our results with the actual regions that showed mutations (discovered at relapse time). We demonstrate that this coupling of the algorithm pipeline can drastically improve the predictive abilities of searching a reliable molecular signature. Arguably, the most important result of our research is its superior performance to other methods like Radial Basis Function Network, Sequential Minimal Optimization, and Gaussian Process. In the final part of this dissertation, we present a detailed significance, stability and statistical analysis of our model. A performance comparison of the results are presented. This work clearly lays a good foundation for future research for other types of cancer.^

Valued occupational roles and life satisfaction among south Florida HIV-infected and non-infected homosexual males: An exploratory study

A study was conducted in order to describe and understand the occupational role behavior of gay men with particular interest on understanding the impact of an HIV diagnosis on their roles and life satisfaction. A 137-item questionnaire was developed for this study and distributed through various gay community groups in south Florida. The process resulted in ranked description of 24 valued occupational roles of gay men (n = 80) along with a general understanding of potential shifts that may occur in those roles as a result of becoming infected with HIV. The study concludes that a diagnosis of HIV infection impacts gay men both by altering their value for particular roles and by darkening the images they hold of their future. The study also identified key factors which may contribute to the greater life satisfaction of gay men including greater confidence in personal knowledge of HIV, a more optimistic outlook an life, the use of stronger coping styles, and perceiving stronger social support and lower stress. ^

The nitrate to ammonia and ceramic (NAC) process for the denitration and immobilization of low-level radioactive liquid waste (LLW)

Hazardous radioactive liquid waste is the legacy of more than 50 years of plutonium production associated with the United States' nuclear weapons program. It is estimated that more than 245,000 tons of nitrate wastes are stored at facilities such as the single-shell tanks (SST) at the Hanford Site in the state of Washington, and the Melton Valley storage tanks at Oak Ridge National Laboratory (ORNL) in Tennessee. In order to develop an innovative, new technology for the destruction and immobilization of nitrate-based radioactive liquid waste, the United State Department of Energy (DOE) initiated the research project which resulted in the technology known as the Nitrate to Ammonia and Ceramic (NAC) process. However, inasmuch as the nitrate anion is highly mobile and difficult to immobilize, especially in relatively porous cement-based grout which has been used to date as a method for the immobilization of liquid waste, it presents a major obstacle to environmental clean-up initiatives. Thus, in an effort to contribute to the existing body of knowledge and enhance the efficacy of the NAC process, this research involved the experimental measurement of the rheological and heat transfer behaviors of the NAC product slurry and the determination of the optimal operating parameters for the continuous NAC chemical reaction process. Test results indicate that the NAC product slurry exhibits a typical non-Newtonian flow behavior. Correlation equations for the slurry's rheological properties and heat transfer rate in a pipe flow have been developed; these should prove valuable in the design of a full-scale NAC processing plant. The 20-percent slurry exhibited a typical dilatant (shear thickening) behavior and was in the turbulent flow regime due to its lower viscosity. The 40-percent slurry exhibited a typical pseudoplastic (shear thinning) behavior and remained in the laminar flow regime throughout its experimental range. The reactions were found to be more efficient in the lower temperature range investigated. With respect to leachability, the experimental final NAC ceramic waste form is comparable to the final product of vitrification, the technology chosen by DOE to treat these wastes. As the NAC process has the potential of reducing the volume of nitrate-based radioactive liquid waste by as much as 70 percent, it not only promises to enhance environmental remediation efforts but also effect substantial cost savings. ^

Comparative analysis of a moderating and mediating model of stress, appraisal, and coping in Hispanic and non-Hispanic Alzheimer's disease caregivers

This dissertation utilizes a cross-sectional study to examine the phenomenon of caregiving within a theoretically grounded stress, appraisal, and coping model. Hispanic and non-Hispanic caregivers were studied to examine the factors associated with variance in caregiver appraisal, coping, and outcomes of caregiving strain (depression and somatic complaints) and caregiving gain (life satisfaction, mastery, and personal gain). A purposive sampling strategy was used to recruit 204 Alzheimer's disease caregivers in South Florida. A self-report questionnaire was used to collect demographic data, and to measure stress, appraisal, coping, and psychological well-being of caregivers. Regression equations were developed to compare moderating and mediating models of appraisal and coping. Emotion-focused coping skills were found to significantly moderate the effects of stress (F [1,195] = 4.62, p < .05), explaining approximately 21% of the variance in satisfaction was found to moderate the effects of stress (F [1,195] = 7.09; p < .05), explaining approximately 27% of the variance in personal gain and approximately 8% of the variance in life satisfaction (F [1,195] = 4.14; p < .05). Appraisal of Burden was found to significantly mediate the effects of stress, explaining approximately 30% of the variance in somatic complaints (F [1,196] = 31.60; p < .001) and 32% of the variance in depression (F [1,196] = 38.18; p < .001). The results of the analyses indicate that appraisal and coping skills are important variables in the stress process. The results of this study underscore the importance of accounting for positive and negative outcomes in providing a fuller understanding of the stress, appraisal and coping process of Alzheimer's Disease caregivers. ^

Parent involvement on school advisory councils: A process evaluation at the middle school level

Increasing parental involvement was made an important goal for all Florida schools in educational reform legislation in the 1990's. A forum for this input was established and became known as the School Advisory Council (SAC). To demonstrate the importance of process and inclusion, a south Florida school district and its local teacher's union agreed on the following five goals for SACs: (a) to foster an environment of professional collaboration among all stakeholders, (b) to assist in the preparation and evaluation of the school improvement plan, (c) to address all state and district goals, (d) to serve as the avenue for authentic and representative input from all stakeholders, and (e) to ensure the continued existence of the consensus-building process on all issues related to the school's instructional program. ^ The purpose of this study was to determine to what extent and in what ways the parent members of one south Florida middle school's SAC achieved the five district goals during its first three years of implementation. The primary participants were 16 parents who served as members of the SAC, while 16 non-parent members provided perspective on parent involvement as “outside sources.” Being qualitative by design, factors such as school climate, leadership styles, and the quality of parental input were described from data collected from four sources: parent interviews, a questionnaire of non-parents, researcher observations, and relevant documents. A cross-case analysis of all data informed a process evaluation that described the similarities and differences of intended and observed outcomes of parent involvement from each source using Stake's descriptive matrix model. A formative evaluation of the process compared the observed outcomes with standards set for successful SACs, such as the district's five goals. ^ The findings indicated that parents elected to the SACs did not meet the intended goals set by the state and district. The school leadership did not foster an environment of professional collaboration and authentic decision-making for parents and other stakeholders. The overall process did not include consensus-building, and there was little if any input by parents on school improvement and other important issues relating to the instructional program. Only two parents gave the SAC a successful rating for involving parents in the decision-making process. Although compliance was met in many of the procedural transactions of the SAC, the reactions of parents to their perceived role and influence often reflected feelings of powerlessness and frustration with a process that many thought lacked meaningfulness and productivity. Two conclusions made from this study are as follows: (a) that the role of the principal in the collaborative process is pivotal, and (b) that the normative-re-educative approach to change would be most appropriate for SACs. ^

Statistical analysis and optimal classification of blood cell populations using Gaussian distributions

This dissertation develops a new figure of merit to measure the similarity (or dissimilarity) of Gaussian distributions through a novel concept that relates the Fisher distance to the percentage of data overlap. The derivations are expanded to provide a generalized mathematical platform for determining an optimal separating boundary of Gaussian distributions in multiple dimensions. Real-world data used for implementation and in carrying out feasibility studies were provided by Beckman-Coulter. It is noted that although the data used is flow cytometric in nature, the mathematics are general in their derivation to include other types of data as long as their statistical behavior approximate Gaussian distributions. ^ Because this new figure of merit is heavily based on the statistical nature of the data, a new filtering technique is introduced to accommodate for the accumulation process involved with histogram data. When data is accumulated into a frequency histogram, the data is inherently smoothed in a linear fashion, since an averaging effect is taking place as the histogram is generated. This new filtering scheme addresses data that is accumulated in the uneven resolution of the channels of the frequency histogram. ^ The qualitative interpretation of flow cytometric data is currently a time consuming and imprecise method for evaluating histogram data. This method offers a broader spectrum of capabilities in the analysis of histograms, since the figure of merit derived in this dissertation integrates within its mathematics both a measure of similarity and the percentage of overlap between the distributions under analysis. ^

Why and how multinational corporations influence the trade negotiation process in Latin America

This thesis examines two research questions: (1) Why do Multinational Enterprises (MNEs) try to influence trade negotiations in the Latin American context? and (2) How do MNEs influence the trade negotiation process in Latin America? The results show that the MNE's main reasons for participation are: (1) to gain market access and, specifically, to reduce tariff and non-tariff barriers; (2) to create a beneficial regulatory environment for the MNE; and (3) to set the rules of the game by influencing the business environment in which its industry or its specific company is required to operate. The main approaches reported by the interviewees as to how MNEs participate are: (1) the MNE directly lobbies domestic government officials, principally the United States Trade Representative office; (2) a business, trade or industry association lobbies domestic government officials on the MNE's behalf; and (3) the MNE lobbies Congress.

Use of the DACUM process in the identification and verification of competencies for the medical administrative assistant

Medicine has changed in recent years. Medicare will all of its rules and regulations, worker's compensation laws, managed care and the trend toward more and larger group practices all contributed to the creation of an extremely structured regulatory environment which in turn demanded highly trained medical administrative assistants.^ The researcher noted three primary problems in the identification of competencies for the medical administrative assistant position: A lack of curricula, diverse roles, and a complex environment which has undergone radical change in recent years and will continue to evolve. Therefore, the purposes of the study were to use the DACUM process to develop a relevant list of competencies required by the medical administrative assistant practicing in physicians' offices in South Florida; determine the rank order of importance of each competency using a scale of one to five; cross-validate the DACUM group scores with a second population who did not participate in the DACUM process; and establish a basis for a curriculum framework for an occupational program.^ The DACUM process of curriculum development was selected because it seemed best suited to the need to develop a list of competencies for an occupation for which no programs existed. A panel of expert medical office administrative staff was selected to attend a 2-day workshop to describe their jobs in great detail. The panel, led by a trained facilitator, listed major duties and the respective tasks of their job. Brainstorming techniques were used to develop a consensus.^ Based upon the DACUM workshop, a survey was developed listing the 8 major duties and 71 tasks identified by the panel. The survey was mailed to the DACUM group and a second, larger population who did not participate in the DACUM. The survey results from the two groups were then compared. The non-DACUM group validated all but 3 of the 71 tasks listed by the DACUM panel. Because the three tasks were rated by the second group as at least "somewhat important" and rated "very important" by the DACUM group, the researcher recommended the inclusion of all 71 tasks in program development for this occupation. ^

Evaluating the effects of initial participation in the group therapy process

Although the effectiveness of group therapy has been highlighted, the underlying mechanisms involved in the group process have been under studied. The purpose of this study is twofold. First, the current study utilized an outcome mediation model to examine whether initial level of participation in the intervention (Control/No intervention, non-participatory, participatory) predicted change in Identity Conflict Resolution (IDCR), Personal Expressiveness (PE) and Informational Identity Style (INFO) at posttest, and Internalizing (INT) and Externalizing (EXT) behaviors at post and follow-up assessment. Secondly, the current study examined whether relationships between variables varied as a result of group differences in initial participation. The study utilized an archival sample of 234 high school students, ages 14 to 18, who participated in the Changing Lives Program of the Youth Development Project (YDP) since 2003. Structural equation modeling (SEM) was used to examine differences in direct effects as a result of initial participation on an outcome meditational model. To further analyze this model, SEM was utilized to conduct a multi-group solution to examine whether group differences based on level of initial participation in the variables^

Discipline And Due Process In The Workplace

In the article - Discipline and Due Process in the Workplace – by Edwin B. Dean, Assistant Professor, the School of Hospitality Management at Florida International University, Assistant Professor Dean prefaces his article with the statement: “Disciplining employees is often necessary for the maintenance of an effective operation. The author discusses situations which require discipline and methods of handling employees, including the need for rules and due process.” In defining what constitutes appropriate discipline and what doesn’t, Dean says, “Fair play is the keystone to discipline in the workplace. Discrimination, caprice, favoritism, and erratic and inconsistent discipline can be costly and harmful to employee relations, and often are a violation of law.” Violation of law is a key phrase in this statement. The author offers a short primer on tact in regard to disciplining an employee. “Discipline must be tailored to the individual,” Dean offers a pearl of wisdom. “A frown for one can cause a tearful outbreak; another employee may need the proverbial two-by-four in order to get his attention.” This is a perceptive comment, indeed, and one in which most would concede but not all would follow. Dean presents a simple outline for steps in the disciplinary process by submitting this suggestion for your approval: “The steps in the disciplinary process begin perhaps with a friendly warning or word of advice. The key here is friendly,” Dean declares. “It could progress to an oral or written reprimand, followed by a disciplinary layoff, terminating in that equivalent of capital punishment, discharge.” Ouch [!]; in order from lenient to strident. Dean suggests these steps are necessary in order to maintain decorum in the workplace. Assistant Professor Dean references the Weingarter Rule. It is a rule that although significant, most employees, at least non-union employees, don’t know is in their quiver. “If an interview is likely to result in discipline, the employee is entitled to have a representative present, whether a union is involved or not,” the rule states. “The employer is not obligated to inform the employee of the rule, but he is obligated to honor the employee's request, if made,” Dean explains. Dean makes an interesting point by revealing that a termination often reflects as much on the institution as it does the employee suffering the termination. The author goes on to list several infractions that could warrant an employee disciplinary action, with possible approaches toward each. Dean also cautions against capricious disciplinary action; if not handled properly a discipline could and can result in a lawsuit against the institution itself.

Medical advice and diabetes self-management reported by Mexican-American, Black- and White-non-Hispanic adults across the United States

Background Diabetes has reached epidemic proportions in the United States, particularly among minorities, and if improperly managed can lead to medical complications and death. Healthcare providers play vital roles in communicating standards of care, which include guidance on diabetes self-management. The background of the client may play a role in the patient-provider communication process. The aim of this study was to determine the association between medical advice and diabetes self care management behaviors for a nationally representative sample of adults with diabetes. Moreover, we sought to establish whether or not race/ethnicity was a modifier for reported medical advice received and diabetes self-management behaviors. Methods We analyzed data from 654 adults aged 21 years and over with diagnosed diabetes [130 Mexican-Americans; 224 Black non-Hispanics; and, 300 White non-Hispanics] and an additional 161 with 'undiagnosed diabetes' [N = 815(171 MA, 281 BNH and 364 WNH)] who participated in the National Health and Nutrition Examination Survey (NHANES) 2007-2008. Logistic regression models were used to evaluate whether medical advice to engage in particular self-management behaviors (reduce fat or calories, increase physical activity or exercise, and control or lose weight) predicted actually engaging in the particular behavior and whether the impact of medical advice on engaging in the behavior differed by race/ethnicity. Additional analyses examined whether these relationships were maintained when other factors potentially related to engaging in diabetes self management such as participants' diabetes education, sociodemographics and physical characteristics were controlled. Sample weights were used to account for the complex sample design. Results Although medical advice to the patient is considered a standard of care for diabetes, approximately one-third of the sample reported not receiving dietary, weight management, or physical activity self-management advice. Participants who reported being given medical advice for each specific diabetes self-management behaviors were 4-8 times more likely to report performing the corresponding behaviors, independent of race. These results supported the ecological model with certain caveats. Conclusions Providing standard medical advice appears to lead to diabetes self-management behaviors as reported by adults across the United States. Moreover, it does not appear that race/ethnicity influenced reporting performance of the standard diabetes self-management behavior. Longitudinal studies evaluating patient-provider communication, medical advice and diabetes self-management behaviors are needed to clarify our findings.

The role of overseas Chinese investment in the emerging countries of Southeast and East Asia: A Confucian model of the foreign direct investment decision-making process using factors unconsidered in the West

The purpose of this study was to gain a better understanding of the foreign direct investment location decision making process through the examination of non-Western investors and their investment strategies in non-traditional markets. This was accomplished through in-depth personal interviews with 50 Overseas Chinese business owners and executives in several different industries from Hong Kong, Singapore, Taiwan, Malaysia, and Thailand about 97 separate investment projects in Southeast and East Asia, including The Philippines, Malaysia, Hong Kong, Singapore, Vietnam, India, Pakistan, South Korea, Australia, Indonesia, Cambodia, Thailand, Burma, Taiwan, and Mainland China.^ Traditional factors utilized in Western models of the foreign direct investment decision making process are reviewed, as well as literature on Asian management systems and the current state of business practices in emerging countries of Southeast and East Asia. Because of the lack of institutionalization in these markets and the strong influences of Confucian and patriarchal value systems on the Overseas Chinese, it was suspected that while some aspects of Western rational economic models of foreign direct investment are utilized, these models are insufficient in this context, and thus are not fully generalizable to the unique conditions of the Overseas Chinese business network in the region without further modification.^ Thus, other factors based on a Confucian value system need to be integrated into these models. Results from the analysis of structured interviews suggest Overseas Chinese businesses rely more heavily on their network and traditional Confucian values than rational economic factors when making their foreign direct investment location decisions in emerging countries in Asia. This effect is moderated by the firm's industry and the age of the firm's owners. ^

Fabrication of Dense Non-Circular Nanomagnetic Device Arrays Using Self-Limiting Low-Energy Glow-Discharge Processing

We describe a low-energy glow-discharge process using reactive ion etching system that enables non-circular device patterns, such as squares or hexagons, to be formed from a precursor array of uniform circular openings in polymethyl methacrylate, PMMA, defined by electron beam lithography. This technique is of a particular interest for bit-patterned magnetic recording medium fabrication, where close packed square magnetic bits may improve its recording performance. The process and results of generating close packed square patterns by self-limiting low-energy glow-discharge are investigated. Dense magnetic arrays formed by electrochemical deposition of nickel over self-limiting formed molds are demonstrated.

Medical Advice and Diabetes Self-Management Reported by Mexican-American, Black- and White-Non-Hispanic Adults Across the United States

Background: Diabetes has reached epidemic proportions in the United States, particularly among minorities, and if improperly managed can lead to medical complications and death. Healthcare providers play vital roles in communicating standards of care, which include guidance on diabetes self-management. The background of the client may play a role in the patient-provider communication process. The aim of this study was to determine the association between medical advice and diabetes self care management behaviors for a nationally representative sample of adults with diabetes. Moreover, we sought to establish whether or not race/ethnicity was a modifier for reported medical advice received and diabetes self-management behaviors. Methods: We analyzed data from 654 adults aged 21 years and over with diagnosed diabetes [130 MexicanAmericans; 224 Black non-Hispanics; and, 300 White non-Hispanics] and an additional 161 with ‘undiagnosed diabetes’ [N = 815(171 MA, 281 BNH and 364 WNH)] who participated in the National Health and Nutrition Examination Survey (NHANES) 2007-2008. Logistic regression models were used to evaluate whether medical advice to engage in particular self-management behaviors (reduce fat or calories, increase physical activity or exercise, and control or lose weight) predicted actually engaging in the particular behavior and whether the impact of medical advice on engaging in the behavior differed by race/ethnicity. Additional analyses examined whether these relationships were maintained when other factors potentially related to engaging in diabetes self management such as participants’ diabetes education, sociodemographics and physical characteristics were controlled. Sample weights were used to account for the complex sample design. Results: Although medical advice to the patient is considered a standard of care for diabetes, approximately onethird of the sample reported not receiving dietary, weight management, or physical activity self-management advice. Participants who reported being given medical advice for each specific diabetes self-management behaviors were 4-8 times more likely to report performing the corresponding behaviors, independent of race. These results supported the ecological model with certain caveats. Conclusions: Providing standard medical advice appears to lead to diabetes self-management behaviors as reported by adults across the United States. Moreover, it does not appear that race/ethnicity influenced reporting performance of the standard diabetes self-management behavior. Longitudinal studies evaluating patient-provider communication, medical advice and diabetes self-management behaviors are needed to clarify our findings.