Comparison of medical and forensic profiling potential of volatile biomarkers from different biological specimens from individuals and across populations

There is limited scientific knowledge on the composition of human odor from different biological specimens and the effect that physiological and psychological health conditions could have on them. There is currently no direct comparison of the volatile organic compounds (VOCs) emanating from different biological specimens collected from healthy individuals as well as individuals with certain diagnosed medical conditions. Therefore the question of matching VOCs present in human odor across various biological samples and across health statuses remains unanswered. The main purpose of this study was to use analytical instrumental methods to compare the VOCs from different biological specimens from the same individual and to compare the populations evaluated in this project. The goals of this study were to utilize headspace solid-phase microextraction gas chromatography mass spectrometry (HS-SPME-GC/MS) to evaluate its potential for profiling VOCs from specimens collected using standard forensic and medical methods over three different populations: healthy group with no diagnosed medical or psychological condition, one group with diagnosed type 2 diabetes, and one group with diagnosed major depressive disorder. The pre-treatment methods of collection materials developed for the study allowed for the removal of targeted VOCs from the sampling kits prior to sampling, extraction and analysis. Optimized SPME-GC/MS conditions has been demonstrated to be capable of sampling, identifying and differentiating the VOCs present in the five biological specimens collected from different subjects and yielded excellent detection limits for the VOCs from buccal swab, breath, blood, and urine with average limits of detection of 8.3 ng. Visual, Spearman rank correlation, and PCA comparisons of the most abundant and frequent VOCs from each specimen demonstrated that each specimen has characteristic VOCs that allow them to be differentiated for both healthy and diseased individuals. Preliminary comparisons of VOC profiles of healthy individuals, patients with type 2 diabetes, and patients with major depressive disorder revealed compounds that could be used as potential biomarkers to differentiate between healthy and diseased individuals. Finally, a human biological specimen compound database has been created compiling the volatile compounds present in the emanations of human hand odor, oral fluids, breath, blood, and urine.

Navigating health sources on the Internet: A mixed-methods examination of online consumer reviews and expert text on psychotropic drugs

Purpose. The Internet has provided an unprecedented opportunity for psychotropic medication consumers, a traditionally silenced group in clinical trial research, to have voice by contributing to the construction of drug knowledge in an immediate, direct manner. Currently, there are no systematic appraisals of the potential of online consumer drug reviews to contribute to drug knowledge. The purpose of this research was to explore the content of drug information on various websites representing themselves as consumer- and expert-constructed, and as a practical consideration, to examine how each source may help and hinder treatment decision-making.^ Methodology. A mixed-methods research strategy utilizing a grounded theory approach was used to analyze drug information on 5 exemplar websites (3 consumer- and 2 expertconstructed) for 2 popularly prescribed psychotropic drugs (escitalopram and quetiapine). A stratified simple random sample was used to select 1,080 consumer reviews from the websites (N=7,114) through February 2009. Text was coded using QDA Miner 3.2 software by Provalis Research. A combination of frequency tables, descriptive excerpts from text, and chi-square tests for association were used throughout analyses.^ Findings. The most frequently mentioned effects by consumers taking either drug were related to psychological/behavioral symptoms and sleep. Consumers reported many of the same effects as found on expert health sites, but provided more descriptive language and situational examples. Expert labels of less serious on certain effects were not congruent with the sometimes tremendous burden described by consumers. Consumers mentioned more than double the themes mentioned in expert text, and demonstrated a diversity and range of discourses around those themes.^ Conclusions. Drug effects from each source were complete relative to the information provided in the other, but each also offered distinct advantages. Expert health sites provided concise summaries of medications’ effects, while consumer reviews had the added advantage of concrete descriptions and greater context. In short, consumer reviews better prepared potential consumers for what it’s like to take psychotropic drugs. Both sources of information benefit clinicians and consumers in making informed treatment-related decisions. Social work practitioners are encouraged to thoughtfully utilize online consumer drug reviews as a legitimate additional source for assisting clients in learning about treatment options.^

The potential role of environmental exposures and genomic signaling in development of central nervous system tumors

The etiology of central nervous system tumors (CNSTs) is mainly unknown. Aside from extremely rare genetic conditions, such as neurofibromatosis and tuberous sclerosis, the only unequivocally identified risk factor is exposure to ionizing radiation, and this explains only a very small fraction of cases. Using meta-analysis, gene networking and bioinformatics methods, this dissertation explored the hypothesis that environmental exposures produce genetic and epigenetic alterations that may be involved in the etiology of CNSTs. A meta-analysis of epidemiological studies of pesticides and pediatric brain tumors revealed a significantly increased risk of brain tumors among children whose mothers had farm-related exposures during pregnancy. A dose response was recognized when this risk estimate was compared to those for risk of brain tumors from maternal exposure to non-agricultural pesticides during pregnancy, and risk of brain tumors among children exposed to agricultural activities. Through meta-analysis of several microarray studies which compared normal tissue to astrocytomas, we were able to identify a list of 554 genes which were differentially expressed in the majority of astrocytomas. Many of these genes have in fact been implicated in development of astrocytoma, including EGFR, HIF-1α, c-Myc, WNT5A, and IDH3A. Reverse engineering of these 554 genes using Bayesian network analysis produced a gene network for each grade of astrocytoma (Grade I-IV), and ‘key genes’ within each grade were identified. Genes found to be most influential to development of the highest grade of astrocytoma, Glioblastoma multiforme (GBM) were: COL4A1, EGFR, BTF3, MPP2, RAB31, CDK4, CD99, ANXA2, TOP2A, and SERBP1. Lastly, bioinformatics analysis of environmental databases and curated published results on GBM was able to identify numerous potential pathways and geneenvironment interactions that may play key roles in astrocytoma development. Findings from this research have strong potential to advance our understanding of the etiology and susceptibility to CNSTs. Validation of our ‘key genes’ and pathways could potentially lead to useful tools for early detection and novel therapeutic options for these tumors.

Hydrogeophysical characterization of anisotropy in the Biscayne Aquifer using geophysical methods

The anisotropy of the Biscayne Aquifer which serves as the source of potable water for Miami-Dade County was investigated by applying geophysical methods. Electrical resistivity imaging, self potential and ground penetration radar techniques were employed in both regional and site specific studies. In the regional study, electrical anisotropy and resistivity variation with depth were investigated with azimuthal square array measurements at 13 sites. The observed coefficient of electrical anisotropy ranged from 1.01 to 1.36. The general direction of measured anisotropy is uniform for most sites and trends W-E or SE-NW irrespective of depth. Measured electrical properties were used to estimate anisotropic component of the secondary porosity and hydraulic anisotropy which ranged from 1 to 11% and 1.18 to 2.83 respectively. 1-D sounding analysis was used to models the variation of formation resistivity with depth. Resistivities decreased from NW (close to the margins of the everglades) to SE on the shores of Biscayne Bay. Porosity calculated from Archie's law, ranged from 18 to 61% with higher values found along the ridge. Higher anisotropy, porosities and hydraulic conductivities were on the Atlantic Coastal Ridge and lower values at low lying areas west of the ridge. The cause of higher anisotropy and porosity is attributed to higher dissolution rates of the oolitic facies of the Miami Formation composing the ridge. The direction of minimum resistivity from this study is similar to the predevelopment groundwater flow direction indicated in published modeling studies. Detailed investigations were carried out to evaluate higher anisotropy at West Perrine Park located on the ridge and Snapper Creek Municipal well field where the anisotropy trend changes with depth. The higher anisotropy is attributed to the presence of solution cavities oriented in the E-SE direction on the ridge. Similarly, the change in hydraulic anisotropy at the well field might be related to solution cavities, the surface canal and groundwater extraction wells.^

Methods for modeling and analyzing concurrent software

Concurrent software executes multiple threads or processes to achieve high performance. However, concurrency results in a huge number of different system behaviors that are difficult to test and verify. The aim of this dissertation is to develop new methods and tools for modeling and analyzing concurrent software systems at design and code levels. This dissertation consists of several related results. First, a formal model of Mondex, an electronic purse system, is built using Petri nets from user requirements, which is formally verified using model checking. Second, Petri nets models are automatically mined from the event traces generated from scientific workflows. Third, partial order models are automatically extracted from some instrumented concurrent program execution, and potential atomicity violation bugs are automatically verified based on the partial order models using model checking. Our formal specification and verification of Mondex have contributed to the world wide effort in developing a verified software repository. Our method to mine Petri net models automatically from provenance offers a new approach to build scientific workflows. Our dynamic prediction tool, named McPatom, can predict several known bugs in real world systems including one that evades several other existing tools. McPatom is efficient and scalable as it takes advantage of the nature of atomicity violations and considers only a pair of threads and accesses to a single shared variable at one time. However, predictive tools need to consider the tradeoffs between precision and coverage. Based on McPatom, this dissertation presents two methods for improving the coverage and precision of atomicity violation predictions: 1) a post-prediction analysis method to increase coverage while ensuring precision; 2) a follow-up replaying method to further increase coverage. Both methods are implemented in a completely automatic tool.

Clean hydrogen production and carbon dioxide capture methods

Fossil fuels constitute a significant fraction of the world's energy demand. The burning of fossil fuels emits huge amounts of carbon dioxide into the atmosphere. Therefore, the limited availability of fossil fuel resources and the environmental impact of their use require a change to alternative energy sources or carriers (such as hydrogen) in the foreseeable future. The development of methods to mitigate carbon dioxide emission into the atmosphere is equally important. Hence, extensive research has been carried out on the development of cost-effective technologies for carbon dioxide capture and techniques to establish hydrogen economy. Hydrogen is a clean energy fuel with a very high specific energy content of about 120MJ/kg and an energy density of 10Wh/kg. However, its potential is limited by the lack of environment-friendly production methods and a suitable storage medium. Conventional hydrogen production methods such as Steam-methane-reformation and Coal-gasification were modified by the inclusion of NaOH. The modified methods are thermodynamically more favorable and can be regarded as near-zero emission production routes. Further, suitable catalysts were employed to accelerate the proposed NaOH-assisted reactions and a relation between reaction yield and catalyst size has been established. A 1:1:1 molar mixture of LiAlH 4, NaNH2 and MgH2 were investigated as a potential hydrogen storage medium. The hydrogen desorption mechanism was explored using in-situ XRD and Raman Spectroscopy. Mesoporous metal oxides were assessed for CO2 capture at both power and non-power sectors. A 96.96% of mesoporous MgO (325 mesh size, surface area = 95.08 ± 1.5 m2/g) was converted to MgCO 3 at 350°C and 10 bars CO2. But the absorption capacity of 1h ball milled zinc oxide was low, 0.198 gCO2 /gZnO at 75°C and 10 bars CO2. Interestingly, 57% mass conversion of Fe and Fe 3O4 mixture to FeCO3 was observed at 200°C and 10 bars CO2. MgO, ZnO and Fe3O4 could be completely regenerated at 550°C, 250°C and 350°C respectively. Furthermore, the possible retrofit of MgO and a mixture of Fe and Fe3O 4 to a 300 MWe coal-fired power plant and iron making industry were also evaluated.

Vocabulary learning through use of the picture-word inductive model for young English learners in China: A mixed methods examination using Cognitive Load Theory

English has been taught as a core and compulsory subject in China for decades. Recently, the demand for English in China has increased dramatically. China now has the world's largest English-learning population. The traditional English-teaching method cannot continue to be the only approach because it merely focuses on reading, grammar and translation, which cannot meet English learners and users' needs (i.e., communicative competence and skills in speaking and writing). ^ This study was conducted to investigate if the Picture-Word Inductive Model (PWIM), a new pedagogical method using pictures and inductive thinking, would benefit English learners in China in terms of potential higher output in speaking and writing. With the gauge of Cognitive Load Theory (CLT), specifically, its redundancy effect, I investigated whether processing words and a picture concurrently would present a cognitive overload for English learners in China. ^ I conducted a mixed methods research study. A quasi-experiment (pretest, intervention for seven weeks, and posttest) was conducted using 234 students in four groups in Lianyungang, China (58 fourth graders and 57 seventh graders as an experimental group with PWIM and 59 fourth graders and 60 seventh graders as a control group with the traditional method). No significant difference in the effects of PWIM was found on vocabulary acquisition based on grade levels. Observations, questionnaires with open-ended questions, and interviews were deployed to answer the three remaining research questions. A few students felt cognitively overloaded when they encountered too many writing samples, too many new words at one time, repeated words, mismatches between words and pictures, and so on. Many students listed and exemplified numerous strengths of PWIM, but a few mentioned weaknesses of PWIM. The students expressed the idea that PWIM had a positive effect on their English teaching. ^ As integrated inferences, qualitative findings were used to explain the quantitative results that there were no significant differences of the effects of the PWIM between the experimental and control groups in both grade levels, from four contextual aspects: time constraints on PWIM implementation, teachers' resistance, how to use PWIM and PWIM implemented in a classroom over 55 students.^

Developing brownfields ranking models using decision analytic methods

The redevelopment of Brownfields has taken off in the 1990s, supported by federal and state incentives, and largely accomplished by local initiatives. Brownfields redevelopment has several associated benefits. These include the revitalization of inner-city neighborhoods, creation of jobs, stimulation of tax revenues, greater protection of public health and natural resources, the renewal and reuse existing civil infrastructure and Greenfields protection. While these benefits are numerous, the obstacles to Brownfields redevelopment are also very much alive. Redevelopment issues typically embrace a host of financial and legal liability concerns, technical and economic constraints, competing objectives, and uncertainties arising from inadequate site information. Because the resources for Brownfields redevelopment are usually limited, local programs will require creativity in addressing these existing obstacles in a manner that extends their limited resources for returning Brownfields to productive uses. Such programs may benefit from a structured and defensible decision framework to prioritize sites for redevelopment: one that incorporates the desired objectives, corresponding variables and uncertainties associated with Brownfields redevelopment. This thesis demonstrates the use of a decision analytic tool, Bayesian Influence Diagrams, and related decision analytic tools in developing quantitative decision models to evaluate and rank Brownfields sites on the basis of their redevelopment potential.

Screening of pharmaceuticals and other pollutants of concern by a combination of chemical and biological methods

This study examined the occurrence of pharmaceuticals and personal care products (PPCP's) in surface waters of Florida and their potential to be use as indicators of wastewater contamination. Previous studies have shown that elimination of pharmaceuticals in municipal sewage treatment plants is often incomplete. Aquatic ecosystems are under increased stress from human activities, particularly in heavily populated areas. The purpose of this study was to find an ideal indicator for wastewater. The applied methods, GC/MS and LC/MS, were suitable for the determination of pharmaceuticals and personal care products in aqueous environmental samples to the lower parts-per-trillion (ng/L) level. As a result of this study a snapshot view of the occurrence of pharmaceuticals and personal care products in south Florida was produced. PPCP's were commonly detected in coastal environments of South Florida at relatively low concentrations. In general, PPCP's were higher inside the canals and contained bodies of water than in open water systems. Caffeine was successfully used to describe impacted versus pristine locations. However, no particular correlation was observed among caffeine and other traditional water quality parameters.

Vocabulary Learning through Use of the Picture-Word Inductive Model for Young English Learners in China: A Mixed Methods Examination Using Cognitive Load Theory

English has been taught as a core and compulsory subject in China for decades. Recently, the demand for English in China has increased dramatically. China now has the world’s largest English-learning population. The traditional English-teaching method cannot continue to be the only approach because it merely focuses on reading, grammar and translation, which cannot meet English learners and users’ needs (i.e., communicative competence and skills in speaking and writing). This study was conducted to investigate if the Picture-Word Inductive Model (PWIM), a new pedagogical method using pictures and inductive thinking, would benefit English learners in China in terms of potential higher output in speaking and writing. With the gauge of Cognitive Load Theory (CLT), specifically, its redundancy effect, I investigated whether processing words and a picture concurrently would present a cognitive overload for English learners in China. I conducted a mixed methods research study. A quasi-experiment (pretest, intervention for seven weeks, and posttest) was conducted using 234 students in four groups in Lianyungang, China (58 fourth graders and 57 seventh graders as an experimental group with PWIM and 59 fourth graders and 60 seventh graders as a control group with the traditional method). No significant difference in the effects of PWIM was found on vocabulary acquisition based on grade levels. Observations, questionnaires with open-ended questions, and interviews were deployed to answer the three remaining research questions. A few students felt cognitively overloaded when they encountered too many writing samples, too many new words at one time, repeated words, mismatches between words and pictures, and so on. Many students listed and exemplified numerous strengths of PWIM, but a few mentioned weaknesses of PWIM. The students expressed the idea that PWIM had a positive effect on their English teaching. As integrated inferences, qualitative findings were used to explain the quantitative results that there were no significant differences of the effects of the PWIM between the experimental and control groups in both grade levels, from four contextual aspects: time constraints on PWIM implementation, teachers’ resistance, how to use PWIM and PWIM implemented in a classroom over 55 students.

Hydrogeophysical Characterization of Anisotropy in the Biscayne Aquifer Using Geophysical Methods

The anisotropy of the Biscayne Aquifer which serves as the source of potable water for Miami-Dade County was investigated by applying geophysical methods. Electrical resistivity imaging, self potential and ground penetration radar techniques were employed in both regional and site specific studies. In the regional study, electrical anisotropy and resistivity variation with depth were investigated with azimuthal square array measurements at 13 sites. The observed coefficient of electrical anisotropy ranged from 1.01 to 1.36. The general direction of measured anisotropy is uniform for most sites and trends W-E or SE-NW irrespective of depth. Measured electrical properties were used to estimate anisotropic component of the secondary porosity and hydraulic anisotropy which ranged from 1 to 11% and 1.18 to 2.83 respectively. 1-D sounding analysis was used to models the variation of formation resistivity with depth. Resistivities decreased from NW (close to the margins of the everglades) to SE on the shores of Biscayne Bay. Porosity calculated from Archie's law, ranged from 18 to 61% with higher values found along the ridge. Higher anisotropy, porosities and hydraulic conductivities were on the Atlantic Coastal Ridge and lower values at low lying areas west of the ridge. The cause of higher anisotropy and porosity is attributed to higher dissolution rates of the oolitic facies of the Miami Formation composing the ridge. The direction of minimum resistivity from this study is similar to the predevelopment groundwater flow direction indicated in published modeling studies. Detailed investigations were carried out to evaluate higher anisotropy at West Perrine Park located on the ridge and Snapper Creek Municipal well field where the anisotropy trend changes with depth. The higher anisotropy is attributed to the presence of solution cavities oriented in the E-SE direction on the ridge. Similarly, the change in hydraulic anisotropy at the well field might be related to solution cavities, the surface canal and groundwater extraction wells.

Methods for Modeling and Analyzing Concurrent Software

Concurrent software executes multiple threads or processes to achieve high performance. However, concurrency results in a huge number of different system behaviors that are difficult to test and verify. The aim of this dissertation is to develop new methods and tools for modeling and analyzing concurrent software systems at design and code levels. This dissertation consists of several related results. First, a formal model of Mondex, an electronic purse system, is built using Petri nets from user requirements, which is formally verified using model checking. Second, Petri nets models are automatically mined from the event traces generated from scientific workflows. Third, partial order models are automatically extracted from some instrumented concurrent program execution, and potential atomicity violation bugs are automatically verified based on the partial order models using model checking. Our formal specification and verification of Mondex have contributed to the world wide effort in developing a verified software repository. Our method to mine Petri net models automatically from provenance offers a new approach to build scientific workflows. Our dynamic prediction tool, named McPatom, can predict several known bugs in real world systems including one that evades several other existing tools. McPatom is efficient and scalable as it takes advantage of the nature of atomicity violations and considers only a pair of threads and accesses to a single shared variable at one time. However, predictive tools need to consider the tradeoffs between precision and coverage. Based on McPatom, this dissertation presents two methods for improving the coverage and precision of atomicity violation predictions: 1) a post-prediction analysis method to increase coverage while ensuring precision; 2) a follow-up replaying method to further increase coverage. Both methods are implemented in a completely automatic tool.