Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients

Chronic bronchopulmonary bacterial infections remain the most common cause of morbidity and mortality among patients with cystic fibrosis (CF). Recent community sequencing work has now shown that the bacterial community in the CF lung is polymicrobial. Identifying bacteria in the CF lung through sequencing can be costly and is not practical for many laboratories. Molecular techniques such as terminal restriction fragment length polymorphism or amplicon length heterogeneity-polymerase chain reaction (LH-PCR) can provide many laboratories with the ability to study CF bacterial communities without costly sequencing. The aim of this study was to determine if the use of LH-PCR with multiple hypervariable regions of the 16S rRNA gene could be used to identify organisms found in sputum DNA. This work also determined if LH-PCR could be used to observe the dynamics of lung infections over a period of time. Nineteen samples were analysed with the V1 and the V1_V2 region of the 16S rRNA gene. Based on the amplicon size present in the V1_V2 region, Pseudomonas aeruginosa was confirmed to be in all 19 samples obtained from the patients. The V1 region provided a higher power of discrimination between bacterial profiles of patients. Both regions were able to identify trends in the bacterial population over a period of time. LH profiles showed that the CF lung community is dynamic and that changes in the community may in part be driven by the patient's antibiotic treatment. LH-PCR is a tool that is well suited for studying bacterial communities and their dynamics.

Discrete time models of the term structure of interest rates and interest rate contingent claims

In this study, discrete time one-factor models of the term structure of interest rates and their application to the pricing of interest rate contingent claims are examined theoretically and empirically. The first chapter provides a discussion of the issues involved in the pricing of interest rate contingent claims and a description of the Ho and Lee (1986), Maloney and Byrne (1989), and Black, Derman, and Toy (1990) discrete time models. In the second chapter, a general discrete time model of the term structure from which the Ho and Lee, Maloney and Byrne, and Black, Derman, and Toy models can all be obtained is presented. The general model also provides for the specification of an additional model, the ExtendedMB model. The third chapter illustrates the application of the discrete time models to the pricing of a variety of interest rate contingent claims. In the final chapter, the performance of the Ho and Lee, Black, Derman, and Toy, and ExtendedMB models in the pricing of Eurodollar futures options is investigated empirically. The results indicate that the Black, Derman, and Toy and ExtendedMB models outperform the Ho and Lee model. Little difference in the performance of the Black, Derman, and Toy and ExtendedMB models is detected. ^

A reliability centered maintenance decision system for a discrete part manufacturing facility

This thesis develops and validates the framework of a specialized maintenance decision support system for a discrete part manufacturing facility. Its construction utilizes a modular approach based on the fundamental philosophy of Reliability Centered Maintenance (RCM). The proposed architecture uniquely integrates System Decomposition, System Evaluation, Failure Analysis, Logic Tree Analysis, and Maintenance Planning modules. It presents an ideal solution to the unique maintenance inadequacies of modern discrete part manufacturing systems. Well established techniques are incorporated as building blocks of the system's modules. These include Failure Mode Effect and Criticality Analysis (FMECA), Logic Tree Analysis (LTA), Theory of Constraints (TOC), and an Expert System (ES). A Maintenance Information System (MIS) performs the system's support functions. Validation was performed by field testing of the system at a Miami based manufacturing facility. Such a maintenance support system potentially reduces downtime losses and contributes to higher product quality output. Ultimately improved profitability is the final outcome. ^

Statistical analysis and meta-analysis of microarray data

The microarray technology provides a high-throughput technique to study gene expression. Microarrays can help us diagnose different types of cancers, understand biological processes, assess host responses to drugs and pathogens, find markers for specific diseases, and much more. Microarray experiments generate large amounts of data. Thus, effective data processing and analysis are critical for making reliable inferences from the data. ^ The first part of dissertation addresses the problem of finding an optimal set of genes (biomarkers) to classify a set of samples as diseased or normal. Three statistical gene selection methods (GS, GS-NR, and GS-PCA) were developed to identify a set of genes that best differentiate between samples. A comparative study on different classification tools was performed and the best combinations of gene selection and classifiers for multi-class cancer classification were identified. For most of the benchmarking cancer data sets, the gene selection method proposed in this dissertation, GS, outperformed other gene selection methods. The classifiers based on Random Forests, neural network ensembles, and K-nearest neighbor (KNN) showed consistently god performance. A striking commonality among these classifiers is that they all use a committee-based approach, suggesting that ensemble classification methods are superior. ^ The same biological problem may be studied at different research labs and/or performed using different lab protocols or samples. In such situations, it is important to combine results from these efforts. The second part of the dissertation addresses the problem of pooling the results from different independent experiments to obtain improved results. Four statistical pooling techniques (Fisher inverse chi-square method, Logit method. Stouffer's Z transform method, and Liptak-Stouffer weighted Z-method) were investigated in this dissertation. These pooling techniques were applied to the problem of identifying cell cycle-regulated genes in two different yeast species. As a result, improved sets of cell cycle-regulated genes were identified. The last part of dissertation explores the effectiveness of wavelet data transforms for the task of clustering. Discrete wavelet transforms, with an appropriate choice of wavelet bases, were shown to be effective in producing clusters that were biologically more meaningful. ^

Development and validation of an instrument to predict online student success using faculty perceptions

Distance learning is growing and transforming educational institutions. The increasing use of distance learning by higher education institutions and particularly community colleges coupled with the higher level of student attrition in online courses than in traditional classrooms suggests that increased attention should be paid to factors that affect online student course completion. The purpose of the study was to develop and validate an instrument to predict community college online student course completion based on faculty perceptions, yielding a prediction model of online course completion rates. Social Presence and Media Richness theories were used to develop a theoretically-driven measure of online course completion. This research study involved surveying 311 community college faculty who taught at least one online course in the past 2 years. Email addresses of participating faculty were provided by two south Florida community colleges. Each participant was contacted through email, and a link to an Internet survey was given. The survey response rate was 63% (192 out of 303 available questionnaires). Data were analyzed through factor analysis, alpha reliability, and multiple regression. The exploratory factor analysis using principal component analysis with varimax rotation yielded a four-factor solution that accounted for 48.8% of the variance. Consistent with Social Presence theory, the factors with their percent of variance in parentheses were: immediacy (21.2%), technological immediacy (11.0%), online communication and interactivity (10.3%), and intimacy (6.3%). Internal consistency of the four factors was calculated using Cronbach's alpha (1951) with reliability coefficients ranging between .680 and .828. Multiple regression analysis yielded a model that significantly predicted 11% of the variance of the dependent variable, the percentage of student who completed the online course. As indicated in the literature (Johnson & Keil, 2002; Newberry, 2002), Media Richness theory appears to be closely related to Social Presence theory. However, elements from this theory did not emerge in the factor analysis.

Long-Term Effects of Adding Nutrients to an Oligotrophic Coastal Environment

Management of ecological disturbances requires an understanding of the time scale and dynamics of community responses to disturbance events. To characterize long-term seagrass bed responses to nutrient enrichment, we established six study sites in Florida Bay, USA. In 24 plots (0.25 m2) at each site, we regularly added nitrogen (N) and phosphorus (P) in a factorial design for 7 years. Five of the six sites exhibited strong P limitation. Over the first 2 years, P enrichment increased Thalassia testudinum cover in the three most P-limited sites. After 3 years, Halodule wrightii began to colonize many of the P-addition plots, but the degree of colonization was variable among sites, possibly due to differences in the supply of viable propagules. Thalassia increased its allocation to aboveground tissue in response to P enrichment; Halodule increased in total biomass but did not appear to change its aboveground: belowground tissue allocation. Nutrient enrichment did not cause macroalgal or epiphytic overgrowth of the seagrass. Nitrogen retention in the study plots was variable but relatively low, whereas phosphorus retention was very high, often exceeding 100% of the P added as fertilizer over the course of our experiments. Phosphorus retentions exceeding 100% may have been facilitated by increases in Thalassia aboveground biomass, which promoted the settlement of suspended particulate matter containing phosphorus. Our study demonstrated that lowintensity press disturbance events such as phosphorus enrichment can initiate a slow, ramped successional process that may alter community structure over many years.

The effect of reciprocal mapping on high-risk sixth-grade students' social studies achievement

Reading deficits in students in Grades 4 to 12 are evident in American schools. Informational text is particularly difficult for students. This quasi-experimental study (N=138) investigated sixth-grade students' achievement in social studies using the Reciprocal Mapping instructional routine, compared to sixth-grade students' achievement taught with a traditional approach. The Reciprocal Mapping instructional routine incorporated explicit instruction in text structure using graphic organizers. Students created their own graphic organizers and used them to write about social studies content. The comparison group used a traditional approach, students' reading the textbook and answering questions. Students for this study included sixth-graders in the seven sixth-grade classrooms in two public schools in a small, rural south Florida school district. A focus of this study was to determine the helpfulness of the intervention for at-risk readers. To determine students considered to be at-risk, the researcher used data from the reading portion of the Florida Comprehensive Assessment Test (FCAT), 2011-2012, that considers Level 1 and 2 as at-risk readers. The quasi-experimental study used a pretest-posttest control group design, with students assigned to treatment groups by class. Two teachers at the two rural sites were trained on the Reciprocal Mapping instructional routine and taught students in both the experimental and control groups for an equivalent amount of time over a 5-week period. Results of the 3 x 2 factorial ANCOVA found a significant positive difference favoring the experimental group's social studies achievement as compared to that of the comparison group as measured by the pre/post unit test from the social studies series (McGraw-Hill, 2013), when controlling for initial differences in students' reading FCAT scores. Interactions for high-risk struggling readers were investigated using the significance level p < .05. Due to no significant interaction the main effects of treatment were interpreted. The pretest was used as a covariate and the multivariate analysis was found to be significant. Therefore, analysis of covariance was run on each of the dependent variable as a follow-up. Reciprocal Mapping was found to be significant in posttest scores, independent of gender and level of risk, and while holding the pretest scores constant. Findings showed there was a significant difference in the performance of the high-risk reading students taught with the Reciprocal Mapping intervention who scored statistically better than students in the control group. Further study findings showed that teacher fidelity of implementation of the treatment had a statistically significant relationship in predicting posttest scores when controlling for pretest scores. Study results indicated that improving students' use of text structure through the Reciprocal Mapping instructional routine positively supported sixth-grade students' social studies achievement.

Acculturation and Hispanic identity/ethnicity as a predictor of change on the brief situational confidence questionnaire

The purpose of this study was to investigate whether level of acculturation among Hispanic adolescent males (n = 174) influenced treatment outcome in a substance abuse program, specifically on the Brief Situational Confidence Questionnaire (BSCQ) which measures relapse confidence. It was hypothesized that lower levels of acculturation were likely to be predictive of positive change, whereas higher levels of acculturation were likely to be predictive of no change or negative change. It was found that adolescents changed over time in BSCQ scores regardless of which acculturation variable was measured. Contrary to expectations, for those adolescents placed in family treatment, place of birth was not significantly associated with treatment response. However, both, U.S. and non-U.S. born adolescents demonstrated a change over time when receiving family treatment, suggesting that the family substance abuse treatment utilized in this intervention effected change over time.

Predictors of Independent Living Outcomes Among Older Women Receiving Informal Care

This study examined the predictors of independent living outcomes among community–living older women who received informal care. The central hypothesis was that older women’s level of functioning is influenced by their relationship with their informal caregiver. The study attempted to understand the independence of older women through the perspective of both informal caregivers and the older women themselves. The following eight variables were measured: 1) the older women’s independence (dependent variable); 2) the relationship between older women and their informal caregivers (independent variable); 3) roles of both the informal caregiver and older women (independent variable); 4) the older women’s attitudes toward aging (independent variable); 5) the older women’s age identity (independent variable); 6) the older women’s health (control variable); 7) the older women’s level of social support (control variable); and 8) the older women’s level of depression (control variable). The variables were measured from the perspective of the older woman herself and her informal caregiver. This study used an ecological and developmental framework along with role theory to understand the interaction among the aforementioned variables through a cross-sectional design. The recruited older women participants of this study were receiving ongoing care and personal assistance from two large home care agencies located in Miami, FL. An analysis was conducted through a mixed-methods incorporated into the study design. The present study aimed to contribute to the understanding of how the relationship between older women and their informal caregivers influences older women’s ability to maintain independent outcomes. The primary finding of this study was that there were both positive and negative experiences within the relationship dynamic of older women and their informal caregivers and that this relationship was either unidirectional or bi-directional.

Valuation of Ecosystem Services for Environmental Decision Making in South Florida

The Greater Everglades system imparts vital ecosystem services (ES) to South Florida residents including high quality drinking water supplies and a habitat for threatened and endangered species. As a result of the altered Everglades system and regional dynamics, restoration may either improve the provision of these services or impose a tradeoff between enhanced environmental goods and services and competing societal demands. The current study aims at understanding public preferences for restoration and generating willingness to pay (WTP) values for restored ES through the implementation of a discrete choice experiment. A previous study (Milon et al., 1999) generated WTP values amongst Floridians of up to $3.42 -$4.07 billion for full restoration over a 10-year period. We have collected data from 2,905 respondents taken from two samples who participated in an online survey designed to elicit the WTP values for selected ecological and social attributes included in the earlier study (Milon et al. 1999). We estimate that the Florida general public is willing to pay up to $854.1- $954.1 million over 10 years to avoid restrictions on their water usage and up to $90.8- $183.7 million over 10 years to restore the hydrological flow within the Water Conservation Area.

The Validity of Broad and Narrow Personality Traits For Predicting Job Performance: The Differential Effects of Time

Research into the dynamicity of job performance criteria has found evidence suggesting the presence of rank-order changes to job performance scores across time as well as intraindividual trajectories in job performance scores across time. These findings have influenced a large body of research into (a) the dynamicity of validities of individual differences predictors of job performance and (b) the relationship between individual differences predictors of job performance and intraindividual trajectories of job performance. In the present dissertation, I addressed these issues within the context of the Five Factor Model of personality. The Five Factor Model is arranged hierarchically, with five broad higher-order factors subsuming a number of more narrowly tailored personality facets. Research has debated the relative merits of broad versus narrow traits for predicting job performance, but the entire body of research has addressed the issue from a static perspective -- by examining the relative magnitude of validities of global factors versus their facets. While research along these lines has been enlightening, theoretical perspectives suggest that the validities of global factors versus their facets may differ in their stability across time. Thus, research is needed to not only compare the relative magnitude of validities of global factors versus their facets at a single point in time, but also to compare the relative stability of validities of global factors versus their facets across time. Also necessary to advance cumulative knowledge concerning intraindividual performance trajectories is research into broad vs. narrow traits for predicting such trajectories. In the present dissertation, I addressed these issues using a four-year longitudinal design. The results indicated that the validities of global conscientiousness were stable across time, while the validities of conscientiousness facets were more likely to fluctuate. However, the validities of emotional stability and extraversion facets were no more likely to fluctuate across time than those of the factors. Finally, while some personality factors and facets predicted performance intercepts (i.e., performance at the first measurement occasion), my results failed to indicate a significant effect of any personality variable on performance growth. Implications for research and practice are discussed.