Evaluation of Some Statistical Methods for the Identification of Differentially Expressed Genes

Microarray platforms have been around for many years and while there is a rise of new technologies in laboratories, microarrays are still prevalent. When it comes to the analysis of microarray data to identify differentially expressed (DE) genes, many methods have been proposed and modified for improvement. However, the most popular methods such as Significance Analysis of Microarrays (SAM), samroc, fold change, and rank product are far from perfect. When it comes down to choosing which method is most powerful, it comes down to the characteristics of the sample and distribution of the gene expressions. The most practiced method is usually SAM or samroc but when the data tends to be skewed, the power of these methods decrease. With the concept that the median becomes a better measure of central tendency than the mean when the data is skewed, the tests statistics of the SAM and fold change methods are modified in this thesis. This study shows that the median modified fold change method improves the power for many cases when identifying DE genes if the data follows a lognormal distribution.

Paleoenvironmental reconstruction of Florida Bay, South Florida, using benthic foraminifera

Efforts that are underway to rehabilitate the Florida Bay ecosystem to a more natural state are best guided by a comprehensive understanding of the natural versus human-induced variability that has existed within the ecosystem. Benthic foraminifera, which are well-known paleoenvironmental indicators, were identified in 203 sediment samples from six sediment cores taken from Florida Bay, and analyzed to understand the environmental variability through anthropogenically unaltered and altered periods. In this research, taxa serving as indicators of (1) seagrass abundance (which is correlated with water quality), (2) salinity, and (3) general habitat change, were studied in detail over the past 120 years, and more generally over the past ~4000 years. Historical seagrass abundance was reconstructed with the proportions of species that prefer living attached to seagrass blades over other substrates. Historical salinity trends were determined by analyzing brackish versus marine faunas, which were defined based on species’ salinity preferences. Statistical methods including cluster analysis, discriminant analysis, analysis of variance and Fisher’s α were used to analyze trends in the data. The changes in seagrass abundance and salinity over the last ~120 years are attributed to anthropogenic activities such as construction of the Flagler Railroad from the mainland to the Florida Keys, the Tamiami Trail that stretches from the east to west coast, and canals and levees in south Florida, as well as natural events such as droughts and increased rainfall from hurricanes. Longer term changes (over ~4000 years) in seagrass abundance and salinity are mostly related to sea level changes. Since seawater entered the Florida Bay area around ~4000 years ago, only one probable sea level drop occurring around ~3000 years was identified.

An assessment of natural and human disturbance effects on Mexican ecosystems: current trends and research gaps

Mexico harbors more than 10% of the planet’s endemic species. However, the integrity and biodiversity of many ecosystems is experiencing rapid transformation under the influence of a wide array of human and natural disturbances. In order to disentangle the effects of human and natural disturbance regimes at different spatial and temporal scales, we selected six terrestrial (temperate montane forests, montane cloud forests, tropical rain forests, tropical semi-deciduous forests, tropical dry forests, and deserts) and four aquatic (coral reefs, mangrove forests, kelp forests and saline lakes) ecosystems. We used semiquantitative statistical methods to assess (1) the most important agents of disturbance affecting the ecosystems, (2) the vulnerability of each ecosystem to anthropogenic and natural disturbance, and (3) the differences in ecosystem disturbance regimes and their resilience. Our analysis indicates a significant variation in ecological responses, recovery capacity, and resilience among ecosystems. The constant and widespread presence of human impacts on both terrestrial and aquatic ecosystems is reflected either in reduced area coverage for most systems, or reduced productivity and biodiversity, particularly in the case of fragile ecosystems (e.g., rain forests, coral reefs). In all cases, the interaction between historical human impacts and episodic high intensity natural disturbance (e.g., hurricanes, fires) has triggered a reduction in species diversity and induced significant changes in habitat distribution or species dominance. The lack of monitoring programs assessing before/after effects of major disturbances in Mexico is one of the major limitations to quantifying the commonalities and differences of disturbance effects on ecosystem properties.

Academic performance of college students in financial management and related prerequisite courses: A comparison of senior high school and commercial high school graduates attending Tamsui Oxford University College in Taiwan

In Taiwan, the college freshmen are recruited graduates of both senior high school and senior vocational school. The Ministry of Education (MOE) of the Republic of China prescribes the standards of curriculum and equipment for schools at all levels and categories. There exists a considerably different curriculum arrangement for senior high schools and vocational high schools in Taiwan at the present time. The present study used a causal-comparative research design to identify the influences of different post-secondary educational background on specialized course performance of college business majors. ^ The students involved in this study were limited to the students of four business-related departments at Tamsui Oxford University College in Taiwan. Students were assigned to comparison groups based on their post-secondary educational background as senior high school graduates and commercial high school graduates. The analysis of this study included a comparison of students' performance on lower level courses and a comparison of students' performance in financial management. The analysis also considered the relationship between the students' performance in financial management and its related prerequisite courses. The Kolb Learning Style Inventory (LSI) survey was administered to categorize subjects' learning styles and to compare the learning styles between the two groups in this study. The applied statistical methods included t-test, correlation, multiple regression, and Chi-square. ^ The findings of this study indicated that there were significant differences between the commercial high school graduates and the senior high school graduates on academic performances in specialized courses but not in general courses. There were no significant differences in learning styles between the two groups. These findings lead to the conclusion that business majors' academic performance in specialized courses were influenced by their post-secondary educational background. ^

Types and amplitudes of touch as reinforcing stimuli in operant conditioning of infant behavior

The reinforcing effects of diverse tactile stimuli were examined in this study. The study had two purposes. First, this study expanded on the Pelaez-Nogueras, Field, Gewirtz, Cigales, Gonzalez, Sanchez and Clasky (1997) finding that stroking increases infants' gaze duration, and smiling and vocalization frequencies more than tickling/poking. Instead of presenting poking and tickling as a single stimulus combination, this study separated poking and tickling in order to measure the effects of each component separately. Further, the effects of poking, tickling/tapping and stroking intensity (i.e., tactile pressure) were compared by having both mild and intense conditions. Second, this study compared the reinforcing efficacy of mother-delivered tactile stimulation to that of infant-originated tactile exploration. Twelve infants from 2- to 5-months of age participated in this study. The experiment was conducted using a repeated measures A-B-A-C-A-D reversal design. The A phases signified baselines and reversals. The B, C, and D phases consisted of alternating treatments (either mild stroking vs. mild poking vs. mild tickling/tapping, intense stroking vs. intense poking vs. intense tickling/tapping, or mother-delivered tactile stimulation vs. infant-originated tactile exploration). Three experimental hypotheses were assessed: (1) infant leg kick rate would be greater when it produced stroking or tickling/tapping (presumptive positive reinforcers), than when it produced poking (a possible punisher), regardless of tactile pressure; (2) infant leg kick rate would be greater when it produced a more intense level of stroking or tickling/tapping and lower when it produced intense poking compared to mild poking; (3) infant leg-kick rate would be greater for mother-delivered tactile stimulation than for infant-originated tactile exploration. Visual inspection and inferential statistical methods were used to analyze the results. The data supported the first two hypotheses. Mixed support emerged for the third hypothesis. This study made several important contributions to the field of psychology. First, this was the first study to quantify the pressure of tactile stimulation, via a pressure meter developed by the researcher. Additionally, the results of this study yielded valuable information about the effects of different modalities of touch. ^

Sales tax enforcement: An empirical analysis of compliance enforcement methodologies and pathologies

Most research on tax evasion has focused on the income tax. Sales tax evasion has been largely ignored and dismissed as immaterial. This paper explored the differences between income tax and sales tax evasion and demonstrated that sales tax enforcement is deserving of and requires the use of different tools to achieve compliance. Specifically, the major enforcement problem with sales tax is not evasion: it is theft perpetrated by companies that act as collection agents for the state. Companies engage in a principal-agent relationship with the state and many retain funds collected as an agent of the state for private use. As such, the act of sales tax theft bears more resemblance to embezzlement than to income tax evasion. It has long been assumed that the sales tax is nearly evasion free, and state revenue departments report voluntary compliance in a manner that perpetuates this myth. Current sales tax compliance enforcement methodologies are similar in form to income tax compliance enforcement methodologies and are based largely on trust. The primary focus is on delinquent filers with a very small percentage of businesses subject to audit. As a result, there is a very large group of noncompliant businesses who file on time and fly below the radar while stealing millions of taxpayer dollars. ^ The author utilized a variety of statistical methods with actual field data derived from operations of the Southern Region Criminal Investigations Unit of the Florida Department of Revenue to evaluate current and proposed sales tax compliance enforcement methodologies in a quasi-experimental, time series research design and to set forth a typology of sales tax evaders. This study showed that current estimates of voluntary compliance in sales tax systems are seriously and significantly overstated and that current enforcement methodologies are inadequate to identify the majority of violators and enforce compliance. Sales tax evasion is modeled using the theory of planned behavior and Cressey’s fraud triangle and it is demonstrated that proactive enforcement activities, characterized by substantial contact with non-delinquent taxpayers, results in superior ability to identify noncompliance and provides a structure through which noncompliant businesses can be rehabilitated.^

*Adoption status: A risk factor or protective factor for children of divorced families

This study examined two competitive hypotheses: the double jeopardy hypothesis and the buffering effect hypothesis on whether parental divorce affects adopted children and non-adopted children similarly or differently. The double jeopardy hypothesis suggests that when adopted children experience their parents' divorce, they perform worse because they carry two risk factors, adoption status and parental divorce, while their non-adopted counterparts carry only the risk factor of their parents' divorce. The buffering effect hypothesis suggests that, being adopted children, their previous experiences of parental loss help them better deal with the later loss of their parents' divorce so their adoption status is a protective factor rather than a risk factor. ^ Secondary analyses of a nation-wide data set were executed using different statistical methods such as ANOVA and Chi-square on different outcome variables. The results indicated that there was no evidence supporting the double-jeopardy hypothesis. That is, adopted children from divorced families did not perform significantly worse than the non-adopted children from divorced families on any outcome variable. The results also indicated that there was only weak evidence supporting the buffering effect hypothesis. The general conclusion based on the results from most of the outcome variables suggest that adopted children from divorced families do not perform differently than the biological children from divorced families. ^

Assessing an automated, information -sharing technology in the post "9 -11" era: Do local law enforcement officers think it meets their needs?

In the wake of the “9-11” terrorists' attacks, the U.S. Government has turned to information technology (IT) to address a lack of information sharing among law enforcement agencies. This research determined if and how information-sharing technology helps law enforcement by examining the differences in perception of the value of IT between law enforcement officers who have access to automated regional information sharing and those who do not. It also examined the effect of potential intervening variables such as user characteristics, training, and experience, on the officers' evaluation of IT. The sample was limited to 588 officers from two sheriff's offices; one of them (the study group) uses information sharing technology, the other (the comparison group) does not. Triangulated methodologies included surveys, interviews, direct observation, and a review of agency records. Data analysis involved the following statistical methods: descriptive statistics, Chi-Square, factor analysis, principal component analysis, Cronbach's Alpha, Mann-Whitney tests, analysis of variance (ANOVA), and Scheffe' post hoc analysis. ^ Results indicated a significant difference between groups: the study group perceived information sharing technology as being a greater factor in solving crime and in increasing officer productivity. The study group was more satisfied with the data available to it. As to the number of arrests made, information sharing technology did not make a difference. Analysis of the potential intervening variables revealed several remarkable results. The presence of a strong performance management imperative (in the comparison sheriff's office) appeared to be a factor in case clearances and arrests, technology notwithstanding. As to the influence of user characteristics, level of education did not influence a user's satisfaction with technology, but user-satisfaction scores differed significantly among years of experience as a law enforcement officer and the amount of computer training, suggesting a significant but weak relationship. ^ Therefore, this study finds that information sharing technology assists law enforcement officers in doing their jobs. It also suggests that other variables such as computer training, experience, and management climate should be accounted for when assessing the impact of information technology. ^

A Review of Merger and Acquisition Wave Literature: Proposing Future Research in the Restaurant Industry

The purpose of this study is to identify research trends in Merger and Acquisition waves in the restaurant industry and propose future research directions by thoroughly reviewing existing Merger and Acquisition related literature. Merger and Acquisition has been extensively used as a strategic management tool for fast growth in the restaurant industry. However, there has been a very limited amount of literature that focuses on Merger & Acquisition in the restaurant industry. Particular, no known study has been identified that examined M&A wave and its determinants. A good understanding of determinants of M&A wave will help practitioners identify important factors that should be considered before making M&A decisions and predict the optimal timing for successful M&A transactions. This study examined literature on six U.S M&A waves and their determinants and summarized main explanatory factors examined, statistical methods, and theoretical frameworks. Inclusion of unique macroeconomic factors of the restaurant industry and the use of factor analysis are suggested for future research.

Comparison of Some Improved Estimators for Linear Regression Model under Different Conditions

Multiple linear regression model plays a key role in statistical inference and it has extensive applications in business, environmental, physical and social sciences. Multicollinearity has been a considerable problem in multiple regression analysis. When the regressor variables are multicollinear, it becomes difficult to make precise statistical inferences about the regression coefficients. There are some statistical methods that can be used, which are discussed in this thesis are ridge regression, Liu, two parameter biased and LASSO estimators. Firstly, an analytical comparison on the basis of risk was made among ridge, Liu and LASSO estimators under orthonormal regression model. I found that LASSO dominates least squares, ridge and Liu estimators over a significant portion of the parameter space for large dimension. Secondly, a simulation study was conducted to compare performance of ridge, Liu and two parameter biased estimator by their mean squared error criterion. I found that two parameter biased estimator performs better than its corresponding ridge regression estimator. Overall, Liu estimator performs better than both ridge and two parameter biased estimator.