New algorithms for automated phylogenetic reconstruction using artificial intelligence and data mining techniques

Academic and industrial research in the late 90s have brought about an exponential explosion of DNA sequence data. Automated expert systems are being created to help biologists to extract patterns, trends and links from this ever-deepening ocean of information. Two such systems aimed on retrieving and subsequently utilizing phylogenetically relevant information have been developed in this dissertation, the major objective of which was to automate the often difficult and confusing phylogenetic reconstruction process. ^ Popular phylogenetic reconstruction methods, such as distance-based methods, attempt to find an optimal tree topology (that reflects the relationships among related sequences and their evolutionary history) by searching through the topology space. Various compromises between the fast (but incomplete) and exhaustive (but computationally prohibitive) search heuristics have been suggested. An intelligent compromise algorithm that relies on a flexible “beam” search principle from the Artificial Intelligence domain and uses the pre-computed local topology reliability information to adjust the beam search space continuously is described in the second chapter of this dissertation. ^ However, sometimes even a (virtually) complete distance-based method is inferior to the significantly more elaborate (and computationally expensive) maximum likelihood (ML) method. In fact, depending on the nature of the sequence data in question either method might prove to be superior. Therefore, it is difficult (even for an expert) to tell a priori which phylogenetic reconstruction method—distance-based, ML or maybe maximum parsimony (MP)—should be chosen for any particular data set. ^ A number of factors, often hidden, influence the performance of a method. For example, it is generally understood that for a phylogenetically “difficult” data set more sophisticated methods (e.g., ML) tend to be more effective and thus should be chosen. However, it is the interplay of many factors that one needs to consider in order to avoid choosing an inferior method (potentially a costly mistake, both in terms of computational expenses and in terms of reconstruction accuracy.) ^ Chapter III of this dissertation details a phylogenetic reconstruction expert system that selects a superior proper method automatically. It uses a classifier (a Decision Tree-inducing algorithm) to map a new data set to the proper phylogenetic reconstruction method. ^

THEORETICAL STUDIES ON THE METHODS OF RECONSTRUCTING PHYLOGENETIC TREES FROM DNA SEQUENCE DATA (MOLECULAR EVOLUTION, HOMINOID EVOLUTION, COMPUTER SIMULATION)

(1) A mathematical theory for computing the probabilities of various nucleotide configurations is developed, and the probability of obtaining the correct phylogenetic tree (model tree) from sequence data is evaluated for six phylogenetic tree-making methods (UPGMA, distance Wagner method, transformed distance method, Fitch-Margoliash's method, maximum parsimony method, and compatibility method). The number of nucleotides (m*) necessary to obtain the correct tree with a probability of 95% is estimated with special reference to the human, chimpanzee, and gorilla divergence. m* is at least 4,200, but the availability of outgroup species greatly reduces m* for all methods except UPGMA. m* increases if transitions occur more frequently than transversions as in the case of mitochondrial DNA. (2) A new tree-making method called the neighbor-joining method is proposed. This method is applicable either for distance data or character state data. Computer simulation has shown that the neighbor-joining method is generally better than UPGMA, Farris' method, Li's method, and modified Farris method on recovering the true topology when distance data are used. A related method, the simultaneous partitioning method, is also discussed. (3) The maximum likelihood (ML) method for phylogeny reconstruction under the assumption of both constant and varying evolutionary rates is studied, and a new algorithm for obtaining the ML tree is presented. This method gives a tree similar to that obtained by UPGMA when constant evolutionary rate is assumed, whereas it gives a tree similar to that obtained by the maximum parsimony tree and the neighbor-joining method when varying evolutionary rate is assumed. ^

A comparative review of water disinfection methods appropriate for developing countries and their efficacy, cost-efficiency, and usability

Developing countries are heavily burdened by limited access to safe drinking water and subsequent water-related diseases. Numerous water treatment interventions combat this public health crisis, encompassing both traditional and less-common methods. Of these, water disinfection serves as an important means to provide safe drinking water. Existing literature discusses a wide range of traditional treatment options and encourages the use of multi-barrier approaches including coagulation-flocculation, filtration, and disinfection. Most sources do not delve into approaches specifically appropriate for developing countries, nor do they exclusively examine water disinfection methods.^ The objective of this review is to focus on an extensive range of chemical, physio-chemical, and physical water disinfection techniques to provide a compilation, description and evaluation of options available. Such an objective provides further understanding and knowledge to better inform water treatment interventions and explores alternate means of water disinfection appropriate for developing countries. Appropriateness for developing countries corresponds to the effectiveness of an available, easy to use disinfection technique at providing safe drinking water at a low cost.^ Among chemical disinfectants, SWS sodium hypochlorite solution is preferred over sodium hypochlorite bleach due to consistent concentrations. Tablet forms are highly recommended chemical disinfectants because they are effective and very easy to use, but also because they are stable. Examples include sodium dichloroisocyanurate, calcium hypochlorite, and chlorine dioxide, which vary in cost depending on location and availability. Among physio-chemical disinfection options, electrolysis which produces mixed oxidants (MIOX) provides a highly effective disinfection option with a higher upfront cost but very low cost over the long term. Among physical disinfection options, solar disinfection (SODIS) applications are effective, but they treat only a fixed volume of water at a time. They come with higher initial costs but very low on-going costs. Additional effective disinfection techniques may be suitable depending on the location, availability and cost.^

Performance tiers: Implementing comparative effectiveness analysis in the health care setting through operations research and spatial methods

This dissertation develops and tests a comparative effectiveness methodology utilizing a novel approach to the application of Data Envelopment Analysis (DEA) in health studies. The concept of performance tiers (PerT) is introduced as terminology to express a relative risk class for individuals within a peer group and the PerT calculation is implemented with operations research (DEA) and spatial algorithms. The analysis results in the discrimination of the individual data observations into a relative risk classification by the DEA-PerT methodology. The performance of two distance measures, kNN (k-nearest neighbor) and Mahalanobis, was subsequently tested to classify new entrants into the appropriate tier. The methods were applied to subject data for the 14 year old cohort in the Project HeartBeat! study.^ The concepts presented herein represent a paradigm shift in the potential for public health applications to identify and respond to individual health status. The resultant classification scheme provides descriptive, and potentially prescriptive, guidance to assess and implement treatments and strategies to improve the delivery and performance of health systems. ^

Policy analysis of iron micronutrient programs at USAID: The FANTA program in East Africa and the micronutrient initiative in Bihar region of India, using comparative cost effective and cost benefit analysis

It is the aim of this paper to examine iron supplementation programs which receive funding from United States Agency for International Development (USAID) but approach combating iron deficiency anemia in two vastly different ways. A brief literature review and background information on iron deficiencies and the differences between supplementation programs and micronutrient fortification were reviewed. Two non-governmental organizations (NGO's) were examined for this paper: the Food and Nutrition Technical Assistance II (FANTA) and the MicroNutrient Initiative. The FANTA program included an educational component to their supplementation program while the MicroNutrient Initiative solely used supplementation of micronutrients to their population. Methods used were cost-benefit analysis and cost-effectiveness analysis to determine the overall effectiveness of each program in reducing iron deficiency anemia in each population, if the added costs of the incentives in the FANTA program changed the cost-effectiveness of the program compared to the MicroNutrient Initiative program and to determine which program imparted the greatest benefit to each population by reducing the disease burden in Disability Adjusted Life Years (DALY). Results showed that the unit cost of the FANTA program per person was higher than the MicroNutrient Initiative program due to the educational component. The FANTA program reduced iron deficiency anemia less overall but cost less for each percentage point of anemia decreased in their respective populations. The MicroNutrient Initiative program had a better benefit cost ratio for the populations it served. The MicroNutrient Initiative's large scale program imparted many advantages by reducing unit cost per person and decreasing iron deficiency anemia. The FANTA program was more effective at decreasing iron deficiency anemia with less money: $5,660 per 1% decrease in iron deficiency anemia versus $18,450 per 1% decrease in iron deficiency anemia for the MicroNutrient Initiative program. ^ In conclusion, economic analysis cannot measure all of the benefits associated with programs that contain an educational component or large scale supplementation. More information needs to be gathered by NGOs and reported to USAID, such as detailed prevalence rates of iron deficiency anemia among the populations served. Further research is needed to determine the effects an educational supplementation program has on compliance rates of participants and motivation to participate in supplementation programs whose aim is to decrease iron deficiency anemia in a targeted population.^

Comparative virulence of enterotoxigenic non-Escherichia coli Enterobacteriaceae species from patients with travelers' diarrhea

Background: Family members of Enterobacteriaceae are found in small numbers associated with acute diarrhea. These species are sometimes mistaken for ETEC. ^ Methods: Forty-four non-E. coli species from travelers' diarrhea are compared to 30 strains of Escherichia coli (ETEC) and 30 strains of normal flora E. coli. Tissue culture supernatants were assayed by enzyme-linked immunosorbent assay for amounts of IL-8, IL-1, and IL-1ra. Amounts of heat-stable (ST) and heat-labile (LT) enterotoxins were assayed from cell culture supernatants by enzyme-linked immunoassay. PCR was use to determine which species was positive colonization factor antigens, CFA/I, CS3, and CS6. ^ Results: Normal flora E. coli significantly induced the production of more IL-8 than non- E. coli and ETEC. Normal E. coli also induced the production of more IL-1and IL-1ra than ETEC. Non-E. coli produced more ST than ETEC. A small percentage of enterotoxigenic non- E. coli gram negatives and ETEC were positive for CFA/I and CS6. None of the strains were positive for CS3. ^ Conclusions: Non-E. coli enterotoxigenic gram negatives were similar to ETEC in their virulence factors. Identification and further study of these non-E.coli strains is important for understanding their pathogenic role in acute diarrhea.^

A comparative state policy analysis of the adoption of birth defects surveillance legislation

Birth defects are the leading cause of infant mortality in the United States and are a major cause of lifetime disability. However, efforts to understand their causes have been hampered by a lack of population-specific data. During 1990–2004, 22 state legislatures responded to this need by proposing birth defects surveillance legislation (BDSL). The contrast between these states and those that did not pass BDSL provides an opportunity to better understand conditions associated with US public health policy diffusion. ^ This study identifies key state-specific determinants that predict: (1) the introduction of birth defects surveillance legislation (BDSL) onto states' formal legislative agenda, and (2) the successful adoption of these laws. Secondary aims were to interpret these findings in a theoretically sound framework and to incorporate evidence from three analytical approaches. ^ The study begins with a comparative case study of Texas and Oregon (states with divergent BDSL outcomes), including a review of historical documentation and content analysis of key informant interviews. After selecting and operationalizing explanatory variables suggested by the case study, Qualitative Comparative Analysis (QCA) was applied to publically available data to describe important patterns of variation among 37 states. Results from logistic regression were compared to determine whether the two methods produced consistent findings. ^ Themes emerging from the comparative case study included differing budgetary conditions and the significance of relationships within policy issue networks. However, the QCA and statistical analysis pointed to the importance of political parties and contrasting societal contexts. Notably, state policies that allow greater access to citizen-driven ballot initiatives were consistently associated with lower likelihood of introducing BDSL. ^ Methodologically, these results indicate that a case study approach, while important for eliciting valuable context-specific detail, may fail to detect the influence of overarching, systemic variables, such as party competition. However, QCA and statistical analyses were limited by a lack of existing data to operationalize policy issue networks, and thus may have downplayed the impact of personal interactions. ^ This study contributes to the field of health policy studies in three ways. First, it emphasizes the importance of collegial and consistent relationships among policy issue network members. Second, it calls attention to political party systems in predicting policy outcomes. Finally, a novel approach to interpreting state data in a theoretically significant manner (QCA) has been demonstrated.^