Report SCRP Monitoring and Data Analysis Training Project

Report on the project activities 2003.

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. ^

Complementary and Alternative Medicine and Pain Management

Over the past several years, there has been a growing interest in CAM therapies at UCHC. There are doctors, nurses, researchers and students all actively learning about, researching and using CAM modalities. Among them is Dr. Mitch Kennedy, the first Naturopathic Physician to treat patients at the University of Connecticut Health Center.

Regional Integration and Industrial Location in a Landlocked Spatial Economy

Regional integration proposals often require agreements between countries that differ in geographic size, resource endowments, transportation assets, technologies, and product quality. In this asymmetric setting, questions arise about the potential for mutual gains and the distribution of benefits among industries and workers in each country. This paper examines how regional integration between a small landlocked country and a large neighboring country--with a unique port facility that both nations must use to export goods--affects the wage and location decisions of firms, the allocation of labor, the welfare of each country's workers and firms, and aggregate measures of economic welfare in each country and the region. A simulated spatial labor market model is used to explore the economic effects of various stages of regional integration. Beginning with autarky as a benchmark case, we consider two forms of regional integration: partial mobility (mobile labor with geographically restricted firms); and full mobility (mobile labor and firms) with convergence of production technologies and product quality.

Understanding treatment-related symptoms, symptom management techniques, and symptom management self-efficacy in a sample of non-muscle invasive bladder cancer patients

The current literature available on bladder cancer symptom management from the perspective of the patients themselves is limited. There is also limited psychosocial research specific to bladder cancer patients and no previous studies have developed and validated measures for bladder cancer patients��� symptom management self-efficacy. The purpose of this study was to investigate non-muscle invasive bladder cancer patients��� health related quality of life through two main study objectives: (1) to describe the treatment related symptoms, reported effectiveness of symptom-management techniques, and the advice a sample of non-muscle invasive bladder cancer patients would convey to physicians and future patients; and (2) to evaluate Lepore���s symptom management self-efficacy measure on a sample of non-muscle invasive bladder cancer patients. Methods. A total of twelve (n=12) non-muscle invasive bladder cancer patients participated in an in-depth interview and a sample of 46 (n=4) non-muscle invasive bladder cancer patients participated in the symptom-management self-efficacy survey. Results. A total of five symptom categories emerged for the participants��� 59 reported symptoms. Four symptom management categories emerged out of the 71 reported techniques. A total of 62% of the participants��� treatment related symptom-management techniques were reported as effective in managing their treatment-related symptoms. Five advice categories emerged out of the in-depth interviews: service delivery; medical advice; physician-patient communication; encouragement; and no advice. An exploratory factor analysis indicated a single-factor structure for the total population and a multiple factor structure for three subgroups: all males, married males, and all married participants. Conclusion. These findings can inform physicians and patients of effective symptom-management techniques thus improving patients��� health-related quality of life. The advice these patients��� impart can improve service-delivery and patient education.^

A comparison of labor and delivery management activities in two settings

Similarities and differences in management activities and patient health outcomes between a traditional physician staffed labor and delivery setting and a certified nurse-midwife staffed Birth Center within the same hospital were described. The 950 study subjects, low income, minority women, were classified as low obstetrical risk by a POPRAS score of 25 points or less at time of admission for labor and delivery. The study subjects were similar in demographic, antepartum and intrapartum characteristics; the labor course was problem free for the majority in both settings. There were no remarkable differences in health outcomes between the groups. Management activities varied between settings; these variations were policy related rather than health related. The POPRAS rating system was an accurate predictor for 93% of BC subjects and 85% of LDU subjects. Charge for service was approximately $600 less for BC women; length of stay did not contribute to the difference in charge. Overall, BC respondents to the attitude survey were more satisfied with their labor and delivery experience than L\&DU women. ^

Standardization of data collection for the Lifetime Surveillance of Astronaut Health (LSAH)

Problems due to the lack of data standardization and data management have lead to work inefficiencies for the staff working with the vision data for the Lifetime Surveillance of Astronaut Health. Data has been collected over 50 years in a variety of manners and then entered into a software. The lack of communication between the electronic health record (EHR) form designer, epidemiologists, and optometrists has led to some level to confusion on the capability of the EHR system and how its forms can be designed to fit all the needs of the relevant parties. EHR form customizations or form redesigns were found to be critical for using NASA's EHR system in the most beneficial way for its patients, optometrists, and epidemiologists. In order to implement a protocol, data being collected was examined to find the differences in data collection methods. Changes were implemented through the establishment of a process improvement team (PIT). Based on the findings of the PIT, suggestions have been made to improve the current EHR system. If the suggestions are implemented correctly, this will not only improve efficiency of the staff at NASA and its contractors, but set guidelines for changes in other forms such as the vision exam forms. Because NASA is at the forefront of such research and health surveillance the impact of this management change could have a drastic improvement on the collection of and adaptability of the EHR. Accurate data collection from this 50+ year study is ongoing and is going to help current and future generations understand the implications of space flight on human health. It is imperative that the vast amount of information is documented correctly.^

The Global Plankton Database: an inventory and data from the Former Soviet Union expeditions

At present time, there is a lack of knowledge on the interannual climate-related variability of zooplankton communities of the tropical Atlantic, central Mediterranean Sea, Caspian Sea, and Aral Sea, due to the absence of appropriate databases. In the mid latitudes, the North Atlantic Oscillation (NAO) is the dominant mode of atmospheric fluctuations over eastern North America, the northern Atlantic Ocean and Europe. Therefore, one of the issues that need to be addressed through data synthesis is the evaluation of interannual patterns in species abundance and species diversity over these regions in regard to the NAO. The database has been used to investigate the ecological role of the NAO in interannual variations of mesozooplankton abundance and biomass along the zonal array of the NAO influence. Basic approach to the proposed research involved: (1) development of co-operation between experts and data holders in Ukraine, Russia, Kazakhstan, Azerbaijan, UK, and USA to rescue and compile the oceanographic data sets and release them on CD-ROM, (2) organization and compilation of a database based on FSU cruises to the above regions, (3) analysis of the basin-scale interannual variability of the zooplankton species abundance, biomass, and species diversity.

Non-tariff barriers, integration and the transatlantic economy

We examine the potential impact of TTIP through trade-cost reductions, applying a mix of econometric and computational methods to develop estimates of the benefits (and costs) for the EU, United States, and third countries. Econometric results point to an approximate 80% growth in bilateral trade with an ambitious trade agreement. However, at the same time, computable general equilibrium (CGE) estimates highlight distributional impacts across countries and factors not evident from econometrics alone. Translated through our CGE framework, while bilateral trade increases roughly 80%, there is a fall of about 2.5% in trade with the rest of the world in our central case. The estimated gains in annual consumption range between 1% and 2.25% for the United States and EU, respectively. A purely discriminatory agreement would harm most countries outside the agreement, while the direction of third-country effects hinges critically on whether NTB reductions end up being discriminatory or not. Within the United States and EU, while labour gains across skill categories, the impact on farmers is mixed.