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. ^

The impact of Medicare, Medicaid and Schip Extension Act of 2007 (MMSEA) on the long term acute care hospitals

The Long Term Acute Care Hospitals (LTACH), which serve medically complex patients, have grown tremendously in recent years, by expanding the number of Medicare patient admissions and thus increasing Medicare expenditures (Stark 2004). In an attempt to mitigate the rapid growth of the LTACHs and reduce related Medicare expenditures, Congress enacted Section 114 of P.L. 110-173 (§114) of the Medicare, Medicaid and SCHIP Extension Act (MMSEA) in December 29, 2007 to regulate the LTCAHs industry. MMSEA increased the medical necessity reviews for Medicare admissions, imposed a moratorium on new LTCAHs, and allowed the Centers for Medicare and Medicaid Services (CMS) to recoup Medicare overpayments for unnecessary admissions. ^ This study examines whether MMSEA impacted LTACH admissions, operating margins and efficiency. These objectives were analyzed by comparing LTACH data for 2008 (post MMSEA) and data for 2006-2007 (pre-MMSEA). Secondary data were utilized from the American Hospital Association (AHA) database and the American Hospital Directory (AHD).^ This is a longitudinal retrospective study with a total sample of 55 LTACHs, selected from 396 LTACHs facilities that were fully operational during the study period of 2006-2008. The results of the research found no statistically significant change in total Medicare admissions; instead there was a small but not statistically significant reduction of 5% in Medicare admissions for 2008 in comparison to those for 2006. A statistically significant decrease in mean operating margins was confirmed between the years 2006 and 2008. The LTACHs' Technical Efficiency (TE), as computed by Data Envelopment Analysis (DEA), showed significant decrease in efficiency over the same period. Thirteen of the 55 LTACHs in the sample (24%) in 2006 were calculated as “efficient” utilizing the DEA analysis. This dropped to 13% (7/55) in 2008. Longitudinally, the decrease in efficiency using the DEA extension technique (Malmquist Index or MI) indicated a deterioration of 10% in efficiency over the same period. Interestingly, however, when the sample was stratified into high efficient versus low efficient subgroups (approximately 25% in each group), a comparison of the MIs suggested a significant improvement in Efficiency Change (EC) for the least efficient (MI 0.92022) and reduction in efficiency for the most efficient LTACHs (MI = 1.38761) over same period. While a reduction in efficiency for the most efficient is unexpected, it is not particularly surprising, since efficiency measure can vary over time. An improvement in efficiency, however, for the least efficient should be expected as those LTACHs begin to manage expenses (and controllable resources) more carefully to offset the payment/reimbursement pressures on their margins from MMSEA.^

Patients' compliance with physician's advice in Costa Rica

The penetration of the western-developed pharmaceutical industry in developing nations has had an impact not only on access to medicines but also on the value attached to medicines and the way they are consumed. People in developing countries have more faith in medicines than in doctors. Medicines constitute a large share of government health expenses but little emphasis has been placed on how medicines are being used. This dissertation includes a discussion on the penetration of pharmaceuticals in the Costa Rican society, a thorough literature review on patients' compliance with medical recommendations (including studies conducted in developed and developing countries, factors affecting adherence, issues involved in measuring compliance, treatment compliance models, and strategies to improve patients' recollection and compliance with medical recommendations), results of a compliance survey conducted in Costa Rica, and a presentation of a compliance model for developing societies.^ The Costa Rican survey includes observations on 505 medical encounters involving 13 general practitioners and 1 pediatrician in 1 urban and 2 rural clinics. Home visits yielded information on patients' adherence to medical recommendations on 404 patients and 988 medicines. The level of patients' adherence in Costa Rica is similar to what has been documented in developed societies but the strategies to improve adherence are different. Costa Ricans are prone to follow the behaviors advertised through the media or recommended by persons they consider knowlegeable in health matters and with whom they can have a personal relationship. Programs to improve adherence to medical regimens should include mass media campaigns, a re-organization of the way drugs are being dispensed, and educating health professionals to communicate and establish meaningful relationships with their patients. ^

Assessing the impact of electronic health record technology adoption on hospital labor efficiency

Information technology (IT) in the hospital organization is fast becoming a key asset, particularly in light of recent reform legislation in the United States calling for expanding the role of IT in our health care system. Future payment reductions to hospitals included in current health reform are based on expected improvements in hospital operating efficiency. Since over half of hospital expenses are for labor, improved efficiency in use of labor resources can be critical in meeting this challenge. Policy makers have touted the value of IT investments to improve efficiency in response to payment reductions. ^ This study was the first to directly examine the relationship between electronic health record (EHR) technology and staffing efficiency in hospitals. As the hospital has a myriad of outputs for inpatient and outpatient care, efficiency was measured using an industry standard performance metric – full time equivalent employees per adjusted occupied bed (FTE/AOB). Three hypotheses were tested in this study.^ To operationalize EHR technology adoption, we developed three constructs to model adoption, each of which was tested by separate hypotheses. The first hypothesis that a larger number of EHR applications used by a hospital would be associated with greater staffing efficiency (or lower values of FTE/AOB) was not accepted. Association between staffing efficiency and specific EHR applications was the second hypothesis tested and accepted with some applications showing significant impacts on observed values for FTE/AOB. Finally, the hypothesis that the longer an EHR application was used in a hospital would be associated with greater labor efficiency was not accepted as the model showed few statistically significant relationships to FTE/AOB performance. Generally, there does not appear a strong relationship between EHR usage and improved labor efficiency in hospitals.^ While returns on investment from EHR usage may not come from labor efficiencies, they may be better sought using measures of quality, contribution to an efficient and effective local health care system, and improved customer satisfaction through greater patient throughput.^

The Colic Clinic---a comprehensive program evaluation

Child abuse correlated with excessive infant crying affects millions of families each year, with consequences of the abuse lasting a lifetime. The University Of Texas School Of Medicine's Colic Clinic is currently in the early stages of testing Dr. Harvey Karp's combinatorial soothing technique for infants called "The Happiest Baby on the Block". In order to gauge the program's potential effectiveness, the Colic Clinic Protocol was examined in order to assess the applicability of the intervention to known causal factors of child abuse associated with excessive infant crying. ^ This evaluation also carried out an anticipated cost-benefit breakout analysis for the implementation of the intervention for 100 children and compared the cost of the program implementation to the cost associated with a single instance of child abuse. The analysis revealed that while accounting for materials, advertising, salaried personnel and other overhead expenses, the cost to implement the intervention was less than half the cost of the medical treatment associated with a single victim of whiplash-shaken infant syndrome. ^ Although the program is still in its early evaluative phase, the future implications of this work are extensive. If this intervention is revealed to be relevant and cost effective, it will precipitate sweeping changes in medical education and training, public health detection and prevention programs, and law enforcement.^

Effects of overweight and obesity on economic outcomes among U.S. adults with kidney disease

Background. Kidney disease is a growing public health phenomenon in the U.S. and in the world. Downstream interventions, dialysis and renal transplants covered by Medicare's renal disease entitlement policy in those who are 65 years and over have been expensive treatments that have been not foolproof. The shortage of kidney donors in the U.S. has grown in the last two decades. Therefore study of upstream events in kidney disease development and progression is justified to prevent the rising prevalence of kidney disease. Previous studies have documented the biological route by which obesity can progress and accelerate kidney disease, but health services literature on quantifying the effects of overweight and obesity on economic outcomes in the context of renal disease were lacking. Objectives . The specific aims of this study were (1) to determine the likelihood of overweight and obesity in renal disease and in three specific adult renal disease sub-populations, hypertensive, diabetic and both hypertensive and diabetic (2) to determine the incremental health service use and spending in overweight and obese renal disease populations and (3) to determine who financed the cost of healthcare for renal disease in overweight and obese adult populations less than 65 years of age. Methods. This study was a retrospective cross-sectional study of renal disease cases pooled for years 2002 to 2009 from the Medical Expenditure Panel Survey. The likelihood of overweight and obesity was estimated using chi-square test. Negative binomial regression and generalized gamma model with log link were used to estimate healthcare utilization and healthcare expenditures for six health event categories. Payments by self/family, public and private insurance were described for overweight and obese kidney disease sub-populations. Results. The likelihood of overweight and obesity was 0.29 and 0.46 among renal disease and obesity was common in hypertensive and diabetic renal disease population. Among obese renal disease population, negative binomial regression estimates of healthcare utilization per person per year as compared to normal weight renal disease persons were significant for office-based provider visits and agency home health visits respectively (p=0.001; p=0.005). Among overweight kidney disease population health service use was significant for inpatient hospital discharges (p=0.027). Over years 2002 to 2009, overweight and obese renal disease sub-populations had 53% and 63% higher inpatient facility and doctor expenditures as compared to normal weight renal disease population and these result were statistically significant (p=0.007; p=0.026). Overweigh renal disease population had significant total expenses per person per year for office-based and outpatient associated care. Overweight and obese renal disease persons paid less from out-of-pocket overall compared to normal weight renal disease population. Medicare and Medicaid had the highest mean annual payments for obese renal disease persons, while mean annual payments per year were highest for private insurance among normal weight renal disease population. Conclusion. Overweight and obesity were common in those with acute and chronic kidney disease and resulted in higher healthcare spending and increased utilization of office-based providers, hospital inpatient department and agency home healthcare. Healthcare for overweight and obese renal disease persons younger than 65 years of age was financed more by private and public insurance and less by out of pocket payments. With the increasing epidemic of obesity in the U.S. and the aging of the baby boomer population, the findings of the present study have implications for public health and for greater dissemination of healthcare resources to prevent, manage and delay the onset of overweight and obesity that can progress and accelerate the course of the kidney disease.^