NONLINEAR TIME SERIES/SYSTEM ANALYSIS (STATE-SPACE, DYNAMICS, INTERVENTION, RESILIENCE, KALMAN)

A discussion of nonlinear dynamics, demonstrated by the familiar automobile, is followed by the development of a systematic method of analysis of a possibly nonlinear time series using difference equations in the general state-space format. This format allows recursive state-dependent parameter estimation after each observation thereby revealing the dynamics inherent in the system in combination with random external perturbations.^ The one-step ahead prediction errors at each time period, transformed to have constant variance, and the estimated parametric sequences provide the information to (1) formally test whether time series observations y(,t) are some linear function of random errors (ELEM)(,s), for some t and s, or whether the series would more appropriately be described by a nonlinear model such as bilinear, exponential, threshold, etc., (2) formally test whether a statistically significant change has occurred in structure/level either historically or as it occurs, (3) forecast nonlinear system with a new and innovative (but very old numerical) technique utilizing rational functions to extrapolate individual parameters as smooth functions of time which are then combined to obtain the forecast of y and (4) suggest a measure of resilience, i.e. how much perturbation a structure/level can tolerate, whether internal or external to the system, and remain statistically unchanged. Although similar to one-step control, this provides a less rigid way to think about changes affecting social systems.^ Applications consisting of the analysis of some familiar and some simulated series demonstrate the procedure. Empirical results suggest that this state-space or modified augmented Kalman filter may provide interesting ways to identify particular kinds of nonlinearities as they occur in structural change via the state trajectory.^ A computational flow-chart detailing computations and software input and output is provided in the body of the text. IBM Advanced BASIC program listings to accomplish most of the analysis are provided in the appendix. ^

Origins and evolution of VNTR loci: The apolipoprotein B 3$\sp\prime$ VNTR

I studied the apolipoprotein (apo) B 3$\sp\prime$ variable number tandem repeat (VNTR) and did computer simulations of the stepwise mutation model to address four questions: (1) How did the apo B VNTR originate? (2) What is the mutational mechanism of repeat number change at the apo B VNTR? (3) To what extent are population and molecular level events responsible for the determination of the contemporary apo B allele frequency distribution? (4) Can VNTR allele frequency distributions be explained by a simple and conservative mutation-drift model? I used three general approaches to address these questions: (1) I characterized the apo B VNTR region in non-human primate species; (2) I constructed haplotypes of polymorphic markers flanking the apo B VNTR in a sample of individuals from Lorrain, France and studied the associations between the flanking-marker haplotypes and apo B VNTR size; (3) I did computer simulations of the one-step stepwise mutation model and compared the results to real data in terms of four allele frequency distribution characteristics.^ The results of this work have allowed me to conclude that the apo B VNTR originated after an initial duplication of a sequence which is still present as a single copy sequence in New World monkey species. I conclude that this locus did not originate by the transposition of an array of repeats from somewhere else in the genome. It is unlikely that recombination is the primary mutational mechanism. Furthermore, the clustered nature of these associations implicates a stepwise mutational mechanism. From the high frequencies of certain haplotype-allele size combinations, it is evident that population level events have also been important in the determination of the apo B VNTR allele frequency distribution. Results from computer simulations of the one-step stepwise mutation model have allowed me to conclude that bimodal and multimodal allele frequency distributions are not unexpected at loci evolving via stepwise mutation mechanisms. Short tandem repeat loci fit the stepwise mutation model best, followed by microsatellite loci. I therefore conclude that there are differences in the mutational mechanisms of VNTR loci as classed by repeat unit size. (Abstract shortened by UMI.) ^

Regulation of the expression of {\it mutS, mutL}, and {\it mutH\/} mismatch repair genes in {\it Escherichia coli\/} K-12

Post-replication DNA mismatch repair plays crucial roles in mutation avoidance and maintenance of chromosome stability in both prokaryotes and eukaryotes. In humans, deficiency in this repair system leads to a predisposition for certain cancers. The biochemistry of this repair system has been best studied in a model bacterium Escherichia coli. In this thesis, regulation of expression of mutS, mutL and mutH genes, whose products mediate methyl-directed mismatch (MDM) repair in E. coli, is investigated. One-step affinity purification schemes were developed to purify E. coli MutS, MutL and MutH proteins fused to a His-6-affinity tag. His-6-MutS exhibited the same mismatch binding activity and specificity as the native MutS protein. Purified His-6-MutS, -MutL and -MutH proteins were used to develop quantitative Western blotting assays for amounts of MutS, MuL and MutH proteins under various conditions. It was found that the three proteins were present in relatively low amounts in exponentially growing cells and MutS and MutH were diminished in stationary-phase cells. Further studies indicated that the drop in the amounts of MutS and MutH proteins in stationary-phase cells was mediated through RpoS, a key global regulator of stationary-phase transition. In both exponential- and stationary-phase cells, MutS amount was also negatively regulated by the Hfq (HF-I) global regulator, which is required for RpoS translation, through an RpoS-independent mechanism. $\beta$-galactosidase assays of mutS-lacZ operon and gene fusions suggested that hfq regulates mutS posttranscriptionally, and RNase T2 protection assays revealed that Hfq destabilizes mutS transcripts in exponentially growing cells. To study the relation between regulation of MDM repair and mutagenesis, amounts of MutS, MutL and MutH were measured in starved cells undergoing adaptive mutagenesis. It was found that MutS amount dropped drastically, MutH amount dropped slightly, whereas MutL amount remained essentially constant in starved cells. Overexpression of MutL did not reverse the drop in the amounts of MutS or MutH protein. These results ruled out several explanations for a phenomenon in which overexpression of MutL, but not MutS, reversed adaptive mutagenesis. The findings further suggested that functional MutL is limiting during adaptive mutagenesis. The implications of regulation of the MDM repair are discussed in the context of mutagenesis, pathogenesis and tumorigenesis. ^

Quantifying uncertainty in cost effectiveness analyses

This study compared four alternative approaches (Taylor, Fieller, percentile bootstrap, and bias-corrected bootstrap methods) to estimating confidence intervals (CIs) around cost-effectiveness (CE) ratio. The study consisted of two components: (1) Monte Carlo simulation was conducted to identify characteristics of hypothetical cost-effectiveness data sets which might lead one CI estimation technique to outperform another. These results were matched to the characteristics of an (2) extant data set derived from the National AIDS Demonstration Research (NADR) project. The methods were used to calculate (CIs) for data set. These results were then compared. The main performance criterion in the simulation study was the percentage of times the estimated (CIs) contained the “true” CE. A secondary criterion was the average width of the confidence intervals. For the bootstrap methods, bias was estimated. ^ Simulation results for Taylor and Fieller methods indicated that the CIs estimated using the Taylor series method contained the true CE more often than did those obtained using the Fieller method, but the opposite was true when the correlation was positive and the CV of effectiveness was high for each value of CV of costs. Similarly, the CIs obtained by applying the Taylor series method to the NADR data set were wider than those obtained using the Fieller method for positive correlation values and for values for which the CV of effectiveness were not equal to 30% for each value of the CV of costs. ^ The general trend for the bootstrap methods was that the percentage of times the true CE ratio was contained in CIs was higher for the percentile method for higher values of the CV of effectiveness, given the correlation between average costs and effects and the CV of effectiveness. The results for the data set indicated that the bias corrected CIs were wider than the percentile method CIs. This result was in accordance with the prediction derived from the simulation experiment. ^ Generally, the bootstrap methods are more favorable for parameter specifications investigated in this study. However, the Taylor method is preferred for low CV of effect, and the percentile method is more favorable for higher CV of effect. ^

Mandating the HPV vaccine

Background. HPV is the underlying cause of cervical cancer, a malignant tumor of the female genital tract. Each year, cervical cancer is newly diagnosed in approximately 10,000 women, and over 3,000 women die from the malignancy. In addition, HPV is implicated as a cause of other cancers involving the genital tract, male and female, and the head and neck. ^ Gardasil, a vaccine against HPV, was licensed by the FDA in June 2006. Early study results have shown Gardasil to be safe and effective at preventing HPV infections that are commonly associated with the development of cervical cancer, as well as other HPV-related cancers and genital warts. The vaccine is most effective when administered in childhood, before initial exposure to HPV, which typically occurs shortly after the onset of sexual activity. Accordingly, the CDC's Advisory Committee on Immunization Practices (ACIP) has recommended routine vaccination of females aged 11-12 years. ^ Taking the ACIP recommendation one step further, many states have considered school-based mandates of the HPV vaccine in an attempt to reduce the burden of HPV-related illness, in particular to reduce the disparately high incidence of cervical cancer in medically underserved populations. These mandate attempts have sparked heated debate—highlighting public concerns regarding adolescent sexuality, corporate greed, and vaccines in general. ^ Methods. My research focuses on publicly available sources of information such as medical journals, government reports (federal and state), NGO reports, newspapers, and books. I begin with a background discussion of HPV, cervical cancer, and the HPV vaccine. I then discuss public health policy issues related to vaccines, vaccine mandates, and HPV-related illness. Specifically, I discuss the public health benefit of previous vaccine mandates, the legality of vaccine mandates, and the undue corporate influence on the politics of instituting HPV vaccine mandates. In addition, I examine some of the causes behind the anti-vaccine movement and the controversy surrounding adolescent sexuality as it pertains to the HPV vaccine. In the final section, I focus on the recent failed attempt by Governor Rick Perry to mandate the HPV vaccine in Texas. A retrospective analysis of Governor Perry's policy decisions is undertaken and recommendations are made regarding future attempts to mandate the HPV vaccine, or other vaccines under development for similar sexually transmitted viral diseases such as HIV and herpes simplex. ^ Results. In Texas, as in other states across the country, HPV vaccine mandates faced opposition from those who, while they may support mandates of other vaccines, oppose mandates for the HPV vaccine based largely on the idea that HPV is a sexually transmitted disease—they see responsible sexual behavior as the appropriate method for preventing HPV-related illness. A second major group of opposition comes from those who are generally opposed to all vaccine mandates, due to concerns that mandates are intended primarily for the financial benefit of the pharmaceutical industry or due to concerns—largely unfounded—that vaccines pose a greater health threat than the illnesses they are designed to prevent. ^ Conclusion. In order to reduce opposition to vaccine mandates, care must be taken to educate the public regarding the benefits of vaccination by mobilizing the public health sector, avoid the impression that the decision to institute mandates is rash or pressured by allowing time for open debate, and minimize lobbying efforts by vaccine manufacturers. ^

Gender disparities in utilization, unmet need and expenditure for mental health care

Objectives: To compare mental health care utilization regarding the source, types, and intensity of mental health services received, unmet need for services, and out of pocket cost among non-institutionalized psychologically distressed women and men. ^ Method: Cross-sectional data for 19,325 non-institutionalized mentally distressed adult respondents to the “The National Survey on Drug Use and Health” (NSDUH), for the years 2006 -2008, representing over twenty-nine millions U.S. adults was analyzed. To assess the relative odds for women compared to men, logistic regression analysis was used for source of service, for types of barriers, for unmet need and cost; zero inflated negative binomial regression for intensity of utilization; and ordinal logistic regression analysis for quantifying out-of-pocket expenditure. ^ Results: Overall, 43% of mentally distressed adults utilized a form of mental health treatment; representing 12.6 million U.S psychologically distressed adults. Females utilized more mental health care compared to males in the previous 12 months (OR: 1. 70; 95% CI: 1.54, 1.83). Similarly, females were 54% more likely to get help for psychological distress in an outpatient setting and females were associated with an increased probability of using medication for mental distress (OR: 1.72; 95% CI: 1.63, 1.98). Women were 1.25 times likelier to visit a mental health center (specialty care) than men. ^ Females were positively associated with unmet needs (OR: 1.50; 95% CI: 1.29, 1.75) after taking into account predisposing, enabling, and need (PEN) characteristics. Women with perceived unmet needs were 23% (OR: 0.77; 95% CI: 0.59, 0.99) less likely than men to report societal accommodation (stigma) as a barrier to mental health care. At any given cutoff point, women were 1.74 times likelier to be in the higher payment categories for inpatient out of pocket cost when other variables in the model are held constant. Conclusions: Women utilize more specialty mental healthcare, report more unmet need, and pay more inpatient out of pocket costs than men. These gender disparities exist even after controlling for predisposing, enabling, and need variables. Creating policies that not only provide mental health care access but also de-stigmatize mental illness will bring us one step closer to eliminating gender disparities in mental health care.^

Interruptions in Workflow for RNs in a Level One Trauma Center

An understanding of interruptions in healthcare is important for the design, implementation, and evaluation of health information systems and for the management of clinical workflow and medical errors. The purpose of this study is to identify and classify the types of interruptions experienced by Emergency Department(ED) nurses working in a Level One Trauma Center. This was an observational field study of Registered Nurses (RNs) employed in a Level One Trauma Center using the shadowing method. Results of the study indicate that nurses were both recipients and initiators of interruptions. Telephones, pagers, and face-to-face conversations were the most common sources of interruptions. Unlike other industries, the healthcare community has not systematically studied interruptions in clinical settings to determine and weigh the necessity of the interruption against their sometimes negative results such as medical errors, decreased efficiency, and increased costs. Our study presented here is an initial step to understand the nature, causes, and effects of interruptions, thereby improving both the quality of healthcare and patient safety. We developed an ethnographic data collection technique and a data coding method for the capturing and analysis of interruptions. The interruption data we collected are systematic, comprehensive, and close to exhaustive. They confirmed the findings from earlier studies by other researchers that interruptions are frequent events in critical care and other healthcare settings. We are currently using these data to analyze the workflow dynamics of ED clinicians, to identify the bottlenecks of information flow, and to develop interventions to improve the efficiency of emergency care through the management of interruptions.

Interruptions in workflow for RNs in a Level One Trauma Center.

An understanding of interruptions in healthcare is important for the design, implementation, and evaluation of health information systems and for the management of clinical workflow and medical errors. The purpose of this study is to identify and classify the types of interruptions experienced by ED nurses working in a Level One Trauma Center. This was an observational field study of Registered Nurses employed in a Level One Trauma Center using the shadowing method. Results of the study indicate that nurses were both recipients and initiators of interruptions. Telephone, pagers, and face-to-face conversations were the most common sources of interruptions. Unlike other industries, the outcomes caused by interruptions resulting in medical errors, decreased efficiency and increased cost have not been systematically studied in healthcare. Our study presented here is an initial step to understand the nature, causes, and effects of interruptions, and to develop interventions to manage interruptions to improve healthcare quality and patient safety. We developed an ethnographic data collection technique and a data coding method for the capturing and analysis of interruptions. The interruption data we collected are systematic, comprehensive, and close to exhaustive. They confirmed the findings from early studies by other researchers that interruptions are frequent events in critical care and other healthcare settings. We are currently using these data to analyze the workflow dynamics of ED clinicians, identify the bottlenecks of information flow, and develop interventions to improve the efficiency of emergency care through the management of interruptions.