20 resultados para complex data
em DigitalCommons@The Texas Medical Center
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Clinical Research Data Quality Literature Review and Pooled Analysis We present a literature review and secondary analysis of data accuracy in clinical research and related secondary data uses. A total of 93 papers meeting our inclusion criteria were categorized according to the data processing methods. Quantitative data accuracy information was abstracted from the articles and pooled. Our analysis demonstrates that the accuracy associated with data processing methods varies widely, with error rates ranging from 2 errors per 10,000 files to 5019 errors per 10,000 fields. Medical record abstraction was associated with the highest error rates (70–5019 errors per 10,000 fields). Data entered and processed at healthcare facilities had comparable error rates to data processed at central data processing centers. Error rates for data processed with single entry in the presence of on-screen checks were comparable to double entered data. While data processing and cleaning methods may explain a significant amount of the variability in data accuracy, additional factors not resolvable here likely exist. Defining Data Quality for Clinical Research: A Concept Analysis Despite notable previous attempts by experts to define data quality, the concept remains ambiguous and subject to the vagaries of natural language. This current lack of clarity continues to hamper research related to data quality issues. We present a formal concept analysis of data quality, which builds on and synthesizes previously published work. We further posit that discipline-level specificity may be required to achieve the desired definitional clarity. To this end, we combine work from the clinical research domain with findings from the general data quality literature to produce a discipline-specific definition and operationalization for data quality in clinical research. While the results are helpful to clinical research, the methodology of concept analysis may be useful in other fields to clarify data quality attributes and to achieve operational definitions. Medical Record Abstractor’s Perceptions of Factors Impacting the Accuracy of Abstracted Data Medical record abstraction (MRA) is known to be a significant source of data errors in secondary data uses. Factors impacting the accuracy of abstracted data are not reported consistently in the literature. Two Delphi processes were conducted with experienced medical record abstractors to assess abstractor’s perceptions about the factors. The Delphi process identified 9 factors that were not found in the literature, and differed with the literature by 5 factors in the top 25%. The Delphi results refuted seven factors reported in the literature as impacting the quality of abstracted data. The results provide insight into and indicate content validity of a significant number of the factors reported in the literature. Further, the results indicate general consistency between the perceptions of clinical research medical record abstractors and registry and quality improvement abstractors. Distributed Cognition Artifacts on Clinical Research Data Collection Forms Medical record abstraction, a primary mode of data collection in secondary data use, is associated with high error rates. Distributed cognition in medical record abstraction has not been studied as a possible explanation for abstraction errors. We employed the theory of distributed representation and representational analysis to systematically evaluate cognitive demands in medical record abstraction and the extent of external cognitive support employed in a sample of clinical research data collection forms. We show that the cognitive load required for abstraction in 61% of the sampled data elements was high, exceedingly so in 9%. Further, the data collection forms did not support external cognition for the most complex data elements. High working memory demands are a possible explanation for the association of data errors with data elements requiring abstractor interpretation, comparison, mapping or calculation. The representational analysis used here can be used to identify data elements with high cognitive demands.
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Random Forests™ is reported to be one of the most accurate classification algorithms in complex data analysis. It shows excellent performance even when most predictors are noisy and the number of variables is much larger than the number of observations. In this thesis Random Forests was applied to a large-scale lung cancer case-control study. A novel way of automatically selecting prognostic factors was proposed. Also, synthetic positive control was used to validate Random Forests method. Throughout this study we showed that Random Forests can deal with large number of weak input variables without overfitting. It can account for non-additive interactions between these input variables. Random Forests can also be used for variable selection without being adversely affected by collinearities. ^ Random Forests can deal with the large-scale data sets without rigorous data preprocessing. It has robust variable importance ranking measure. Proposed is a novel variable selection method in context of Random Forests that uses the data noise level as the cut-off value to determine the subset of the important predictors. This new approach enhanced the ability of the Random Forests algorithm to automatically identify important predictors for complex data. The cut-off value can also be adjusted based on the results of the synthetic positive control experiments. ^ When the data set had high variables to observations ratio, Random Forests complemented the established logistic regression. This study suggested that Random Forests is recommended for such high dimensionality data. One can use Random Forests to select the important variables and then use logistic regression or Random Forests itself to estimate the effect size of the predictors and to classify new observations. ^ We also found that the mean decrease of accuracy is a more reliable variable ranking measurement than mean decrease of Gini. ^
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Manuscript 1: “Conceptual Analysis: Externalizing Nursing Knowledge” We use concept analysis to establish that the report tool nurses prepare, carry, reference, amend, and use as a temporary data repository are examples of cognitive artifacts. This tool, integrally woven throughout the work and practice of nurses, is important to cognition and clinical decision-making. Establishing the tool as a cognitive artifact will support new dimensions of study. Such studies can characterize how this report tool supports cognition, internal representation of knowledge and skills, and external representation of knowledge of the nurse. Manuscript 2: “Research Methods: Exploring Cognitive Work” The purpose of this paper is to describe a complex, cross-sectional, multi-method approach to study of personal cognitive artifacts in the clinical environment. The complex data arrays present in these cognitive artifacts warrant the use of multiple methods of data collection. Use of a less robust research design may result in an incomplete understanding of the meaning, value, content, and relationships between personal cognitive artifacts in the clinical environment and the cognitive work of the user. Manuscript 3: “Making the Cognitive Work of Registered Nurses Visible” Purpose: Knowledge representations and structures are created and used by registered nurses to guide patient care. Understanding is limited regarding how these knowledge representations, or cognitive artifacts, contribute to working memory, prioritization, organization, cognition, and decision-making. The purpose of this study was to identify and characterize the role a specific cognitive artifact knowledge representation and structure as it contributed to the cognitive work of the registered nurse. Methods: Data collection was completed, using qualitative research methods, by shadowing and interviewing 25 registered nurses. Data analysis employed triangulation and iterative analytic processes. Results: Nurse cognitive artifacts support recall, data evaluation, decision-making, organization, and prioritization. These cognitive artifacts demonstrated spatial, longitudinal, chronologic, visual, and personal cues to support the cognitive work of nurses. Conclusions: Nurse cognitive artifacts are an important adjunct to the cognitive work of nurses, and directly support patient care. Nurses need to be able to configure their cognitive artifact in ways that are meaningful and support their internal knowledge representations.
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The haloarchaeal phototaxis receptor sensory rhodopsin I (SRI) in complex with its transducer HtrI delivers an attractant signal from excitation with an orange photon and a repellent signal from a second near-UV photon excitation. Using a proteoliposome system with purified SRI in complex with its transducer HtrI, we identified by site-directed fluorescence labeling a site (Ser(155)) on SRI that is conformationally active in signal relay to HtrI. Using site-directed spin labeling of Ser(155)Cys with a nitroxide side chain, we detected a change in conformation following one-photon excitation such that the spin probe exhibits a splitting of the outer hyperfine extrema (2A'(zz)) significantly smaller than that of the electron paramagnetic resonance spectrum in the dark state. The dark conformations of five mutant complexes that do not discriminate between orange and near-UV excitation show shifts to lower or higher 2A'(zz) values correlated with the alterations in their motility behavior to one- and two-photon stimuli. These data are interpreted in terms of a model in which the dark complex is populated by two conformers in the wild type, one that inhibits the CheA kinase (A) and the other that activates it (R), shifted in the dark by mutations and shifted in the wild-type SRI-HtrI complex in opposite directions by one-photon and two-photon reactions.
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Type IV secretion (T4S) systems translocate DNA and protein effectors through the double membrane of Gram-negative bacteria. The paradigmatic T4S system in Agrobacterium tumefaciens is assembled from 11 VirB subunits and VirD4. Two subunits, VirB9 and VirB7, form an important stabilizing complex in the outer membrane. We describe here the NMR structure of a complex between the C-terminal domain of the VirB9 homolog TraO (TraO(CT)), bound to VirB7-like TraN from plasmid pKM101. TraO(CT) forms a beta-sandwich around which TraN winds. Structure-based mutations in VirB7 and VirB9 of A. tumefaciens show that the heterodimer interface is conserved. Opposite this interface, the TraO structure shows a protruding three-stranded beta-appendage, and here, we supply evidence that the corresponding region of VirB9 of A. tumefaciens inserts in the membrane and protrudes extracellularly. This complex structure elucidates the molecular basis for the interaction between two essential components of a T4S system.
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Tumor specific immunity is mediated by cytotoxic T lymphocytes (CTL) that recognize peptide antigen (Ag) in the context of major histocompatibility complex (MHC) class I molecules and by helper T (Th) lymphocytes that recognize peptide Ag in the context of MHC class II molecules. The purpose of this study is (1) to induce or augment the immunogenicity of nonimmunogenic or weakly immunogenic tumors by genetic modification of tumor cells, and (2) to use these genetically altered cells in cancer immunotherapy. To study this, I transfected a highly tumorigenic murine melanoma cell line (K1735) that did not express constitutively either MHC class I or II molecules with syngeneic cloned MHC class I and/or class II genes, and then determined the tumorigenicity of transfected cells in normal C3H mice. K1735 transfectants expressing either $\rm K\sp{k}$ or $\rm A\sp{k}$ molecules alone produced tumors in normal C3H mice, whereas most transfectants that expressed both molecules were rejected in normal C3H mice but produced tumors in nude mice. The rejection of K1735 transfectants expressing $\rm K\sp{k}$ and $\rm A\sp{k}$ Ag in normal C3H mice required both $\rm CD4\sp+$ and $\rm CD8\sp+$ T cells. Interestingly, the $\rm A\sp{k}$ requirement can be substituted by IL-2 because transfection of $\rm K\sp{k}$-positive/A$\sp{\rm k}$-negative K1735 cells with the IL-2 gene also resulted in abrogation of tumorigenicity in normal C3H mice but not in nude mice. In addition, 1735 $(\rm I\sp+II\sp+)$ transfected cells can function as antigen presenting cells (APC) since they could process and present native hen egg lysozyme (HEL) to HEL specific T cell hybridomas. Furthermore, the transplantation immunity induced by K1735 transfectants expressing both $\rm K\sp{k}$ and $\rm A\sp{k}$ molecules completely cross-protected mice against challenge with $\rm K\sp{k}$-positive transfectants but weakly protected them against challenge with parental K1735 cells or $\rm A\sp{k}$-positive transfectants. Finally, I demonstrated that MHC $(\rm I\sp+II\sp+)$ or $\rm K\sp{k}$-positive/IL-2-positive cells can function as anti-cancer vaccines since they can abrogate the growth of established tumors and metastasis.^ In summary, my results indicate that expression of either MHC class I or II molecule alone is insufficient to cause the rejection of K1735 melanoma in syngeneic hosts and that both molecules are necessary. In addition, my data suggest that the failure of $\rm K\sp{k}$-positive K1735 cells to induce a primary tumor-rejection response in normal C3H mice may be due to their inability to induce the helper arm of the anti-tumor immune response. Finally, the ability of MHC $(\rm I\sp+II\sp+)$ or $\rm K\sp{k}$-positive/IL-2-positive cells to prevent growth of established tumors or metastasis suggests that these cell lines can serve as potential vaccines for the immunotherapy of cancer. (Abstract shortened by UMI.) ^
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This study describes the patterns of occurrence of amyotrophic lateral sclerosis (ALS) and parkinsonism-dementia complex (PDC) of Guam during 1950-1989. Both ALS and PDC occur with high frequency among the indigenous Chamorro population, first recognized in the early 1950's. Reports in the early 1980's indicated that both ALS and PDC were disappearing, due to a purported reduction in exposure to harmful environmental factors as a result of the dramatic changes in lifestyle that took place after World War II. However, this study provides compelling evidence that ALS and PDC have not disappeared on Guam and that rates for both are higher during 1980-1989 than previously reported.^ The patterns of occurrence for both ALS and PDC overlap in most respects: (1) incidence and mortality are decreasing; (2) median age at onset is increasing; (3) males are at increased risk for developing disease; (4) risk is higher for those residing in the south compared to the non-south; and (5) age-specific incidence is decreasing over time except in the oldest age groups.^ Age-specific incidence of ALS and PDC, separately and together, is generally higher for cohorts born before 1920 than for those born after 1920. A significant birth cohort effect on the incidence of PDC for the 1906-1915 birth cohort was found, but not for ALS and for ALS and PDC together. Whether or not a cohort effect, period effect, or both are associated with incidence of ALS and PDC cannot be determined from the data currently available and will require additional follow-up of individuals born after 1920.^ The epidemiological data amassed over this 40-year period provide evidence that supports an environmental exposure model for disease occurrence as opposed to a simple genetic or infectious disease model. Whether neurodegenerative disease in this population occurs as a consequence of a single exposure or is explained by a multifactorial model such as a genetic predisposition with some environmental interaction is yet to be determined. However, descriptive studies such as this can provide clues concerning timing and location of potential adverse exposures but cannot determine etiology, underscoring the urgent need for analytic studies of ALS and PDC to further investigate existing etiologic hypotheses and to test new hypotheses. ^
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mRNA 3′ polyadenylation is central to mRNA biogenesis in prokaryotes and eukaryotes, and is implicated in numerous aspects of mRNA metabolism, including efficiency of mRNA export from the nucleus, message stability, and initiation of translation. However, due to the great complexity of the eukaryotic polyadenylation apparatus, the mechanisms of RNA 3 ′ end processing have remained elusive. Although the RNA processing reactions leading to polyadenylated messenger RNA have been studied in many systems, and much progress has been made, a complete understanding of the biochemistry of the poly(A) polymerase enzyme is still lacking. My research uses Vaccinia virus as a model system to gain a better understanding of this complicated polyadenylation process, which consist of RNA binding, catalysis and polymerase translocation. ^ Vaccinia virus replicates in the cytoplasm of its host cell, so it must employ its own poly(A) polymerase (PAP), a heterodimer of two virus encoded proteins, VP55 and VP39. VP55 is the catalytic subunit, adding 30 adenylates to a non-polyadenylated RNA in a rapid processive manner before abruptly changing to a slow, non-processive mode of adenylate addition and dissociating from the RNA. VP39 is the stimulatory subunit. It has no polyadenylation catalytic activity by itself, but when associated with VP55 it facilitates the semi-processive synthesis of tails several hundred adenylates in length. ^ Oligonucleotide selection and competition studies have shown that the heterodimer binds a minimal motif of (rU)2 (N)25 U, the “heterodimer binding motif”, within an oligonucleotide, and its primer selection for polyadenylation is base-type specific. ^ Crosslinking studies using photosensitive uridylate analogs show that within a VP55-VP39-primer ternary complex, VP55 comes into contact with all three required uridylates, while VP39 only contacts the downstream uridylate. Further studies, using a backbone-anchored photosensitive crosslinker show that both PAP subunits are in close proximity to the downstream −10 to −21 region of 50mer model primers containing the heterodimer binding motif. This equal crosslinking to both subunits suggests that the dimerization of VP55 and VP39 creates either a cleft or a channel between the two subunits through which this region of RNA passes. ^ Peptide mapping studies of VP39 covalently crosslinked to the oligonucleotide have identified residue R107 as the amino acid in close proximity to the −10 uridylate. This helps us project a conceptual model onto the known physical surface of this subunit. In the absence of any tertiary structural data for VP55, we have used a series of oligonucleotide selection assays, as well as crosslinking, nucleotide transfer assays, and gel shift assays to gain insight into the requirements for binding, polyadenylation and translocation. Collectively, these data allow us to put together a comprehensive model of the structure and function of the polyadenylation ternary complex consisting of VP39, VP55 and RNA. ^
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Mycobacterium avium complex (MAC) is a ubiquitous organism responsible for most pulmonary and disseminated disease caused by non-tuberculosis (NTM) mycobacteria. Though MAC lung disease without predisposing factors is uncommon, in recent years it has been increasingly described in middle-aged and elderly women. Recognition and correct diagnosis, is often delayed due to the indolent nature of the disease. It is unclear if these women have significant clinical disease as or if their airways are simply colonized by the bacterium. This study describes the clinical presentation, identifies risk factors, and describes the clinical significance of MAC lung disease in HIV-negative women aged 50 or greater. ^ A hybrid study design utilizing both cross-sectional and case-control methodologies was used. A comparison population was selected from previously identified tuberculosis suspects found throughout Harris County. The study population had at least one acid fast bacillus pulmonary culture performed between 1/1/1998 and 12/31/2000 from a pulmonary source. Clinical presentation and symptoms were analyzed using a cross-sectional design. Past medical history and other risk factors were evaluated using a traditional case-control study design. Differences in categorical variables were estimated with the Chi Square or Fisher's Exact test as appropriate. Odds ratios and 95% confidence intervals were utilized to evaluate associations. Multivariate logistic regression was used to identify predictive factors for MAC. All statistical tests were two-sided and P-values <0.05 were considered statistically significant. ^ Culture confirmed MAC pulmonary cases were more likely to be white, have bronchiectasis, scoliosis, evidence of cavitation and pleural changes on chest radiography and granulomas on histopathologic examination than women whose pulmonary cultures were AFB negative. After controlling for selected risk factors, white race continued to be significantly associated with MAC lung disease (OR = 4.6, 95% CI = 2.3, 9.2). In addition, asthma history, smoking history and alcohol use were less likely to be evident among MAC cases in a multivariate analysis. Right upper and right middle lobe disease was further noted among clinically significant cases. Based on population data, MAC lung disease appears to represent a significant clinical syndrome in HIV-negative women thus supporting the theory of the Lady Windermere Syndrome. ^
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Linkage and association studies are major analytical tools to search for susceptibility genes for complex diseases. With the availability of large collection of single nucleotide polymorphisms (SNPs) and the rapid progresses for high throughput genotyping technologies, together with the ambitious goals of the International HapMap Project, genetic markers covering the whole genome will be available for genome-wide linkage and association studies. In order not to inflate the type I error rate in performing genome-wide linkage and association studies, multiple adjustment for the significant level for each independent linkage and/or association test is required, and this has led to the suggestion of genome-wide significant cut-off as low as 5 × 10 −7. Almost no linkage and/or association study can meet such a stringent threshold by the standard statistical methods. Developing new statistics with high power is urgently needed to tackle this problem. This dissertation proposes and explores a class of novel test statistics that can be used in both population-based and family-based genetic data by employing a completely new strategy, which uses nonlinear transformation of the sample means to construct test statistics for linkage and association studies. Extensive simulation studies are used to illustrate the properties of the nonlinear test statistics. Power calculations are performed using both analytical and empirical methods. Finally, real data sets are analyzed with the nonlinear test statistics. Results show that the nonlinear test statistics have correct type I error rates, and most of the studied nonlinear test statistics have higher power than the standard chi-square test. This dissertation introduces a new idea to design novel test statistics with high power and might open new ways to mapping susceptibility genes for complex diseases. ^
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Pulmonary fibrosis (PF) is the result of a variety of environmental and cancer treatment related insults and is characterized by excessive deposition of collagen. Gas exchange in the alveoli is impaired as the normal lung becomes dense and collapsed leading to a loss of lung volume. It is now accepted that lung injury and fibrosis are in part genetically regulated. ^ Bleomycin is a chemotherapeutic agent used for testicular cancer and lymphomas that induces significant pulmonary toxicity. We delivered bleomycin to mice subcutaneously via a miniosmotic pump in order to elicit lung injury (LI) and quantified the %LI morphometrically using video imaging software. We previously identified a quantitative trait loci, Blmpf-1(LOD=17.4), in the Major Histocompatibility Complex (MHC), but the exact genetic components involved have remained unknown. ^ In the current studies, Blmpf-1 was narrowed to an interval spanning 31.9-32.9Mb on Chromosome 17 using MHC Congenic mice. This region includes the MHC Class II and III genes, and is flanked by the TNF-alpha super locus and MHC Class I genes. Knockout mice of MHC Class I genes (B2mko), MHC Class II genes (Cl2ko), and TNF-alpha (TNF-/-) and its receptors (p55-/-, p75-/-, and p55/p75-/-) were treated with bleomycin in order to ascertain the role of these genes in the pathogenesis of lung injury. ^ Cl2ko mice had significantly better survival and %LI when compared to treated background BL/6 (B6, P<.05). In contrast, B2mko showed no differences in survival or %LI compared to B6. This suggests that the MHC Class II locus contains susceptibility genes for bleomycin-induced lung injury. ^ TNF-alpha, a Class III gene, was examined and it was found that TNF-/- and p55-/- mice had higher %LI and lower survival when compared to B6 (P<.05). In contrast, p75-/- mice had significantly reduced %LI when compared to TNF-/-, p55-/-, and B6 mice as well as higher survival (P<.01). These data contradict the current paradigm that TNF-alpha is a profibrotic mediator of lung injury and suggest a novel and distinct role for the p55 and p75 receptors in mediating lung injury. ^
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Cancer is the second leading cause of death in the United States. With the advent of new technologies, changes in health care delivery, and multiplicity of provider types that patients must see, cancer care management has become increasingly complex. The availability of cancer health information has been shown to help cancer patients cope with the management and effects of their cancers. As a result, more cancer patients are using the internet to find resources that can aid in decision-making and recovery. ^ The Health Information National Trends Survey (HINTS) is a nationally representative survey designed to collect information about the experiences of cancer and non-cancer adults with health information sources. The HINTS survey focused on both conventional sources as well as newer technologies, particularly the internet. This study is a descriptive analysis of the HINTS 2003 and HINTS 2005 survey data. The purpose of the research is to explore the general trends in health information seeking and use by US adults, and especially by cancer patients. ^ From 2003 to 2005, internet use for various health-related activities appears to have increased among adults with and without cancer. Differences were found between the groups in the general trust in information media, particularly the internet. Non-cancer respondents tended to have greater trust in information media than cancer respondents. ^ The latter portion of this work examined characteristics of HINTS respondents that were thought to be relevant to how much trust individuals placed in the internet as a source of health information. Trust in health information from the internet was significantly greater among younger adults, higher-earning households, internet users, online seekers of health or cancer information, and those who found online cancer information useful. ^
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In the United States, “binge” drinking among college students is an emerging public health concern due to the significant physical and psychological effects on young adults. The focus is on identifying interventions that can help decrease high-risk drinking behavior among this group of drinkers. One such intervention is Motivational interviewing (MI), a client-centered therapy that aims at resolving client ambivalence by developing discrepancy and engaging the client in change talk. Of late, there is a growing interest in determining the active ingredients that influence the alliance between the therapist and the client. This study is a secondary analysis of the data obtained from the Southern Methodist Alcohol Research Trial (SMART) project, a dismantling trial of MI and feedback among heavy drinking college students. The present project examines the relationship between therapist and client language in MI sessions on a sample of “binge” drinking college students. Of the 126 SMART tapes, 30 tapes (‘MI with feedback’ group = 15, ‘MI only’ group = 15) were randomly selected for this study. MISC 2.1, a mutually exclusive and exhaustive coding system, was used to code the audio/videotaped MI sessions. Therapist and client language were analyzed for communication characteristics. Overall, therapists adopted a MI consistent style and clients were found to engage in change talk. Counselor acceptance, empathy, spirit, and complex reflections were all significantly related to client change talk (p-values ranged from 0.001 to 0.047). Additionally, therapist ‘advice without permission’ and MI Inconsistent therapist behaviors were strongly correlated with client sustain talk (p-values ranged from 0.006 to 0.048). Simple linear regression models showed a significant correlation between MI consistent (MICO) therapist language (independent variable) and change talk (dependent variable) and MI inconsistent (MIIN) therapist language (independent variable) and sustain talk (dependent variable). The study has several limitations such as small sample size, self-selection bias, poor inter-rater reliability for the global scales and the lack of a temporal measure of therapist and client language. Future studies might consider a larger sample size to obtain more statistical power. In addition the correlation between therapist language, client language and drinking outcome needs to be explored.^
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The purpose of this Continuing Education Course is to provide oral health professionals with information to address the unique dental needs of medically complex children. The objective is to train dentists to treat special needs patients so these children have more access to oral healthcare. ^ Under the auspice of Dell Children Hospital of Austin, Lisa Jacob DDS MS is administering this Continuing Education Course for dentists and dental staff from the 46 counties of central Texas served by the hospital.^ Needs assessment was determined through a survey questionnaire to collect data about the number of special needs patients seen by general dentists in Central Texas.^ In recent years, an increasing number of continuing education courses have been developed to help dentists learn techniques for providing dentistry in more understanding ways to patients with special needs. Dentists and dental staff are trained to provide care specifically in dentistry, regardless of who the patient is. This means dentists can perform a clinical examination, carry out procedures to diagnose and treat oral diseases, and provide restorations such as fillings and crowns. ^ Four prominent speakers will provide an instructional tool to address the need for dentists to increase their competence and comfort level in caring for individuals with developmental disabilities. Each speaker will address one of the most frequently encountered cases of medically complex children. The four topics selected by Dr. Lisa Jacob are Cancer, Mental Disability, Downs Syndrome, and Craniofacial Syndromes.^ The public health implications of this continuing education course are presented in providing dental service to this underserved population. When general dentist turn away patients with special needs because of lack of knowledge to treat them, these patients will, more than likely, postpone or abandon needed dental visits because of difficulties reaching pediatric dentists who may not be available in certain areas.^
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Next-generation DNA sequencing platforms can effectively detect the entire spectrum of genomic variation and is emerging to be a major tool for systematic exploration of the universe of variants and interactions in the entire genome. However, the data produced by next-generation sequencing technologies will suffer from three basic problems: sequence errors, assembly errors, and missing data. Current statistical methods for genetic analysis are well suited for detecting the association of common variants, but are less suitable to rare variants. This raises great challenge for sequence-based genetic studies of complex diseases.^ This research dissertation utilized genome continuum model as a general principle, and stochastic calculus and functional data analysis as tools for developing novel and powerful statistical methods for next generation of association studies of both qualitative and quantitative traits in the context of sequencing data, which finally lead to shifting the paradigm of association analysis from the current locus-by-locus analysis to collectively analyzing genome regions.^ In this project, the functional principal component (FPC) methods coupled with high-dimensional data reduction techniques will be used to develop novel and powerful methods for testing the associations of the entire spectrum of genetic variation within a segment of genome or a gene regardless of whether the variants are common or rare.^ The classical quantitative genetics suffer from high type I error rates and low power for rare variants. To overcome these limitations for resequencing data, this project used functional linear models with scalar response to develop statistics for identifying quantitative trait loci (QTLs) for both common and rare variants. To illustrate their applications, the functional linear models were applied to five quantitative traits in Framingham heart studies. ^ This project proposed a novel concept of gene-gene co-association in which a gene or a genomic region is taken as a unit of association analysis and used stochastic calculus to develop a unified framework for testing the association of multiple genes or genomic regions for both common and rare alleles. The proposed methods were applied to gene-gene co-association analysis of psoriasis in two independent GWAS datasets which led to discovery of networks significantly associated with psoriasis.^