THE NATURAL AND ORTHOGONAL INTERACTION (NOIA) MODELS FOR QUANTITATIVE TRAITS (QTs) AND COMPLEX DISEASES

My dissertation focuses on developing methods for gene-gene/environment interactions and imprinting effect detections for human complex diseases and quantitative traits. It includes three sections: (1) generalizing the Natural and Orthogonal interaction (NOIA) model for the coding technique originally developed for gene-gene (GxG) interaction and also to reduced models; (2) developing a novel statistical approach that allows for modeling gene-environment (GxE) interactions influencing disease risk, and (3) developing a statistical approach for modeling genetic variants displaying parent-of-origin effects (POEs), such as imprinting. In the past decade, genetic researchers have identified a large number of causal variants for human genetic diseases and traits by single-locus analysis, and interaction has now become a hot topic in the effort to search for the complex network between multiple genes or environmental exposures contributing to the outcome. Epistasis, also known as gene-gene interaction is the departure from additive genetic effects from several genes to a trait, which means that the same alleles of one gene could display different genetic effects under different genetic backgrounds. In this study, we propose to implement the NOIA model for association studies along with interaction for human complex traits and diseases. We compare the performance of the new statistical models we developed and the usual functional model by both simulation study and real data analysis. Both simulation and real data analysis revealed higher power of the NOIA GxG interaction model for detecting both main genetic effects and interaction effects. Through application on a melanoma dataset, we confirmed the previously identified significant regions for melanoma risk at 15q13.1, 16q24.3 and 9p21.3. We also identified potential interactions with these significant regions that contribute to melanoma risk. Based on the NOIA model, we developed a novel statistical approach that allows us to model effects from a genetic factor and binary environmental exposure that are jointly influencing disease risk. Both simulation and real data analyses revealed higher power of the NOIA model for detecting both main genetic effects and interaction effects for both quantitative and binary traits. We also found that estimates of the parameters from logistic regression for binary traits are no longer statistically uncorrelated under the alternative model when there is an association. Applying our novel approach to a lung cancer dataset, we confirmed four SNPs in 5p15 and 15q25 region to be significantly associated with lung cancer risk in Caucasians population: rs2736100, rs402710, rs16969968 and rs8034191. We also validated that rs16969968 and rs8034191 in 15q25 region are significantly interacting with smoking in Caucasian population. Our approach identified the potential interactions of SNP rs2256543 in 6p21 with smoking on contributing to lung cancer risk. Genetic imprinting is the most well-known cause for parent-of-origin effect (POE) whereby a gene is differentially expressed depending on the parental origin of the same alleles. Genetic imprinting affects several human disorders, including diabetes, breast cancer, alcoholism, and obesity. This phenomenon has been shown to be important for normal embryonic development in mammals. Traditional association approaches ignore this important genetic phenomenon. In this study, we propose a NOIA framework for a single locus association study that estimates both main allelic effects and POEs. We develop statistical (Stat-POE) and functional (Func-POE) models, and demonstrate conditions for orthogonality of the Stat-POE model. We conducted simulations for both quantitative and qualitative traits to evaluate the performance of the statistical and functional models with different levels of POEs. Our results showed that the newly proposed Stat-POE model, which ensures orthogonality of variance components if Hardy-Weinberg Equilibrium (HWE) or equal minor and major allele frequencies is satisfied, had greater power for detecting the main allelic additive effect than a Func-POE model, which codes according to allelic substitutions, for both quantitative and qualitative traits. The power for detecting the POE was the same for the Stat-POE and Func-POE models under HWE for quantitative traits.

Understanding and Characterizing Shared Decision-Making and Behavioral Intent in Medical Uncertainty

Applying Theoretical Constructs to Address Medical Uncertainty Situations involving medical reasoning usually include some level of medical uncertainty. Despite the identification of shared decision-making (SDM) as an effective technique, it has been observed that the likelihood of physicians and patients engaging in shared decision making is lower in those situations where it is most needed; specifically in circumstances of medical uncertainty. Having identified shared decision making as an effective, yet often a neglected approach to resolving a lack of information exchange in situations involving medical uncertainty, the next step is to determine the way(s) in which SDM can be integrated and the supplemental processes that may facilitate its integration. SDM involves unique types of communication and relationships between patients and physicians. Therefore, it is necessary to further understand and incorporate human behavioral elements - in particular, behavioral intent - in order to successfully identify and realize the potential benefits of SDM. This paper discusses the background and potential interaction between the theories of shared decision-making, medical uncertainty, and behavioral intent. Identifying Shared Decision-Making Elements in Medical Encounters Dealing with Uncertainty A recent summary of the state of medical knowledge in the U.S. reported that nearly half (47%) of all treatments were of unknown effectiveness, and an additional 7% involved an uncertain tradeoff between benefits and harms. Shared decision-making (SDM) was identified as an effective technique for managing uncertainty when two or more parties were involved. In order to understand which of the elements of SDM are used most frequently and effectively, it is necessary to identify these key elements, and understand how these elements related to each other and the SDM process. The elements identified through the course of the present research were selected from basic principles of the SDM model and the “Data, Information, Knowledge, Wisdom” (DIKW) Hierarchy. The goal of this ethnographic research was to identify which common elements of shared decision-making patients are most often observed applying in the medical encounter. The results of the present study facilitated the understanding of which elements patients were more likely to exhibit during a primary care medical encounter, as well as determining variables of interest leading to more successful shared decision-making practices between patients and their physicians. Understanding Behavioral Intent to Participate in Shared Decision-Making in Medically Uncertain Situations Objective: This article describes the process undertaken to identify and validate behavioral and normative beliefs and behavioral intent of men between the ages of 45-70 with regard to participating in shared decision-making in medically uncertain situations. This article also discusses the preliminary results of the aforementioned processes and explores potential future uses of this information which may facilitate greater understanding, efficiency and effectiveness of doctor-patient consultations.Design: Qualitative Study using deductive content analysisSetting: Individual semi-structure patient interviews were conducted until data saturation was reached. Researchers read the transcripts and developed a list of codes.Subjects: 25 subjects drawn from the Philadelphia community.Measurements: Qualitative indicators were developed to measure respondents’ experiences and beliefs related to behavioral intent to participate in shared decision-making during medical uncertainty. Subjects were also asked to complete the Krantz Health Opinion Survey as a method of triangulation.Results: Several factors were repeatedly described by respondents as being essential to participate in shared decision-making in medical uncertainty. These factors included past experience with medical uncertainty, an individual’s personality, and the relationship between the patient and his physician.Conclusions: The findings of this study led to the development of a category framework that helped understand an individual’s needs and motivational factors in their intent to participate in shared decision-making. The three main categories include 1) an individual’s representation of medically uncertainty, 2) how the individual copes with medical uncertainty, and 3) the individual’s behavioral intent to seek information and participate in shared decision-making during times of medically uncertain situations.

An evaluation of the centers for Medicare & Medicaid Services' Hospital Acquired Conditions and Present on Admission Indicator Reporting program

Objective: This dissertation evaluated three aspects of the Centers for Medicare and Medicaid Services' Hospital Acquired Conditions and Present on Admission Indicator Reporting program (HACPOA program) to produce three journal articles for publication. ^ Methods: All payer admission records from state inpatient databases from Arizona, New Jersey and Washington states were analyzed for the year 2008. However some analyses required a sample of adult only Medicare patients in the first two studies. California's inpatient data (2004 – 2010) was also analyzed in the third study to examine the reporting and non-payment program elements' impact on the incidence of hospital acquired conditions. ^ Results: Majority diagnoses reported in inpatient prospective payment systems hospitals were present on admission. However, some diagnoses are still coded as "not present on admission" and "insufficient documentation to determine whether or not conditions are present on admission or not". This is important because it reveals that hospital complications still occur in hospitals. Hospital fall and trauma injuries were the most common hospital acquired conditions observed in this study. Predictors of hospital fall injuries include age, gender, number of diagnoses, number of procedures, number of chronic conditions while predictors of hospital trauma injuries include number of e-codes, number of diagnoses and the presence of chronic conditions on a patient's admission records. Finally, the implementation of the present on admission reporting requirement increased reports of certain hospital acquired conditions while the non-payment policy element in the Hospital Acquired Conditions program reduced the incidence of hospital fall and trauma injuries in particular. ^ Conclusion: The implementation of the Hospital Acquired Conditions and Present on Admission Indicator Reporting program has made the state inpatient database a more useful source of data capable of now identifying hospital complications. The reporting and nonpayment program elements in the HACPOA program have also impacted the incidence of hospital acquired conditions. ^

Estimates of hospital and physician costs of epilepsy in the United States for 1995 comparing the provider -based survey method and a patient -based medical charts and billing method

This investigation compares two different methodologies for calculating the national cost of epilepsy: provider-based survey method (PBSM) and the patient-based medical charts and billing method (PBMC&BM). The PBSM uses the National Hospital Discharge Survey (NHDS), the National Hospital Ambulatory Medical Care Survey (NHAMCS) and the National Ambulatory Medical Care Survey (NAMCS) as the sources of utilization. The PBMC&BM uses patient data, charts and billings, to determine utilization rates for specific components of hospital, physician and drug prescriptions. ^ The 1995 hospital and physician cost of epilepsy is estimated to be $722 million using the PBSM and $1,058 million using the PBMC&BM. The difference of $336 million results from $136 million difference in utilization and $200 million difference in unit cost. ^ Utilization. The utilization difference of $136 million is composed of an inpatient variation of $129 million, $100 million hospital and $29 million physician, and an ambulatory variation of $7 million. The $100 million hospital variance is attributed to inclusion of febrile seizures in the PBSM, $−79 million, and the exclusion of admissions attributed to epilepsy, $179 million. The former suggests that the diagnostic codes used in the NHDS may not properly match the current definition of epilepsy as used in the PBMC&BM. The latter suggests NHDS errors in the attribution of an admission to the principal diagnosis. ^ The $29 million variance in inpatient physician utilization is the result of different per-day-of-care physician visit rates, 1.3 for the PBMC&BM versus 1.0 for the PBSM. The absence of visit frequency measures in the NHDS affects the internal validity of the PBSM estimate and requires the investigator to make conservative assumptions. ^ The remaining ambulatory resource utilization variance is $7 million. Of this amount, $22 million is the result of an underestimate of ancillaries in the NHAMCS and NAMCS extrapolations using the patient visit weight. ^ Unit cost. The resource cost variation is $200 million, inpatient is $22 million and ambulatory is $178 million. The inpatient variation of $22 million is composed of $19 million in hospital per day rates, due to a higher cost per day in the PBMC&BM, and $3 million in physician visit rates, due to a higher cost per visit in the PBMC&BM. ^ The ambulatory cost variance is $178 million, composed of higher per-physician-visit costs of $97 million and higher per-ancillary costs of $81 million. Both are attributed to the PBMC&BM's precise identification of resource utilization that permits accurate valuation. ^ Conclusion. Both methods have specific limitations. The PBSM strengths are its sample designs that lead to nationally representative estimates and permit statistical point and confidence interval estimation for the nation for certain variables under investigation. However, the findings of this investigation suggest the internal validity of the estimates derived is questionable and important additional information required to precisely estimate the cost of an illness is absent. ^ The PBMC&BM is a superior method in identifying resources utilized in the physician encounter with the patient permitting more accurate valuation. However, the PBMC&BM does not have the statistical reliability of the PBSM; it relies on synthesized national prevalence estimates to extrapolate a national cost estimate. While precision is important, the ability to generalize to the nation may be limited due to the small number of patients that are followed. ^

Mineral composition and major element oxides of gabbros from ODP Hole 179-1105A, southwest Indian Ridge

Hole 1105A penetrated 158 m of gabbros at a site offset 1.3 km east-northeast from Hole 735B on the Atlantis Bank near the Atlantis II Fracture Zone. A total of 118 m of dominantly medium- to coarse-grained intercalated Fe-Ti oxide gabbro and olivine gabbro was recovered from Hole 1105A that shows many petrographic features similar to those recovered from the upper part of Hole 735B. The main rock types are distinguished based on the constituent cumulus phases, with the most primitive gabbros consisting of olivine, plagioclase, and clinopyroxene. The inferred crystallization order is subsequently Fe-Ti oxides (ilmenite and titanomagnetite), followed by orthopyroxene, then apatite, and finally biotite. Orthopyroxene appears to replace olivine in a narrow middle interval. The magmatic evolution is likewise reflected in the mineral compositions. Plagioclase varies from An66 to An28. Olivine varies from Fo78 to Fo35. The gap in olivine crystallization occurs between Fo46 and Fo40 and coincides approximately with the appearance of orthopyroxene (~En50). The clinopyroxenes show large compositional variation in Mg/(Mg + Fe total) from 0.84 to 0.51. The nonquadrilateral cations of clinopyroxene similarly show large variations with Ti increasing for the olivine gabbros and decreasing for the Fe-Ti oxide gabbros with the decrease in Mg/(Mg + Fe total). The apatites are mainly flourapatites. The compositional variation in the gabbros is interpreted as a comagmatic suite resulting from fractional crystallization. Pyroxene geothermometry suggests equilibration temperatures from 1100°C and below. The coexisting Fe-Ti oxide minerals indicate subsolidus equilibration temperatures from 900°C for olivine gabbros to 700°C for the most evolved apatite-bearing gabbros. The cryptic variation in the olivine gabbros defines two or three lenses, 40 to 60 m thick, each characterized by a distinct convex zoning with a lower segment indicating upward reverse fractionation, a central maximum, and an upper segment showing normal fractionation. The Fe-Ti oxide gabbros show cryptic variations independent of the host olivine gabbros and reveal a systematic upward normal fractionation trend transgressing host olivine gabbro boundaries. Forward fractional crystallization modeling, using a likely parental magma composition from the Atlantis II Fracture Zone (MgO = 7.2 wt%; Mg/[Mg + Fe2+] = 0.62), closely matches the compositions of coexisting olivine, plagioclase, and clinopyroxene. This modeling suggests cosaturation of olivine, plagioclase, and clinopyroxene from 1155°C and the addition of Fe-Ti oxides from 1100°C. The liquid line of descent initially shows increasing FeO with moderately increasing SiO2. After saturation of Fe-Ti oxides, the liquid strongly decreases in FeO and TiO2 and increases in SiO2, reaching dacitic compositions at ~10% liquid remaining. The calculations indicate that formation of olivine gabbros can be accounted for by <65% fractionation and that only the residual 35% liquid was saturated in Fe-Ti oxides. The modeling of the solid fractionation products shows that both the olivine gabbro and the Fe-Ti oxide gabbros contain very small amounts of trapped liquid (<5%). The implications are that the gabbros represent crystal mush that originated in a recharging and tapping subaxial chamber. Compaction and upward melt migration in the crystal mush appear to have been terminated with relatively large amounts of interstitial liquid remaining in the upper parts of the cumulate mush. This termination may have been caused by tectonic disturbances, uplift, and associated withdrawal of magma into the subaxial dike and sill system. Prolonged compaction and cooling of the trapped melt in the mush formed small differentiated bodies and lenses by pressure release migration and crystallization along syntectonic channels. This resulted in differentiation products along lateral and vertical channelways in the host gabbro that vary from olivine gabbro, to Fe-Ti oxide gabbro, gabbronorite, and apatite gabbros and show large compositional variations independent of the host olivine gabbros.

Paleomagnetic and rock magnetic properties of IODP Expedition 318 cores

The Integrated Ocean Drilling Program Expedition 318 to the Wilkes Land margin of Antarctica recovered a sedimentary succession ranging in age from lower Eocene to the Holocene. Excellent stratigraphic control is key to understanding the timing of paleoceanographic events through critical climate intervals. Drill sites recovered the lower and middle Eocene, nearly the entire Oligocene, the Miocene from about 17 Ma, the entire Pliocene and much of the Pleistocene. The paleomagnetic properties are generally suitable for magnetostratigraphic interpretation, with well-behaved demagnetization diagrams, uniform distribution of declinations, and a clear separation into two inclination modes. Although the sequences were discontinuously recovered with many gaps due to coring, and there are hiatuses from sedimentary and tectonic processes, the magnetostratigraphic patterns are in general readily interpretable. Our interpretations are integrated with the diatom, radiolarian, calcareous nannofossils and dinoflagellate cyst (dinocyst) biostratigraphy. The magnetostratigraphy significantly improves the resolution of the chronostratigraphy, particularly in intervals with poor biostratigraphic control. However, Southern Ocean records with reliable magnetostratigraphies are notably scarce, and the data reported here provide an opportunity for improved calibration of the biostratigraphic records. In particular, we provide a rare magnetostratigraphic calibration for dinocyst biostratigraphy in the Paleogene and a substantially improved diatom calibration for the Pliocene. This paper presents the stratigraphic framework for future paleoceanographic proxy records which are being developed for the Wilkes Land margin cores. It further provides tight constraints on the duration of regional hiatuses inferred from seismic surveys of the region.

A virtual species set for robust and reproducible Species Distribution Modelling tests

Predicting species potential and future distribution has become a relevant tool in biodiversity monitoring and conservation. In this data article we present the suitability map of a virtual species generated based on two bioclimatic variables, and a dataset containing more than 700.000 random observations at the extent of Europe. The dataset includes spatial attributes such as, distance to roads, protected areas, country codes, and the habitat suitability of two spatially clustered species (grassland and forest species) and a wide spread species.