Latent variable models in statistical genetics

Understanding the complexities that are involved in the genetics of multifactorial diseases is still a monumental task. In addition to environmental factors that can influence the risk of disease, there is also a number of other complicating factors. Genetic variants associated with age of disease onset may be different from those variants associated with overall risk of disease, and variants may be located in positions that are not consistent with the traditional protein coding genetic paradigm. Latent Variable Models are well suited for the analysis of genetic data. A latent variable is one that we do not directly observe, but which is believed to exist or is included for computational or analytic convenience in a model. This thesis presents a mixture of methodological developments utilising latent variables, and results from case studies in genetic epidemiology and comparative genomics. Epidemiological studies have identified a number of environmental risk factors for appendicitis, but the disease aetiology of this oft thought useless vestige remains largely a mystery. The effects of smoking on other gastrointestinal disorders are well documented, and in light of this, the thesis investigates the association between smoking and appendicitis through the use of latent variables. By utilising data from a large Australian twin study questionnaire as both cohort and case-control, evidence is found for the association between tobacco smoking and appendicitis. Twin and family studies have also found evidence for the role of heredity in the risk of appendicitis. Results from previous studies are extended here to estimate the heritability of age-at-onset and account for the eect of smoking. This thesis presents a novel approach for performing a genome-wide variance components linkage analysis on transformed residuals from a Cox regression. This method finds evidence for a dierent subset of genes responsible for variation in age at onset than those associated with overall risk of appendicitis. Motivated by increasing evidence of functional activity in regions of the genome once thought of as evolutionary graveyards, this thesis develops a generalisation to the Bayesian multiple changepoint model on aligned DNA sequences for more than two species. This sensitive technique is applied to evaluating the distributions of evolutionary rates, with the finding that they are much more complex than previously apparent. We show strong evidence for at least 9 well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least 7 classes in an alignment of four mammals, including human. A pattern of enrichment and depletion of genic regions in the profiled segments suggests they are functionally significant, and most likely consist of various functional classes. Furthermore, a method of incorporating alignment characteristics representative of function such as GC content and type of mutation into the segmentation model is developed within this thesis. Evidence of fine-structured segmental variation is presented.

A critical analysis of sperm donation practices : the personal and social effects of disrupting the unity of biological and social relatedness for the offspring

This thesis critically analyses sperm donation practices from a child-centred perspective. It examines the effects, both personal and social, of disrupting the unity of biological and social relatedness in families affected by donor conception. It examines how disruption is facilitated by a process of mediation which is detailed using a model provided by Sunderland (2002). This model identifies mediating movements - alienation, translation, re-contextualisation and absorption - which help to explain the powerful and dominating material, and social and political processes which occur in biotechnology, or in reproductive technology in this case. The understanding of such movements and mediation of meanings is inspired by the complementary work of Silverstone (1999) and Sunderland. This model allows for a more critical appreciation of the movement of meaning from previously inalienable aspects of life to alienable products through biotechnology (Sunderland, 2002). Once this mediation in donor conception is subjected to critical examination here, it is then approached from different angles of investigation. The thesis posits that two conflicting notions of the self are being applied to fertility-frustrated adults and the offspring of reproductive interventions. Adults using reproductive interventions receive support to maximise their genetic continuity, but in so doing they create and dismiss the corresponding genetic discontinuity produced for the offspring. The offspring’s kinship and identity are then framed through an experimental postmodernist notion, presenting them as social rather than innate constructs. The adults using the reproductive intervention, on the other hand, have their identity and kinship continuity framed and supported as normative, innate, and based on genetic connection. This use of shifting frameworks is presented as unjust and harmful, creating double standards and a corrosion of kinship values, connection and intelligibility between generations; indeed, it is put forward as adult-centric. The analysis of other forms of human kinship dislocation provided by this thesis explores an under-utilised resource which is used to counter the commonly held opinion that any disruption of social and genetic relatedness for donor offspring is insignificant. The experiences of adoption and the stolen generations are used to inform understanding of the personal and social effects of such kinship disruption and potential reunion for donor offspring. These examples, along with laws governing international human rights, further strengthen the appeal here for normative principles and protections based on collective knowledge and standards to be applied to children of reproductive technology. The thesis presents the argument that the framing and regulation of reproductive technology is excessively influenced by industry providers and users. The interests of these parties collide with and corrode any accurate assessments and protections afforded to the children of reproductive technology. The thesis seeks to counter such encroachments and concludes by presenting these protections, frameworks, and human experiences as resources which can help to address the problems created for the offspring of such reproductive interventions, thereby illustrating why these reproductive interventions should be discontinued.

Effects of pediatric obesity on joint kinematics and kinetics during 2 walking cadences

Objective: To determine whether differences existed in lower-extremity joint biomechanics during self-selected walking cadence (SW) and fast walking cadence (FW) in overweight- and normal-weight children.---------- Design: Survey.---------- Setting: Institutional gait study center.---------- Participants: Participants (N=20; mean age ± SD, 10.4±1.6y) from referred and volunteer samples were classified based on body mass index percentiles and stratified by age and sex. Exclusion criteria were a history of diabetes, neuromuscular disorder, or recent lower-extremity injury.---------- Main Outcome Measures: Sagittal, frontal, and transverse plane angular displacements (degrees) and peak moments (newton meters) at the hip, knee, and ankle joints.---------- Results: The level of significance was set at P less than .008. Compared with normal-weight children, overweight children had greater absolute peak joint moments at the hip (flexor, extensor, abductor, external rotator), the knee (flexor, extensor, abductor, adductor, internal rotator), and the ankle (plantarflexor, inverter, external/internal rotators). After including body weight as a covariate, overweight children had greater peak ankle dorsiflexor moments than normal-weight children. No kinematic differences existed between groups. Greater peak hip extensor moments and less peak ankle inverter moments occurred during FW than SW. There was greater angular displacement during hip flexion as well as less angular displacement at the hip (extension, abduction), knee (flexion, extension), and ankle (plantarflexion, inversion) during FW than SW.---------- Conclusions: Overweight children experienced increased joint moments, which can have long-term orthopedic implications and suggest a need for more nonweight-bearing activities within exercise prescription. The percent of increase in joint moments from SW to FW was not different for overweight and normal-weight children. These findings can be used in developing an exercise prescription that must involve weight-bearing activity.

Infrared spectroscopic investigation of the effects of titania photocatalyst on the degradation of linear low density polyethylene film for commercial applications

There is a need in industry for a commodity polyethylene film with controllable degradation properties that will degrade in an environmentally neutral way, for applications such as shopping bags and packaging film. Additives such as starch have been shown to accelerate the degradation of plastic films, however control of degradation is required so that the film will retain its mechanical properties during storage and use, and then degrade when no longer required. By the addition of a photocatalyst it is hoped that polymer film will breakdown with exposure to sunlight. Furthermore, it is desired that the polymer film will degrade in the dark, after a short initial exposure to sunlight. Research has been undertaken into the photo- and thermo-oxidative degradation processes of 25 ìm thick LLDPE (linear low density polyethylene) film containing titania from different manufacturers. Films were aged in a suntest or in an oven at 50 °C, and the oxidation product formation was followed using IR spectroscopy. Degussa P25, Kronos 1002, and various organic-modified and doped titanias of the types Satchleben Hombitan and Hunstsman Tioxide incorporated into LLDPE films were assessed for photoactivity. Degussa P25 was found to be the most photoactive with UVA and UVC exposure. Surface modification of titania was found to reduce photoactivity. Crystal phase is thought to be among the most important factors when assessing the photoactivity of titania as a photocatalyst for degradation. Pre-irradiation with UVA or UVC for 24 hours of the film containing 3% Degussa P25 titania prior to aging in an oven resulted in embrittlement in ca. 200 days. The multivariate data analysis technique PCA (principal component analysis) was used as an exploratory tool to investigate the IR spectral data. Oxidation products formed in similar relative concentrations across all samples, confirming that titania was catalysing the oxidation of the LLDPE film without changing the oxidation pathway. PCA was also employed to compare rates of degradation in different films. PCA enabled the discovery of water vapour trapped inside cavities formed by oxidation by titania particles. Imaging ATR/FTIR spectroscopy with high lateral resolution was used in a novel experiment to examine the heterogeneous nature of oxidation of a model polymer compound caused by the presence of titania particles. A model polymer containing Degussa P25 titania was solvent cast onto the internal reflection element of the imaging ATR/FTIR and the oxidation under UVC was examined over time. Sensitisation of 5 ìm domains by titania resulted in areas of relatively high oxidation product concentration. The suitability of transmission IR with a synchrotron light source to the study of polymer film oxidation was assessed as the Australian Synchrotron in Melbourne, Australia. Challenges such as interference fringes and poor signal-to-noise ratio need to be addressed before this can become a routine technique.

Stroke education : promising effects on the health beliefs of those at risk

Background: The effect of patient education on reducing stroke has had mixed effects, raising questions about how to achieve optimal benefit. Because past evaluations have typically lacked an appropriate theoretical base, the design of past research may have missed important effects. --------- Method: This study used a social cognitive framework to identify variables that might change in response to education. A mixed design was used to evaluate two approaches to an intervention, both of which included education. Fifty seniors completed a measure of stroke knowledge and beliefs twice: before and after an intervention that was either standard (educational brochure plus activities that were not about stroke) or enhanced (educational brochure plus activities designed to enhance beliefs about stroke). Outcome measures were health beliefs, intention to exercise to reduce stroke, and stroke knowledge. --------- Results: Selected beliefs changed significantly over time but not differentially across conditions. Beliefs that changed were (a) perceived susceptibility to stroke and (b) perceived benefit of exercise to reduce risk. Benefit beliefs, in particular, were strongly and positively associated with intention to exercise. -------- Conclusion: Findings suggest that basic approaches to patient education may influence health beliefs. More effective stroke prevention programs may result from continued consideration of the role of health beliefs in such programs.

Effects of age on peripheral ocular aberrations

On-axis monochromatic higher-order aberrations increase with age. Few studies have been made of peripheral refraction along the horizontal meridian of older eyes, and none of their off-axis higher-order aberrations. We measured wave aberrations over the central 42°x32° visual field for a 5mm pupil in 10 young and 7 older emmetropes. Patterns of peripheral refraction were similar in the two groups. Coma increased linearly with field angle at a significantly higher rate in older than in young emmetropes (−0.018±0.007 versus −0.006±0.002 µm/deg). Spherical aberration was almost constant over the measured field in both age groups and mean values across the field were significantly higher in older than in young emmetropes (+0.08±0.05 versus +0.02±0.04 µm). Total root-mean-square and higher-order aberrations increased more rapidly with field angle in the older emmetropes. However, the limits to monochromatic peripheral retinal image quality are largely determined by the second-order aberrations, which do not change markedly with age, and under normal conditions the relative importance of the increased higher-order aberrations in older eyes is lessened by the reduction in pupil diameter with age. Therefore it is unlikely that peripheral visual performance deficits observed in normal older individuals are primarily attributable to the increased impact of higher-order aberration.

Direct and indirect effects on households’ intentions to replace the old car

With the purpose of testing the hypothesis that households’ intentions to replace their old car have a direct negative relationship to its perceived quality (‘current level’) and a direct positive relationship to their aspirations for a new car (‘aspiration level’), a rotating panel of car owners were interviewed every fourth month during 2 years. In this data set the hypothesis received support. In addition the results showed that the age of the car, the total number of miles driven, and the number of anticipated repairs affected the current level, whereas marital status, the number of children, consumer confidence, and environmental concern affected the aspiration level.

Modeling the effects of strategic flexibility, organisational learning on e-business adoption and competitive advantage : an empirical investigation

The role of intangible firm capabilities as a source of competitive advantage has come into prominence in marketing strategy literature, due to the Resource Based View. This paper applies the Resource Based View and hypothesizes that strategic flexibility and organisation learning, conceptualised as capabilities, positively effect e-business adoption and competitive advantage. Partial Lease Squares analysis suggest that theoretical constructs function as hypothesised and explain a significant variation on e-business adoption and competitive advantage. Firms adopting e-business should develop capabilities such as strategic flexibility and organisation learning and that vendor firms may segment their potential clients based on these capabilities.

Effects of starting strategy on 5-min cycling time-trial performance

The importance of pacing for middle-distance performance is well recognized, yet previous research has produced equivocal results. Twenty-six trained male cyclists (O2peak 62.8 ± 5.9 ml · kg-1 · min-1; maximal aerobic power output 340 ± 43 W; mean ± s) performed three cycling time-trials where the total external work (102.7 ± 13.7 kJ) for each trial was identical to the best of two 5-min habituation trials. Markers of aerobic and anaerobic metabolism were assessed in 12 participants. Power output during the first quarter of the time-trials was fixed to control external mechanical work done (25.7 ± 3.4 kJ) and induce fast-, even-, and slow-starting strategies (60, 75, and 90 s, respectively). Finishing times for the fast-start time-trial (4:53 ± 0:11 min:s) were shorter than for the even-start (5:04 ± 0:11 min:s; 95% CI = 5 to 18 s, effect size = 0.65, P < 0.001) and slow-start time-trial (5:09 ± 0:11 min:s; 95% CI = 7 to 24 s, effect size = 1.00, P < 0.001). Mean O2 during the fast-start trials (4.31 ± 0.51 litres · min-1) was 0.18 ± 0.19 litres · min-1 (95% CI = 0.07 to 0.30 litres · min-1, effect size = 0.94, P = 0.003) higher than the even- and 0.18 ± 0.20 litres · min-1 (95% CI = 0.5 to 0.30 litres · min-1, effect size = 0.86, P = 0.007) higher than the slow-start time-trial. Oxygen deficit was greatest during the first quarter of the fast-start trial but was lower than the even- and slow-start trials during the second quarter of the trial. Blood lactate and pH were similar between the three trials. In conclusion, performance during a 5-min cycling time-trial was improved with the adoption of a fast- rather than an even- or slow-starting strategy.

Effects of lead exposure on hippocampal metabotropic glutamate receptor subtype 3 and 7 in developmental rats

Background A complete explanation of the mechanisms by which Pb2+ exerts toxic effects on developmental central nervous system remains unknown. Glutamate is critical to the developing brain through various subtypes of ionotropic or metabotropic glutamate receptors (mGluRs). Ionotropic N-methyl-D-aspartate receptors have been considered as a principal target in lead-induced neurotoxicity. The relationship between mGluR3/mGluR7 and synaptic plasticity had been verified by many recent studies. The present study aimed to examine the role of mGluR3/mGluR7 in lead-induced neurotoxicity. Methods Twenty-four adult and female rats were randomly selected and placed on control or 0.2% lead acetate during gestation and lactation. Blood lead and hippocampal lead levels of pups were analyzed at weaning to evaluate the actual lead content at the end of the exposure. Impairments of short -term memory and long-term memory of pups were assessed by tests using Morris water maze and by detection of hippocampal ultrastructural alterations on electron microscopy. The impact of lead exposure on mGluR3 and mGluR7 mRNA expression in hippocampal tissue of pups were investigated by quantitative real-time polymerase chain reaction and its potential role in lead neurotoxicity were discussed. Results Lead levels of blood and hippocampi in the lead-exposed rats were significantly higher than those in the controls (P < 0.001). In tests using Morris Water Maze, the overall decrease in goal latency and swimming distance was taken to indicate that controls had shorter latencies and distance than lead-exposed rats (P = 0.001 and P < 0.001 by repeated-measures analysis of variance). On transmission electron microscopy neuronal ultrastructural alterations were observed and the results of real-time polymerase chain reaction showed that exposure to 0.2% lead acetate did not substantially change gene expression of mGluR3 and mGluR7 mRNA compared with controls. Conclusion Exposure to lead before and after birth can damage short-term and long-term memory ability of young rats and hippocampal ultrastructure. However, the current study does not provide evidence that the expression of rat hippocampal mGluR3 and mGluR7 can be altered by systemic administration of lead during gestation and lactation, which are informative for the field of lead-induced developmental neurotoxicity noting that it seems not to be worthwhile to include mGluR3 and mGluR7 in future studies. Background

A Knight without a Sword? The Effects of Audit Courts on Tax Morale

The intention of this paper is to analyse how audit courts affect tax morale, controlling in a multivariate analysis for a broad variety of potential factors. Switzerland, with its variety of audit-court competence among the cantons, has been analysed. With data from the ISSP [1998] (Swiss data 1999), evidence has been found that higher audit-court competence has a significantly positive effect on tax morale. Thus, the results in Switzerland suggest that in the cantons where audit courts are not just knights without swords; they help improve taxpayers' tax morale and thus citizens' intrinsic motivation to pay taxes.

Evaluation of piezoelectric PVDF polymers for use in space environments. III. Comparison of the effects of vacuum UV and gamma radiation

Films of piezoelectric PVDF and P(VDF-TrFE) were exposed to vacuum UV (115-300 nm VUV) and -radiation to investigate how these two forms of radiation affect the chemical, morphological, and piezoelectric properties of the polymers. The extent of crosslinking was almost identical in both polymers after -irradiation, but surprisingly, was significantly higher for the TrFE copolymer after VUV-irradiation. Changes in the melting behavior were also more significant in the TrFE copolymer after VUV-irradiation due to both surface and bulk crosslinking, compared with only surface crosslinking for the PVDF films. The piezoelectric properties (measured using d33 piezoelectric coefficients and D-E hysteresis loops) were unchanged in the PVDF homopolymer, while the TrFE copolymer exhibited more narrow D-E loops after exposure to either - or VUV-radiation. The more severe damage to the TrFE copolymer in comparison with the PVDF homopolymer after VUV-irradiation is explained by different energy deposition characteristics. The short wavelength, highly energetic photons are undoubtedly absorbed in the surface layers of both polymers, and we propose that while the longer wavelength components of the VUV-radiation are absorbed by the bulk of the TrFE copolymer causing crosslinking, they are transmitted harmlessly in the PVDF homopolymer.

Evaluation of piezoelectric PVDF polymers for use in space environments. II. Effects of atomic oxygen and vacuum UV exposure

The effects of atomic oxygen (AO) and vacuum UV radiation simulating low Earth orbit conditions on two commercially available piezoelectric polymer films, poly(vinylidene fluoride) (PVDF) and poly(vinylidene fluoride-trifluoroethylene) P(VDF-TrFE), have been studied. Surface erosion and pattern development are significant for both polymers. Erosion yields were determined as 2.8 � 10�24 cm3/atom for PVDF and 2.5 � 10�24 cm3/atom for P(VDF-TrFE). The piezoelectric properties of the residual material of both polymers were largely unchanged after exposure, although a slight shift in the Curie transition of the P(VDF-TrFE) was observed. A lightly cross-linked network was formed in the copolymer presumably because of penetrating vacuum ultraviolet (VUV) radiation, while the homopolymer remained uncross-linked. These differences were attributed to varying degrees of crystallinity and potentially greater absorption, and hence damage, of VUV radiation in P(VDFTrFE) compared with PVDF.