Resequencing and fine-mapping of the chromosome 12q13-14 locus associated with multiple sclerosis refines the number of implicated genes

Multiple sclerosis (MS) is a common chronic inflammatory disease of the central nervous system. Susceptibility to the disease is affected by both environmental and genetic factors. Genetic factors include haplotypes in the histocompatibility complex (MHC) and over 50 non-MHC loci reported by genome-wide association studies. Amongst these, we previously reported polymorphisms in chromosome 12q13-14 with a protective effect in individuals of European descent. This locus spans 288 kb and contains 17 genes, including several candidate genes which have potentially significant pathogenic and therapeutic implications. In this study, we aimed to fine-map this locus. We have implemented a two-phase study: a variant discovery phase where we have used next-generation sequencing and two target-enrichment strategies [long-range polymerase chain reaction (PCR) and Nimblegen's solution phase hybridization capture] in pools of 25 samples; and a genotyping phase where we genotyped 712 variants in 3577 healthy controls and 3269 MS patients. This study confirmed the association (rs2069502, P = 9.9 × 10−11, OR = 0.787) and narrowed down the locus of association to an 86.5 kb region. Although the study was unable to pinpoint the key-associated variant, we have identified a 42 (genotyped and imputed) single-nucleotide polymorphism haplotype block likely to harbour the causal variant. No evidence of association at previously reported low-frequency variants in CYP27B1 was observed. As part of the study we compared variant discovery performance using two target-enrichment strategies. We concluded that our pools enriched with Nimblegen's solution phase hybridization capture had better sensitivity to detect true variants than the pools enriched with long-range PCR, whilst specificity was better in the long-range PCR-enriched pools compared with solution phase hybridization capture enriched pools; this result has important implications for the design of future fine-mapping studies.

Comparison of genomic DNA extraction techniques from whole blood samples : a time, cost and quality evaluation study

Genomic DNA obtained from patient whole blood samples is a key element for genomic research. Advantages and disadvantages, in terms of time-efficiency, cost-effectiveness and laboratory requirements, of procedures available to isolate nucleic acids need to be considered before choosing any particular method. These characteristics have not been fully evaluated for some laboratory techniques, such as the salting out method for DNA extraction, which has been excluded from comparison in different studies published to date. We compared three different protocols (a traditional salting out method, a modified salting out method and a commercially available kit method) to determine the most cost-effective and time-efficient method to extract DNA. We extracted genomic DNA from whole blood samples obtained from breast cancer patient volunteers and compared the results of the product obtained in terms of quantity (concentration of DNA extracted and DNA obtained per ml of blood used) and quality (260/280 ratio and polymerase chain reaction product amplification) of the obtained yield. On average, all three methods showed no statistically significant differences between the final result, but when we accounted for time and cost derived for each method, they showed very significant differences. The modified salting out method resulted in a seven- and twofold reduction in cost compared to the commercial kit and traditional salting out method, respectively and reduced time from 3 days to 1 hour compared to the traditional salting out method. This highlights a modified salting out method as a suitable choice to be used in laboratories and research centres, particularly when dealing with a large number of samples.

Tailoring surface properties and structure of layered double hydroxides using silanes with different number of functional groups

Four silanes, trimethylchlorosilane (TMCS), dimethyldiethoxylsilane (DMDES), 3-aminopropyltriethoxysilane (APTES) and tetraethoxysilane (TEOS), were adopted to graft layered double hydroxides (LDH) via an induced hydrolysis silylation method (IHS). Fourier transform infrared spectra (FTIR) and 29Si MAS nuclear magnetic resonance spectra (29Si MAS NMR) indicated that APTES and TEOS can be grafted onto LDH surfaces via condensation with hydroxyl groups of LDH, while TMCS and DMDES could only be adsorbed on the LDH surface with a small quantity. A combination of X-ray diffraction patterns (XRD) and 29Si MAS NMR spectra showed that silanes were exclusively present in the external surface and had little influence on the long range order of LDH. The surfactant intercalation experiment indicated that the adsorbed and/or grafted silane could not fix the interlamellar spacing of the LDH. However, they will form crosslink between the particles and affect the further surfactant intercalation in the silylated samples. The replacement of water by ethanol in the tactoids and/or aggregations and the polysiloxane oligomers formed during silylation procedure can dramatically increase the value of BET surface area (SBET) and total pore volumes (Vp) of the products.

Smoothing a Discrete Hazard Function for the Number of Patients Colonized with Methicillin-Resistance Staphylococcus Aureus in an Intensive Care Unit

A new method for estimating the time to colonization of Methicillin-resistant Staphylococcus Aureus (MRSA) patients is developed in this paper. The time to colonization of MRSA is modelled using a Bayesian smoothing approach for the hazard function. There are two prior models discussed in this paper: the first difference prior and the second difference prior. The second difference prior model gives smoother estimates of the hazard functions and, when applied to data from an intensive care unit (ICU), clearly shows increasing hazard up to day 13, then a decreasing hazard. The results clearly demonstrate that the hazard is not constant and provide a useful quantification of the effect of length of stay on the risk of MRSA colonization which provides useful insight.

Measuring episodic memory: A novel approach with an indefinite number of alternative forms

Both clinical practice and clinical research settings can require successive administrations of a memory test, particularly when following the trajectory of suspected memory decline in older adults. However, relatively few verbal episodic memory tests have alternative forms. We set out to create a broad based memory test to allow for the use of an essentially unlimited number of alternative forms. Four tasks for inclusion in such a test were developed. These tasks varied the requirement for recall as opposed to recognition, the need to form an association between unrelated words, and the need to discriminate the most recent list from earlier lists, all of which proved useful. A total of 115 participants completed the battery of tests and were used to show that the test could differentiate between older and younger adults; a sub-sample of 73 participants completed alternative forms of the tests to determine test-retest reliability and the amount of learning to learn.

Practical improvements to simultaneous computation of multi-view geometry and radial lens distortion

This paper discusses practical issues related to the use of the division model for lens distortion in multi-view geometry computation. A data normalisation strategy is presented, which has been absent from previous discussions on the topic. The convergence properties of the Rectangular Quadric Eigenvalue Problem solution for computing division model distortion are examined. It is shown that the existing method can require more than 1000 iterations when dealing with severe distortion. A method is presented for accelerating convergence to less than 10 iterations for any amount of distortion. The new method is shown to produce equivalent or better results than the existing method with up to two orders of magnitude reduction in iterations. Through detailed simulation it is found that the number of data points used to compute geometry and lens distortion has a strong influence on convergence speed and solution accuracy. It is recommended that more than the minimal number of data points be used when computing geometry using a robust estimator such as RANSAC. Adding two to four extra samples improves the convergence rate and accuracy sufficiently to compensate for the increased number of samples required by the RANSAC process.

Controls on iron in soils and soil waters of a forested, coastal catchment in subtropical Australia

Soluble organic matter derived from exotic Pinus vegetation forms stronger complexes with iron (Fe) than the soluble organic matter derived from most native Australian species. This has lead to concern about the environmental impacts related to the establishment of extensive exotic Pinus plantations in coastal southeast Queensland, Australia. It has been suggested that the Pinus plantations may enhance the solubility of Fe in soils by increasing the amount of organically complexed Fe. While this remains inconclusive, the environmental impacts of an increased flux of dissolved, organically complexed Fe from soils to the fluvial system and then to sensitive coastal ecosystems are potentially damaging. Previous work investigated a small number of samples, was largely laboratory based and had limited application to field conditions. These assessments lacked field-based studies, including the comparison of the soil water chemistry of sites associated with Pinus vegetation and undisturbed native vegetation. In addition, the main controls on the distribution and mobilisation of Fe in soils of this subtropical coastal region have not been determined. This information is required in order to better understand the relative significance of any Pinus enhanced solubility of Fe. The main aim of this thesis is to determine the controls on Fe distribution and mobilisation in soils and soil waters of a representative coastal catchment in southeast Queensland (Poona Creek catchment, Fraser Coast) and to test the effect of Pinus vegetation on the solubility and speciation of Fe. The thesis is structured around three individual papers. The first paper identifies the main processes responsible for the distribution and mobilisation of labile Fe in the study area and takes a catchment scale approach. Physicochemical attributes of 120 soil samples distributed throughout the catchment are analysed, and a new multivariate data analysis approach (Kohonen’s self organising maps) is used to identify the conditions associated with high labile Fe. The second paper establishes whether Fe nodules play a major role as an iron source in the catchment, by determining the genetic mechanism responsible for their formation. The nodules are a major pool of Fe in much of the region and previous studies have implied that they may be involved in redox-controlled mobilisation and redistribution of Fe. This is achieved by combining a detailed study of a ferric soil profile (morphology, mineralogy and micromorphology) with the distribution of Fe nodules on a catchment scale. The third component of the thesis tests whether the concentration and speciation of Fe in soil solutions from Pinus plantations differs significantly from native vegetation soil solutions. Microlysimeters are employed to collect unaltered, in situ soil water samples. The redox speciation of Fe is determined spectrophotometrically and the interaction between Fe and dissolved organic matter (DOM) is modelled with the Stockholm Humic Model. The thesis provides a better understanding of the controls on the distribution, concentration and speciation of Fe in the soils and soil waters of southeast Queensland. Reductive dissolution is the main mechanism by which mobilisation of Fe occurs in the study area. Labile Fe concentrations are low overall, particularly in the sandy soils of the coastal plain. However, high labile Fe is common in seasonally waterlogged and clay-rich soils which are exposed to fluctuating redox conditions and in organic-rich soils adjacent to streams. Clay-rich soils are most common in the upper parts of the catchment. Fe nodules were shown to have a negligible role in the redistribution of dissolved iron in the catchment. They are formed by the erosion, colluvial transport and chemical weathering of iron-rich sandstones. The ferric horizons, in which nodules are commonly concentrated, subsequently form through differential biological mixing of the soil. Whereas dissolution/ reprecipitation of the Fe cements is an important component of nodule formation, mobilised Fe reprecipitates locally. Dissolved Fe in the soil waters is almost entirely in the ferrous form. Vegetation type does not affect the concentration and speciation of Fe in soil waters, although Pinus DOM has greater acidic functional group site densities than DOM from native vegetation. Iron concentrations are highest in the high DOM soil waters collected from sandy podosols, where they are controlled by redox potential. Iron concentrations are low in soil solutions from clay and iron oxide rich soils, in spite of similar redox potentials. This is related to stronger sorption to the reactive clay and iron oxide mineral surfaces in these soils, which reduces the amount of DOM available for microbial metabolisation and reductive dissolution of Fe. Modelling suggests that Pinus DOM can significantly increase the amount of truly dissolved ferric iron remaining in solution in oxidising conditions. Thus, inputs of ferrous iron together with Pinus DOM to surface waters may reduce precipitation of hydrous ferric oxides and increase the flux of dissolved iron out of the catchment. Such inputs are most likely from the lower catchment, where podosols planted with Pinus are most widely distributed. Significant outcomes other than the main aims were also achieved. It is shown that mobilisation of Fe in podosols can occur as dissolved Fe(II) rather than as Fe(III)-organic complexes. This has implications for the large body of work which assumes that Fe(II) plays a minor role. Also, the first paper demonstrates that a data analysis approach based on Kohonen’s self organising maps can facilitate the interpretation of complex datasets and can help identify geochemical processes operating on a catchment scale.

Scaling for the Prandtl number of the natural convection boundary layer of an inclined flat plate under uniform surface heat flux

An improved scaling analysis and direct numerical simulations are performed for the unsteady natural convection boundary layer adjacent to a downward facing inclined plate with uniform heat flux. The development of the thermal or viscous boundary layers may be classified into three distinct stages: a start-up stage, a transitional stage and a steady stage, which can be clearly identified in the analytical as well as the numerical results. Previous scaling shows that the existing scaling laws of the boundary layer thickness, velocity and steady state time scale for the natural convection flow on a heated plate of uniform heat flux provide a very poor prediction of the Prandtl number dependency of the flow. However, those scalings perform very well with Rayleigh number and aspect ratio dependency. In this study, a modified Prandtl number scaling is developed using a triple layer integral approach for Pr > 1. It is seen that in comparison to the direct numerical simulations, the modified scaling performs considerably better than the previous scaling.

Proactive management of collision risks in port waters using navigational traffic conflicts

Navigational collisions are one of the major safety concerns in many seaports. To address this safety concern, a comprehensive and structured method of collision risk management is necessary. Traditionally management of port water collision risks has been relied on historical collision data. However, this collision-data-based approach is hampered by several shortcomings, such as randomness and rarity of collision occurrence leading to obtaining insufficient number of samples for a sound statistical analysis, insufficiency in explaining collision causation, and reactive approach to safety. A promising alternative approach that overcomes these shortcomings is the navigational traffic conflict technique that uses traffic conflicts as an alternative to the collision data. This paper proposes a collision risk management method by utilizing the principles of this technique. This risk management method allows safety analysts to diagnose safety deficiencies in a proactive manner, which, consequently, has great potential for managing collision risks in a fast, reliable and efficient manner.

A mixed-method study to investigate the relationship between the number of social support people present during labour, women’s perceptions and birth outcomes

The birth of a baby is a significant event for women and their families, with the event being influenced by the prevailing social and cultural context. Historically, women throughout the world have given birth at home assisted by other women who helped them cope with the stress of labour and birth. In the middle of the twentieth century, the togetherness, caring and support that were provided within the social and cultural context of childbirth began to change; women in most developed countries, and to some extent in developing countries, laboured and gave birth in institutions that isolated them from the support of family and friends. This practice is referred to as the medical model of childbirth and, over time, birthing within this model has come to be viewed by women as a dehumanising experience. In an attempt to secure a more supportive experience, women began to demand the presence of a supportive companion; namely their partner. This event became the catalyst for a number of studies focusing on different types of support providers and their contribution to the phenomenon of social support during labour. More recently, it has become a common practice for some women to be supported during labour by a number of people from their social network. However, research on the influence of such supportive people on women’s experience of labour and birth and on birth outcomes is scarce. The aim of this study is to examine the influence of various support arrangements from a woman’s family and social network on her experience of labour and birth and on birth outcomes. The mixed-method study was conducted to answer three research questions: 1. Do women with more than one support person present during labour and birth have similar perceptions and experiences of support compared to women with one support person? 2. Do women with more than one support person present during labour and birth have similar birth outcomes compared to women with one support person? 3. Do women with different types of support providers during labour and birth have similar birth outcomes? Methods Phase one of this study developed, pilot tested and administered a newly developed instrument designed to measure women’s perceptions of supportive behaviours provided during labour. Specific birth outcome data were extracted from the medical records. Phase two consisted of in-depth interviews with a sample of women who had completed the survey. Results: The results identified a statistically significant relationship between women’s perceptions of social support and the number of support providers: women supported by one person only rated the supportive behaviours of that person more highly compared to women who were supported by a number of people. The results also identified that women supported by one person used less analgesia. An additional qualitative finding was that some women sacrificed the support of female relatives at the request of their partners. Conclusion: By using a mixed-method approach, this study found that women were selective in their choice of support providers, as they chose individuals with whom they had an enduring affectionate attachment. Women place more emphasis on a support person’s ability to fulfil their attachment needs of close proximity and a sense of security and safety, rather than their ability to provide the expected functional supportive behaviours.

History behind the IVF egg: Are women's comprehensive histories associated with the number of eggs collected, or fertilised normally, from repeated IVF cycles? [abstract]

Most studies of in vitro fertilisation (IVF) outcomes use cycle-based data and fail to account for women who use repeated IVF cycles. The objective of this study was to examine the association between the number of eggs collected (EC) and the percentage fertilised normally, and women’s self-reported medical, personal and social histories. This study involved a crosssectional survey of infertile women (aged 27-46 years) recruited from four privately-owned fertility clinics located in major cities of Australia. Regression modeling was used to estimate the mean EC and mean percentage of eggs fertilised normally: adjusted for age at EC. Appropriate statistical methods were used to take account of repeated IVF cycles by the same women. Among 121 participants who returned the survey and completed 286 IVF cycles, the mean age at EC was 35.2 years (SD 4.5). Women’s age at EC was strongly associated with the number of EC: <30 years, 11.7 EC; 30.0-< 35 years, 10.6 EC; 35.0-<40.0 years, 7.3 EC; 40.0+ years, 8.1 EC; p<.0001. Prolonged use of oral contraceptives was associated with lower numbers of EC: never used, 14.6 EC; 0-2 years, 11.7 EC; 3-5 years, 8.5 EC; 6þ years, 8.2 EC; p=.04. Polycystic ovary syndrome (PCOS) was associated with more EC: have PCOS, 11.5 EC; no, 8.3 EC; p=.01. Occupational exposures may be detrimental to normal fertilisation: professional roles, 58.8%; trade and service roles, 51.8%; manual and other roles, 63.3%; p=.02. In conclusion, women’s age remains the most significant characteristic associated with EC but not the percentage of eggs fertilised normally.

Adaptive sizing of populations and number of islands in distributed genetic algorithms

Deciding the appropriate population size and number of is- lands for distributed island-model genetic algorithms is often critical to the algorithm’s success. This paper outlines a method that automatically searches for good combinations of island population sizes and the number of islands. The method is based on a race between competing parameter sets, and collaborative seeding of new parameter sets. This method is applicable to any problem, and makes distributed genetic algorithms easier to use by reducing the number of user-set parameters. The experimental results show that the proposed method robustly and reliably finds population and islands settings that are comparable to those found with traditional trial-and-error approaches.