A novel approach for prediction of vitamin D status using support vector regression

BACKGROUND Epidemiological evidence suggests that vitamin D deficiency is linked to various chronic diseases. However direct measurement of serum 25-hydroxyvitamin D (25(OH)D) concentration, the accepted biomarker of vitamin D status, may not be feasible in large epidemiological studies. An alternative approach is to estimate vitamin D status using a predictive model based on parameters derived from questionnaire data. In previous studies, models developed using Multiple Linear Regression (MLR) have explained a limited proportion of the variance and predicted values have correlated only modestly with measured values. Here, a new modelling approach, nonlinear radial basis function support vector regression (RBF SVR), was used in prediction of serum 25(OH)D concentration. Predicted scores were compared with those from a MLR model. METHODS Determinants of serum 25(OH)D in Caucasian adults (n = 494) that had been previously identified were modelled using MLR and RBF SVR to develop a 25(OH)D prediction score and then validated in an independent dataset. The correlation between actual and predicted serum 25(OH)D concentrations was analysed with a Pearson correlation coefficient. RESULTS Better correlation was observed between predicted scores and measured 25(OH)D concentrations using the RBF SVR model in comparison with MLR (Pearson correlation coefficient: 0.74 for RBF SVR; 0.51 for MLR). The RBF SVR model was more accurately able to identify individuals with lower 25(OH)D levels (<75 nmol/L). CONCLUSION Using identical determinants, the RBF SVR model provided improved prediction of serum 25(OH)D concentrations and vitamin D deficiency compared with a MLR model, in this dataset.Dr. Guo is funded by an Australian Postgraduate Award. Prof. Lucas is funded by a National Health and Medical Research (NHMRC) Career Development Fellowship and receives research funding from Cancer Australia, NHMRC, and MS Research Australia. Prof. Ponsonby is funded by a NHMRC Research Fellowship and receives research funding from NHMRC and MS Research Australia. The Ausimmune Study was funded by the US National Multiple Sclerosis Society, NHMRC, and MS Research Australia

The ecology of otters in an urban environment

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the Degree of Doctor of Philosophy. Johannesburg, 2018Urban development has rapidly become the largest contributing factor of biodiversity decline across the planet. Regardless, certain species can survive these novel environments due to their opportunistic nature or occurrence in niche specific areas within urban areas. The aim of my study was to establish whether two otter species, the African clawless otter (Aonyx capensis) and the spotted-necked otter (Hydrictis maculicollis), in an urban environment showed similar ecological patterns in distribution (spatial arrangement), diet, and habitat use compared to conspecific individuals in areas with moderate to low levels of human disturbance. Firstly, I investigated the distribution and frequency of each species based on occurrence of signs (e.g. spraints and footprints) in relation to urban and peri-urban areas of central Gauteng, South Africa. Both species were present in central Gauteng, with a greater number of A. capensis signs found. No difference was observed between the number of signs found in urban and peri-urban areas for both species. Secondly, habitat variables measured near otter signs showed several differences in variables between urban and peri-urban areas. Otter movement through urban areas appeared to be associated with tall grass species, reed beds, and trees, which provided means of concealment for the animals, as well as avoidance of buildings to reduce human encounters. Thirdly, diet analysis based on prey remains in otter faecal samples resulted in lower than expected levels of crab and fish, and revealed higher than expected numbers of less common prey (e.g. birds and mammals) being consumed. Finally, the genetic diversity of individuals was measured using allele frequency to determine the level of reproductive success (ability to survive and produce viable offspring; Fisher, 1915) of A. capensis. Results showed a high level of genetic recombination between individuals in the population suggesting no movement restrictions are being experienced by otters, but genetic diversity was low. Otters are able to utilise resources available in this novel environment, which does not appear to be affecting movement, habitat utilisation or diet. A high genetic flow suggests successful use of urban areas, although there is concern about future genetic health in Gauteng based on the lower level of genetic variance.MT 201

Vitamin D sufficiency in pregnancy

One year ago, the chief medical officers of the United Kingdom recommended that “All pregnant and breastfeeding women should take a daily supplement containing 10 μg (400 IU) of vitamin D,” to counter the high prevalence of vitamin D deficiency in pregnant women. This was aimed at reducing the associated consequences of deficiency, such as rickets in children and osteomalacia in adults

Low maternal exposure to ultraviolet radiation in pregnancy, month of birth, and risk of multiple sclerosis in offspring: longitudinal analysis

Objectives To investigate the distribution of month of birth in people with multiple sclerosis in Australia. To use the large regional and seasonal variation in ambient ultraviolet radiation in Australia to explore the association between exposure to ultraviolet radiation during pregnancy and subsequent risk of multiple sclerosis in offspring

Biochar: an improver of nutrient and soil water availability - what is the evidence?

Biochar has consistently been proposed as a way of improving soil fertility by increasing nutrient and soil water availability. This review critically investigates recent literature, focussing particularly on these agronomic aspects of biochar. We clarify the differences between biochar made from plant (plant derived biochar, PDB) and animal feedstock (animal derived biochar, ADB) and show how pyrolysis temperature affects biochar properties. We also tabulate crop yield data against production variables using recent field and greenhouse studies. We find evidence to suggest that ADB supplies many more nutrients than PDB and that, in general, biochar can improve nutrient availability indirectly through changes in pH, CEC, soil structure, improved fertiliser efficiency, decreased nutrient leaching and may effect nutrient availability by changing nitrogenous gas release and by changing the soil microbial community, which under some circumstances translates into short term, increased crop yield. Few studies however show complete nutrient, especially N budgets and elaborate on the underlying mechanisms of interaction, especially with regards to microbial induced changes. Also the longevity of the different beneficial effects is questionable as most studies are less than a year long. A synopsis of the literature concludes that biochar application promotes soil water availability, particularly in soils which are degraded or of low quality. Despite this conclusion it is hard to find studies that have adopted methodologies which are fully appropriate to support this notion such as available water capacity and how this changes in response to crop uptake and soil drying. We conclude that the variability in biochar due to variable feedstock and pyrolysis process, as well as particle size and application method, necessitates and also enables production of specific purpose–driven biochars to benefit particular aspects of crop production

Measurement of Epstein-Barr virus DNA load using a novel quantification standard containing two EBV DNA targets and SYBR Green I dye

BACKGROUND Reactivation of Epstein-Barr virus (EBV) infection may cause serious, life-threatening complications in immunocompromised individuals. EBV DNA is often detected in EBV-associated disease states, with viral load believed to be a reflection of virus activity. Two separate real-time quantitative polymerase chain reaction (QPCR) assays using SYBR Green I dye and a single quantification standard containing two EBV genes, Epstein-Barr nuclear antigen-1 (EBNA-1) and BamHI fragment H rightward open reading frame-1 (BHRF-1), were developed to detect and measure absolute EBV DNA load in patients with various EBV-associated diseases. EBV DNA loads and viral capsid antigen (VCA) IgG antibody titres were also quantified on a population sample. RESULTS EBV DNA was measurable in ethylenediaminetetraacetic acid (EDTA) whole blood, peripheral blood mononuclear cells (PBMCs), plasma and cerebrospinal fluid (CSF) samples. EBV DNA loads were detectable from 8.0 × 10² to 1.3 × 10⁸ copies/ml in post-transplant lymphoproliferative disease (n = 5), 1.5 × 10³ to 2.0 × 10⁵ copies/ml in infectious mononucleosis (n = 7), 7.5 × 10⁴ to 1.1 × 10⁵ copies/ml in EBV-associated haemophagocytic syndrome (n = 1), 2.0 × 10² to 5.6 × 10³ copies/ml in HIV-infected patients (n = 12), and 2.0 × 10² to 9.1 × 10⁴ copies/ml in the population sample (n = 218). EBNA-1 and BHRF-1 DNA were detected in 11.0% and 21.6% of the population sample respectively. There was a modest correlation between VCA IgG antibody titre and BHRF-1 DNA load (rho = 0.13, p = 0.05) but not EBNA-1 DNA load (rho = 0.11, p = 0.11). CONCLUSION Two sensitive and specific real-time PCR assays using SYBR Green I dye and a single quantification standard containing two EBV DNA targets, were developed for the detection and measurement of EBV DNA load in a variety of clinical samples. These assays have application in the investigation of EBV-related illnesses in immunocompromised individuals.The Ausimmune Study is funded by the National Multiple Sclerosis Society of the USA, the National Health & Medical Research Council (Project Grant 316901) and Multiple Sclerosis Research Australia

Ecologic analysis of some immune-related disorders, including type 1 diabetes, in Australia: latitude, regional ultraviolet radiation, and disease prevalence

The apparent immune-suppressive effect of ultraviolet radiation (UVR) has suggested that this environmental exposure may influence the development of immune-related disorders. Self-reported prevalence rates of type 1 diabetes mellitus, rheumatoid arthritis (RA) , eczema/dermatitis, and asthma, from the 1995 Australian National Health Survey, were therefore examined by latitude and ambient level of UVR. A positive association of type 1 diabetes mellitus prevalence was found with both increasing southern latitude of residence (r = 0.77 ; p = 0.026) and decreasing regional annual ambient UVR (r = -0.80 ; p = 0.018) ; a 3-fold increase in prevalence from the northernmost region to the southernmost region was evident. In contrast, asthma correlated negatively with latitude (r = -0.72 ; p = 0.046) , although the change in asthma prevalence from the north to the south of Australia was only 0.7-fold. For both RA and eczema/dermatitis, there were no statistically significant associations between latitude/UVR and disease prevalence. These ecologic data provide some support for a previously proposed beneficial effect of UVR on T-helper 1-mediated autoimmune disorders such as type 1 diabetes. The inverse association of type 1 diabetes prevalence with UVR is consistent with that previously reported for another autoimmune disease, multiple sclerosis, in Australia, and also with type 1 diabetes latitudinal gradients in the Northern Hemisphere. The finding also accords with photoimmunologic evidence of UVR-induced immunosuppression and may suggest a beneficial effect of UVR in reducing the incidence of such autoimmune conditions. In light of this study, analytic epidemiologic studies investigating risk of immune disorders in relation to personal UVR exposure in humans are require

Methodological lessons and findings from an impact evaluation of a WASH project in Indonesia

Internationally, there is growing emphasis on evaluations that aim not only at output and performance data but also show the project’s impacts. This paper reports on the experiences, findings and lessons from the impact evaluation of the Second Water and Sanitation for Low Income Communities Project (WSLIC-2) in the Ministry of Health of Indonesia. During project formulation an impact study was planned using the strongest model of a double difference evaluation (differences between before and after situations and practices in project and matched control villages). In this paper, the team that designed and implemented the study reports on the problems and how they were addressed, followed by a brief summary of the findings. It concludes that the classical double difference study is becoming ever harder to practice in development research and suggests ways to address the challenge