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Search Results: 1 - 10 of 318698 matches for " Nicholas H de Klerk "
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Translating microarray data for diagnostic testing in childhood leukaemia
Katrin Hoffmann, Martin J Firth, Alex H Beesley, Nicholas H de Klerk, Ursula R Kees
BMC Cancer , 2006, DOI: 10.1186/1471-2407-6-229
Abstract: We examined published microarray data from 104 ALL patients specimens, that represent six different subgroups defined by cytogenetic features and immunophenotypes. Using the decision-tree based supervised learning algorithm Random Forest (RF), we determined a small set of genes for optimal subgroup distinction and subsequently validated their predictive power in an independent patient cohort.We achieved very high overall ALL subgroup prediction accuracies of about 98%, and were able to verify the robustness of these genes in an independent panel of 68 specimens obtained from a different institution and processed in a different laboratory. Our study established that the selection of discriminating genes is strongly dependent on the analysis method. This may have profound implications for clinical use, particularly when the classifier is reduced to a small set of genes. We have demonstrated that as few as 26 genes yield accurate class prediction and importantly, almost 70% of these genes have not been previously identified as essential for class distinction of the six ALL subgroups.Our finding supports the feasibility of qRT-PCR technology for standardized diagnostic testing in paediatric ALL and should, in conjunction with conventional cytogenetics lead to a more accurate classification of the disease. In addition, we have demonstrated that microarray findings from one study can be confirmed in an independent study, using an entirely independent patient cohort and with microarray experiments being performed by a different research team.Acute lymphoblastic leukaemia (ALL) is a heterogeneous disease characterized by the presence of several subtypes that are of prognostic relevance. These subtypes can be distinguished based on immunophenotype, differentiation status, as well as chromosomal and molecular abnormalities. The identification of different ALL subtypes, the characterization of prognostic features, and the finding that ALL subtypes differ in their response to t
Optimal fetal growth for the Caucasian singleton and assessment of appropriateness of fetal growth: an analysis of a total population perinatal database
Eve M Blair, Yingxin Liu, Nicholas H de Klerk, David M Lawrence
BMC Pediatrics , 2005, DOI: 10.1186/1471-2431-5-13
Abstract: Fractional polynomial regression models including terms for non-pathological determinants of fetal size (gestational duration, fetal gender and maternal height, age and parity) were used to predict birth weight, birth length and head circumference from a population without any major risk factors for sub-optimal intra-uterine growth. This population was selected from a total population of all singleton, Caucasian births in Western Australia 1998–2002. Births were excluded if the pregnancy was exposed to factors known to influence fetal growth pathologically. The values predicted by these models were treated as the optimal values, given infant gender, gestational age, maternal height, parity, and age.The selected sample (N = 62,746) comprised 60.5% of the total Caucasian singleton birth cohort. Equations are presented that predict optimal birth weight, birth length and head circumference given gestational duration, fetal gender, maternal height, age and parity. The best fitting models explained 40.5% of variance for birth weight, 32.2% for birth length, and 25.2% for head circumference at birth.Proportion of optimal birth weight (length or head circumference) provides a method of assessing appropriateness of intrauterine growth that is less dependent on the health of the reference population or the quality of their morphometric data than is percentile position on a birth weight distribution.Being born small for one's gestational age is associated with adverse outcomes in both the short and long term [1-3]. However assessing whether a neonate is at risk of compromise on account of inappropriate intrauterine growth is complicated because not all fetuses should grow at the same rate [4]. Currently the appropriateness of fetal growth is usually inferred from the percentile position that the neonate's birth weight occupies on a gestation-specific birth weight distribution, that may also be specific for gender. This practice is unsuitable if the most appropriate birth weigh
Statistical adjustment of genotyping error in a case–control study of childhood leukaemia
Cooper Matthew N,de Klerk Nicholas H,Greenop Kathryn R,Jamieson Sarra E
BMC Medical Research Methodology , 2012, DOI: 10.1186/1471-2288-12-141
Abstract: Background Genotyping has become more cost-effective and less invasive with the use of buccal cell sampling. However, low or fragmented DNA yields from buccal cells collected using FTA cards often requires additional whole genome amplification to produce sufficient DNA for genotyping. In our case–control study of childhood leukaemia, discordance was found between genotypes derived from blood and whole genome amplified FTA buccal DNA samples. We aimed to develop a user-friendly method to correct for this genotype misclassification, as existing methods were not suitable for use in our study. Methods Discordance between the results of blood and buccal-derived DNA was assessed in childhood leukaemia cases who had both blood and FTA buccal samples. A method based on applying misclassification probabilities to measured data and combining results using multiple imputations, was devised to correct for error in the genotypes of control subjects, for whom only buccal samples were available, to minimize bias in the odds ratios in the case–control analysis. Results Application of the correction method to synthetic datasets showed it was effective in producing correct odds ratios from data with known misclassification. Moreover, when applied to each of six bi-allelic loci, correction altered the odds ratios in the logically anticipated manner given the degree and direction of the misclassification revealed by the investigations in cases. The precision of the effect estimates decreased with decreasing size of the misclassification data set. Conclusions Bias arising from differential genotype misclassification can be reduced by correcting results using this method whenever data on concordance of genotyping results with those from a different and probably better DNA source are available.
Plasma retinol, carotene and vitamin E concentrations and lung function in a crocidolite-exposed cohort from Wittenoom, Western Australia: a cohort study
Helman S Alfonso, Lin Fritschi, Nicholas H de Klerk, Gina Ambrosini, John Beilby, Nola Olsen, A William Musk
Nutrition Journal , 2005, DOI: 10.1186/1475-2891-4-16
Abstract: Annual measurements of forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) and plasma concentrations of retinol, carotene and vitamin E have been made since 1992. Mixed effects models were used to examine the associations between lung function and the plasma vitamin levels of retinol, carotene and vitamin E.After adjusting for potential confounders, higher plasma retinol and carotene concentrations were significantly associated with higher levels of lung function at entry into the study, while vitamin E concentrations were associated with lower entry lung function. Retinol was associated with a less steep decline of lung function over time, while carotene concentrations were associated with an increased decline of lung function over time and vitamin E levels were not associated with changes of lung function over time.These results support a beneficial relationship between plasma concentrations of retinol on the levels and rates of change of lung function, while showing no such consistent beneficial effect for plasma levels of beta-carotene or vitamin E.Respiratory impairment is an important cause of disability in asbestos-exposed people. Cross-sectional and longitudinal studies have shown that greater intensity and duration of asbestos exposure are associated with greater impairment of pulmonary function [1]. A protective effect of fruit and vegetable consumption on lung function has been reported, and a number of studies have found positive associations between pulmonary function and dietary intake and blood levels of both carotenoids and retinoids [2-4].Crocidolite (blue asbestos) was mined at Wittenoom, Western Australia from 1943 until 1966. Approximately 7000 workers were employed in the mining and milling operations [5]. In addition, about 5000 people, who did not work in the production of asbestos, are documented to have lived in the nearby town, where they received environmental exposure to asbestos [6]. Former workers and residents w
Tegnologie van die landbou
J.H. de Klerk
Koers : Bulletin for Christian Scholarship , 1998, DOI: 10.4102/koers.v63i3.531
Abstract: Technology of agriculture Technicism, i.e., the human pretence to change reality in an autonomous way to man's own liking via a technical-scientific way has become a leading principle in science and technology. This principle has already attained the character of an idolatrous conviction. The power of technology has started to change science via technicism into a controlling instrument. In this sense the potential of technology is much overrated. In this discussion attention will be paid to the meaning of technology and the power it manifests nowadays, with specific attention to the technology of agriculture. Attention is not only paid to the dark side of technology (namely the power of technology), but also to a liberating perspective on technology according to some selected normative principles. Finally, these principles will be applied to a few agricultural case studies, among others also to a South African example.
A retrospective population-based cohort study identifying target areas for prevention of acute lower respiratory infections in children
Hannah C Moore, Nicholas de Klerk, Peter Richmond, Deborah Lehmann
BMC Public Health , 2010, DOI: 10.1186/1471-2458-10-757
Abstract: A retrospective population-based data linkage study of 245,249 singleton births in Western Australia. Population attributable fractions of known maternal and infant risk factors for hospitalisation with ALRI between 1996 and 2005 were calculated using multiple logistic regression.The overall ALRI hospitalisation rate was 16.1/1,000 person-years for non-Aboriginal children and 93.0/1,000 for Aboriginal children. Male gender, being born in autumn, gestational age <33 weeks, and multiple previous pregnancies were significant risk factors for ALRI in both Aboriginal and non-Aboriginal children. In non-Aboriginal children, maternal smoking during pregnancy accounted for 6.3% (95%CI: 5.0, 7.6) of the population attributable fraction for ALRI, being born in autumn accounted for 12.3% (10.8, 13.8), being born to a mother with three or more previous pregnancies accounted for 15.4% (14.1, 17.0) and delivery by elective caesarean accounted for 4.1% (2.8, 5.3). In Aboriginal children, being born to a mother with three or more previous pregnancies accounted for 16.5% (11.8, 20.9), but remote location at birth accounted for 11.7% (8.5, 14.8), maternal age <20 years accounted for 11.2% (7.8, 14.5), and being in the most disadvantaged socio-economic group accounted for 18.4% (-6.5, 37.4) of the population attributable fraction.The population attributable fractions estimated in this study should help in guiding public health interventions to prevent ALRI. A key risk factor for all children is maternal smoking during pregnancy, and multiple previous pregnancies and autumnal births are important high-risk groups. Specific key target areas are reducing elective caesareans in non-Aboriginal women and reducing teenage pregnancies and improving access to services and living conditions for the Aboriginal population.Acute lower respiratory infections (ALRIs) are a leading cause of hospitalisation in young children, particularly in those under the age of 2 years [1]. Factors leading to an in
Development of a socio-cognitive model for examining consumers' adoption of the Internet for the purchase of apparel
B. M. Jacobs,H. M. de Klerk
South African Journal of Information Management , 2010, DOI: 10.4102/sajim.v5i2.337
Prevalence and characteristics of erectile dysfunction in black and mixed race primary care populations of the Cape Flats and Helderberg Basin area of the Western Cape, South Africa
H De Klerk, PJT De Villiers, S Isaacs
South African Family Practice , 2003,
Abstract: Objective: To estimate the prevalence of erectile dysfunction (ED) among users of primary care in a Black and Mixed Race urban population in the Western Cape, and to describe any associated health and psychosocial factors. Design: Cross-sectional survey by interviewer administered questionnaire. Setting: Two primary care medical centres, 40km apart, in Cape Town metropolitan area. Serve different ethnic groups, with no cross-contamination between them. Study period: March-June 1999 Patients: 833 Males (35-70 years old) attending these health centres for primary care. Systematic selection of all attendees. Main outcome measures: Prevalence of ED and presence of associated health and psychosocial factors. Describe patient demographics, physical attributes, sexual relationships. Results: Results of 730 males with current sexual partners: Mean ages 48 years (SD:7 years) all; 46 years (SD:9 years) Black group; 51 years (SD: 9 years) Mixed Race group. All degrees of ED prevalence: All 77.1% (95% CI: 74.0-80.2), Black 76.4% (95% CI: 71.8-80.4) and Mixed Race 77.7% (95% CI: 72.8-82.0). Significantly associated diseases: hypertension, diabetes, gastrointestinal and heart disease. Alcohol consumption (younger patients), smoking (older patients) significantly related to ED. Males with ED: more sexual partners than males without ED. More than 90% choose primary care physician/ generalist as primary ED care-giver. Conclusions: ED is very common in both study groups. Primary care workers must be prepared to manage associated risk factors and health implications. ED sufferers in this population may also be at higher risk for sexually transmitted diseases due to multiple sexual partners. (SA Fam Pract 2003;45(1):14-20)
Plant communities of the Ebenhaezer section of the Mountain Zebra National Park
J. de Klerk,L.R. Brown,H. Bezuidenhout
Koedoe : African Protected Area Conservation and Science , 2003, DOI: 10.4102/koedoe.v46i2.47
Abstract: The long-term conservation of viable ecosystems requires a broader understanding of the ecological processes involved. Because ecosystems react differently to different management practices, it is important to have a description and classification of the vegetation of an area available. As part of a vegetation survey programme for the newly acquired farms to be incorporated into the Mountain Zebra National Park, the vegetation of the Ebenhaezer section was investigated. Ahierarchical classification, vegetation map, description and ecological interpretation of the plant communities of the study area are presented. ATWINSPAN classification, refined by Braun-Blanquet procedures revealed eight distinct plant communities. Habitat factors associated with differences in vegetation include topography, soil form and grazing. Descriptions of the plant communities include diagnostic species as well as prominent and less conspicuous species of the tree, shrub and herbaceous layers.
Predictive Potential of FDG-PET/CT for Histological Transformation in Patients with Indolent Lymphoma  [PDF]
Peter E. Blase, Pieternel C. M. Pasker-de Jong, Anton Hagenbeek, Rob Fijnheer, Marie J. de Haas, John M. H. de Klerk
Advances in Molecular Imaging (AMI) , 2014, DOI: 10.4236/ami.2014.41001

Backgrounds and PurposeIn indolent non-Hodgkin lymphoma, histological transformation is a dramatic event which reduces the prognosis significantly. SUVmax values from FDG-PET/CT help differentiate between aggressive and indolent lymphomas, and transformed indolent lymphomas also show an increased FDG uptake. Possibly FDG uptake increases early in the clinical course and could predict histological transformation. Our objective was to predict histological transformation in indolent lymphomas from initial staging FDG-PET/CT. Patients and MethodsA retrospective study was performed. Patients with biopsy-proven indolent lymphoma who had had initial staging FDG-PET/CT were included. Qualitative (foci compared with FDG uptake liver) and semiquantitative (SUVmax-value per focus) analyses were performed of all abnormal foci. Patient characteristics and outcome were evaluated. ResultsWe included 88 patients, 5 of whom developed a histological transformation. Semiquantitative analysis showed a relation between maximum standardized uptake value and histological transformation (odds ratio 1.25, 95% CI 1.024 - 1.513). Qualitative analysis showed a negative predictive relation of FDG uptake less than or equal to liver in the occurrence of histological transformation. Transformation-free survival was 100% over 30 months in those with FDG uptake lower than or equal to liver. More FDG uptake than liver showed transformation-free survival of 88% over 30 months. ConclusionQualitative analysis of staging FDG-PET/CT in indolent lymphomas could be useful to rule out transformation in the next 30 months. In our study, semiquantitative analysis was statistically significantly associated with histological transformation and maximum standardized uptake value. However, because of the small number of patients, cautious interpretation of the results is warranted. More studies are needed to investigate the role of staging PET/CT in patient with

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