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Search Results: 1 - 10 of 12679 matches for " Stephen Knight "
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Sequential Variable Selection as Bayesian Pragmatism in Linear Factor Models  [PDF]
John Knight, Stephen Satchell, Jessica Qi Zhang
Journal of Mathematical Finance (JMF) , 2013, DOI: 10.4236/jmf.2013.31A022

We examine a popular practitioner methodology used in the construction of linear factor models whereby particular factors are increased or decreased in relative importance within the model. This allows model builders to customise models and, as such, reflect those factors that the client and modeller may think important. We call this process Pragmatic Bayesianism (or prag-Bayes for short) and we provide analysis which shows when such a procedure is likely to be successful.

A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
Robin D Knight, Stephen J Freeland, Laura F Landweber
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-4-research0010
Abstract: Codons respond to genome composition on the basis of their GC content relative to their synonyms (explaining 71-87% of the variance in response among the different codons, depending on measure). Amino-acid responses are determined by the mean GC content of their codons (explaining 71-79% of the variance). Similar trends hold for genes within a genome. Position-dependent selection for error minimization explains why individual bases respond differently to directional mutation pressure.Our model suggests that GC content drives codon usage (rather than the converse). It unifies a large body of empirical evidence concerning relationships between GC content and amino-acid or codon usage in disparate systems. The relationship between GC content and codon and amino-acid usage is ahistorical; it is replicated independently in the three domains of living organisms, reinforcing the idea that genes and genomes at mutation/selection equilibrium reproduce a unique relationship between nucleic acid and protein composition. Thus, the model may be useful in predicting amino-acid or nucleotide sequences in poorly characterized taxa.Different organisms have idiosyncratic, and sometimes extremely biased, preferences for one synonymous codon over another. Although differences in codon usage among genes and species have been widely studied, general principles have been difficult to find. Although it has been known for some time that the frequencies of some codons and amino acids correlate with genome GC content [1], the causality has remained unclear: correlations could exist because selection for a particular codon or amino-acid usage produces a particular genome GC content, or because mutation towards a particular GC content determines codon and amino-acid usage according to combinatorial principles. Here we show that codon and amino-acid usage is consistent with forces acting on nucleotides, rather than on codons or amino acids, although both mutation and selection play important rol
The use of non-bronchoscopic brushings to study the paediatric airway
Catherine Lane, Scott Burgess, Anthony Kicic, Darryl Knight, Stephen Stick
Respiratory Research , 2005, DOI: 10.1186/1465-9921-6-53
Abstract: Non-bronchoscopic brushing was investigated in a non-selected cohort of healthy, and mildly asthmatic children presenting for surgery unrelated to respiratory conditions, at the major children's hospital in Perth. Safety and side-effects of the procedure were assessed. Cell number, phenotype and viability were measured for all samples. The potential of these cells for use in long-term cell culture, immunohistochemistry, western blotting, quantitative PCR and gene arraying was examined.Non-bronchoscopic brushing was well tolerated in all children. The only significant side effect following the procedure was cough: nursing staff reported cough in 20% of patients; parents reported cough in 40% of patients. Cells sampled were of sufficient quantity and quality to allow cell culture in 93% of samples. Similarly, protein and RNA extracted from the cells was suitable for investigation of both gene and protein expression using micro-array and real-time PCR.Non-bronchoscopic brushing in children is safe and easy to perform, and is not associated with any complications. Using this technique, adequate numbers of epithelial cells can be retrieved to allow cell culture, western blotting, real time PCR, and microarray analysis. The purpose of this study is to demonstrate the utility of non-bronchoscopic airway brushing to obtain and study epithelial cells and to encourage others so that we can accelerate our knowledge regarding the role of the epithelium in childhood respiratory disease.The use of cytology brushes for the purpose of obtaining respiratory cells from adults for clinical and research purposes is well established. This technique is generally reported to be safe, both in adults with pulmonary disease and in healthy volunteers [1]. Samples are usually obtained under direct vision using a bronchoscope. However, we and others have recently used non-bronchoscopic brushing to sample airway epithelial cells from children [2,3]. This method has several advantages over bronch
Total Hip Arthroplasty – over 100 years of operative history
Stephen Richard Knight,Randeep Aujla,Satya Prasad Biswas
Orthopedic Reviews , 2011, DOI: 10.4081/or.2011.e16
Abstract: Total hip arthroplasty (THA) has completely revolutionised the nature in which the arthritic hip is treated, and is considered to be one of the most successful orthopaedic interventions of its generation (1). With over 100 years of operative history, this review examines the progression of the operation from its origins, together with highlighting the materials and techniques that have contributed to its development. Knowledge of its history contributes to a greater understanding of THA, such as the reasons behind selection of prosthetic materials in certain patient groups, while demonstrating the importance of critically analyzing research to continually determine best operative practice. Finally, we describe current areas of research being undertaken to further advance techniques and improve outcomes.
Why Are Women Dying When They Reach Hospital on Time? A Systematic Review of the ‘Third Delay’
Hannah E. Knight, Alice Self, Stephen H. Kennedy
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0063846
Abstract: Background The ‘three delays model’ attempts to explain delays in women accessing emergency obstetric care as the result of: 1) decision-making, 2) accessing services and 3) receipt of appropriate care once a health facility is reached. The third delay, although under-researched, is likely to be a source of considerable inequity in access to emergency obstetric care in developing countries. The aim of this systematic review was to identify and categorise specific facility-level barriers to the provision of evidence-based maternal health care in developing countries. Methods and Findings Five electronic databases were systematically searched using a 4-way strategy that combined search terms related to: 1) maternal health care; 2) maternity units; 3) barriers, and 4) developing countries. Forty-three original research articles were eligible to be included in the review. Thirty-two barriers to the receipt of timely and appropriate obstetric care at the facility level were identified and categorised into six emerging themes (Drugs and equipment; Policy and guidelines; Human resources; Facility infrastructure; Patient-related and Referral-related). Two investigators independently recorded the frequency with which barriers relating to the third delay were reported in the literature. The most commonly cited barriers were inadequate training/skills mix (86%); drug procurement/logistics problems (65%); staff shortages (60%); lack of equipment (51%) and low staff motivation (44%). Conclusions This review highlights how a focus on patient-side delays in the decision to seek care can conceal the fact that many health facilities in the developing world are still chronically under-resourced and unable to cope effectively with serious obstetric complications. We stress the importance of addressing supply-side barriers alongside demand-side factors if further reductions in maternal mortality are to be achieved.
Understanding the Profile of Tuberculosis and Human Immunodeficiency Virus Coinfection: Insights from Expanded HIV Surveillance at a Tuberculosis Facility in Durban, South Africa
Rubeshan Perumal,Nesri Padayatchi,Kogieleum Naidoo,Stephen Knight
ISRN AIDS , 2014, DOI: 10.1155/2014/260329
Abstract: Background. Expanded HIV surveillance in TB patients forms part of the World Health Organization framework for strategic collaborative activity. Surveillance helps understand the epidemiology of the local dual epidemic and enables design of a tailored response to these challenges. Methods. We conducted an observational, cross-sectional study of anonymous unlinked HIV testing for 741 consecutive TB suspects attending an urban TB facility during a seven-week period in 2008. Results. A total of 512 patients were found to have TB. The mean age was 35.7 years, and 63% were male. The prevalence of HIV was 72.2% (95% CI: 68.2–75.9) in all TB cases, 69.8% (95% CI: 65.3–74.2) in pulmonary tuberculosis (PTB), 81.6% (95% CI: 72.9–90.3) in extrapulmonary disease, and 66.8% (95% CI: 60.7–72.9) in those without TB disease. HIV prevalence in TB patients was higher in females than males and in younger age groups (18–29 years). The sex ratio of PTB patients correlated with the sex ratio of the prevalence of HIV in the respective age groups . Conclusion. The use of a rapid HIV test performed on sputum anonymously provides an opportunity for HIV surveillance in this high-burdened setting, which has the potential to lend valuable insight into the coepidemics. 1. Background In South Africa, the global epicenter of both tuberculosis (TB) and human immunodeficiency virus (HIV), the menacing convergence of these diseases: one viral and one bacterial, one emergent, and one ancient, presents a near insurmountable challenge to health, social, economic, and developmental welfare [1]. These dual epidemics threaten to undo the health care gains of the past decades in an already ailing health care system. Women now account for nearly a half of all global infections and 77% of all women living with HIV are in sub-Saharan African [2]. Acquired immune deficiency syndrome (AIDS) accounts for more deaths in women than all causes of maternal mortality combined [2]. While the global incidence of HIV is decreasing, new infections among young women aged 15 to 24 years have steadily increased in South Africa, which is due to multifactorial and complex biological, social, economic and behavioural factors. The World Health Organization (WHO), in an effort to address the challenges of HIV associated TB, has proposed a framework of strategic collaborative activities for TB and HIV services which foster a more comprehensive approach to the synergistic dual epidemics [3]. In settings of generalized HIV and AIDS epidemics, like South Africa, WHO recommends expanding HIV surveillance to include TB
The Nucleus of Comet 10P/Tempel 2 in 2013 and Consequences Regarding Its Rotational State: Early Science from the Discovery Channel Telescope
David G. Schleicher,Matthew M. Knight,Stephen E. Levine
Physics , 2013, DOI: 10.1088/0004-6256/146/5/137
Abstract: We present new lightcurve measurements of Comet 10P/Tempel 2 carried out with Lowell Observatory's Discovery Channel Telescope in early 2013 when the comet was at aphelion. These data represent some of the first science obtained with this new 4.3-m facility. With Tempel 2 having been observed to exhibit a small but ongoing spin-down in its rotation period for over two decades, our primary goals at this time were two-fold. First, to determine its current rotation period and compare it to that measured shortly after its most recent perihelion passage in 2010, and second, to disentangle the spin-down from synodic effects due to the solar day and the Earth's orbital motion and to determine the sense of rotation, i.e. prograde or retrograde. At our midpoint of 2013 Feb 24, the observed synodic period is 8.948+/-0.001 hr, exactly matching the predicted prograde rotation solution based on 2010 results, and yields a sidereal period of the identical value due to the solar and Earth synodic components just canceling out during the interval of the 2013 observations. The retrograde solution is ruled out because the associated sidereal periods in 2010 and 2013 are quite different even though we know that extremely little outgassing, needed to produce torques, occurred in this interval. With a definitive sense of rotation, the specific amounts of spin-down to the sidereal period could be assessed. The nominal values imply that the rate of spin-down has decreased over time, consistent with the secular drop in water production since 1988. Our data also exhibited an unexpectedly small lightcurve amplitude which appears to be associated with viewing from a large, negative sub-Earth latitude, and a lightcurve shape deviating from a simple sinusoid implying a highly irregularly shaped nucleus.
Bone Density and Cortical Thickness in Normal, Osteopenic, and Osteoporotic Sacra
Andrew M. Richards,Nathan W. Coleman,Trevor A. Knight,Stephen M. Belkoff,Simon C. Mears
Journal of Osteoporosis , 2010, DOI: 10.4061/2010/504078
Abstract: It is unclear if a decrease in cancellous bone density or cortical bone thickness is related to sacral insufficiency fractures. We hypothesized that reduction in overall bone density leads to local reductions in bone density and cortical thickness in cadaveric sacra that match clinically observed fracture patterns in patients with sacral insufficiency fractures. We used quantitative computed tomography to measure cancellous density and cortical thickness in multiple areas of normal, osteopenic, and osteoporotic sacra. Cancellous bone density was significantly lower in osteoporotic specimens in the central and anterior regions of the sacral ala compared with other regions of these specimens. Cortical thickness decreased uniformly in all regions of osteopenic and osteoporotic specimens. These results support our hypothesis that areas of the sacrum where sacral insufficiency fractures often occur have significantly larger decreases in cancellous bone density; however, they do not support the hypothesis that these areas have local reduction of cortical bone thickness.
A retrospective study of Human Immunodeficiency Virus transmission, mortality and loss to follow-up among infants in the first 18 months of life in a prevention of mother-to-child transmission programme in an urban hospital in KwaZulu-Natal, South Africa
Terusha Chetty, Stephen Knight, Janet Giddy, Tamaryn L Crankshaw, Lisa M Butler, Marie-Louise Newell
BMC Pediatrics , 2012, DOI: 10.1186/1471-2431-12-146
Abstract: We conducted a retrospective cohort study of infants born to women in the PMTCT programme at McCord Hospital, where mothers paid a fee for service. Data were abstracted from patient records for live-born infants delivered between 1 May 2008 and 31 May 2009. The infants’ LTFU status and age was based on the date of the last visit. HIV transmission was calculated as a proportion of infants followed and tested at six weeks. Mortality rates were analyzed using Kaplan-Meier (K-M), with censoring on 15 January 2010, LTFU or death.Of 260 infants, 155 (59.6%) remained in care at McCord beyond 28 weeks: one died at?<?28 days, three died between one to six months; 34 were LTFU within seven days, 60 were LTFU by six months. K-M mortality rate: 1.7% at six months (95% confidence interval (CI): 0.6% to 4.3%). Of 220 (83%) infants tested for HIV at six weeks, six (2.7%, 95% CI: 1.1% to 5.8%) were HIV-infected. In Cox regression analysis, late antenatal attendance (≥ 28 weeks gestation) relative to attending in the first trimester was a predictor for infant LTFU (adjusted hazards ratio?=?2.3; 95% CI: 1.0 to 5.1; p?=?0.044).This urban PMTCT programme achieved low transmission rates at six weeks, but LTFU in the first six months limited our ability to examine HIV transmission up to 18 months and determinants of mortality. The LTFU of infants born to women who attended antenatal care at 28 weeks gestation or later emphasizes the need to identify late antenatal attendees for follow up care to educate and support them regarding the importance of follow up care for themselves and their infants.Globally, approximately 370 000 children were newly infected with Human Immunodeficiency Virus (HIV) in 2009; the vast majority in sub-Saharan Africa [1], mostly due to mother-to-child transmission. In resource-constrained settings, with little or no antiretroviral treatment, approximately one-third of HIV-infected children die before one year and more than half die before two years of age [2]. In
Function of the Airway Epithelium in Asthma
Teal S. Hallstrand,Prescott G. Woodruff,Stephen T. Holgate,Darryl A. Knight
Journal of Allergy , 2012, DOI: 10.1155/2012/160586
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