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Graham DJ, McCoy EJ, Stephens DA. Quantifying Causal Effects of Road Network Capacity Expansions on Traffic Volume and Density via a Mixed Model Propensity Score Estimator. J Am Stat Assoc 2014. [DOI: 10.1080/01621459.2014.956871] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Hanley JA, Saarela O, Stephens DA, Thalabard JC. hGH isoform differential immunoassays applied to blood samples from athletes: decision limits for anti-doping testing. Growth Horm IGF Res 2014; 24:205-215. [PMID: 24973245 DOI: 10.1016/j.ghir.2014.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 06/02/2014] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To detect hGH doping in sport, the World Anti-Doping Agency (WADA)-accredited laboratories use the ratio of the concentrations of recombinant hGH ('rec') versus other 'natural' pituitary-derived isoforms of hGH ('pit'), measured with two different kits developed specifically to detect the administration of exogenous hGH. The current joint compliance decision limits (DLs) for ratios derived from these kits, designed so that they would both be exceeded in fewer than 1 in 10,000 samples from non-doping athletes, are based on data accrued in anti-doping labs up to March 2010, and later confirmed with data up to February-March 2011. In April 2013, WADA asked the authors to analyze the now much larger set of ratios collected in routine hGH testing of athletes, and to document in the peer-reviewed literature a statistical procedure for establishing DLs, so that it be re-applied as more data become available. DESIGN We examined the variation in the rec/pit ratios obtained for 21,943 screened blood (serum) samples submitted to the WADA accredited laboratories over the period 2009-2013. To fit the relevant sex- and kit-specific centiles of the logs of the ratios, we classified 'rec/pit' ratios based on low 'rec' and 'pit' values as 'negative' and fitted statistical distributions to the remaining log-ratios. The flexible data-driven quantile regression approach allowed us to deal with the fact that the location, scale and shape of the distribution of the modeled 'rec/pit' ratios varied with the concentrations of the 'rec' and 'pit' values. The between-kit correlation of the ratios was included in the fitting of the DLs, and bootstrap samples were used to quantify the estimation error in these limits. We examined the performance of these limits by applying them to the data obtained from investigator-initiated hGH administration studies, and in athletes in a simulated cycling stage race. RESULTS The mean and spread of the distribution of the modeled log-ratios depended in different ways on the magnitude of the rec and pit concentrations. Ultimately, however, the estimated limits were almost invariant to the concentrations, and similar to those obtained by fitting simpler (marginal) log-normal and Box-Cox transformed distributions. The estimated limits were similar to the (currently-used) limits fitted to the smaller datasets analyzed previously. In investigator-initiated instances, the limits distinguished recent use of rec-hGH from non-use. CONCLUSIONS The distributions of the rec/pit ratios varied as a function of the rec and pit concentrations, but the patterns in their medians and spreads largely canceled each other. Thus, ultimately, the kit- and sex-specific ratio DL obtained from the simpler model was very close to the 'curve of DLs' obtained from the more complex one. Both were close to previously established limits.
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Rich B, Moodie EEM, Stephens DA. Simulating sequential multiple assignment randomized trials to generate optimal personalized warfarin dosing strategies. Clin Trials 2014; 11:435-444. [DOI: 10.1177/1740774513517063] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background Due to the cost and complexity of conducting a sequential multiple assignment randomized trial (SMART), it is desirable to pre-define a small number of personalized regimes to study. Purpose We proposed a simulation-based approach to studying personalized dosing strategies in contexts for which a therapeutic agent’s pharmacokinetic and pharmacodynamics properties are well understood. We take dosing of warfarin as a case study, as its properties are well understood. We consider a SMART in which there are five intervention points in which dosing may be modified, following a loading phase of treatment. Methods Realistic SMARTs are simulated, and two methods of analysis, G-estimation and Q-learning, are used to assess potential personalized dosing strategies. Results In settings where outcome modelling may be complex due to the highly non-linear nature of the pharmacokinetic and pharmacodynamics mechanisms of the therapeutic agent, G-estimation provides for which the more promising method of estimating an optimal dosing strategy. Used in combination with the simulated SMARTs, we were able to improve simulated patient outcomes and suggest which patient characteristics were needed to best individually tailor dosing. In particular, our simulations suggest that current dosing should be determined by an individual’s current coagulation time as measured by the international normalized ratio (INR), their last measured INR, and their last dose. Tailoring treatment only based on current INR and last warfarin dose provided inferior control of INR over the course of the trial. Limitations The ability of the simulated SMARTs to suggest optimal personalized dosing strategies relies on the pharmacokinetic and pharmacodynamic models used to generate the hypothetical patient profiles. This approach is best suited to therapeutic agents whose effects are well studied. Conclusion Prior to investing in a complex randomized trial that involves sequential treatment allocations, simulations should be used where possible in order to guide which dosing strategies to evaluate.
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Moodie EE, Stephens DA, Klein MB. A marginal structural model for multiple-outcome survival data:assessing the impact of injection drug use on several causes of death in the Canadian Co-infection Cohort. Stat Med 2013; 33:1409-25. [DOI: 10.1002/sim.6043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 10/25/2013] [Accepted: 10/26/2013] [Indexed: 11/11/2022]
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Wallace MP, Stewart CE, Moseley MJ, Stephens DA, Fielder AR. Compliance with occlusion therapy for childhood amblyopia. Invest Ophthalmol Vis Sci 2013; 54:6158-66. [PMID: 23882695 DOI: 10.1167/iovs.13-11861] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Explore compliance with occlusion treatment of amblyopia in the Monitored and Randomized Occlusion Treatment of Amblyopia Studies (MOTAS and ROTAS), using objective monitoring. METHODS Both studies had a three-phase protocol: initial assessment, refractive adaptation, and occlusion. In the occlusion phase, participants were instructed to dose for 6 hours/day (MOTAS) or randomized to 6 or 12 hour/day (ROTAS). Dose was monitored continuously using an occlusion dose monitor (ODM). RESULTS One hundred and fifty-two patients (71 male, 81 female; 122 Caucasian, 30 non-Caucasian) of mean ± SD age 68 ± 18 months participated. Amblyopia was defined as an interocular acuity difference of at least 0.1 logMAR and was associated with anisometropia in 50, strabismus in 44, and both (mixed) in 58. Median duration of occlusion was 99 days (interquartile range 72 days). Mean compliance was 44%, mean proportion of days with no patch worn was 42%. Compliance was lower (39%) on weekends compared with weekdays (46%, P = 0.04), as was the likelihood of dosing at all (52% vs. 60%, P = 0.028). Compliance was lower when attendance was less frequent (P < 0.001) and with prolonged treatment duration (P < 0.001). Age, sex, amblyopia type, and severity were not associated with compliance. Mixture modeling suggested three subpopulations of patch day doses: less than 30 minutes; doses that achieve 30% to 80% compliance; and doses that achieve around 100% compliance. CONCLUSIONS This study shows that compliance with patching treatment averages less than 50% and is influenced by several factors. A greater understanding of these influences should improve treatment outcome. (ClinicalTrials.gov number, NCT00274664).
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Vincent C, Stephens DA, Loo VG, Edens TJ, Behr MA, Dewar K, Manges AR. Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection. MICROBIOME 2013; 1:18. [PMID: 24450844 PMCID: PMC3971611 DOI: 10.1186/2049-2618-1-18] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 06/21/2013] [Indexed: 05/10/2023]
Abstract
BACKGROUND Antimicrobial use is thought to suppress the intestinal microbiota, thereby impairing colonization resistance and allowing Clostridium difficile to infect the gut. Additional risk factors such as proton-pump inhibitors may also alter the intestinal microbiota and predispose patients to Clostridium difficile infection (CDI). This comparative metagenomic study investigates the relationship between epidemiologic exposures, intestinal bacterial populations and subsequent development of CDI in hospitalized patients. We performed a nested case-control study including 25 CDI cases and 25 matched controls. Fecal specimens collected prior to disease onset were evaluated by 16S rRNA gene amplification and pyrosequencing to determine the composition of the intestinal microbiota during the at-risk period. RESULTS The diversity of the intestinal microbiota was significantly reduced prior to an episode of CDI. Sequences corresponding to the phylum Bacteroidetes and to the families Bacteroidaceae and Clostridiales Incertae Sedis XI were depleted in CDI patients compared to controls, whereas sequences corresponding to the family Enterococcaceae were enriched. In multivariable analyses, cephalosporin and fluoroquinolone use, as well as a decrease in the abundance of Clostridiales Incertae Sedis XI were significantly and independently associated with CDI development. CONCLUSIONS This study shows that a reduction in the abundance of a specific bacterial family - Clostridiales Incertae Sedis XI - is associated with risk of nosocomial CDI and may represent a target for novel strategies to prevent this life-threatening infection.
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Stewart CE, Wallace MP, Stephens DA, Fielder AR, Moseley MJ. The effect of amblyopia treatment on stereoacuity. J AAPOS 2013; 17:166-73. [PMID: 23622448 DOI: 10.1016/j.jaapos.2012.10.021] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 10/17/2012] [Accepted: 10/17/2012] [Indexed: 11/18/2022]
Abstract
PURPOSE To explore how stereoacuity changes in patients while they are being treated for amblyopia. METHODS The Monitored Occlusion Treatment for Amblyopia Study (MOTAS) comprised 3 distinct phases. In the first phase, baseline, assessments of visual function were made to confirm the initial visual and binocular visual deficit. The second phase, refractive adaptation, now commonly termed "optical treatment," was an 18-week period of spectacle wear with measurements of logMAR visual acuity and stereoacuity with the Frisby test at weeks 0, 6, 12, and 18. In the third phase, occlusion, participants were prescribed 6 hours of patching per day. RESULTS A total of 85 children were enrolled (mean age, 5.1 ± 1.5 years). In 21 children amblyopia was associated with anisometropia; in 29, with strabismus; and in 35, with both. At study entry, poor stereoacuity was associated with poor visual acuity (P < 0.001) in the amblyopic eye and greater angle of strabismus (P < 0.001). Of 66 participants, 25 (38%) who received refractive adaptation and 19 (29%) who received occlusion improved by at least one octave in stereoacuity, exceeding test-retest variability. Overall, 38 (45%) improved one or more octaves across both treatment phases. Unmeasureable stereoacuity was observed in 56 participants (66%) at study entry and in 37 (43%) at study exit. CONCLUSIONS Stereoacuity improved for almost one half of the study participants. Improvement was observed in both treatment phases. Factors associated with poor or nil stereoacuity at study entry and exit were poor visual acuity of the amblyopic eye and large-angle strabismus.
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Spry NA, Taaffe DR, England PJ, Judge JS, Stephens DA, Peddle-McIntyre C, Baker MK, Newton RU, Galvão DA. Long-term effects of intermittent androgen suppression therapy on lean and fat mass: a 33-month prospective study. Prostate Cancer Prostatic Dis 2012; 16:67-72. [DOI: 10.1038/pcan.2012.33] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Weston DJ, Adams NM, Russell RA, Stephens DA, Freemont PS. Analysis of spatial point patterns in nuclear biology. PLoS One 2012; 7:e36841. [PMID: 22615822 PMCID: PMC3353971 DOI: 10.1371/journal.pone.0036841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 04/16/2012] [Indexed: 12/31/2022] Open
Abstract
There is considerable interest in cell biology in determining whether, and to what extent, the spatial arrangement of nuclear objects affects nuclear function. A common approach to address this issue involves analyzing a collection of images produced using some form of fluorescence microscopy. We assume that these images have been successfully pre-processed and a spatial point pattern representation of the objects of interest within the nuclear boundary is available. Typically in these scenarios, the number of objects per nucleus is low, which has consequences on the ability of standard analysis procedures to demonstrate the existence of spatial preference in the pattern. There are broadly two common approaches to look for structure in these spatial point patterns. First a spatial point pattern for each image is analyzed individually, or second a simple normalization is performed and the patterns are aggregated. In this paper we demonstrate using synthetic spatial point patterns drawn from predefined point processes how difficult it is to distinguish a pattern from complete spatial randomness using these techniques and hence how easy it is to miss interesting spatial preferences in the arrangement of nuclear objects. The impact of this problem is also illustrated on data related to the configuration of PML nuclear bodies in mammalian fibroblast cells.
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Moodie EEM, Stephens DA. Using Directed Acyclic Graphs to detect limitations of traditional regression in longitudinal studies. Int J Public Health 2010; 55:701-3. [PMID: 20838848 DOI: 10.1007/s00038-010-0184-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 06/17/2010] [Accepted: 07/16/2010] [Indexed: 10/19/2022] Open
Abstract
INTRODUCTION Longitudinal data are increasingly available to health researchers; these present challenges not encountered in cross-sectional data, not the least of which is the presence of time-varying confounding variables and intermediate effects. OBJECTIVES We review confounding and mediation in a longitudinal setting and introduce causal graphs to explain the bias that arises from conventional analyses. CONCLUSIONS When both time-varying confounding and mediation are present in the data, traditional regression models result in estimates of effect coefficients that are systematically incorrect, or biased. In a companion paper (Moodie and Stephens in Int J Publ Health, 2010b, this issue), we describe a class of models that yield unbiased estimates in a longitudinal setting.
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Sagoo P, Perucha E, Sawitzki B, Tomiuk S, Stephens DA, Miqueu P, Chapman S, Craciun L, Sergeant R, Brouard S, Rovis F, Jimenez E, Ballow A, Giral M, Rebollo-Mesa I, Le Moine A, Braudeau C, Hilton R, Gerstmayer B, Bourcier K, Sharif A, Krajewska M, Lord GM, Roberts I, Goldman M, Wood KJ, Newell K, Seyfert-Margolis V, Warrens AN, Janssen U, Volk HD, Soulillou JP, Hernandez-Fuentes MP, Lechler RI. Development of a cross-platform biomarker signature to detect renal transplant tolerance in humans. J Clin Invest 2010; 120:1848-61. [PMID: 20501943 DOI: 10.1172/jci39922] [Citation(s) in RCA: 426] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 03/16/2010] [Indexed: 12/13/2022] Open
Abstract
Identifying transplant recipients in whom immunological tolerance is established or is developing would allow an individually tailored approach to their posttransplantation management. In this study, we aimed to develop reliable and reproducible in vitro assays capable of detecting tolerance in renal transplant recipients. Several biomarkers and bioassays were screened on a training set that included 11 operationally tolerant renal transplant recipients, recipient groups following different immunosuppressive regimes, recipients undergoing chronic rejection, and healthy controls. Highly predictive assays were repeated on an independent test set that included 24 tolerant renal transplant recipients. Tolerant patients displayed an expansion of peripheral blood B and NK lymphocytes, fewer activated CD4+ T cells, a lack of donor-specific antibodies, donor-specific hyporesponsiveness of CD4+ T cells, and a high ratio of forkhead box P3 to alpha-1,2-mannosidase gene expression. Microarray analysis further revealed in tolerant recipients a bias toward differential expression of B cell-related genes and their associated molecular pathways. By combining these indices of tolerance as a cross-platform biomarker signature, we were able to identify tolerant recipients in both the training set and the test set. This study provides an immunological profile of the tolerant state that, with further validation, should inform and shape drug-weaning protocols in renal transplant recipients.
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Moodie EEM, Stephens DA. Estimation of dose-response functions for longitudinal data using the generalised propensity score. Stat Methods Med Res 2010; 21:149-66. [PMID: 20442194 DOI: 10.1177/0962280209340213] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In a longitudinal study of dose-response, it is often necessary to adjust for confounding or non-compliance, which may otherwise compromise the estimation of the true effect of a treatment. Using an approach based on the generalised propensity score (GPS)--a generalisation of the classical, binary treatment propensity score--it is possible to construct a balancing score that provides an estimation procedure for the true (unconfounded) direct effect of dose on response. Previously, the GPS has been applied only in a single interval setting; in this article, we extend the GPS methodology to the longitudinal setting to estimate the direct effect of a continuous dose on a longitudinal response. The methodology is applied to two simulated examples, and a real longitudinal dose-response investigation, the Monitored Occlusion Treatment of Amblyopia Study (MOTAS). In the treatment of childhood amblyopia, a common ophthalmological condition, occlusion therapy (patching) was for many decades the standard medical treatment, despite the fact that its efficacy was not quantified. MOTAS was revolutionary, as it was the first study to obtain precise measurements of the amount of occlusion each study participant received over the course of the study.
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Russell RA, Adams NM, Stephens DA, Batty E, Jensen K, Freemont PS. Segmentation of fluorescence microscopy images for quantitative analysis of cell nuclear architecture. Biophys J 2009; 96:3379-89. [PMID: 19383481 DOI: 10.1016/j.bpj.2008.12.3956] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Revised: 11/18/2008] [Accepted: 12/15/2008] [Indexed: 12/24/2022] Open
Abstract
Considerable advances in microscopy, biophysics, and cell biology have provided a wealth of imaging data describing the functional organization of the cell nucleus. Until recently, cell nuclear architecture has largely been assessed by subjective visual inspection of fluorescently labeled components imaged by the optical microscope. This approach is inadequate to fully quantify spatial associations, especially when the patterns are indistinct, irregular, or highly punctate. Accurate image processing techniques as well as statistical and computational tools are thus necessary to interpret this data if meaningful spatial-function relationships are to be established. Here, we have developed a thresholding algorithm, stable count thresholding (SCT), to segment nuclear compartments in confocal laser scanning microscopy image stacks to facilitate objective and quantitative analysis of the three-dimensional organization of these objects using formal statistical methods. We validate the efficacy and performance of the SCT algorithm using real images of immunofluorescently stained nuclear compartments and fluorescent beads as well as simulated images. In all three cases, the SCT algorithm delivers a segmentation that is far better than standard thresholding methods, and more importantly, is comparable to manual thresholding results. By applying the SCT algorithm and statistical analysis, we quantify the spatial configuration of promyelocytic leukemia nuclear bodies with respect to irregular-shaped SC35 domains. We show that the compartments are closer than expected under a null model for their spatial point distribution, and furthermore that their spatial association varies according to cell state. The methods reported are general and can readily be applied to quantify the spatial interactions of other nuclear compartments.
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Metcalf CJE, Stephens DA, Rees M, Louda SM, Keeler KH. Using Bayesian inference to understand the allocation of resources between sexual and asexual reproduction. J R Stat Soc Ser C Appl Stat 2009. [DOI: 10.1111/j.1467-9876.2008.00652.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Graham DJ, Stephens DA. Decomposing the impact of deprivation on child pedestrian casualties in England. ACCIDENT; ANALYSIS AND PREVENTION 2008; 40:1351-1364. [PMID: 18606266 DOI: 10.1016/j.aap.2008.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 02/18/2008] [Accepted: 02/20/2008] [Indexed: 05/26/2023]
Abstract
The incidence of child injury due to road traffic accidents appears to be positively associated with socio-economic deprivation. However, the reasons behind this relationship have proven difficult to identify. In this paper, we present results from a cross-sectional analysis using generalized linear regression models of child pedestrian casualties for the wards of England. We find that there are distinct and substantial effects on casualty rates from characteristics associated with area deprivation across diverse environments. These associations exist over and above influences arising from local environmental characteristics. Distinct dimensions of deprivation appear to affect the incidence of pedestrian casualties to varying degrees and sometimes in different directions. The results identify a relationship between income deprivation and the incidence of child pedestrian casualties, but they also show that poverty is only one aspect of deprivation that matters. In particular, we find a consistent positive influence from crime related deprivation.
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Stewart CE, Stephens DA, Fielder AR, Moseley MJ. Objectively monitored patching regimens for treatment of amblyopia: randomised trial. BMJ 2007; 335:707. [PMID: 17855283 PMCID: PMC2001048 DOI: 10.1136/bmj.39301.460150.55] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES To compare visual outcome in response to two prescribed rates of occlusion (six hours a day and 12 hours a day). DESIGN Unmasked randomised trial. SETTING Research clinics in two London hospitals. PARTICIPANTS 97 children with a confirmed diagnosis of amblyopia associated with strabismus, anisometropia, or both. INTERVENTIONS 18 week period of wearing glasses (refractive adaptation) followed by occlusion prescribed ("patching") for six or 12 hours a day. MAIN OUTCOME MEASURES Visual acuity measured by logMAR letter recognition; objectively monitored rate of occlusion (hours a day). RESULTS The mean age of children at study entry was 5.6 (SD 1.5) years. Ninety were eligible for occlusion but 10 dropped out in this phase, leaving 80 children who were randomised to a prescribed dose rate of six (n=40) or 12 (n=40) hours a day. The mean change in visual acuity of the amblyopic eye was not significantly different (P=0.64) between the two groups (0.26 (95% confidence interval 0.21 to 0.31) log units in six hour group; 0.24 (0.19 to 0.29) log units in 12 hour group). The mean dose rates (hours a day) actually received, however, were also not significantly different (4.2 (3.7 to 4.7) in six hour group v 6.2 (5.1 to 7.3) in 12 hour group; P=0.06). The visual outcome was similar for those children who received three to six hours a day or more than six to 12 hours a day, but significantly better than that in children who received less than three hours a day. Children aged under 4 required significantly less occlusion than older children. Visual outcome was not influenced by type of amblyopia. CONCLUSIONS Substantial (six hours a day) and maximal (12 hours a day) prescribed occlusion results in similar visual outcome. On average, the occlusion dose received in the maximal group was only 50% more than in the substantial group and in both groups was much less than that prescribed. Younger children required the least occlusion. TRIALS REGISTRATION Clinical Trials NCT00274664.
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Gander MP, Stephens DA. Stochastic volatility modelling in continuous time with general marginal distributions: Inference, prediction and model selection. J Stat Plan Inference 2007. [DOI: 10.1016/j.jspi.2006.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
A dynamic regime is a function that takes treatment and covariate history and baseline covariates as inputs and returns a decision to be made. Murphy (2003, Journal of the Royal Statistical Society, Series B 65, 331-366) and Robins (2004, Proceedings of the Second Seattle Symposium on Biostatistics, 189-326) have proposed models and developed semiparametric methods for making inference about the optimal regime in a multi-interval trial that provide clear advantages over traditional parametric approaches. We show that Murphy's model is a special case of Robins's and that the methods are closely related but not equivalent. Interesting features of the methods are highlighted using the Multicenter AIDS Cohort Study and through simulation.
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Stewart CE, Stephens DA, Fielder AR, Moseley MJ. Modeling dose-response in amblyopia: toward a child-specific treatment plan. Invest Ophthalmol Vis Sci 2007; 48:2589-94. [PMID: 17525188 DOI: 10.1167/iovs.05-1243] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE This article describes an empirically derived mathematical model of the treatment dose-response of occlusion therapy for amblyopia based on outcome data obtained from the Monitored Occlusion Treatment for Amblyopia Study (MOTAS). METHODS The MOTAS protocol comprised three discrete phases: baseline, refractive adaptation, and occlusion. Only data from the occlusion phase were used in this dose-response model. Seventy-two participants, 3 to 8 years of age, mean +/- SD age 5.2 +/- 1.4 years (anisometropia [n = 18]); strabismus [n = 22]); both anisometropia and strabismus [n = 32]) completed the occlusion phase. All participants were prescribed 6-h/d patching, which was objectively monitored by an occlusion dose monitor (ODM). RESULTS Simple normal linear regression modeling of the data on an interval-by-interval basis (interval between clinic visits) indicates that increasing cumulative dose within interval (hours) yields an increase in visual acuity (R2 = 0.918; 684 data points). Most of the children achieved their best visual acuity with 150 to 250 hours' cumulative dose. Specific patient characteristics (especially age) modify the steepness of this function. For example, a 0.20-logMAR (2-line logarithm of the minimum angle of resolution) gain in visual acuity requires a cumulative dose of 170 hours for children at age 48 months and 236 hours at age 72 months. CONCLUSIONS Mathematical modeling of amblyopia therapy is a novel approach that elucidates the kinetics of the therapeutic response in humans. This response is age-influenced so that older children require a greater dose to achieve the same outcome--evidence of altered plasticity of the visual system. Fine-tuning the dose-response in amblyopia therapy will facilitate the development of child-specific, evidence-based treatment plans.
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Abstract
There are almost 1,300 entries for higher eukaryotes in the Nuclear Protein Database. The proteins' subcellular distribution patterns within interphase nuclei can be complex, ranging from diffuse to punctate or microspeckled, yet they all work together in a coordinated and controlled manner within the three-dimensional confines of the nuclear volume. In this review we describe recent advances in the use of quantitative methods to understand nuclear spatial organisation and discuss some of the practical applications resulting from this work.
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McManus KJ, Stephens DA, Adams NM, Islam SA, Freemont PS, Hendzel MJ. The transcriptional regulator CBP has defined spatial associations within interphase nuclei. PLoS Comput Biol 2006; 2:e139. [PMID: 17054391 PMCID: PMC1617132 DOI: 10.1371/journal.pcbi.0020139] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 09/08/2006] [Indexed: 01/19/2023] Open
Abstract
It is becoming increasingly clear that nuclear macromolecules and macromolecular complexes are compartmentalized through binding interactions into an apparent three-dimensionally ordered structure. This ordering, however, does not appear to be deterministic to the extent that chromatin and nonchromatin structures maintain a strict 3-D arrangement. Rather, spatial ordering within the cell nucleus appears to conform to stochastic rather than deterministic spatial relationships. The stochastic nature of organization becomes particularly problematic when any attempt is made to describe the spatial relationship between proteins involved in the regulation of the genome. The CREB-binding protein (CBP) is one such transcriptional regulator that, when visualised by confocal microscopy, reveals a highly punctate staining pattern comprising several hundred individual foci distributed within the nuclear volume. Markers for euchromatic sequences have similar patterns. Surprisingly, in most cases, the predicted one-to-one relationship between transcription factor and chromatin sequence is not observed. Consequently, to understand whether spatial relationships that are not coincident are nonrandom and potentially biologically important, it is necessary to develop statistical approaches. In this study, we report on the development of such an approach and apply it to understanding the role of CBP in mediating chromatin modification and transcriptional regulation. We have used nearest-neighbor distance measurements and probability analyses to study the spatial relationship between CBP and other nuclear subcompartments enriched in transcription factors, chromatin, and splicing factors. Our results demonstrate that CBP has an order of spatial association with other nuclear subcompartments. We observe closer associations between CBP and RNA polymerase II-enriched foci and SC35 speckles than nascent RNA or specific acetylated histones. Furthermore, we find that CBP has a significantly higher probability of being close to its known in vivo substrate histone H4 lysine 5 compared with the closely related H4 lysine 12. This study demonstrates that complex relationships not described by colocalization exist in the interphase nucleus and can be characterized and quantified. The subnuclear distribution of CBP is difficult to reconcile with a model where chromatin organization is the sole determinant of the nuclear organization of proteins that regulate transcription but is consistent with a close link between spatial associations and nuclear functions.
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Grudell ABM, Camilleri M, Burton DD, Stephens DA. Effect of a proton pump inhibitor on postprandial gastric volume, emptying and symptoms in healthy human subjects: a pilot study. Aliment Pharmacol Ther 2006; 24:1037-43. [PMID: 16984497 DOI: 10.1111/j.1365-2036.2006.03102.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND In consensus guidelines, proton pump inhibitors (PPIs) are recommended for the treatment of functional dyspepsia. It is unclear whether PPIs change gastric volume or emptying. AIM To assess the effect of a PPI, rabeprazole, on gastric volume and emptying and postprandial symptoms. METHODS In a double-blind, parallel-group placebo-controlled trial, 13 healthy participants were randomized to rabeprazole, 20 mg b.d., or placebo. On day 3, fasting gastric volume was measured using intravenous (99m)Tc-pertechnate and single photon emission computed tomography (SPECT). After the last dose of study medication, an (111)In-chloride egg meal (300 kcal) was ingested, and postprandial gastric volume and emptying were measured by SPECT. Symptom ratings using a visual analogue scale (fullness, nausea, bloating, abdominal pain, aggregate score) were obtained at baseline and 15, 30, 45, 60 and 75 min postprandially. Group comparisons were performed using Mann-Whitney rank sum test. RESULTS There were no statistically significant differences in gastric volume or emptying in the two groups. However, there was a borderline increase in gastric volume with rabeprazole compared with placebo. Rabeprazole treatment reduced aggregate postprandial symptoms, particularly fullness, 30 min after the meal (P = 0.01). CONCLUSIONS In healthy participants, rabeprazole, 20 mg b.d., did not significantly change gastric emptying, but reduced symptoms and had a borderline effect on gastric volume postprandially. The mechanism of reduced postprandial symptoms with a PPI requires further study.
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Gonenne J, Esfandyari T, Camilleri M, Burton DD, Stephens DA, Baxter KL, Zinsmeister AR, Bharucha AE. Effect of female sex hormone supplementation and withdrawal on gastrointestinal and colonic transit in postmenopausal women. Neurogastroenterol Motil 2006; 18:911-8. [PMID: 16961694 DOI: 10.1111/j.1365-2982.2006.00808.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Females are disproportionately affected by constipation, which is often aggravated during pregnancy. Bowel function also changes during the luteal phase of the menstrual cycle. The aim was to compare the effects of acute administration of female sex steroids on gastric emptying, small bowel transit and colonic transit in healthy postmenopausal subjects. A second aim was to determine whether withdrawal of the hormones was associated with a change in transit. Forty-nine postmenopausal females were randomized to receive for 7 days 400 mg day(-1) micronized progesterone, 0.2 mg day(-1) oestradiol, combination of the two, or placebo. Treatment groups were balanced on age. Participants underwent whole gut transit measurement by scintigraphy using a 99m-labeled technetium-egg meal and 111-labeled indium-charcoal via a delayed-release capsule. Transit measurement was repeated after withdrawal of the study medications. The primary endpoints were ascending colon (AC) emptying half-life time (t1/2) and colonic geometric centre (GC) at 24 h. Secondary analysis variables were GC at 4 and 48 h, gastric emptying t1/2 and colonic filling at 6 h. There was a significant overall effect of progesterone on colonic transit with shorter AC emptying t1/2 and significantly greater colonic GC at 48 h. No transit endpoints were altered by oestradiol or combined hormonal treatment relative to placebo. Oestradiol and progesterone resulted in looser stool consistency. Withdrawal of the hormone supplement was not associated with significant alteration in transit. Micronized progesterone does not retard colonic transit in postmenopausal females.
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Stephens DA, Crowder MJ. Bayesian analysis of quasi-life tables. LIFETIME DATA ANALYSIS 2006; 12:117-41. [PMID: 16868838 DOI: 10.1007/s10985-006-9003-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Accepted: 03/30/2006] [Indexed: 05/11/2023]
Abstract
Quasi-life tables, in which the data arise from many concurrent, independent, discrete-time renewal processes, were defined by Baxter (1994, Biometrika 81:567-577), who outlined some methods for estimation. The processes are not observed individually; only the total numbers of renewals at each time point are observed. Crowder and Stephens (2003, Lifetime Data Anal 9:345-355) implemented a formal estimating-equation approach that invokes large-sample theory. However, these asymptotic methods fail to yield sensible estimates for smaller samples. In this paper, we implement a Bayesian analysis based on MCMC computation that works equally well for large and small sample sizes. We give three simulated examples, studying the Bayesian results, the impact of changing prior specification, and empirical properties of the Bayesian estimators of the lifetime distribution parameters. We also study the Baxter (1994, Biometrika 81:567-577) data, and uncover structure that has not been commented upon previously.
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Jasra A, Stephens DA, Gallagher K, Holmes CC. Bayesian Mixture Modelling in Geochronology via Markov Chain Monte Carlo. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s11004-005-9019-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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