Biomedical subjects

David A Stephens

Publications and source records attributed to David A Stephens.

7 recordsLinked to original sources

PubMed2006

The transcriptional regulator CBP has defined spatial associations within interphase nuclei.

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.

Acetylation↗

PubMed2006

Bayesian analysis of quasi-life tables.

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.

Bayes Theorem↗

PubMed2006

Intermediate spatial frequency letter contrast sensitivity: its relation to visual resolution before and during amblyopia treatment.

We examined the loss of letter contrast sensitivity (LCS) measured using the Pelli-Robson chart, and the extent to which any such loss was modulated by spectacle wear and occlusion therapy in children participating in an amblyopia treatment trial. Their initial mean interocular difference in logMAR acuity was approximately three times that of their LCS (0.45 vs 0.14 log units). Log LCS was weakly though significantly correlated with logMAR visual acuity (VA) for all VAs better than 0.90 (r = -0.19, 95% CI: -0.28 to -0.10) whereas for all VAs of 0.90 or poorer, log LCS was markedly and significantly correlated with VA (r = -0.72, 95% CI: -0.83 to -0.53). LCS in those children with a > or =0.1 log unit interocular difference on this test improved commensurately with VA during treatment. We conjecture that the spatial visual loss in all but the most severe amblyopes occurs in an area of resolution and contrast space that lies beyond that sampled by the Pelli-Robson chart.

Adaptation, Physiological↗

PubMed2005

Bayesian coclustering of Anopheles gene expression time series: study of immune defense response to multiple experimental challenges.

We present a method for Bayesian model-based hierarchical coclustering of gene expression data and use it to study the temporal transcription responses of an Anopheles gambiae cell line upon challenge with multiple microbial elicitors. The method fits statistical regression models to the gene expression time series for each experiment and performs coclustering on the genes by optimizing a joint probability model, characterizing gene coregulation between multiple experiments. We compute the model using a two-stage Expectation-Maximization-type algorithm, first fixing the cross-experiment covariance structure and using efficient Bayesian hierarchical clustering to obtain a locally optimal clustering of the gene expression profiles and then, conditional on that clustering, carrying out Bayesian inference on the cross-experiment covariance using Markov chain Monte Carlo simulation to obtain an expectation. For the problem of model choice, we use a cross-validatory approach to decide between individual experiment modeling and varying levels of coclustering. Our method successfully generates tightly coregulated clusters of genes that are implicated in related processes and therefore can be used for analysis of global transcript responses to various stimuli and prediction of gene functions.

Algorithms↗

PubMed2005

Treatment of unilateral amblyopia: factors influencing visual outcome.

PURPOSE: To identify factors that influence the outcome of treatment for unilateral amblyopia, as a part of the Monitored Occlusion Treatment of Amblyopia Study (MOTAS). METHODS: This was an intervention study consisting of three nonoverlapping phases: "Baseline", "refractive adaptation" (18 weeks of full-time spectacle wear), and "occlusion" (6 hours of patching per day, objectively monitored). Condition factors: type of amblyopia, age of participant, initial severity of amblyopia, fixation, and binocular vision status; treatment factors: refractive adaptation and occlusion (total dose [hours] and dose rate [hours per day]) were assessed for their influence on visual outcome. Visual outcome was expressed in three ways: logMAR (logarithm of the minimum angle of resolution) change, residual amblyopia, and proportion of the deficit corrected. RESULTS: The study included 85 participants (mean age, 5.1 +/- 1.4 years) with amblyopia associated with strabismus (n = 32) or anisometropia (n = 20) or associated with both anisometropia and strabismus (n = 33). Treatment factors: cumulative occlusion dose exceeding 50 hours, and dose rates > or =1 hour per day resulted in (P < or = 0.01) lower residual amblyopia and a greater proportion of the deficit corrected. Condition factors associated with poor outcome (high residual amblyopia) were presence of eccentric fixation, severe initial amblyopia, and no binocular vision. CONCLUSIONS: Factors influencing outcome with treatment for amblyopia are occlusion dose (the rate of delivery and cumulative dose worn), the initial severity of the amblyopia, binocular vision status, fixation of the amblyopic eye, and the age of the subject at the start of treatment.

Age Factors↗

PubMed2004

Triiodothyronine stimulates food intake via the hypothalamic ventromedial nucleus independent of changes in energy expenditure.

Increased food intake is characteristic of hyperthyroidism, although this is presumed to compensate for a state of negative energy balance. However, here we show that the thyroid hormone T(3) directly stimulates feeding at the level of the hypothalamus. Peripheral administration of T(3) doubled food intake in ad libitum-fed rats over 2 h and induced expression of the immediate early gene, early growth response-1, in the hypothalamic ventromedial nucleus (VMN), whereas maintaining plasma-free T(3) levels within the normal range. T(3)-induced feeding occurred without altering energy expenditure or locomotion. Injection of T(3) directly into the VMN produced a 4-fold increase in food intake in the first hour. The majority of T(3) in the brain is reported to be produced by tissue-specific conversion of T(4) to T(3) by the enzyme type 2 iodothyronine deiodinase (D2). Hypothalamic D2 mRNA expression showed a diurnal variation, with a peak in the nocturnal feeding phase. Hypothalamic D2 mRNA levels also increased after a 12- and 24-h fast, suggesting that local production of T(3) may play a role in this T(3) feeding circuit. Thus, we propose a novel hypothalamic feeding circuit in which T(3), from the peripheral circulation or produced by local conversion, stimulates food intake via the VMN.

Adipose Tissue↗

PubMed2004

Treatment dose-response in amblyopia therapy: the Monitored Occlusion Treatment of Amblyopia Study (MOTAS).

PURPOSE: Amblyopia is the commonest visual disorder of childhood. Yet the contributions of the two principal treatments (spectacle wear and occlusion) to outcome are unknown. This study was undertaken to investigate the dose-response relationship of amblyopia therapy. METHODS: The study comprised three distinct phases: baseline, in which repeat measures of visual function were undertaken to confirm the initial visual deficit; refractive adaptation: an 18-week period of spectacle wear with six weekly measurements of logarithm of the minimum angle of resolution (logMAR) visual acuity; occlusion: in which participants were prescribed 6 hours of "patching" per day. In the latter phase, occlusion was objectively monitored and logMAR visual acuity recorded at 2-week intervals until any observed gains had ceased. RESULTS: Data were obtained from 94 participants (mean age, 5.1 +/- 1.4 years) with amblyopia associated with strabismus (n = 34), anisometropia (n = 23), and both anisometropia and strabismus (n = 37). Eighty-six underwent refractive adaptation. Average concordance with patching was 48%. The relationship between logMAR visual acuity gain and total occlusion dose was monotonic and linear. Increasing dose rate beyond 2 h/d hastened the response but did not improve outcome. More than 80% of the improvement during occlusion occurred within 6 weeks. Treatment outcome was significantly better for children younger than 4 years (n = 17) than in those older than 6 years (n = 24; P = 0.0014). CONCLUSIONS: Continuous objective monitoring of the amount of patching therapy received has provided insight into the dose-response relationship of occlusion therapy for amblyopia. Patching is most effective within the first few weeks of treatment, even for those in receipt of a relatively small dose. Further studies are needed to elucidate the neural basis for the dose-response functions.

Adaptation, Physiological↗