Designs for generalized linear models with several variables and model uncertainty

Standard factorial designs sometimes may be inadequate for experiments that aim to estimate a generalized linear model, for example, for describing a binary response in terms of several variables. A method is proposed for finding exact designs for such experiments that uses a criterion allowing for uncertainty in the link function, the linear predictor, or the model parameters, together with a design search. Designs are assessed and compared by simulation of the distribution of efficiencies relative to locally optimal designs over a space of possible models. Exact designs are investigated for two applications, and their advantages over factorial and central composite designs are demonstrated.

Microbial Fuel Cells: Methodology and Technology

Microbial fuel cell (MFC) research is a rapidly evolving field that lacks established terminology and methods for the analysis of system performance. This makes it difficult for researchers to compare devices on an equivalent basis. The construction and analysis of MFCs requires knowledge of different scientific and engineering fields, ranging from microbiology and electrochemistry to materials and environmental engineering. DescribingMFCsystems therefore involves an understanding of these different scientific and engineering principles. In this paper, we provide a review of the different materials and methods used to construct MFCs, techniques used to analyze system performance, and recommendations on what information to include in MFC studies and the most useful ways to present results.

Stochastic models for regulatory networks of the genetic toggle switch

Bistability arises within a wide range of biological systems from the A phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. in this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

Transcriptome analysis of Neotyphodium and Epichloë grass endophytes

Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloe festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource, They permit the interrogation of 3806 Neotyphodium genes (Nchip (TM) rnicroarray), and 4195 Neotyphodium and 920 Epichloe genes (EndoChip (TM) microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloe was performed. (c) 2006 Elsevier

Prolonged prevention of squamous cell carcinoma of the skin by regular sunscreen use

Half of all cancers in the United States are skin cancers. We have previously shown in a 4.5-year randomized controlled trial in an Australian community that squamous cell carcinomas (SCC) but not basal cell carcinomas (BCC) can be prevented by regular sunscreen application to the head, neck, hands, and forearms. Since cessation of the trial, we have followed participants for a further 8 years to evaluate possible latency of preventive effect on BCCs and SCCs. After prolonged follow-up, BCC tumor rates tended to decrease but not significantly in people formerly randomized to daily sunscreen use compared with those not applying sunscreen daily. By contrast, corresponding SCC tumor rates were significantly decreased by almost 40% during the entire follow-up period (rate ratio, 0.62; 95% confidence interval, 0.38-0.99). Regular application of sunscreen has prolonged preventive effects on SCC but with no clear benefit in reducing BCC.

Childhood ethnic differences in ametropia and ocular biometry:the Aston Eye Study

Purpose: To describe the methodology, sampling strategy and preliminary results for the Aston Eye Study (AES), a cross-sectional study to determine the prevalence of refractive error and its associated ocular biometry in a large multi-racial sample of school children from the metropolitan area of Birmingham, England. Methods: A target sample of 1700 children aged 6–7 years and 1200 aged 12–13 years is being selected from Birmingham schools selected randomly with stratification by area deprivation index (a measure of socio-economic status). Schools with pupils predominantly (>70%) from a single race are excluded. Sample size calculations account for the likely participation rate and the clustering of individuals within schools. Procedures involve standardised protocols to allow for comparison with international population-based data. Visual acuity, non-contact ocular biometry (axial length, corneal radius of curvature and anterior chamber depth) and cycloplegic autorefraction are measured in both eyes. Distance and near oculomotor balance, height and weight are also assessed. Questionnaires for parents and older children will allow the influence of environmental factors on refractive error to be examined. Results: Recruitment and data collection are ongoing (currently N = 655). Preliminary cross-sectional data on 213 South Asian, 44 black African Caribbean and 70 white European children aged 6–7 years and 114 South Asian, 40 black African Caribbean and 115 white European children aged 12–13 years found myopia prevalence of 9.4% and 29.4% for the two age groups respectively. A more negative mean spherical equivalent refraction (SER) was observed in older children (-0.21 D vs +0.87 D). Ethnic differences in myopia prevalence are emerging with South Asian children having higher levels than white European children 36.8% vs 18.6% (for the older children). Axial length, corneal radius of curvature and anterior chamber depth were normally distributed, while SER was leptokurtic (p < 0.001) with a slight negative skew. Conclusions: The AES will allow ethnic differences in the ocular characteristics of children from a large metropolitan area of the UK to be examined. The findings to date indicate the emergence of higher levels of myopia by early adolescence in second and third generation British South Asians, compared to white European children. The continuation of the AES will allow the early determinants of these ethnic differences to be studied.

Sampling and measurement methods for a study of childhood refractive error in a UK population

Background There is a paucity of data describing the prevalence of childhood refractive error in the United Kingdom. The Northern Ireland Childhood Errors of Refraction study, along with its sister study the Aston Eye Study, are the first population-based surveys of children using both random cluster sampling and cycloplegic autorefraction to quantify levels of refractive error in the United Kingdom. Methods Children aged 6–7 years and 12–13 years were recruited from a stratified random sample of primary and post-primary schools, representative of the population of Northern Ireland as a whole. Measurements included assessment of visual acuity, oculomotor balance, ocular biometry and cycloplegic binocular open-field autorefraction. Questionnaires were used to identify putative risk factors for refractive error. Results 399 (57%) of 6–7 years and 669 (60%) of 12–13 years participated. School participation rates did not vary statistically significantly with the size of the school, whether the school is urban or rural, or whether it is in a deprived/non-deprived area. The gender balance, ethnicity and type of schooling of participants are reflective of the Northern Ireland population. Conclusions The study design, sample size and methodology will ensure accurate measures of the prevalence of refractive errors in the target population and will facilitate comparisons with other population-based refractive data.

Refractive error and visual impairment in school children in Northern Ireland

To describe the prevalence of refractive error (myopia and hyperopia) and visual impairment in a representative sample of white school children.

Ocular blood flow measurements in healthy human myopic eyes

Background. To evaluate the haemodynamic features of young healthy myopes and emmetropes, in order to ascertain the perfusion profile of human myopia and its relationship with axial length prior to reaching a degenerative state. Methods The retrobulbar, microretinal and pulsatile ocular blood flow (POBF) of one eye of each of twenty-two high myopes (N=22, mean spherical equivalent (MSE) =-5.00D), low myopes (N=22, MSE-1.00 to-4.50D) and emmetropes (N=22, MSE±0.50D) was analyzed using color Doppler Imaging, Heidelberg retinal flowmetry and ocular blood flow analyser (OBF) respectively. Intraocular pressure, axial length (AL), systemic blood pressure, and body mass index were measured. Results. When compared to the emmetropes and low myopes, the AL was greater in high myopia (p<0.0001). High myopes showed higher central retinal artery resistance index (CRA RI) (p=0.004), higher peak systolic to end diastolic velocities ratio (CRA ratio) and lower end diastolic velocity (CRA EDv) compared to low myopes (p=0.014, p=0.037). Compared to emmetropes, high myopes showed lower OBFamplitude (OBFa) (p=0.016). The POBF correlated significantly with the systolic and diastolic blood velocities of the CRA (p=0.016, p=0.036). MSE and AL correlated negatively with OBFa (p=0.03, p=0.003), OBF volume (p=0.02, p<0.001), POBF (p=0.01, p<0.001) and positively with CRA RI (p=0.007, p=0.05). Conclusion. High myopes exhibited significantly reduced pulse amplitude and CRA blood velocity, the first of which may be due to an OBF measurement artefact or real decreased ocular blood flow pulsatility. Axial length and refractive error correlated moderately with the ocular pulse and with the resistance index of the CRA, which in turn correlated amongst themselves. It is hypothesized that the compromised pulsatile and CRA haemodynamics observed in young healthy myopes is an early feature of the decrease in ocular blood flow reported in pathological myopia. Such vascular features would increase the susceptibility for vascular and age-related eye diseases.

Matrix-free mass spectrometric imaging using laser desorption ionisation Fourier transform ion cyclotron resonance mass spectrometry

Mass spectrometry imaging (MSI) is a powerful tool in metabolomics and proteomics for the spatial localization and identification of pharmaceuticals, metabolites, lipids, peptides and proteins in biological tissues. However, sample preparation remains a crucial variable in obtaining the most accurate distributions. Common washing steps used to remove salts, and solvent-based matrix application, allow analyte spreading to occur. Solvent-free matrix applications can reduce this risk, but increase the possibility of ionisation bias due to matrix adhesion to tissue sections. We report here the use of matrix-free MSI using laser desorption ionisation performed on a 12 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. We used unprocessed tissue with no post-processing following thaw-mounting on matrix-assisted laser desorption ionisation (MALDI) indium-tin oxide (ITO) target plates. The identification and distribution of a range of phospholipids in mouse brain and kidney sections are presented and compared with previously published MALDI time-of-flight (TOF) MSI distributions.

Reproducibility-repeatability of choroidal thickness calculation using optical coherence tomography

Purpose. To evaluate the repeatability and reproducibility of subfoveal choroidal thickness (CT) calculations performed manually using optical coherence tomography (OCT). Methods. The CT was imaged in vivo at each of two visits on 11 healthy volunteers (mean age, 35.72 ± 13.19 years) using the spectral domain OCT. CT was manually measured after applying ImageJ processing filters on 15 radial subfoveal scans. Each radial scan was spaced 12° from each other and contained 2500 A-scans. The coefficient of variability, coefficient of repeatability (CoR), coefficient of reproducibility, and intraclass correlation coefficient determined the reproducibility and repeatability of the calculation. Axial length (AL) and mean spherical equivalent refractive error were measured with the IOLMaster and an open view autorefractor to study their potential relationship with CT. Results. The within-visit and between-visit coefficient of variability, CoR, coefficient of reproducibility, and intraclass correlation coefficient were 0.80, 2.97% 2.44%, and 99%, respectively. The subfoveal CT correlated significantly with AL (R = -0.60, p = 0.05). Conclusions. The subfoveal CT could be measured manually in vivo using OCT and the readings obtained from the healthy subjects evaluated were repeatable and reproducible. It is proposed that OCT could be a useful instrument to perform in vivo assessment and monitoring of CT changes in retinal disease. The preliminary results suggest a negative correlation between subfoveal CT and AL in such a way that it decreases with increasing AL but not with refractive error.

Refractive and corneal astigmatism in white school children in Northern Ireland

To study the prevalence of and relation between refractive and corneal astigmatism in white school children in Northern Ireland and to describe the association between refractive astigmatism and refractive error.

Three-dimensional modeling of the human eye based on magnetic resonance imaging

PURPOSE. A methodology for noninvasively characterizing the three-dimensional (3-D) shape of the complete human eye is not currently available for research into ocular diseases that have a structural substrate, such as myopia. A novel application of a magnetic resonance imaging (MRI) acquisition and analysis technique is presented that, for the first time, allows the 3-D shape of the eye to be investigated fully. METHODS. The technique involves the acquisition of a T2-weighted MRI, which is optimized to reveal the fluid-filled chambers of the eye. Automatic segmentation and meshing algorithms generate a 3-D surface model, which can be shaded with morphologic parameters such as distance from the posterior corneal pole and deviation from sphericity. Full details of the method are illustrated with data from 14 eyes of seven individuals. The spatial accuracy of the calculated models is demonstrated by comparing the MRI-derived axial lengths with values measured in the same eyes using interferometry. RESULTS. The color-coded eye models showed substantial variation in the absolute size of the 14 eyes. Variations in the sphericity of the eyes were also evident, with some appearing approximately spherical whereas others were clearly oblate and one was slightly prolate. Nasal-temporal asymmetries were noted in some subjects. CONCLUSIONS. The MRI acquisition and analysis technique allows a novel way of examining 3-D ocular shape. The ability to stratify and analyze eye shape, ocular volume, and sphericity will further extend the understanding of which specific biometric parameters predispose emmetropic children subsequently to develop myopia. Copyright © Association for Research in Vision and Ophthalmology.

Ametropia and ocular biometry in a UK university student population

Purpose. The prevalence of myopia is known to vary with age, ethnicity, level of education, and socioeconomic status, with a high prevalence reported in university students and in people from East Asian countries. This study determines the prevalence of ametropia in a mixed ethnicity U.K. university student population and compares associated ocular biometric measures. Methods. Refractive error and related ocular component data were collected on 373 first-year U.K. undergraduate students (mean age = 19.55 years ± 2.99, range = 17-30 years) at the start of the academic year at Aston University, Birmingham, and the University of Bradford, West Yorkshire. The ethnic variation of the students was as follows: white 38.9%, British Asian 58.2%, Chinese 2.1%, and black 0.8%. Noncycloplegic refractive error was measured with an infrared open-field autorefractor, the Shin-Nippon NVision-K 5001 (Shin Nippon, Ryusyo Industrial Co. Ltd, Osaka, Japan). Myopia was defined as a mean spherical equivalent (MSE) less than or equal to -0.50 D. Hyperopia was defined as an MSE greater than or equal to +0.50 D. Axial length, corneal curvature, and anterior chamber depth were measured using the Zeiss IOLMaster (Carl Zeiss, Jena, GmBH). Results. The analysis was carried out only for white and British Asian groups. The overall distribution of refractive error exhibited leptokurtosis, and prevalence levels were similar for white and British Asian (the predominant ethnic group) students across each ametropic group: myopia (50% vs. 53.4%), hyperopia (18.8% vs. 17.3%), and emmetropia (31.2% vs. 29.3%). There were no significant differences in the distribution of ametropia and biometric components between white and British Asian samples. Conclusion. The absence of a significant difference in refractive error and ocular components between white and British Asian students exposed to the same educational system is of interest. However, it is clear that a further study incorporating formal epidemiologic methods of analysis is required to address adequately the recent proposal that juvenile myopia develops principally from myopiagenic environments and is relatively independent of ethnicity.