Publications by authors named "Andrew C James"

38 Publications

Dichoptic multifocal pupillography reveals afferent visual field defects in early type 2 diabetes.

Invest Ophthalmol Vis Sci 2010 Jan 30;51(1):602-8. Epub 2009 Jul 30.

ARC Centre of Excellence in Vision Science and Centre for Visual Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia.

Purpose: Multifocal pupillographic perimetry was used to examine differences in the visual fields of 23 subjects with early type 2 diabetes (T2D) and 23 age- and sex-matched control subjects.

Methods: Independent stimuli were delivered to 44 regions of each eye while pupil responses were recorded with infrared cameras. The stimuli were presented in 8 segments of 30 seconds, and both eyes of each subject were tested twice. The direct and consensual responses provided 88 responses per eye. The diagnostic power of the method was then examined by applying receiver operator analysis to the peak regional contraction amplitudes, time to peaks, and linear combinations of those.

Results: Dichoptic multifocal pupillography provided response amplitudes with a median z-score of 2.63 +/- 0.26 (SE). The diagnostic performance (expressed as areas under ROC plots) of the eight subjects (32 fields) who had had T2D for at least 10 years was 0.87 +/- 0.06 (mean +/- SE) for response amplitude deviations from normative data, rising to 0.95 +/- 0.04 when between-eye symmetry was considered. Mean pupil size did not have diagnostic power. Comparison of direct and consensual response fields indicated that the observed localized field defects were afferent.

Conclusions: Reasonable diagnostic power was obtained, especially for the 16 eyes that had had T2D for more than 10 years, inferring that even in the near absence of visible diabetic retinopathy, some retinal damage had been sustained. This result, if confirmed in a wider group, suggests the that the method may be clinically useful in screening for early damage to the retina in T2D diabetes.
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http://dx.doi.org/10.1167/iovs.09-3659DOI Listing
January 2010

Quantitative multifocal fMRI shows active suppression in human V1.

Hum Brain Mapp 2008 Sep;29(9):1001-14

Brain Research Unit, Low Temperature Laboratory, Helsinki University of Technology, Espoo, Finland.

Multifocal functional magnetic resonance imaging has recently been introduced as an alternative method for retinotopic mapping, and it enables effective functional localization of multiple regions-of-interest in the visual cortex. In this study we characterized interactions in V1 with spatially and temporally identical stimuli presented alone, or as a part of a nine-region multifocal stimulus. We compared stimuli at different contrasts, collinear and orthogonal orientations and spatial frequencies one octave apart. Results show clear attenuation of BOLD signal from the central region in the multifocal condition. The observed modulation in BOLD signal could be produced either by neural suppression resulting from stimulation of adjacent regions of visual field, or alternatively by hemodynamic saturation or stealing effects in V1. However, we find that attenuation of the central response persists through a range of contrasts, and that its strength varies with relative orientation and spatial frequency of the central and surrounding stimulus regions, indicating active suppression mechanisms of neural origin. Our results also demonstrate that the extent of the signal spreading is commensurate with the extent of the horizontal connections in primate V1.
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http://dx.doi.org/10.1002/hbm.20442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6870839PMC
September 2008

Multifocal blue-on-yellow visual evoked potentials in early glaucoma.

Ophthalmology 2007 Sep;114(9):1613-21

Department of Ophthalmology, Save Sight Institute, University of Sydney, Sydney, Australia.

Objective: To determine the sensitivity and specificity of blue-on-yellow multifocal visual evoked potentials (mfVEPs) in early glaucoma.

Design: Cross-sectional study.

Participants: Fifty patients with a confirmed diagnosis of early glaucoma and 60 normal participants.

Methods: Black-and-white mfVEPs and blue-on-yellow mfVEPs were recorded using the Accumap version 2.0 (ObjectiVision Pty. Ltd., Sydney, Australia). All patients also underwent achromatic standard automated perimetry (SAP).

Main Outcome Measures: Multifocal VEP amplitude and latency values in glaucoma patients were analyzed and compared with those of the normal controls.

Results: Based on the definition of visual field defect, in the group of glaucomatous eyes with SAP defects, amplitude of blue-on-yellow mfVEP was abnormal in all 64 cases (100% sensitivity), whereas black-and-white mfVEP missed 5 cases (92.2% sensitivity). Generally, larger scotomata were noted on blue-on-yellow mfVEP compared with black-and-white mfVEP for the same eyes. There was high topographic correspondence between SAP and amplitude of blue-on-yellow mfVEP and significant (P<0.0001) correlation between them (correlation coefficient, 0.73). Abnormal amplitude was detected in 3 of 60 eyes of control subjects (95% specificity). There was, however, no correlation between visual field defect and latency delay in glaucoma patients. Although there was a significant difference between averaged latency of control and glaucoma eyes, values considerably overlapped.

Conclusions: The blue-on-yellow mfVEP is a sensitive and specific tool for detecting early glaucoma based on amplitude analysis.
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http://dx.doi.org/10.1016/j.ophtha.2006.11.037DOI Listing
September 2007

Isolation and characterization of the mating type locus of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana.

Mol Plant Pathol 2007 Jan;8(1):111-20

Centro de Investigación Científica de Yucatán (CICY), Calle 43 no. 130, Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, México.

SUMMARY Idiomorphs mat1-1 and mat1-2 from Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana, were isolated. Degenerate oligos were used to amplify the HMG box of the mat1-2 idiomorph from M. fijiensis, showing homology with the HMG box of Mycosphaerella graminicola. Using a DNA walking strategy, anchored on the DNA lyase gene towards the HMG box, a 9-kb-long region of mat1-2 was obtained. A 5-kb fragment from the mat1-1 region was obtained by long-range PCR using primers on the flanking regions, which have close to 100% identity between both idiomorphs. High-identity (77-89%), inverted regions within both idiomorphs were found, which suggest unique inversion events, which have not been found before, and that could have been significant in the evolution of this species. The predicted genes showed the conserved introns in both idiomorphs as well as an additional intron within the alpha box. The implications for the evolution of species in the Mycosphaerella complex on banana are discussed.
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http://dx.doi.org/10.1111/j.1364-3703.2006.00376.xDOI Listing
January 2007

Hierarchical decomposition of dichoptic multifocal visual evoked potentials.

Vis Neurosci 2006 Sep-Oct;23(5):703-12

Centre for Visual Sciences, Research School of Biological Sciences, Australian National University, Canberra, ACT, Australia.

Visual evoked responses to dichoptically presented multifocal stimuli were recorded for 92 eyes. Two stimulus variants were explored: temporally sparse and rapidly contrast reversing. We used hierarchical decomposition (HD) to represent the multifocal responses in terms of a small number of potentially unique component waveforms that are interrelated in a multivariate linear autoregressive (MLAR) relationship. The HD method exploits temporal correlations over a range of delays in the responses to estimate parallel, feedforward and feedback relationships between the HD components. Three HD components having temporal interrelationships constrained (at P < 0.05) to a moving approximately 20 ms window could describe the multifocal responses well (median r2-values up to 90%). HD components were similar for both stimulus types and the component waveforms were temporally correlated, especially the first and third components. The data set was large enough to estimate separate HD components for each multifocal stimulus region. The component waveforms differed somewhat by region but the MLAR relationships were similar. At short delays parallel processing dominated. At longer delays the proportion of response drives that were attributed to feedback and feedforward relationships grew. Overall HD analysis seems to provide an informed summary of multifocal responses and insights into their sources.
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http://dx.doi.org/10.1017/S0952523806230013DOI Listing
December 2006

Sparse multifocal stimuli for the detection of multiple sclerosis.

Ann Neurol 2005 Jun;57(6):904-13

Centre for Visual Sciences, Research School of Biological Sciences, Canberra, Australia.

We compared the diagnostic capabilities of contrast reversal and sparse pattern pulse stimulation for dichoptic multifocal visual evoked potentials (mfVEPs) measured in normal subjects and multiple sclerosis (MS) patients. Multifocal responses were obtained from 27 normal subjects and 50 relapsing-remitting patients, 26 of whom had experienced optic neuritis (ON+). The patient groups were matched for length of disease and number of clinical attacks. Compared with the responses of normal subjects those of MS patients had significantly smaller response amplitudes, lower signal-to-noise ratios, more complex response waveforms, and longer response delays. The effects were larger for sparser stimuli. Sensitivities and specificities for the different stimulus types were estimated from receiver operator characteristic (ROC) plots. Bootstrap estimates of the accuracies of the ROCs for the most promising measure, the template delays, indicated the sparsest stimulus would deliver 92% sensitivity at a false-positive rate of 0%. In contrast, at 92% sensitivity the conventional mfVEP stimulus misdiagnosed more than 20% of the normal population. The results were similar for patients with no history of ON (ON-). In performing well in patients with no history of ON, the sparse mfVEPs seem to measure progressive damage associated with axon and gray matter losses rather than damage associated with a history of serious inflammation.
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http://dx.doi.org/10.1002/ana.20504DOI Listing
June 2005

Effect of temporal sparseness and dichoptic presentation on multifocal visual evoked potentials.

Vis Neurosci 2005 Jan-Feb;22(1):45-54

Centre for Visual Sciences, Research School of Biological Sciences, Australian National University, Canberra, Australia.

Multifocal VEP (mfVEP) responses were obtained from 13 normal human subjects for nine test conditions, covering three viewing conditions (dichoptic and left and right monocular), and three different temporal stimulation forms (rapid contrast reversal, rapid pattern pulse presentation, and slow pattern pulse presentation). The rapid contrast reversal stimulus had pseudorandomized reversals of checkerboards in each visual field region at a mean rate of 25 reversals/s, similar to most mfVEP studies to date. The rapid pattern pulse presentation had pseudorandomized presentations of a checkerboard for one frame, interspersed with uniform grey frames, with a mean rate of 25 presentations/s per region per eye. The slow pattern pulse stimulus had six presentations/s per region per eye. Recording time was 5.3 min/condition. For dichoptic presentation slow pattern pulse responses were 4.6 times larger in amplitude than the contrast reversal responses. Binocular suppression was greatest for the contrast reversal stimulus. Consideration of the signal-to-noise ratios indicated that to achieve a given level of reliability, slow pattern pulse stimuli would require half the recording time of contrast reversal stimuli for monocular viewing, and 0.4 times the recording time for dichoptically presented stimuli. About half the responses to the slow pattern pulse stimuli had peak value exceeding five times their estimated standard error. Responses were about 20% smaller in the upper visual field locations. Space-time decomposition showed that responses to slow pattern pulse were more consistent across visual field locations. We conclude that the pattern pulse stimuli, which we term temporally sparse, maintain the visual system in a high contrast gain state. This more than compensates for the smaller number of presentations in the run, and provides signal-to-noise advantages that may be valuable in clinical application.
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http://dx.doi.org/10.1017/S0952523805221053DOI Listing
June 2005

Sensitivity and specificity of five abundance estimators for high-density oligonucleotide microarrays.

Bioinformatics 2004 May 5;20(7):1060-5. Epub 2004 Feb 5.

Research School of Biological Sciences, Australian National University, PO Box 475, Canberra ACT 2601, Australia.

Motivation: A number of algorithms have been proposed for the processing of feature-level data from high-density oligonucleotide microarrays to give estimates of transcript abundance. Performance in the common task of detecting differential expression between samples can be quantified by the statistical concepts of sensitivity and specificity, and represented by the use of receiver operating characteristic curves. These have been previously presented for small numbers of genes known to be differentially present in spiked-in samples. We present here a study of performance over a large number (thousands) of transcripts for which there is strong evidence of differential expression, with corresponding false positive rates controlled by comparisons between replicates.

Results: The straight-line regression analysis of a mixture series with replicates by five estimation algorithms produces a consensus set of 4462 transcripts with differential expression of agreed direction and high significance (p < 0.01) according to all algorithms. The more difficult task of two-sample tests between adjacent mixture levels produces performance curves of fraction true positive detected against significance level. Performance varies significantly between algorithms: at the p < 0.01 level, the detection rate varies between 41 and 66%. A control using comparisons between replicates at the same levels indicates that the tests produce empirical false positive rates closely matching the nominal p-values.
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http://dx.doi.org/10.1093/bioinformatics/bth038DOI Listing
May 2004