ORCID Profile
0000-0002-2720-8739
Current Organisations
University of Queensland
,
CSIRO (Data61)
,
Queensland University of Technology
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Publisher: Elsevier BV
Date: 06-2007
Publisher: Elsevier BV
Date: 05-2010
DOI: 10.1016/J.JNEUMETH.2010.02.020
Abstract: In magnetic resonance imaging (MRI), accuracy and precision with which brain structures may be quantified are frequently affected by the partial volume (PV) effect. PV is due to the limited spatial resolution of MRI compared to the size of anatomical structures. Accurate classification of mixed voxels and correct estimation of the proportion of each pure tissue (fractional content) may help to increase the precision of cortical thickness estimation in regions where this measure is particularly difficult, such as deep sulci. The contribution of this work is twofold: on the one hand, we propose a new method to label voxels and compute tissue fractional content, integrating a mechanism for detecting sulci with topology preserving operators. On the other hand, we improve the computation of the fractional content of mixed voxels using local estimation of pure tissue intensity means. Accuracy and precision were assessed using simulated and real MR data and comparison with other existing approaches demonstrated the benefits of our method. Significant improvements in gray matter (GM) classification and cortical thickness estimation were brought by the topology correction. The fractional content root mean squared error diminished by 6.3% (p<0.01) on simulated data. The reproducibility error decreased by 8.8% (p<0.001) and the Jaccard similarity measure increased by 3.5% on real data. Furthermore, compared with manually guided expert segmentations, the similarity measure was improved by 12.0% (p<0.001). Thickness estimation with the proposed method showed a higher reproducibility compared with the measure performed after partial volume classification using other methods.
Publisher: Elsevier BV
Date: 03-2012
DOI: 10.1016/J.COMPMEDIMAG.2011.08.004
Abstract: Due to physical limitations inherent in magnetic resonance imaging scanners, three dimensional volumetric scans are often acquired with anisotropic voxel resolution. We investigate several interpolation approaches to reduce the anisotropy and present a novel approach - constrained reverse diffusion for thick slice interpolation. This technique was compared to common methods: linear and cubic B-Spline interpolation and a technique based on non-rigid registration of neighboring slices. The methods were evaluated on artificial MR phantoms and real MR scans of human brain. The constrained reverse diffusion approach delivered promising results and provides an alternative for thick slice interpolation, especially for higher anisotropy factors.
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.CMPB.2018.07.011
Abstract: Biomedical imaging analysis typically comprises a variety of complex tasks requiring sophisticated algorithms and visualising high dimensional data. The successful integration and deployment of the enabling software to clinical (research) partners, for rigorous evaluation and testing, is a crucial step to facilitate adoption of research innovations within medical settings. In this paper, we introduce the Simple Medical Imaging Library Interface (SMILI), an object oriented open-source framework with a compact suite of objects geared for rapid biomedical imaging (cross-platform) application development and deployment. SMILI supports the development of both command-line (shell and Python scripting) and graphical applications utilising the same set of processing algorithms. It provides a substantial subset of features when compared to more complex packages, yet it is small enough to ship with clinical applications with limited overhead and has a license suitable for commercial use. After describing where SMILI fits within the existing biomedical imaging software ecosystem, by comparing it to other state-of-the-art offerings, we demonstrate its capabilities in creating a clinical application for manual measurement of cam-type lesions of the femoral head-neck region for the investigation of femoro-acetabular impingement (FAI) from three dimensional (3D) magnetic resonance (MR) images of the hip. This application for the investigation of FAI proved to be convenient for radiological analyses and resulted in high intra (ICC=0.97) and inter-observer (ICC=0.95) reliabilities for measurement of α-angles of the femoral head-neck region. We believe that SMILI is particularly well suited for prototyping biomedical imaging applications requiring user interaction and/or visualisation of 3D mesh, scalar, vector or tensor data.
Publisher: Elsevier BV
Date: 2008
Publisher: SPIE
Date: 03-03-2011
DOI: 10.1117/12.877915
Publisher: Oxford University Press (OUP)
Date: 11-2013
Publisher: Elsevier BV
Date: 10-2009
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 05-2006
Publisher: American Society of Neuroradiology (ASNR)
Date: 18-10-2013
DOI: 10.3174/AJNR.A3315
Publisher: Elsevier BV
Date: 06-2010
DOI: 10.1016/J.COMPMEDIMAG.2009.12.003
Abstract: 3D shape context is a method to define matching points between similar shapes. It can be used as a pre-processing step in a non-rigid registration. The main limitation of the method is point mismatching, which includes long geodesic distance mismatch causing wrong topological structure, and neighbors crossing mismatch between two adjacent points. In this paper, we propose a topological structure verification method to correct the long geodesic distance mismatch and a correspondence field smoothing method to correct the neighbors crossing mismatch. A robust 3D shape context model is generated and further combined with thin-plate spline model for non-rigid registration. The method was tested on phantoms and applied to rat hind limb and mouse hind limb skeletons registration from micro-CT images. Errors between the registered surfaces were reduced by using the proposed method. The robustness of the method is demonstrated.
Publisher: Elsevier BV
Date: 03-2008
Abstract: Understanding the relationship between the gender of insects and their ability to act as vectors of insect-borne diseases (IBDs) could provide clues as to the origin of the intimate interplay among insect, pathogen and vertebrate hosts. The vector activity of several species of blood-feeding insects is linked to adult females. Interestingly, the only known exception is the transmission of canine and human thelaziosis by a male dipteran fly. This biological difference raises the question as to whether the parasitic behaviour of male and female insects transmitting IBDs is an expression of a co-evolution of vectors and pathogens.
Publisher: SPIE
Date: 23-02-2012
DOI: 10.1117/12.911752
Publisher: Springer Science and Business Media LLC
Date: 12-2007
Abstract: The accurate analysis of genetic variation has major implications in many areas of biomedical research, including the identification of infectious agents (such as parasites), the diagnosis of infections, and the detection of unknown or known disease-causing mutations. Mutation scanning methods, including PCR-coupled single-strand conformation polymorphism (SSCP), have significant advantages over many other nucleic acid techniques for the accurate analysis of allelic and mutational sequence variation. The present protocol describes the SSCP method of analysis, including all steps from the small-scale isolation of genomic DNA and PCR lification of target sequences, through to the gel-based separation of licons and scanning for mutations by SSCP (either by the analysis of radiolabeled licons in mutation detection enhancement (MDE) gels or by non-isotopic SSCP using precast GMA gels). The subsequent sequence analysis of polymorphic bands isolated from gels is also detailed. The SSCP protocol can readily detect point mutations for licon sizes of up to 450-500 bp, and usually takes 1-2 days to carry out. This user-friendly, low-cost, potentially high-throughput platform has demonstrated the utility to study a wide range of pathogens and diseases, and has the potential to be applied to any gene of any organism.
Publisher: SPIE
Date: 03-03-2011
DOI: 10.1117/12.877921
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.NEUROIMAGE.2011.10.014
Abstract: The hippoc us is affected at an early stage in the development of Alzheimer's disease (AD). With the use of structural magnetic resonance (MR) imaging, we can investigate the effect of AD on the morphology of the hippoc us. The hippoc al shape variations among a population can be usually described using statistical shape models (SSMs). Conventional SSMs model the modes of variations among the population via principal component analysis (PCA). Although these modes are representative of variations within the training data, they are not necessarily discriminative on labeled data or relevant to the differences between the subpopulations. We use the shape descriptors from SSM as features to classify AD from normal control (NC) cases. In this study, a Hotelling's T2 test is performed to select a subset of landmarks which are used in PCA. The resulting variation modes are used as predictors of AD from NC. The discrimination ability of these predictors is evaluated in terms of their classification performances with bagged support vector machines (SVMs). Restricting the model to landmarks with better separation between AD and NC increases the discrimination power of SSM. The predictors extracted on the subregions also showed stronger correlation with the memory-related measurements such as Logical Memory, Auditory Verbal Learning Test (AVLT) and the memory subscores of Alzheimer Disease Assessment Scale (ADAS).
Publisher: SPIE
Date: 29-04-2005
DOI: 10.1117/12.596220
Publisher: Elsevier BV
Date: 04-2013
Publisher: SPIE
Date: 23-02-2012
DOI: 10.1117/12.911746
Publisher: Springer Science and Business Media LLC
Date: 11-10-2012
Abstract: Older adults free of dementia but with subjective memory complaints (SMC) or mild cognitive impairment (MCI) are considered at increased risk of cognitive decline. Vascular risk factors (VRF), including hypertension, heart disease, smoking, hypercholesterolemia and lack of physical activity (PA) have been identified as modifiable risk factors contributing to cognitive decline, and white matter hyperintensities (WMH) are associated with VRF, SMC and cognitive impairment. Findings from a growing number of clinical trials with older adults are providing strong evidence for the benefits of physical activity for maintaining cognitive function, but few studies are investigating these benefits in high-risk populations. The aim of AIBL Active is to determine whether a 24-month physical activity program can delay the progression of white matter changes on magnetic resonance imaging (MRI). This single-blind randomized controlled trial (RCT) is offered to 156 participants, aged 60 and older, in the Melbourne arm of the Australian Imaging Biomarkers and Lifestyle Flagship Study of Aging (AIBL). Participants must have SMC with or without MCI and at least one VRF. The PA intervention is a modification of the intervention previously trialed in older adults with SMC and MCI (Fitness for the Ageing Brain Study). It comprises 24 months of moderate, home-based PA (150 minutes per week) and a behavioral intervention package. The primary outcome measure will be change in WMH after 24 months on MRI. Cognition, quality of life, functional fitness, level of physical activity, plasma biomarkers for cerebrovascular disease and amyloid positron emission tomography (PET) imaging comprise secondary measures. Currently, there is no effective pharmacological treatment available to delay cognitive decline and dementia in older adults at risk. Should our findings show that physical activity can slow down the progression of WMH, this RCT would provide an important proof of concept. Since imbedded in AIBL this RCT will also be able to investigate the interaction between vascular and Alzheimer's disease pathologies. Australia New Zealand Clinical Trials Registry ACTRN12611000612910
Publisher: Wiley
Date: 17-05-2011
DOI: 10.1002/JMRI.22188
Abstract: To compare automated segmentation of the quadratus lumborum (QL) based on statistical shape modeling (SSM) with conventional manual processing of magnetic resonance (MR) images for segmentation of this paraspinal muscle. The automated SSM scheme for QL segmentation was developed using an MR database of 7 mm axial images of the lumbar region from 20 subjects (cricket fast bowlers and athletic controls). Specifically, a hierarchical 3D-SSM scheme for segmentation of the QL, and surrounding psoas major (PS) and erector spinae+multifidus (ES+MT) musculature, was implemented after image preprocessing (bias field correction, partial volume interpolation) followed by image registration procedures to develop average and probabilistic MR atlases for initializing and constraining the SSM segmentation of the QL. The automated and manual QL segmentations were compared using spatial overlap and average surface distance metrics. The spatial overlap between the automated SSM and manual segmentations had a median Dice similarity metric of 0.87 (mean = 0.86, SD = 0.08) and mean average surface distance of 1.26 mm (SD = 0.61) and 1.32 mm (SD = 0.60) for the right and left QL muscles, respectively. The current SSM scheme represents a promising approach for future automated morphometric analyses of the QL and other paraspinal muscles from MR images.
Publisher: SPIE
Date: 04-03-2010
DOI: 10.1117/12.844067
Publisher: Hindawi Limited
Date: 2006
Abstract: Many medical images suffer from the partial volume effect where a boundary between two structures of interest falls in the midst of a voxel giving a signal value that is a mixture of the two. We propose a method to restore the ideal boundary by splitting a voxel into subvoxels and reapportioning the signal into the subvoxels. Each voxel is ided by nearest neighbor interpolation. The gray level of each subvoxel is considered as “material” able to move between subvoxels but not between voxels. A partial differential equation is written to allow the material to flow towards the highest gradient direction, creating a “reverse” diffusion process. Flow is subject to constraints that tend to create step edges. Material is conserved in the process thereby conserving signal. The method proceeds until the flow decreases to a low value. To test the method, synthetic images were downs led to simulate the partial volume artifact and restored. Corrected images were remarkably closer both visually and quantitatively to the original images than those obtained from common interpolation methods: on simulated data standard deviation of the errors were 3.8 % , 6.6 % , and 7.1 % of the dynamic range for the proposed method, bicubic, and bilinear interpolation, respectively. The method was relatively insensitive to noise. On gray level, scanned text, MRI physical phantom, and brain images, restored images processed with the new method were visually much closer to high-resolution counterparts than those obtained with common interpolation methods.
Publisher: Informa UK Limited
Date: 11-2010
Publisher: Oxford University Press (OUP)
Date: 22-02-2008
DOI: 10.1111/J.1567-1364.2008.00358.X
Abstract: Malassezia pachydermatis isolates (n=185) from skin sites from dogs (n=30) were characterized genetically and biochemically following in vitro culture. Two regions in the chitin synthase-2 gene (chs-2) and the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA were sequenced, and the phospholipase activity of each isolate was assessed. Three chs-2 (i.e. Ac, Bc and Cc) and eight ITS-1 (i.e. AI1, AI2, AI3, AI4, BI1, CI1, CI2 and CI3) sequence types were defined for all 185 s les. The findings revealed that multiple M. pachydermatis genotypes/subgenotypes could be cultured from healthy dogs or from dogs with single or multiple, generalized skin lesions. Subgenotypes AI1 and BI1 were associated with all skin sites of dogs s led, whereas subgenotype CI2 was mostly linked to a particular location. Isolates derived from skin lesions showed a significantly higher phospholipase activity compared with those from skin sites with no detectable lesions. Genotype B was mainly cultured from healthy skin only four isolates (9.3%) had low phospholipase activity, whereas other genotypes/subgenotypes were predominantly associated with skin lesions and had a high phospholipase activity. The results of the present study suggest that the distribution pattern of particular genotypes or subgenotypes of M. pachydermatis on the skin of dogs relates to the affinity of the yeast to the host and to particular skin sites.
Publisher: Elsevier BV
Date: 2020
Publisher: Wiley
Date: 27-11-2008
Publisher: Elsevier BV
Date: 04-2007
DOI: 10.1016/J.MEDIA.2006.12.001
Abstract: Intensity based registration (e.g., mutual information) suffers from a scalloping artifact giving rise to local maxima and sometimes a biased global maximum in a similarity objective function. Here, we demonstrate that scalloping is principally due to the noise reduction filtering that occurs when image s les are interpolated. Typically at a much smaller scale (100 times less in our test cases), there are also fluctuations in the similarity objective function due to interpolation of the signal and to s ling of a continuous, band-limited image signal. Focusing on the larger problem from noise, we show that this phenomenon can even bias global maxima, giving inaccurate registrations. This phenomenon is readily seen when one registers an image onto itself with different noise realizations but is absent when the same noise realization is present in both images. For linear interpolation, local maxima and global bias are removed if one filters the interpolated image using a new constant variance filter for linear interpolation (cv-lin filter), which equalizes the variance across the interpolated image. We use 2D synthetic and MR images and characterize the effect of cv-lin on similarity objective functions. With a reduction of local and biased maxima, image registration becomes more robust and accurate. An efficient implementation adds insignificant computation time per iteration, and because optimization proceeds more smoothly, sometimes fewer iterations are needed.
Publisher: Society for Neuroscience
Date: 05-05-2010
DOI: 10.1523/JNEUROSCI.5180-09.2010
Abstract: Alzheimer's disease (AD) is the most common age-related dementia. Unfortunately due to a lack of validated biomarkers definitive diagnosis relies on the histological demonstration of amyloid-β (Aβ) plaques and tau neurofibrillary tangles. Aβ processing is implicated in AD progression and many therapeutic strategies target various aspects of this biology. While Aβ deposition is the most prominent feature of AD, oligomeric forms of Aβ have been implicated as the toxic species inducing the neuronal dysfunction. Currently there are no methods allowing routine monitoring of levels of such species in living populations. We have used surface enhanced laser desorption ionization time of flight (SELDI-TOF) mass spectrometry incorporating antibody capture to investigate whether the cellular membrane-containing fraction of blood provides a new source of biomarkers. There are significant differences in the mass spectra profiles of AD compared with HC subjects, with significantly higher levels of Aβ monomer and dimer in the blood of AD subjects. Furthermore, levels of these species correlated with clinical markers of AD including brain Aβ burden, cognitive impairment and brain atrophy. These results indicate that fundamental biochemical events relevant to AD can be monitored in blood, and that the species detected may be useful clinical biomarkers for AD.
Publisher: Wiley
Date: 2011
DOI: 10.1002/ANA.22248
Publisher: Elsevier BV
Date: 03-2011
DOI: 10.1016/J.RADONC.2011.01.012
Abstract: Dose planning requires a CT scan which provides the electron density distribution for dose calculation. MR provides superior soft tissue contrast compared to CT and the use of MR-alone for prostate planning would provide further benefits such as lower cost to the patient. This study compares the accuracy of MR-alone based dose calculations with bulk electron density assignment to CT-based dose calculations for prostate radiotherapy. CT and whole pelvis MR images were contoured for 39 prostate patients. Plans with uniform density and plans with bulk density values assigned to bone and tissue were compared to the patient's gold standard full density CT plan. The optimal bulk density for bone was calculated using effective depth measurements. The plans were evaluated using ICRU point doses, dose volume histograms, and Chi comparisons. Differences in spatial uniformity were investigated for the CT and MR scans. The calculated dose for CT bulk bone and tissue density plans was 0.1±0.6% (mean±1 SD) higher than the corresponding full density CT plan. MR bulk bone and tissue density plans were 1.3±0.8% lower than the full density CT plan. CT uniform density plans and MR uniform density plans were 1.4±0.9% and 2.6±0.9% lower, respectively. Paired t-tests performed on specific points on the DVH graphs showed that points on DVHs for all bulk electron density plans were equivalent with two exceptions. There was no significant difference between doses calculated on Pinnacle and Eclipse. The dose distributions of six patients produced Chi values outside the acceptable range of values when MR-based plans were compared to the full density plan. MR-alone bulk density planning is feasible provided bone is assigned a density, however, manual segmentation of bone on MR images will have to be replaced with automatic methods. The major dose differences for MR bulk density plans are due to differences in patient external contours introduced by the MR couch-top and pelvic coil.
Publisher: Springer Science and Business Media LLC
Date: 26-02-2013
DOI: 10.1038/TP.2012.150
Publisher: SPIE
Date: 04-03-2010
DOI: 10.1117/12.844624
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 04-2012
DOI: 10.1109/TOH.2011.66
Publisher: SPIE
Date: 02-03-2006
DOI: 10.1117/12.649093
Publisher: Elsevier BV
Date: 02-2012
DOI: 10.1016/J.NEUROIMAGE.2011.10.045
Abstract: This article proposes a new measure called Apparent Fibre Density (AFD) for the analysis of high angular resolution diffusion-weighted images using higher-order information provided by fibre orientation distributions (FODs) computed using spherical deconvolution. AFD has the potential to provide specific information regarding differences between populations by identifying not only the location, but also the orientations along which differences exist. In this work, analytical and numerical Monte-Carlo simulations are used to support the use of the FOD litude as a quantitative measure (i.e. AFD) for population and longitudinal analysis. To perform robust voxel-based analysis of AFD, we present and evaluate a novel method to modulate the FOD to account for changes in fibre bundle cross-sectional area that occur during spatial normalisation. We then describe a novel approach for statistical analysis of AFD that uses cluster-based inference of differences extended throughout space and orientation. Finally, we demonstrate the capability of the proposed method by performing voxel-based AFD comparisons between a group of Motor Neurone Disease patients and healthy control subjects. A significant decrease in AFD was detected along voxels and orientations corresponding to both the corticospinal tract and corpus callosal fibres that connect the primary motor cortices. In addition to corroborating previous findings in MND, this study demonstrates the clear advantage of using this type of analysis by identifying differences along single fibre bundles in regions containing multiple fibre populations.
Publisher: SPIE
Date: 12-05-2004
DOI: 10.1117/12.535958
Publisher: SPIE
Date: 04-03-2010
DOI: 10.1117/12.844058
Publisher: American Society of Parasitologists
Date: 08-2006
DOI: 10.1645/GE-823R.1
Publisher: Informa UK Limited
Date: 2012
Publisher: Elsevier BV
Date: 03-2012
Abstract: Morphologic and sonographic features of endobronchial ultrasound (EBUS) convex probe images are helpful in predicting metastatic lymph nodes. Grey scale texture analysis is a well-established methodology that has been applied to ultrasound images in other fields of medicine. The aim of this study was to determine if this methodology could differentiate between benign and malignant lymphadenopathy of EBUS images. Lymph nodes from digital images of EBUS procedures were manually mapped to obtain a region of interest and were analyzed in a prediction set. The regions of interest were analyzed for the following grey scale texture features in MATLAB (version 7.8.0.347 [R2009a]): mean pixel value, difference between maximal and minimal pixel value, SEM pixel value, entropy, correlation, energy, and homogeneity. Significant grey scale texture features were used to assess a validation set compared with fluoro-D-glucose (FDG)-PET-CT scan findings where available. Fifty-two malignant nodes and 48 benign nodes were in the prediction set. Malignant nodes had a greater difference in the maximal and minimal pixel values, SEM pixel value, entropy, and correlation, and a lower energy (P < .0001 for all values). Fifty-one lymph nodes were in the validation set 44 of 51 (86.3%) were classified correctly. Eighteen of these lymph nodes also had FDG-PET-CT scan assessment, which correctly classified 14 of 18 nodes (77.8%), compared with grey scale texture analysis, which correctly classified 16 of 18 nodes (88.9%). Grey scale texture analysis of EBUS convex probe images can be used to differentiate malignant and benign lymphadenopathy. Preliminary results are comparable to FDG-PET-CT scan.
Publisher: American Medical Association (AMA)
Date: 07-2013
Publisher: Wiley
Date: 03-2010
DOI: 10.1002/ANA.21955
Abstract: Elucidating the role of aggregated beta-amyloid in relation to gray matter atrophy is crucial to the understanding of the pathological mechanisms of Alzheimer disease and for the development of therapeutic trials. The present study aims to assess this relationship. Brain magnetic resonance imaging and [(11)C]Pittsburgh compound B (PiB)-positron emission tomography scans were obtained from 94 healthy elderly subjects (49 with subjective cognitive impairment), 34 patients with mild cognitive impairment, and 35 patients with Alzheimer disease. The correlations between global and regional neocortical PiB retention and atrophy were analyzed in each clinical group. Global and regional atrophy were strongly related to beta-amyloid load in participants with subjective cognitive impairment but not in patients with mild cognitive impairment or Alzheimer disease. Global neocortical beta-amyloid deposition correlated to atrophy in a large brain network including the hippoc us, medial frontal and parietal areas, and lateral temporoparietal cortex, whereas regional beta-amyloid load was related to local atrophy in the areas of highest beta-amyloid load only, that is, medial orbitofrontal and anterior and posterior cingulate recuneus areas. There is a strong relationship between beta-amyloid deposition and atrophy very early in the disease process. As the disease progresses to mild cognitive impairment and Alzheimer disease clinical stages, pathological events other than, and probably downstream from, aggregated beta-amyloid deposition might be responsible for the ongoing atrophic process. These findings suggest that antiamyloid therapy should be administered very early in the disease evolution to minimize synaptic and neuronal loss.
Publisher: Wiley
Date: 04-2007
Abstract: Members of the genus Malassezia are budding yeasts, characterized by a thick cell wall. Recently, these yeasts have received attention as emerging pathogens. They are common commensals on the skin of animals and can become pathogenic under the influence of various predisposing factors. Central to studying their taxonomy, systematics, and ecology and to diagnosis is the accurate identification of species or operational taxonomic units. To overcome the limitations of current phenotypic and biochemical methods of identification, a PCR-coupled SSCP approach, utilizing sequence variation (0.4-33.5%) in short regions (approximately 250-270 bp) of the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA and the chitin synthase-2 gene (chs-2), was assessed for the identification and differentiation of different species/genotypes of Malassezia, characterized previously by DNA sequencing. Genomic DNA s les (n = 30) from Malassezia isolates cultured from canine skin scrapings were assessed by SSCP analysis of the two different genetic loci, and unequivocal delineation between genotypes and species was achieved. This SSCP approach is considered to provide a practical tool for the rapid and reliable genetic characterization of Malassezia genotypes/species from dogs and for investigating their population genetics and ecology. It will also provide a powerful tool for studies of Malassezia isolates from other animal species.
Publisher: Wiley
Date: 05-2010
DOI: 10.1016/J.JALZ.2010.03.009
Abstract: The Australian Imaging Biomarkers and Lifestyle (AIBL) study is a longitudinal study of 1112 volunteers from healthy, mild cognitive impairment, and Alzheimer's disease (AD) populations who can be assessed and followed up for prospective research into aging and AD. AIBL aims to improve understanding of the pathogenesis, early clinical manifestation, and diagnosis of AD, and identify diet and lifestyle factors that influence the development of AD. For AIBL, the magnetic resonance imaging parameters of Alzheimer's Disease Neuroimaging Initiative (ADNI) were adopted and the Pittsuburgh compound B ((11)C-PiB) positron emission tomography (PET) acquisition and neuropsychological tests were designed to permit comparison and pooling with ADNI data. Differences to ADNI include assessment every 18-months, imaging in 25% (magnetic resonance imaging, (11)C-PiB PET but no fluorodeoxyglucose PET), more comprehensive neuropsychological testing, and detailed collection of diet and lifestyle data. AIBL has completed the first 18-month follow-up and is making imaging and clinical data available through the ADNI website. Cross-sectional analysis of baseline data is revealing links between cognition, brain amyloid burden, structural brain changes, biomarkers, and lifestyle.
Publisher: Springer Science and Business Media LLC
Date: 10-06-2009
Publisher: IOP Publishing
Date: 30-11-2012
DOI: 10.1088/0031-9155/57/24/8357
Abstract: Recent advances in high resolution magnetic resonance (MR) imaging of the spine provide a basis for the automated assessment of intervertebral disc (IVD) and vertebral body (VB) anatomy. High resolution three-dimensional (3D) morphological information contained in these images may be useful for early detection and monitoring of common spine disorders, such as disc degeneration. This work proposes an automated approach to extract the 3D segmentations of lumbar and thoracic IVDs and VBs from MR images using statistical shape analysis and registration of grey level intensity profiles. The algorithm was validated on a dataset of volumetric scans of the thoracolumbar spine of asymptomatic volunteers obtained on a 3T scanner using the relatively new 3D T2-weighted SPACE pulse sequence. Manual segmentations and expert radiological findings of early signs of disc degeneration were used in the validation. There was good agreement between manual and automated segmentation of the IVD and VB volumes with the mean Dice scores of 0.89 ± 0.04 and 0.91 ± 0.02 and mean absolute surface distances of 0.55 ± 0.18 mm and 0.67 ± 0.17 mm respectively. The method compares favourably to existing 3D MR segmentation techniques for VBs. This is the first time IVDs have been automatically segmented from 3D volumetric scans and shape parameters obtained were used in preliminary analyses to accurately classify (100% sensitivity, 98.3% specificity) disc abnormalities associated with early degenerative changes.
Publisher: SPIE
Date: 02-03-2006
DOI: 10.1117/12.655617
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 04-2010
Publisher: Oxford University Press (OUP)
Date: 09-02-2011
DOI: 10.1093/BRAIN/AWQ383
Abstract: The relationship between β-amyloid deposition and memory deficits in early Alzheimer's disease is unresolved, as past studies show conflicting findings. The present study aims to determine the relative contribution of regional β-amyloid deposition, hippoc al atrophy and white matter integrity to episodic memory deficits in non-demented older in iduals harbouring one of the characteristic hallmarks of Alzheimer's disease, i.e. with β-amyloid pathology. Understanding these relationships is critical for effective therapeutic development. Brain magnetic resonance imaging and [(11)C]Pittsburgh Compound B-positron emission tomography scans were obtained in 136 non-demented in iduals aged over 60 years, including 93 healthy elderly and 43 patients with mild cognitive impairment. Voxel-based correlations were computed between a memory composite score and grey matter volume, white matter volume and β-amyloid deposition imaging datasets. Hierarchical linear regression analyses were then performed using values extracted in regions of most significant correlations to determine the relative contribution of each modality to memory deficits. All analyses were conducted pooling all groups together as well as within separate subgroups of cognitively normal elderly, patients with mild cognitive impairment and in iduals with high versus low neocortical β-amyloid. Brain areas of highest correlation with episodic memory deficits were the hippoc i for grey matter volume, the perforant path for white matter volume and the temporal neocortex for β-amyloid deposition. When considering these three variables together, only hippoc al volume and temporal β-amyloid deposition provided independent contributions to memory deficits. In contrast to global β-amyloid deposition, temporal β-amyloid deposition was still related to memory independently from hippoc al atrophy within subgroups of cognitively normal elderly, patients with mild cognitive impairment or cases with high neocortical β-amyloid. In the pre-dementia stage of Alzheimer's disease, subtle episodic memory impairment is related to β-amyloid deposition, especially in the temporal neocortex, and independently from hippoc al atrophy, suggesting that both factors should be independently targeted in therapeutic trials aimed at reducing cognitive decline.
Publisher: Oxford University Press (OUP)
Date: 23-05-2012
DOI: 10.1093/BRAIN/AWS125
Abstract: Amyloid-β deposition in Alzheimer's disease is thought to start while in iduals are still cognitively unimpaired and it is hypothesized that after an early phase of fast accumulation, a plateau is reached by the time of cognitive decline. However, few longitudinal Pittsburgh compound B-positron emission tomography studies have tested this hypothesis, and with conflicting results. The purpose of this work is to further our understanding of the dynamics of amyloid-β deposition in a large longitudinal cohort. A total of 32 patients with Alzheimer's disease, 49 subjects with mild cognitive impairment and 103 healthy controls underwent two Pittsburgh compound B-positron emission tomography scans 18 months apart. For each participant, a parametric map of Pittsburgh compound B-positron emission tomography rate of change was created [(follow-up scan - baseline scan)/follow-up duration] and entered in a voxelwise three-way analysis of covariance, with clinical status (healthy controls, mild cognitive impairment or Alzheimer's disease), disease progression (clinical conversion from healthy controls to mild cognitive impairment or Alzheimer's disease, or from mild cognitive impairment to Alzheimer's disease) and Pittsburgh compound B status (positive versus negative) as independent factors. Only a significant effect of the Pittsburgh compound B status was found: both Pittsburgh compound B-positive and -negative subjects showed a significant increase in amyloid-β deposition, with this increase being significantly higher in Pittsburgh compound B-positive in iduals. This finding suggests either that Pittsburgh compound B-negative in iduals have slower rates of amyloid-β accumulation than positive, or that the proportion of in iduals showing significant increase in amyloid-β deposition, termed 'Pittsburgh compound B accumulators', is higher within the Pittsburgh compound B-positive group than within the Pittsburgh compound B-negative group. The bimodal distribution of the in idual rates of neocortical amyloid-β accumulation observed support the existence of 'Pittsburgh compound B non-accumulators' and 'Pittsburgh compound B accumulators' and different clustering analyses led to a consistent threshold to separate these two subgroups (0.014-0.022 standardized uptake value ratio(pons)/year). The voxelwise three-way analysis of covariance was thus recomputed with the 'Pittsburgh compound B accumulators' only and the results were almost unchanged, with the Pittsburgh compound B-positive group showing higher accumulation than the Pittsburgh compound B-negative group. Finally, a significant negative correlation was found between Pittsburgh compound B rate of change and Pittsburgh compound B baseline burden, but only in the Pittsburgh compound B-positive group (r= -0.24 P=0.025). Higher rates of amyloid-β deposition are associated with higher amyloid-β burden suggesting that amyloid-β deposition does not reach a plateau when cognitive impairments manifest but is instead an ongoing process present even at the Alzheimer's disease stage. amyloid-β accumulation also seems to slow down at the latest stages of the process, i.e. in participants with the highest amyloid burden. Furthermore, this study identified the existence of Pittsburgh compound 'accumulators' and 'non-accumulators', notably within the Pittsburgh compound B-negative group, which may be a relevant concept for future studies.
Publisher: Wiley
Date: 19-12-2012
DOI: 10.1002/MRM.23058
Abstract: Using high angular resolution diffusion-weighted images, spherical deconvolution enables multiple white matter fiber populations to be resolved within a single voxel by computing the fiber orientation distribution (FOD). Higher order information provided by FODs could improve several methods for investigating population differences in white matter, including image registration, voxel-based analysis, atlas-based segmentation and labeling, and group average fiber tractography. All of these methods require spatial normalization of FODs. In this article, a novel method to reorient the FOD is presented, which is an important step required for FOD spatial normalization. The proposed method was assessed using both qualitative and quantitative experiments, with numerical simulations and in vivo human data. Results demonstrate that the proposed method improves FOD reorientation accuracy, removes undesired artefacts, and decreases computation time compared to a previous approach. The utility of the proposed method is illustrated by nonlinear FOD spatial normalization of 10 human subjects. Accurate reorientation and normalization of FODs is a critical step toward investigating white matter tissue in the context of multiple fiber orientations.
Publisher: Elsevier BV
Date: 05-2012
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 03-2011
Publisher: Oxford University Press (OUP)
Date: 25-08-2010
DOI: 10.1093/BRAIN/AWQ187
Abstract: β-Amyloid deposition is one of the main hallmarks of Alzheimer's disease thought to eventually cause neuronal death. Post-mortem and neuroimaging studies have consistently reported cases with documented normal cognition despite high β-amyloid burden. It is of great interest to understand what differentiates these particular subjects from those without β-amyloid deposition or with both β-amyloid deposition and cognitive deficits, i.e. what allows these subjects to resist the damage of the pathological lesions. [¹¹C]Pittsburgh compound B positron emission tomography and magnetic resonance brain scans were obtained in 149 participants including healthy controls and patients with subjective cognitive impairment, mild cognitive impairment and Alzheimer's disease. Magnetic resonance data were compared between high versus low-[11C]Pittsburgh compound B cases, and between high-[¹¹C]Pittsburgh compound B cases with versus those without cognitive deficits. Larger temporal (including hippoc al) grey matter volume, associated with better episodic memory performance, was found in high- versus low-[¹¹C]Pittsburgh compound B healthy controls. The same finding was obtained using different [¹¹C]Pittsburgh compound B thresholds, correcting [¹¹C]Pittsburgh compound B data for partial averaging, using age, education, Mini-Mental State Examination, apolipoprotein E4 and sex-matched subs les, and using manual hippoc al delineation instead of voxel-based analysis. By contrast, in participants with subjective cognitive impairment, significant grey matter atrophy was found in high-[¹¹C]Pittsburgh compound B cases compared to low-[¹¹C]Pittsburgh compound B cases, as well as in high-[¹¹C]Pittsburgh compound B cases with subjective cognitive impairment, mild cognitive impairment and Alzheimer's disease compared to high-[¹¹C]Pittsburgh compound B healthy controls. Larger grey matter volume in high-[¹¹C]Pittsburgh compound B healthy controls may reflect either a tissue reactive response to β-amyloid or a combination of higher 'brain reserve' and under-representation of subjects with standard/low temporal volume in the high-[¹¹C]Pittsburgh compound B healthy controls. Our complementary analyses tend to support the latter hypotheses. Overall, our findings suggest that the deleterious effects of β-amyloid on cognition may be delayed in those subjects with larger brain (temporal) volume.
Publisher: SPIE
Date: 03-03-2011
DOI: 10.1117/12.877866
Publisher: SPIE
Date: 04-03-2010
DOI: 10.1117/12.844088
Publisher: Cold Spring Harbor Laboratory
Date: 05-04-2019
DOI: 10.1101/597856
Abstract: Participant movement can deleteriously affect MR image quality. Further, for the visualization and segmentation of small anatomical structures, there is a need to improve image quality, specifically signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), by acquiring multiple anatomical scans consecutively. We aimed to ameliorate movement artefacts and increase SNR in a high-resolution turbo spin-echo (TSE) sequence acquired thrice using non-linear realignment in order to improve segmentation consistency of the hippoc us subfields. We assessed the method in young healthy participants, Motor Neurone Disease patients, and age matched controls. Results show improved image segmentation of the hippoc us subfields when comparing template-based segmentations with in idual segmentations with Dice overlaps N=51 ps 0.001 (Friedman’s test) and higher sharpness ps 0.001 in non-linearly realigned scans as compared to linearly, and arithmetically averaged scans.
Publisher: SPIE
Date: 03-03-2011
DOI: 10.1117/12.877869
Publisher: Elsevier BV
Date: 06-2011
DOI: 10.1016/J.NEUROIMAGE.2011.02.014
Abstract: Registration of diffusion-weighted images is an important step in comparing white matter fibre bundles across subjects, or in the same subject at different time points. Using diffusion-weighted imaging, Spherical Deconvolution enables multiple fibre populations within a voxel to be resolved by computing the fibre orientation distribution (FOD). In this paper, we present a novel method that employs FODs for the registration of diffusion-weighted images. Registration was performed by optimising a symmetric diffeomorphic non-linear transformation model, using image metrics based on the mean squared difference, and cross-correlation of the FOD spherical harmonic coefficients. The proposed method was validated by recovering known displacement fields using FODs represented with maximum harmonic degrees (l(max)) of 2, 4 and 6. Results demonstrate a benefit in using FODs at l(max)=4 compared to l(max)=2. However, a decrease in registration accuracy was observed when l(max)=6 was used this was likely caused by noise in higher harmonic degrees. We compared our proposed method to fractional anisotropy driven registration using an identical code base and parameters. FOD registration was observed to perform significantly better than FA in all experiments. The cross-correlation metric performed significantly better than the mean squared difference. Finally, we demonstrated the utility of this method by computing an unbiased group average FOD template that was used for probabilistic fibre tractography. This work suggests that using crossing fibre information aids in the alignment of white matter and could therefore benefit several methods for investigating population differences in white matter, including voxel based analysis, tensor based morphometry, atlas based segmentation and labelling, and group average fibre tractography.
Publisher: SPIE
Date: 04-03-2010
DOI: 10.1117/12.844048
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/AN12366
Abstract: The aim of this study was to determine the effect of potassium (K) supplementation on the calcium (Ca) absorption capacity from the rumen and abomasum of sheep. The Ca absorption capacity from the rumen and abomasum of sheep was measured using stable strontium (Sr) as a Ca-analogue tracer method. The sheep, cannulated at either the rumen or abomasum, were randomly allocated to one of two groups (control or K-supplemented) and fed in in idual metabolism pens twice daily with a diet comprising oaten hay, lucerne chaff and barley fortified with or without potassium carbonate (K2CO3). The K content of the diet of the K-supplemented animals was 3.1% of dry matter compared with 1.4% for the control animals. The animals were fed their respective diets for a period of 2 weeks. The fractional absorption capacity (FC) of Ca was estimated before, during and after the treatment period. Supplementation with K decreased the FC of Ca in both the rumen and abomasum during treatment and increased the FC of Ca in the abomasum post-treatment. Supplementation with K also increased the fractional excretion of K in the urine, but decreased the fractional excretion of Ca and magnesium (Mg) (P 0.05), showing that K supplementation significantly affected Ca and Mg metabolism. Results suggest that renal conservation of Ca and Mg is an important mechanism controlling the Ca and Mg pool for vital functions of the body. In times of high demand for these minerals during lactation and pregnancy, high K in the diets may predispose sheep to hypomagnesaemia and hypocalcaemia, which in turn will have a negative impact on productivity and economic returns.
Publisher: Wiley
Date: 10-2009
Abstract: Dermatophytes are fungi that can be contagious and cause infections in the keratinized skin of mammals, including humans. The etiological diagnosis of dermatophytosis relies on a combination of in vitro-culture and microscopic methods. Effective molecular tools could overcome the limitations of conventional methods of identification. In the present study, following phenetic identification as M. canis, M. fulvum, M. gypseum, T. mentagrophytes and T. terrestre, we genetically characterized key dermatophytes, employing the sequences of the first and second internal transcribed spacers of nuclear ribosomal DNA as well as part of the chitin synthase-1 gene, and assessed the utility of these DNA regions (based on levels of nucleotide variation within and among species/taxa) as markers for the classification of species and genotypes. Employing partial chitin synthase-1 gene as the marker, we also established a PCR-coupled SSCP approach as a diagnostic/analytical mutation-scanning tool. This tool should facilitate fundamental investigations of the ecology, epidemiology and population genetics of dermatophytes and, importantly, should assist in allowing a more rapid diagnosis of dermatophytoses in humans and other animals, thus overcoming the significant delays in targeted chemotherapy following diagnosis using conventional methods. (Nucleotide sequence data reported in this paper are available in the EMBL, GenBank and DDJB datadases under accession numbers FJ897707-FJ897713 (ITS-1), FJ897714-FJ897720 (ITS-2) and FJ897700-FJ897706 (pchs-1)).
Publisher: Elsevier BV
Date: 11-2013
DOI: 10.1016/J.NEUROBIOLAGING.2013.05.006
Abstract: Brain-derived neurotrophic factor (BDNF) Val66Met polymorphism has previously been implicated in Alzheimer's disease (AD)-related cognitive impairment. We aimed to determine the relationship between BDNF Val66Met and beta-amyloid (Aβ) on cognitive decline, hippoc al atrophy, and Aβ accumulation over 36 months in 165 healthy adults enrolled in the Australian Imaging, Biomarkers and Lifestyle study. In healthy adults with high Aβ, Met carriers showed significant and moderate-to-large declines in episodic memory, executive function, and language, and greater hippoc al atrophy over 36 months, compared with Val/Val homozygotes. BDNF Val66Met was not found to be related to rates of change in cognition or hippoc al volume in healthy adults with low Aβ. BDNF Val66Met did not relate to the amount of Aβ or to the rate of Aβ accumulation in either group. High Aβ levels coupled with Met carriage may be useful prognostic markers of accelerated cognitive decline and hippoc al degeneration in in iduals in the preclinical stage of AD.
Publisher: Elsevier BV
Date: 04-2008
DOI: 10.1016/J.VETPAR.2007.12.028
Abstract: Coccidiosis of chickens is one of the commonest and economically most important parasitic diseases of poultry worldwide. Given the limitations of traditional approaches, molecular tools have been developed for the specific diagnosis of coccidiosis. Recently, a polymerase chain reaction (PCR)-based capillary electrophoresis (CE) method, employing genetic markers in the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA, was established for both analytical and diagnostic purposes. The application of this method to investigate the epidemiology of coccidiosis and genetic structures of Eimeria populations on commercial chicken establishments has discovered genetic variants of Eimeria (i.e., new operational taxonomic units OTU-X, OTU-Y and OTU-Z) which were (based on CE analysis) distinct from those of species of Eimeria identified previously in chickens in Australia. The present characterization of these OTUs, based on their ITS-2 sequences and phylogenetic analyses of selected sequence data, provides first evidence to support that OTU-X represents a population variant of Eimeria maxima, and that OTU-Y and OTU-Z represent cryptic species of Eimeria. Further biological and genetic studies are needed to rigorously test these proposals and establish the specific status of these OTUs and their importance as pathogens in chickens. An understanding of the epidemiology of these population variants or cryptic species in Australia is central to designing and implementing effective vaccination and control strategies.
No related grants have been discovered for Olivier Salvado.