Leigh Johnston

The impact of Alzheimer's disease on the functional connectivity between brain regions underlying pain perception

Publisher: Wiley

Date: 07-2010

DOI: 10.1016/J.EJPAIN.2010.10.010

Abstract: Patients with Alzheimer's disease (AD) are administered fewer analgesics and report less clinical pain compared with their cognitively-intact peers, prompting much speculation about the likely impact of neurodegeneration on pain perception and processing. This study used functional connectivity analysis to examine the impact of AD on the integrated functioning of brain regions mediating the sensory, emotional, and cognitive aspects of pain. Fourteen patients with AD and 15 controls attended two experimental sessions. In an initial psychophysical testing session, a random staircase procedure was used to assess sensitivity to noxious mechanical pressure applied to the thumbnail. In a subsequent brain imaging session, fMRI data were collected as participants received noxious or innocuous thumbnail pressure, delivered at intensities corresponding with previously identified subjective pain thresholds. Two approaches to functional connectivity analysis were utilised. A seed-based correlation method was first used to identify regions showing significant functional connectivity with the right dorsolateral prefrontal cortex (DLPFC). Functional connectivity between a network of 17 predefined pain processing regions was then assessed. Between-group comparisons revealed enhanced functional connectivity between the DLPFC and the anterior mid cingulate cortex, periaqueductal grey, thalamus, hypothalamus, and several motor areas in patients with AD compared with control group. Likewise, inter-regional functional connectivity across most regions of the predefined pain network was shown to be greater in the patient group, with the enhanced functional connectivity centred on three nodes: the DLPFC-R, hypothalamus, and PAG. The results of this study support previous research suggesting an interplay between pain and cognitive processes in patients with AD.

Sodium selenate reduces hyperphosphorylated tau and improves outcomes after traumatic brain injury

Publisher: Oxford University Press (OUP)

Date: 13-03-2015

DOI: 10.1093/BRAIN/AWV053

Spatially dependent filtering for removing phase distortions at the cortical surface

Publisher: Wiley

Date: 09-03-2011

DOI: 10.1002/MRM.22825

Abstract: Recent advances in high field magnetic resonance technology have increased the interest in the phase of the complex data. Processed phase images are derived from the phase signal by removing the bias field and phase wraps from the initial data. However, the usefulness of this data has been hindered by artifacts at the brain/non-brain surface, particularly in cortical regions. A method is proposed that efficiently removes surface artifacts by performing Gaussian filtering with spatially varying parameters of unwrapped or complex filtered phase images. The proposed method is shown to produce improved images, revealing underlying structure and detail that are otherwise obscured by surface artifacts in images produced by traditional phase processing methods.

Video Imaging and Spatiotemporal Maps to Analyze Gastrointestinal Motility in Mice

Publisher: MyJove Corporation

Date: 03-02-2016

DOI: 10.3791/53828

2D IIR filter for parallel magnetic resonance image reconstruction

Publisher: IEEE

Date: 12-2009

DOI: 10.1109/ICCA.2009.5410221

Altered Speeds and Trajectories of Neurons Migrating in the Ventricular and Subventricular Zones of the Reeler Neocortex

Publisher: Oxford University Press (OUP)

Date: 16-09-2010

DOI: 10.1093/CERCOR/BHQ168

Abstract: The Reelin signaling pathway is essential for proper cortical development, but it is unclear to whether Reelin function is primarily important for cortical layering or neuron migration. It has been proposed that Reelin is perhaps required only for somal translocation but not glial-dependent locomotion. This implies that the location of neurons responding to Reelin is restricted to the outer regions of the cortical plate (CP). To determine whether Reelin is required for migration outside of the CP, we used time-lapse imaging to track the behavior of cells undergoing locomotion in the germinal zones. We focused on the migratory activity in the ventricular/subventricular zones where the first transition of bipolar to multipolar migration occurs and where functional Reelin receptors are known to be expressed. Despite Reelin loss, neurons had no difficulty in undergoing radial migration and indeed displayed greater migratory speed. Additionally, compared with the wild-type, reeler neurons displayed altered trajectories with greater deviation from a radial path. These results suggest that Reelin loss has early consequences for migration in the germinal zones that are portrayed as defective radial trajectories and migratory speeds. Together, these abnormalities can give rise to the increased cell dispersion observed in the reeler cortex.

Automated differentiation of pre-diagnosis Huntington's disease from healthy control individuals based on quadratic discriminant analysis of the basal ganglia: The IMAGE-HD study

Publisher: Elsevier BV

Date: 03-2013

DOI: 10.1016/J.NBD.2012.10.001

Abstract: We investigated two measures of neural integrity, T1-weighted volumetric measures and diffusion tensor imaging (DTI), and explored their combined potential to differentiate pre-diagnosis Huntington's disease (pre-HD) in iduals from healthy controls. We applied quadratic discriminant analysis (QDA) to discriminate pre-HD in iduals from controls and we utilised feature selection and dimension reduction to increase the robustness of the discrimination method. Thirty six symptomatic HD (symp-HD), 35 pre-HD, and 36 control in iduals participated as part of the IMAGE-HD study and underwent T1-weighted MRI, and DTI using a Siemens 3 Tesla scanner. Volume and DTI measures [mean diffusivity (MD) and fractional anisotropy (FA)] were calculated for each group within five regions of interest (ROI caudate, putamen, pallidum, accumbens and thalamus). QDA was then performed in a stepwise manner to differentiate pre-HD in iduals from controls, based initially on unimodal analysis of motor or neurocognitive measures, or on volume, MD or FA measures from within the caudate, pallidum and putamen. We then tested for potential improvements to this model, by examining multi-modal MRI classifications (volume, FA and MD), and also included motor and neurocognitive measures, and additional brain regions (i.e., accumbens and thalamus). Volume, MD and FA differed across the three groups, with pre-HD characterised by significant volumetric reductions and increased FA within caudate, putamen and pallidum, relative to controls. The QDA results demonstrated that the differentiation of pre-HD from controls was highly accurate when both volumetric and diffusion data sets from basal ganglia (BG) regions were used. The highest discriminative accuracy however was achieved in a multi-modality approach and when including all available measures: motor and neurocognitive scores and multi-modal MRI measures from the BG, accumbens and thalamus. Our QDA findings provide evidence that combined multi-modal imaging measures can accurately classify in iduals up to 15 years prior to onset when therapeutic intervention is likely to have maximal effects in slowing the trajectory of disease development.

Inter-scanner Aβ-amyloid PET harmonization using barrel phantom spatial resolution matching

Publisher: Cold Spring Harbor Laboratory

Date: 18-07-2023

DOI: 10.1101/2023.07.16.23292733

Abstract: The standardized uptake value ratio (SUVR) is used to measure Aβ uptake in PET images of the brain. Variations in PET scanner technologies and image reconstruction techniques can lead to variability in images acquired from different scanners. This poses a challenge for Aβ-PET studies conducted across multiple centers. The aim of harmonization is to achieve consistent Aβ-PET measurements across scanners. In this study, the procedure of matching the spatial resolution of a barrel phantom measured in each PET scanner is proposed as a method of Aβ-PET harmonization, validated using subject data. Three different PET scanners were used: the Siemens Biograph Vision 600, Siemens Biograph mCT, and Philips Gemini TF64. A total of five, eight, and five subjects were each scanned twice with [ 18 F]-NAV4694 across Vision-mCT, mCT-Philips, and Vision-Philips scanner pairs. The Vision and mCT scans were reconstructed using various iterations, subsets, and post-reconstruction Gaussian smoothing, while one reconstruction configuration was used for the Philips scans. The full-width at half-maximum (FWHM) of each reconstruction configuration was calculated using [ 18 F]-filled barrel phantom scans with the SNMMI phantom analysis toolkit. Regional SUVRs were calculated from 72 brain regions using the AAL3 atlas for each subject and reconstruction configuration. Statistical similarity between SUVRs was assessed using paired (within subject) t-tests for each pair of reconstructions across scanners the higher the p-value, the greater the similarity between the SUVRs. maximal statistical similarity (i.e., p -value) between regional SUVRs was achieved using a 4.10 mm FWHM Vision reconstruction with a 4.30 mm FWHM mCT reconstruction. maximal statistical similarity between regional SUVRs was achieved using an 8.2 mm FWHM Philips reconstruction with a 9.35 mm FWHM mCT reconstruction. a 9.1 mm FWHM Vision reconstruction had maximum statistical similarity with regional SUVRs from an 8.2mm FWHM Philips reconstruction. Reconstruction pairs that maximized statistical similarity, and supported a null hypothesis of being drawn from the same distribution, were selected as harmonised for each scanner pair. Using data obtained from three sets of participants, each scanned on a different pair of PET scanners, using reconstruction configurations with matched barrel phantom spatial resolutions, we have demonstrated that Aβ-PET quantitation can be harmonised across scanners, producing SUVR values statistically likely to be drawn from the same distribution. This finding is encouraging for the use of different PET scanners in multi-centre trials, or updates during longitudinal studies.

A Comprehensive Atlas of the Adult Mouse Penis

Publisher: S. Karger AG

Date: 2015

DOI: 10.1159/000431010

Abstract: Mice are routinely used to study the development of the external genitalia and, in particular, the process of male urethral closure. This is because misplacement of the male penile urethra, or hypospadias, is amongst the most common birth defects reported in humans. While mice present a tractable model to study penile development, several structures differ between mice and humans, and there is a lack of consensus in the literature on their annotation and developmental origins. Defining the ontology of the mouse prepuce is especially important for the relevance and interpretation of mouse models of hypospadias to human conditions. We have developed a detailed annotation of the adult mouse penis that addresses these differences and enables an accurate comparison of murine and human hypospadias phenotypes. Through MRI data, gross morphology and section histology, we define the origin of the mouse external and internal prepuces, their relationship to the single human foreskin as well as provide a comprehensive view of the various structures of the mouse penis and their associated muscle attachments within the body. These data are combined to annotate structures in a novel 3D adult penis atlas that can be downloaded, viewed at any angle, and manipulated to examine the relationship of various structures.

3D model-based approach to identification of laminar structures of the cerebral cortex: Application to Brodmann areas 17 and 18

Publisher: Elsevier BV

Date: 11-2013

DOI: 10.1016/J.BSPC.2013.08.005

Limitations of two-component diffusion models for axon diameter density estimation

Publisher: IEEE

Date: 04-2015

DOI: 10.1109/ISBI.2015.7164082

A tracking approach to parcellation of the cerebral cortex

Publisher: Springer Berlin Heidelberg

Date: 2005

DOI: 10.1007/11566465_37

Abstract: The cerebral cortex is composed of regions with distinct laminar structure. Functional neuroimaging results are often reported with respect to these regions, usually by means of a brain "atlas". Motivated by the need for more precise atlases, and the lack of model-based approaches in prior work in the field, this paper introduces a novel approach to parcellating the cortex into regions of distinct laminar structure, based on the theory of target tracking. The cortical layers are modelled by hidden Markov models and are tracked to determine the Bayesian evidence of layer hypotheses. This model-based parcellation method, evaluated here on a set of histological images of the cortex, is extensible to 3-D images.

Solving the bloch equation with periodic excitation using harmonic balancing: Application to Rabi modulated excitation

Publisher: Institute of Electrical and Electronics Engineers (IEEE)

Date: 10-2015

DOI: 10.1109/TMI.2015.2423313

A longitudinal diffusion tensor imaging study in symptomatic Huntington's disease

Publisher: BMJ

Date: 22-02-2010

DOI: 10.1136/JNNP.2007.142786

Abstract: The striatum and its projections are thought to be the earliest sites of Huntington's disease (HD) pathology. This study aimed to investigate progression of striatal pathology in symptomatic HD using diffusion tensor imaging. Diffusion weighted images were acquired in 18 HD patients and in 17 healthy controls twice, 1 year apart. Mean diffusivity (MD) was calculated in the caudate, putamen, thalamus and corpus callosum, and compared between groups. In addition, caudate width was measured using T1 high resolution images and correlated with caudate MD. Correlation analyses were also performed in HD between caudate utamen MD and clinical measures. MD was significantly higher in the caudate and putamen bilaterally for patients compared with controls at both time points although there were no significant MD differences in the thalamus or corpus callosum. For both groups, MD did not change significantly in any region from baseline to year 1. There was a significant negative correlation between caudate width and MD in patients at baseline but no correlation between these parameters in controls. There was also a significant negative correlation between Mini-Mental State Examination scores and caudate MD and putamen MD at both time points in HD. It appears that microstructural changes influence cognitive status in HD. Although MD was significantly higher in HD compared with controls at both time points, there were no longitudinal changes in either group. This finding does not rule out the possibility that MD could be a sensitive biomarker for detecting early change in preclinical HD.

Extending Communication for Patients with Disorders of Consciousness

Publisher: Wiley

Date: 28-08-2012

DOI: 10.1111/J.1552-6569.2012.00744.X

Abstract: The difficulty of distinguishing disorders of consciousness from certain disorders of communication leads to the possibility of false diagnosis. Our aim is to communicate with patients with disorders of consciousness through asking them to answer questions with "yes/no" by performing mental imagery tasks using functional magnetic resonance imaging (fMRI). A 1.5 T fMRI study with 5 patients and a control group is presented. Speech comprehension, mental imagery, and question-answer tests were performed. The imagery task of mental calculation produced equally distinct activation patterns when compared to navigation and motor imagery in controls. For controls, we could infer answers to questions based on imagery activations. Two patients produced activations in similar areas to controls for certain imagery tasks, however, no activations were observed for the question-answer task. The results from 2 patients provide independent support of similar work by others with 3 T fMRI, and demonstrate broader clinical utility for these tests at 1.5 T despite lower signal-to-noise ratio. Based on the control results, mental calculation adds a robust imagery task for use in future studies of this kind.

A stochastic linear model for fMRI activation analyses

Publisher: Springer Berlin Heidelberg

Date: 2011

DOI: 10.1007/978-3-642-23629-7_36

Abstract: The debate regarding how best to model variability of the hemodynamic response function in fMRI data has focussed on the linear vs. nonlinear nature of the optimal signal model, with few studies exploring the deterministic vs. stochastic nature of the dynamics. We propose a stochastic linear model (SLM) of the hemodynamic signal and noise dynamics to more robustly infer fMRI activation estimates. The SLM models the hemodynamic signal by an exogenous input autoregressive model driven by Gaussian state noise. Activation weights are inferred by a joint state-parameter iterative coordinate descent algorithm based on the Kalman smoother. The SLM produced more accurate parameter estimates than the GLM for event-design simulated data. In application to block-design experimental visuo-motor task fMRI data, the SLM resulted in more punctate and well-defined motor cortex activation maps than the GLM, and was able to track variations in the hemodynamics, as expected from a stochastic model. We demonstrate in application to both simulated and experimental fMRI data that in comparison to the GLM, the SLM produces more flexible, consistent and enhanced fMRI activation estimates.

A review of beta-amyloid neuroimaging in Alzheimer's disease

Publisher: Frontiers Media SA

Date: 31-10-2014

DOI: 10.3389/FNINS.2014.00327

A multistage parallel magnetic resonance image reconstruction method

Publisher: IEEE

Date: 2008

DOI: 10.1109/DICTA.2008.53

Continuous monitoring of plant sodium transport dynamics using clinical PET

Publisher: Springer Science and Business Media LLC

Date: 19-01-2021

DOI: 10.1186/S13007-021-00707-8

Abstract: The absorption, translocation, accumulation and excretion of substances are fundamental processes in all organisms including plants, and have been successfully studied using radiotracers labelled with 11 C, 13 N, 14 C and 22 Na since 1939. Sodium is one of the most damaging ions to the growth and productivity of crops. Due to the significance of understanding sodium transport in plants, a significant number of studies have been carried out to examine sodium influx, compartmentation, and efflux using 22 Na- or 24 Na-labeled salts. Notably, however, most of these studies employed destructive methods, which has limited our understanding of sodium flux and distribution characteristics in real time, in live plants. Positron emission tomography (PET) has been used successfully in medical research and diagnosis for decades. Due to its ability to visualise and assess physiological and metabolic function, PET imaging has also begun to be employed in plant research. Here, we report the use of a clinical PET scanner with a 22 Na tracer to examine 22 Na-influx dynamics in barley plants ( Hordeum vulgare L. spp. Vulgare —cultivar Bass) under variable nutrient levels, alterations in the day/night light cycle, and the presence of sodium channel inhibitors. 3D dynamic PET images of whole plants show readily visible 22 Na translocation from roots to shoots in each examined plant, with rates influenced by both nutrient status and channel inhibition. PET images show that plants cultivated in low-nutrient media transport more 22 Na than plants cultivated in high-nutrient media, and that 22 Na uptake is suppressed in the presence of a cation-channel inhibitor. A distinct diurnal pattern of 22 Na influx was discernible in curves displaying rates of change of relative radioactivity. Plants were found to absorb more 22 Na during the light period, and anticipate the change in the light/dark cycle by adjusting the sodium influx rate downward in the dark period, an effect not previously described experimentally. We demonstrate the utility of clinical PET/CT scanners for real-time monitoring of the temporal dynamics of sodium transport in plants. The effects of nutrient deprivation and of ion channel inhibition on sodium influx into barley plants are shown in two proof-of-concept experiments, along with the first-ever 3D-imaging of the light and dark sodium uptake cycles in plants. This method carries significant potential for plant biology research and, in particular, in the context of genetic and treatment effects on sodium acquisition and toxicity in plants.

Diffusion Tensor Imaging in Huntington's disease reveals distinct patterns of white matter degeneration associated with motor and cognitive deficits

Publisher: Springer Science and Business Media LLC

Date: 26-03-2011

DOI: 10.1007/S11682-011-9121-8

Abstract: White matter (WM) degeneration is an important feature of Huntington's disease (HD) neuropathology. To investigate WM degeneration we used Diffusion Tensor Imaging and Tract-Based Spatial Statistics to compare Fractional Anisotropy, Mean Diffusivity (MD), parallel diffusivity and perpendicular diffusivity (λ⊥) in WM throughout the whole brain in 17 clinically diagnosed HD patients and 16 matched controls. Significant WM diffusivity abnormalities were identified primarily in the corpus callosum (CC) and external/extreme capsules in HD patients compared to controls. Significant correlations were observed between motor symptoms and MD in the CC body, and between global cognitive impairment and λ⊥ in the CC genu. Probabilistic tractography from these regions revealed degeneration of functionally relevant interhemispheric WM tracts. Our findings suggest that WM degeneration within interhemispheric pathways plays an important role in the deterioration of cognitive and motor function in HD patients, and that improved understanding of WM pathology early in the disease is required.

Bayesian model evidence for order selection and correlation testing

Publisher: IEEE

Date: 08-2011

DOI: 10.1109/IEMBS.2011.6091250

Diffusion tensor imaging of the optic radiations after optic neuritis

Publisher: Wiley

Date: 13-09-2012

DOI: 10.1002/HBM.21343

A method for shape analysis and segmentation in MRI

Publisher: IEEE

Date: 2008

DOI: 10.1109/DICTA.2008.71

Fourier Tract Sampling (FouTS): A framework for improved inference of white matter tracts from diffusion MRI by explicitly modelling tract volume

Publisher: Elsevier BV

Date: 10-2015

DOI: 10.1016/J.NEUROIMAGE.2015.05.090

Abstract: Diffusion MRI tractography algorithm development is increasingly moving towards global techniques to incorporate "downstream" information and conditional probabilities between neighbouring tracts. Such approaches also enable white matter to be represented more tangibly than the abstract lines generated by the most common approaches to fibre tracking. However, previously proposed algorithms still use fibre-like models of white matter corresponding to thin strands of white matter tracts rather than the tracts themselves, and therefore require many components for accurate representations, which leads to poorly constrained inverse problems. We propose a novel tract-based model of white matter, the 'Fourier tract', which is able to represent rich tract shapes with a relatively low number of parameters, and explicitly decouples the spatial extent of the modelled tract from its 'Apparent Connection Strength (ACS)'. The Fourier tract model is placed within a novel Bayesian framework, which relates the tract parameters directly to the observed signal, enabling a wide range of acquisition schemes to be used. The posterior distribution of the Bayesian framework is characterised via Markov-chain Monte-Carlo s ling to infer probable values of the ACS and spatial extent of the imaged white matter tracts, providing measures that can be directly applied to many research and clinical studies. The robustness of the proposed tractography algorithm is demonstrated on simulated basic tract configurations, such as curving, twisting, crossing and kissing tracts, and sections of more complex numerical phantoms. As an illustration of the approach in vivo, fibre tracking is performed on a central section of the brain in three subjects from 60 direction HARDI datasets.

Preservation of Vision by the Pulvinar following Early-Life Primary Visual Cortex Lesions

Publisher: Elsevier BV

Date: 02-2015

DOI: 10.1016/J.CUB.2014.12.028

Abstract: Conscious vision is believed to depend upon an intact primary visual cortex (V1), although injury in early life is often accompanied by the preservation of visual capacity, unlike in adulthood. The middle temporal area (MT) receives input from the retinorecipient koniocellular layers of the lateral geniculate nucleus (LGN) and the more recently described medial sub ision of the inferior pulvinar (PIm) of the thalamus, pathways that potentially contribute to preservation of vision after early damage to V1. We examined the potential of these pathways to the long-term preservation of vision after permanent lesions of primate V1 in early and adult life by using a combination of neural tracing and diffusion MRI. We show that early-life V1 lesions lead to less pruning of the retina-pulvinar-MT pathway than is observed in control or adult lesion animals. These findings suggest that sustained visual input through the pulvinar to MT following a lesion of V1 in early life has the capacity to afford improved visual outcomes.

Continuous monitoring of plant sodium transport dynamics using clinical PET

Publisher: Research Square Platform LLC

Date: 05-05-2020

DOI: 10.21203/RS.3.RS-25187/V1

Abstract: Background The absorption, translocation, accumulation and excretion of substances are fundamental processes in all organisms including plants, and have been successfully studied using radiotracers labelled with and since 1939. Sodium is one of the most damaging ions to the growth and productivity of crops. Due to the significance of understanding sodium transport in plants, a significant number of studies have been carried out to examine sodium influx, compartmentation, and efflux using - or 24 Na-labeled salts. Notably, however, most of these studies employed destructive methods, which has limited our understanding of sodium flux and distribution characteristics in real time, in live plants.Positron emission tomography (PET) has been used successfully in medical research and diagnosis for decades. Due to its ability to visualise and assess physiological and metabolic function, PET imaging has also begun to be employed in plant research. Here, we report the use of a clinical PET scanner with a tracer to examine -influx dynamics in barley plants ( Hordeum vulgare L. spp. vulgare – cultivar Bass) under variable nutrient levels, alterations in the day/night light cycle, and the presence of sodium channel inhibitors. Results 3D dynamic PET images of whole plants show readily visible translocation from roots to shoots in each examined plant, with rates influenced by both nutrient status and channel inhibition. PET images show that plants cultivated in low-nutrient media transport more than plants cultivated in high-nutrient media, and that uptake is suppressed in the presence of a cation-channel inhibitor. A distinct diurnal pattern of influx was discernible in curves displaying rates of change of relative radioactivity. Plants were found to absorb significantly more during the light period, and anticipate the change in the light/dark cycle by adjusting the sodium influx rate downward in the dark period, an effect not previously described experimentally. Conclusions We demonstrate the utility of clinical PET/CT scanners for real-time monitoring of the temporal dynamics of sodium transport in plants. The effects of nutrient deprivation and of ion channel inhibition on sodium influx into barley plants are shown in two proof-of-concept experiments, along with the first-ever 3D-imaging of the light and dark sodium uptake cycles in plants. This method carries significant potential for plant biology research and, in particular, in the context of genetic and treatment effects on sodium acquisition and toxicity in plants. * The authors contributed equally

Continuous monitoring of plant sodium transport dynamics using clinical PET

Publisher: Research Square Platform LLC

Date: 07-01-2021

DOI: 10.21203/RS.3.RS-25187/V3

Abstract: Background The absorption, translocation, accumulation and excretion of substances are fundamental processes in all organisms including plants, and have been successfully studied using radiotracers labelled with 11 C, 13 N, 14 C and 22 Na since 1939. Sodium is one of the most damaging ions to the growth and productivity of crops. Due to the significance of understanding sodium transport in plants, a significant number of studies have been carried out to examine sodium influx, compartmentation, and efflux using 22 Na- or 24 Na-labeled salts. Notably, however, most of these studies employed destructive methods, which has limited our understanding of sodium flux and distribution characteristics in real time, in live plants.Positron emission tomography (PET) has been used successfully in medical research and diagnosis for decades. Due to its ability to visualise and assess physiological and metabolic function, PET imaging has also begun to be employed in plant research. Here, we report the use of a clinical PET scanner with a 22 Na tracer to examine 22 Na-influx dynamics in barley plants ( Hordeum vulgare L. spp. vulgare – cultivar Bass) under variable nutrient levels, alterations in the day/night light cycle, and the presence of sodium channel inhibitors. Results 3D dynamic PET images of whole plants show readily visible 22 Na translocation from roots to shoots in each examined plant, with rates influenced by both nutrient status and channel inhibition. PET images show that plants cultivated in low-nutrient media transport more 22 Na than plants cultivated in high-nutrient media, and that 22 Na uptake is suppressed in the presence of a cation-channel inhibitor. A distinct diurnal pattern of 22 Na influx was discernible in curves displaying rates of change of relative radioactivity. Plants were found to absorb more 22 Na during the light period, and anticipate the change in the light/dark cycle by adjusting the sodium influx rate downward in the dark period, an effect not previously described experimentally. Conclusions We demonstrate the utility of clinical PET/CT scanners for real-time monitoring of the temporal dynamics of sodium transport in plants. The effects of nutrient deprivation and of ion channel inhibition on sodium influx into barley plants are shown in two proof-of-concept experiments, along with the first-ever 3D-imaging of the light and dark sodium uptake cycles in plants. This method carries significant potential for plant biology research and, in particular, in the context of genetic and treatment effects on sodium acquisition and toxicity in plants.

Optic nerve diffusion changes and atrophy jointly predict visual dysfunction after optic neuritis

Publisher: Elsevier BV

Date: 04-2009

DOI: 10.1016/J.NEUROIMAGE.2008.12.047

Abstract: Recently, there has been strong interest in the development of imaging techniques to quantify axonal and myelin pathology in patients with multiple sclerosis (MS). Optic neuritis, a condition characterised by inflammatory demyelination of the optic nerve, is one of the commonest sites of MS relapse, and exhibits similar pathological alterations to MS lesions elsewhere in the central nervous system (CNS). Unlike other regions of the CNS, however, the function of the optic nerve can be accurately assessed using clinical measures, as well as electrophysiological techniques such as visual evoked potential recordings. Therefore, optic neuritis is useful for investigating the relationship between abnormalities in optic nerve structure, assessed using magnetic resonance imaging (MRI), and visual dysfunction, assessed clinically and electrophysiologically. The aims of the present study were to assess optic nerve structural abnormalities in patients with a history of unilateral optic neuritis using MRI, and then to identify correlations between abnormalities in optic nerve MRI and visual dysfunction. Ten controls and sixteen patients underwent high resolution optic nerve diffusion tensor imaging (DTI), T2- and T1-weighted MRI. In addition, Snellen visual acuity and the latency and litude of multifocal visual evoked potentials (mfVEP) were tested in all patients. Diffusion and volumetric MRI indices were correlated to mfVEP functional indices. Significant abnormalities were detected in MRI and mfVEP measures in patients' affected nerves compared to unaffected optic nerves or optic nerves from healthy controls. Reduced mfVEP litude in the affected side significantly correlated with both affected optic nerve atrophy (R=0.58, p=0.02) and reduced fractional anisotropy (FA) (R=0.52, p=0.04). However, atrophy and reduced FA did not correlate with each other. To further investigate this disassociation, we used linear regression analysis with optic nerve atrophy and optic nerve FA as independent variables and mfVEP litude as the dependent variable. The resulting linear regression model was highly significant (R=0.819, p=0.001). These results show that, 4 years after unilateral optic neuritis, MRI-based measures of optic nerve structural abnormalities (decreased anisotropy and volume) independently predict visual dysfunction.

Continuous monitoring of plant sodium transport dynamics using clinical PET

Publisher: Research Square Platform LLC

Date: 03-11-2020

DOI: 10.21203/RS.3.RS-25187/V2

Abstract: Background The absorption, translocation, accumulation and excretion of substances are fundamental processes in all organisms including plants, and have been successfully studied using radiotracers labelled with 11 C, 13 N, 14 C and 22 Na since 1939. Sodium is one of the most damaging ions to the growth and productivity of crops. Due to the significance of understanding sodium transport in plants, a significant number of studies have been carried out to examine sodium influx, compartmentation, and efflux using 22 Na- or 24 Na-labeled salts. Notably, however, most of these studies employed destructive methods, which has limited our understanding of sodium flux and distribution characteristics in real time, in live plants.Positron emission tomography (PET) has been used successfully in medical research and diagnosis for decades. Due to its ability to visualise and assess physiological and metabolic function, PET imaging has also begun to be employed in plant research. Here, we report the use of a clinical PET scanner with a 22 Na tracer to examine 22 Na-influx dynamics in barley plants ( Hordeum vulgare L. spp. vulgare – cultivar Bass) under variable nutrient levels, alterations in the day/night light cycle, and the presence of sodium channel inhibitors. Results 3D dynamic PET images of whole plants show readily visible 22 Na translocation from roots to shoots in each examined plant, with rates influenced by both nutrient status and channel inhibition. PET images show that plants cultivated in low-nutrient media transport more 22 Na than plants cultivated in high-nutrient media, and that 22 Na uptake is suppressed in the presence of a cation-channel inhibitor. A distinct diurnal pattern of 22 Na influx was discernible in curves displaying rates of change of relative radioactivity. Plants were found to absorb more 22 Na during the light period, and anticipate the change in the light/dark cycle by adjusting the sodium influx rate downward in the dark period, an effect not previously described experimentally. Conclusions We demonstrate the utility of clinical PET/CT scanners for real-time monitoring of the temporal dynamics of sodium transport in plants. The effects of nutrient deprivation and of ion channel inhibition on sodium influx into barley plants are shown in two proof-of-concept experiments, along with the first-ever 3D-imaging of the light and dark sodium uptake cycles in plants. This method carries significant potential for plant biology research and, in particular, in the context of genetic and treatment effects on sodium acquisition and toxicity in plants.

An optimised framework for reconstructing and processing MR phase images

Publisher: Elsevier BV

Date: 2010

DOI: 10.1016/J.NEUROIMAGE.2009.09.071

Abstract: Phase contrast imaging holds great potential for in vivo biodistribution studies of paramagnetic molecules and materials. However, in vivo quantification of iron storage and other paramagnetic materials requires improvements in reconstruction and processing of MR complex images. To achieve this, we have developed a framework including (i) an optimal coil sensitivity smoothing filter for phase imaging determined at the maximal signal to noise ratio, (ii) a phase optimised and a complex image optimised reconstruction approach, and (iii) a magnitude and phase correlation test criterion to determine the low pass filter parameter for background phase removal. The method has been evaluated using 3T and 7T MRI data containing cortical regions, the basal ganglia including the caudate, and the midbrain including the substantia nigra. The optimised reconstruction improves phase image contrast and noise suppression compared with conventional reconstruction approaches, and the correlation test criterion provides an objective method for separation of the local phase signal from the background phase measurements. Phase values of several brain regions of interest have been calculated, including gray matter (-1.23 Hz at 7T and -0.55 Hz at 3T), caudate (-3.8 Hz at 7T), and the substantia nigra (-6.2 Hz at 7T).

Nonlinear estimation of the BOLD signal

Publisher: Elsevier BV

Date: 04-2008

DOI: 10.1016/J.NEUROIMAGE.2007.11.024

Abstract: Signal variations in functional Magnetic Resonance Imaging experiments essentially reflect the vascular system response to increased demand for oxygen caused by neuronal activity, termed the blood oxygenation level dependent (BOLD) effect. The most comprehensive model to date of the BOLD signal is formulated as a mixed continuous-discrete-time system of nonlinear stochastic differential equations. Previous approaches to the analysis of this system have been based on linearised approximations of the dynamics, which are limited in their ability to capture the inherent nonlinearities in the physiological system. In this paper we present a nonlinear filtering method for simultaneous estimation of the hidden physiological states and the system parameters, based on an iterative coordinate descent framework. State estimates of the cerebral blood flow, cerebral blood volume and deoxyhaemoglobin content are determined using a particle filter, demonstrated via simulation to be accurate, robust and efficient in comparison to linearisation-based techniques. The adaptive state and parameter estimation algorithm generates physiologically reasonable parameter estimates for experimental fMRI data. It is anticipated that signal processing techniques for modelling and estimation will become increasingly important in fMRI analyses as limitations of linear and linearised modelling are reached.

Venous vessel boundary delineation at high field using sigmoid-SWI

Publisher: IEEE

Date: 08-2011

DOI: 10.1109/IEMBS.2011.6090779

Biomechanisms for modelling cerebral cortical folding

Publisher: Elsevier BV

Date: 12-2009

DOI: 10.1016/J.MEDIA.2008.12.005

Abstract: Understanding the biomechanical mechanisms by which the cerebral cortex folds is a fundamental problem in neuroscience. Current mathematical models of cortical folding do not include three dimensional geometry or measurement of cortical growth in developing brains extracted from experimental data. We present two biomechanical models of cortical folding which integrate 3D geometry and information taken from MRI scans of fetal sheep brains at a number of key developmental stages. The first model utilises diffusion tensor imaging (DTI) measurements of white matter fibre orientation in the fetal sheep brains as a cue to the tension forces that may regulate folding. In the second model, tangential cortical growth is modelled by osmotic expansion of the tissue and regulated by inhomogeneous white matter rigidity as a biomechanism of cortical folding. This is based on quantitative analysis of cortical growth and inhomogeneous white matter anisotropy measured from the MRI data. We demonstrate that structural and diffusion tensor MRI can be combined with finite element modelling and an explicit growth mechanism of the cortex to create biologically meaningful models of the cortical folding process common to higher order mammals.

Characterization of the corpus callosum in very preterm and full-term infants utilizing MRI

Publisher: Elsevier BV

Date: 03-2011

DOI: 10.1016/J.NEUROIMAGE.2010.12.025

Filtering induces correlation in fMRI resting state data

Publisher: Elsevier BV

Date: 2013

DOI: 10.1016/J.NEUROIMAGE.2012.08.022

Abstract: Correlation-based functional MRI connectivity methods typically impose a temporal s le independence assumption on the data. However, the conventional use of temporal filtering to address the high noise content of fMRI data may introduce s le dependence. Violation of the independence assumption has ramifications for the distribution of s le correlation which, if unaccounted for, may invalidate connectivity results. To enable the use of temporal filtering for noise suppression while maintaining the integrity of connectivity results, we derive the distribution of s le correlation between filtered timeseries as a function of the filter frequency response. Corrected distributions are also derived for statistical inference tests of s le correlation between filtered timeseries, including Fisher's z-transformation and the Student's t-test. Crucially, the proposed corrections are valid for any unknown true correlation and arbitrary filter specifications. Empirical simulations demonstrate the potential for temporal filtering to artificially induce connectivity by introducing s le dependence, and verify the utility of the proposed corrections in mitigating this effect. The importance of our corrections is exemplified in a resting state fMRI connectivity analysis: seed-voxel correlation maps generated from filtered data using uncorrected test variates yield an unfeasible number of connections to the left primary motor cortex, suggesting artificially induced connectivity, while maps acquired from filtered data using corrected test variates exhibit bilateral connectivity in the primary motor cortex, in conformance with expected results as seen in the literature.

Impact of PET reconstruction on Aβ-amyloid quantitation in cross-sectional and longitudinal analyses

Publisher: Cold Spring Harbor Laboratory

Date: 03-07-2023

DOI: 10.1101/2023.07.03.23292155

Abstract: Amyloid beta (Aβ) accumulation in Alzheimer’s disease (AD) is typically measured using standardized uptake value ratio (SUVR) and the Centiloid scale (CL). The low spatial resolution of PET images is known to degrade quantitative metrics due to the partial volume effect (PVE). This paper examines the impact of spatial resolution, as determined by the reconstruction configuration, on the Aβ-PET quantitation in both cross-sectional and longitudinal data. Cross-sectional Study -89 subjects with [ 18 F]-florbetapir scans (44 Aβ-, 45 Aβ+) were reconstructed using 69 reconstruction configurations. For each reconstruction, Aβ SUVR was calculated and the spatial resolution was calculated as full-width-at-half-maximum (FWHM) using the barrel phantom method (Lodge et al , 2018). The change of SUVR and the effect size of the difference in SUVR between Aβ- and Aβ+ groups with FWHM were examined. Longitudinal study -79 subjects (46 Aβ-, 33 Aβ+) with three [ 18 F]-flutemetamol scans were analysed. All scans were reconstructed using low-, medium- and high-resolution reconstruction configurations and Aβ CLs were calculated. Since linear Aβ accumulation was assumed over a 10-year interval, for each reconstruction configuration, Aβ accumulation rate differences (ARD) between the second and first periods were calculated for all the subjects and compared. Zero ARD was used as a consistency metric. The number of Aβ-accumulators was also used to compare reconstruction configurations. Cross-sectional- SUVRs in both Aβ- and Aβ+ groups were impacted by the FWHM of the reconstruction method Aβ- SUVRs increased for FWHM ≥ 4.5 mm, while Aβ+ SUVRs decreased across the FWHM range. High-resolution reconstructions provided the best statistical separation between groups. Longitudinal study -In the Aβ-group, the median ARD of low-resolution reconstructed data was greater than zero whereas the ARDs of higher-resolution reconstructions were not significantly different to zero, indicating less consistent rates in the low-than the higher-resolution data. Higher-resolution reconstructions identified 10 additional Aβ-accumulators in the Aβ-group, resulting in a 22% increased group size compared to the low-resolution reconstructions. Higher-resolution reconstructions reduced the average CL values of the negative group by 12 points. High-resolution PET reconstructions, inherently less impacted by PVE, may improve Aβ-PET quantitation in both cross-sectional and longitudinal data. In the cross-sectional analysis, separation of Aβ groups’ SUVRs increased with spatial resolution. Longitudinal analysis showed better Aβ accumulation consistency in higher-resolution compared to low-resolution reconstructions. The identification of more Aβ-accumulators from the higher-resolution reconstruction may be helpful in early-stage AD therapies.

Rabi resonance in spin systems: Theory and experiment

Publisher: Elsevier BV

Date: 05-2014

DOI: 10.1016/J.JMR.2014.02.014

Abstract: The response of a magnetic resonance spin system is predicted and experimentally verified for the particular case of a continuous wave litude modulated radiofrequency excitation. The experimental results demonstrate phenomena not previously observed in magnetic resonance systems, including a secondary resonance condition when the litude of the excitation equals the modulation frequency. This secondary resonance produces a relatively large steady state magnetisation with Fourier components at harmonics of the modulation frequency. Experiments are in excellent agreement with the theoretical prediction derived from the Bloch equations, which provides a sound theoretical framework for future developments in NMR spectroscopy and imaging.

The power of spectral density analysis for mapping endogenous BOLD signal fluctuations

Publisher: Wiley

Date: 02-05-2008

DOI: 10.1002/HBM.20601

Granulocyte-macrophage colony-stimulating factor is neuroprotective in experimental traumatic brain injury

Publisher: Mary Ann Liebert Inc

Date: 15-05-2014

DOI: 10.1089/NEU.2013.3106

QSMART: Quantitative susceptibility mapping artifact reduction technique

Publisher: Elsevier BV

Date: 05-2021

DOI: 10.1016/J.NEUROIMAGE.2020.117701

IIR GRAPPA for parallel MR image reconstruction

Publisher: Wiley

Date: 26-10-2010

DOI: 10.1002/MRM.22197

Abstract: Accelerated parallel MRI has advantage in imaging speed, and its image quality has been improved continuously in recent years. This paper introduces a two-dimensional infinite impulse response model of inverse filter to replace the finite impulse response model currently used in generalized autocalibrating partially parallel acquisitions class image reconstruction methods. The infinite impulse response model better characterizes the correlation of k-space data points and better approximates the perfect inversion of parallel imaging process, resulting in a novel generalized image reconstruction method for accelerated parallel MRI. This k-space-based reconstruction method includes the conventional generalized autocalibrating partially parallel acquisitions class methods as special cases and has a new infinite impulse response data estimation mechanism for effective improvement of image quality. The experiments on in vivo MRI data show that the proposed method significantly reduces reconstruction errors compared with the conventional two-dimensional generalized autocalibrating partially parallel acquisitions method, particularly at the high acceleration rates.

What can we gain from subpopulation universal pulses? A simulation‐based study

Publisher: Wiley

Date: 17-10-2023

DOI: 10.1002/MRM.29884

The equivalence of linear Gaussian connectivity techniques

Publisher: Wiley

Date: 19-05-2013

DOI: 10.1002/HBM.22043

Anti-lysophosphatidic acid antibodies improve traumatic brain injury outcomes

Publisher: Springer Science and Business Media LLC

Date: 2014

DOI: 10.1186/1742-2094-11-37

A software tool to generate simulated white matter structures for the assessment of fibre-tracking algorithms

Publisher: Elsevier BV

Date: 10-2009

DOI: 10.1016/J.NEUROIMAGE.2009.03.077

Abstract: The assessment of Diffusion-Weighted MRI (DW-MRI) fibre-tracking algorithms has been limited by the lack of an appropriate 'gold standard'. Practical limitations of alternative methods and physical models have meant that numerical simulations have become the method of choice in practice. However, previous numerical phantoms have consisted of separate fibres embedded in homogeneous backgrounds, which do not capture the true nature of white matter. In this paper we describe a method that is able to randomly generate numerical structures consisting of densely packed bundles of fibres, which are much more representative of human white matter, and simulate the DW-MR images that would arise from them under many imaging conditions. User-defined parameters may be adjusted to produce structures with a range of complexities that spans the levels we would expect to find in vivo. These structures are shown to contain many different features that occur in human white matter and which could confound fibre-tracking algorithms, such as tract kissing and crossing. Furthermore, combinations of such features can be s led by the random generation of many different structures with consistent levels of complexity. The proposed software provides means for quantitative assessment via direct comparison between tracking results and the exact location of the generated fibres. This should greatly improve our understanding of algorithm performance and therefore prove an important tool for fibre tracking development.

Discovery Projects - Grant ID: DP170104080

Start Date: 2017

End Date: 12-2021

Amount: $386,000.00

Funder: Australian Research Council

Linkage - International - Grant ID: LX0882711

Start Date: 2008

End Date: 12-2011

Amount: $34,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP0985143

Start Date: 2009

End Date: 12-2013

Amount: $255,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP110103292

Start Date: 2011

End Date: 12-2015

Amount: $474,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP230101628

Start Date: 10-2023

End Date: 10-2026

Amount: $512,607.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE230100150

Start Date: 2023

End Date: 12-2023

Amount: $930,213.00

Funder: Australian Research Council