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• Journal article
  Bangerter NK, Taylor MD, Tarbox GJ, Palmer AJ, Park DJet al., 2016,

  Quantitative techniques for musculoskeletal MRI at 7 Tesla

  , Quantitative Imaging in Medicine and Surgery, Vol: 6, Pages: 715-730, ISSN: 2223-4292
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• Journal article
  Bangerter NK, Tarbox GJ, Taylor MD, Kaggie JDet al., 2016,

  Quantitative sodium magnetic resonance imaging of cartilage, muscle, and tendon

  , Quantitative Imaging in Medicine and Surgery, Vol: 6, Pages: 699-714, ISSN: 2223-4292
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• Journal article
  Serbanovic-Canic J, de Luca A, Warboys C, Ferreira PF, Luong LA, Hsiao S, Gauci I, Mahmoud M, Feng S, Souilhol C, Bowden N, Ashton JP, Walczak H, Firmin D, Krams R, Mason JC, Haskard DO, Sherwin S, Ridger V, Chico TJ, Evans PCet al., 2016,

  Zebrafish model for functional screening of flow-responsive genes

  , Arteriosclerosis Thrombosis and Vascular Biology, Vol: 36, ISSN: 1524-4636

  OBJECTIVE: Atherosclerosis is initiated at branches and bends of arteries exposed to disturbed blood flow that generates low shear stress. This mechanical environment promotes lesions by inducing endothelial cell (EC) apoptosis and dysfunction via mechanisms that are incompletely understood. Although transcriptome-based studies have identified multiple shear-responsive genes, most of them have an unknown function. To address this, we investigated whether zebrafish embryos can be used for functional screening of mechanosensitive genes that regulate EC apoptosis in mammalian arteries. APPROACH AND RESULTS: First, we demonstrated that flow regulates EC apoptosis in developing zebrafish vasculature. Specifically, suppression of blood flow in zebrafish embryos (by targeting cardiac troponin) enhanced that rate of EC apoptosis (≈10%) compared with controls exposed to flow (≈1%). A panel of candidate regulators of apoptosis were identified by transcriptome profiling of ECs from high and low shear stress regions of the porcine aorta. Genes that displayed the greatest differential expression and possessed 1 to 2 zebrafish orthologues were screened for the regulation of apoptosis in zebrafish vasculature exposed to flow or no-flow conditions using a knockdown approach. A phenotypic change was observed in 4 genes; p53-related protein (PERP) and programmed cell death 2-like protein functioned as positive regulators of apoptosis, whereas angiopoietin-like 4 and cadherin 13 were negative regulators. The regulation of perp, cdh13, angptl4, and pdcd2l by shear stress and the effects of perp and cdh13 on EC apoptosis were confirmed by studies of cultured EC exposed to flow. CONCLUSIONS: We conclude that a zebrafish model of flow manipulation coupled to gene knockdown can be used for functional screening of mechanosensitive genes in vascular ECs, thus providing potential therapeutic targets to prevent or treat endothelial injury at atheroprone sites.

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• Journal article
  Newbould R, Muraro P, Bishop C, Waldman Aet al., 2016,

  Analysis of ageing-associated grey matter volume in patients with multiple sclerosis shows excess atrophy in subcortical regions

  , NeuroImage-Clinical, Vol: 13, Pages: 9-15, ISSN: 2213-1582

  Age of onset in multiple sclerosis (MS) exerts an influence on the course of disease. This study examined whether global and regional brain volumes differed between “younger” and “older” onset MS subjects who were matched for short disease duration, mean 1.9 years and burden as measured by the MS Severity Score and relapses.21 younger-onset MS subjects (age 30.4 ± 3.2 years) were compared with 17 older-onset (age 48.7 ± 3.3 years) as well as age-matched controls (n = 31, 31.9 ± 3.5 years and n = 21, 47.3 ± 4.0 years). All subjects underwent 3D volumetric T1 and T2-FLAIR imaging. White matter (WM) and grey matter (GM) lesions were outlined manually. Lesions were filled prior to tissue and structural segmentation to reduce classification errors.Volume loss versus control was predominantly in the subcortical GM, at > 13% loss. Younger and older-onset MS subjects had similar, strong excess loss in the putamen, thalamus, and nucleus accumbens. No excess loss was detected in the amygdala or pallidum. The hippocampus and caudate showed significant excess loss in the younger group (p < 0.001) and a strong trend in the older-onset group.These results provide a potential imaging correlate of published neuropsychological studies that reported the association of younger age at disease onset with impaired cognitive performance, including decreased working memory.

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• Journal article
  Miller KL, Alfaro-Almagro F, Bangerter NK, Thomas DL, Yacoub E, Xu J, Bartsch AJ, Jbabdi S, Sotiropoulos SN, Andersson JL, Griffanti L, Douaud G, Okell TW, Weale P, Dragonu I, Garratt S, Hudson S, Collins R, Jenkinson M, Matthews PM, Smith SMet al., 2016,

  Multimodal population brain imaging in the UK Biobank prospective epidemiological study

  , Nature Neuroscience, Vol: 19, Pages: 1523-1536, ISSN: 1097-6256

  Medical imaging has enormous potential for early disease prediction, but is impeded by the difficulty and expense of acquiring data sets before symptom onset. UK Biobank aims to address this problem directly by acquiring high-quality, consistently acquired imaging data from 100,000 predominantly healthy participants, with health outcomes being tracked over the coming decades. The brain imaging includes structural, diffusion and functional modalities. Along with body and cardiac imaging, genetics, lifestyle measures, biological phenotyping and health records, this imaging is expected to enable discovery of imaging markers of a broad range of diseases at their earliest stages, as well as provide unique insight into disease mechanisms. We describe UK Biobank brain imaging and present results derived from the first 5,000 participants' data release. Although this covers just 5% of the ultimate cohort, it has already yielded a rich range of associations between brain imaging and other measures collected by UK Biobank.

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• Journal article
  Wang H, Adluru G, Chen L, Kholmovski EG, Bangerter NK, DiBella EVRet al., 2016,

  Radial simultaneous multi-slice CAIPI for ungated myocardial perfusion

  , Magnetic Resonance Imaging, Vol: 34, Pages: 1329-1336, ISSN: 0730-725X
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• Journal article
  De Simoni S, Grover PJ, Jenkins PO, Honeyfield L, Quest R, Scott G, Wilson WH, Majewska P, Waldman AD, Patel MC, Sharp DJet al., 2016,

  Disconnection between the default mode network and medial temporal lobes in post-traumatic amnesia

  , Brain, Vol: 139, Pages: 3137-3150, ISSN: 0006-8950

  Post-traumatic amnesia is very common immediately after traumatic brain injury. It is characterised by a confused, agitated state and a pronounced inability to encode new memories and sustain attention. Clinically, post-traumatic amnesia is an important predictor of functional outcome. However, despite its prevalence and functional importance, the pathophysiology of post-traumatic amnesia is not understood. Memory processing relies on limbic structures such as the hippocampus, parahippocampus and parts of the cingulate cortex. These structures are connected within an intrinsic connectivity network, the Default Mode Network. Interactions within the Default Mode Network can be assessed using resting state functional magnetic resonance imaging, which can be acquired in confused patients unable to perform tasks in the scanner. Here we used this approach to test the hypothesis that the mnemonic symptoms of post-traumatic amnesia are caused by functional disconnection within the Default Mode Network. We assessed whether the hippocampus and parahippocampus showed evidence of transient disconnection from cortical brain regions involved in memory processing. 19 traumatic brain injury patients were classified into post-traumatic amnesia and traumatic brain injury control groups, based on their performance on a paired associates learning task. Cognitive function was also assessed with a detailed neuropsychological test battery. Functional interactions between brain regions were investigated using resting-state functional magnetic resonance imaging. Together with impairments in associative memory patients in post-traumatic amnesia demonstrated impairments in information processing speed and spatial working memory. Patients in post-traumatic amnesia showed abnormal functional connectivity between the parahippocampal gyrus and posterior cingulate cortex. The strength of this functional connection correlated with both associative memory and information processing speed and normal

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• Journal article
  Giannakidis A, Melkus G, Yang G, Gullberg GTet al., 2016,

  On the Averaging of Cardiac Diffusion Tensor MRI Data: The Effect of Distance Function Selection

  , Physics in Medicine and Biology, Vol: 61, ISSN: 1361-6560

  Diffusion tensor magnetic resonance imaging (DT-MRI) allows a unique insightinto the microstructure of highly-directional tissues. The selection of the mostproper distance function for the space of diffusion tensors is crucial in enhancingthe clinical application of this imaging modality. Both linear and nonlinearmetrics have been proposed in the literature over the years. The debate on themost appropriate DT-MRI distance function is still ongoing. In this paper, we presenteda framework to compare the Euclidean, affine-invariant Riemannian andlog-Euclidean metrics using actual high-resolution DT-MRI rat heart data. We employedtemporal averaging at the diffusion tensor level of three consecutive andidentically-acquired DT-MRI datasets from each of five rat hearts as a means torectify the background noise-induced loss of myocyte directional regularity. Thisprocedure is applied here for the first time in the context of tensor distance functionselection. When compared with previous studies that used a different concrete applicationto juxtapose the various DT-MRI distance functions, this work is uniquein that it combined the following: (i) Metrics were judged by quantitative –ratherthan qualitative– criteria, (ii) the comparison tools were non-biased, (iii) a longitudinalcomparison operation was used on a same-voxel basis. The statisticalanalyses of the comparison showed that the three DT-MRI distance functions tendto provide equivalent results. Hence, we came to the conclusion that the tensormanifold for cardiac DT-MRI studies is a curved space of almost zero curvature. The signal to noise ratio dependence of the operations was investigated throughsimulations. Finally, the “swelling effect” occurrence following Euclidean averagingwas found to be too unimportant to be worth consideration.

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• Journal article
  Forte E, Inglese M, Infante T, Schiano C, Napoli C, Soricelli A, Salvatore M, Tedeschi Cet al., 2016,

  Anomalous left main coronary artery detected by CT angiography

  , SURGICAL AND RADIOLOGIC ANATOMY, Vol: 38, Pages: 987-990, ISSN: 0930-1038
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  • Citations: 10
• Journal article
  Soltaninejad M, Yang G, Lambrou T, Allinson N, Jones TL, Barrick TR, Howe FA, Ye Xet al., 2016,

  Automated brain tumour detection and segmentation using superpixel-based extremely randomized trees in FLAIR MRI

  , International Journal of Computer Assisted Radiology and Surgery, Vol: 12, Pages: 183-203, ISSN: 1861-6410

  Purpose: We propose a fully automated method for detection and segmentation of the abnormal tissue associated with brain tumour (tumour core and oedema) from Fluid- Attenuated Inversion Recovery (FLAIR) Magnetic Resonance Imaging (MRI). Methods: The method is based on superpixel technique and classification of each superpixel. A number of novel image features including intensity-based, Gabor textons, fractal analysis and curvatures are calculated from each superpixel within the entire brain area in FLAIR MRI to ensure a robust classification. Extremely randomized trees (ERT) classifier is compared with support vector machine (SVM) to classify each superpixel into tumour and non-tumour. Results: The proposed method is evaluated on two datasets: (1) Our own clinical dataset: 19 MRI FLAIR images of patients with gliomas of grade II to IV, and (2) BRATS 2012 dataset: 30 FLAIR images with 10 low-grade and 20 high-grade gliomas. The experimental results demonstrate the high detection and segmentation performance of the proposed method using ERT classifier. For our own cohort, the average detection sensitivity, balanced error rate and the Dice overlap measure for the segmented tumour against the ground truth are 89.48 %, 6 % and 0.91, respectively, while, for the BRATS dataset, the corresponding evaluation results are 88.09 %, 6 % and 0.88, respectively. Conclusions: This provides a close match to expert delineation across all grades of glioma, leading to a faster and more reproducible method of brain tumour detection and delineation to aid patient management.

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