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Neuroimaging of animal models of brain disease

Mark F Lythgoe, Nicola R Sibson, Neil G Harris
2003 British Medical Bulletin  
J Cereb Blood Flow Metab 1998; 18: 911-20 33 Lythgoe MF, Thomas DL, Calamante F et al.  ...  J Cereb Blood Flow Metab 1995; 15: 578-86Imaging neuroscience: clinical frontiers for diagnosis and management 29 Calamante F, Lythgoe MF, Pell GS et al.  ... 
doi:10.1093/bmb/65.1.235 pmid:12697629 fatcat:qbeykmes2jhs5jqa7siffzynza

Deep learning diffusion fingerprinting to detect brain tumour response to chemotherapy [article]

Thomas A. Roberts, Ben Hipwell, Giulia Agliardi, Angela d'Esposito, Valerie Taylor, Mark F. Lythgoe, Simon Walker-Samuel
2017 bioRxiv   pre-print
Artificial neural networks are being widely implemented for a range of different biomedical imaging applications. Convolutional neural networks are by far the most popular type of deep learning architecture, but often require very large datasets for robust training and evaluation. We introduce deep learning diffusion fingerprinting (DLDF), which we have used to classify diffusion-weighted magnetic resonance imaging voxels in a mouse model of glioblastoma (GL261 cell line), both prior to and in
more » ... esponse to Temozolomide (TMZ) chemotherapy. We show that, even with limited training, DLDF can automatically segment brain tumours from normal brain, can automatically distinguish between young and older (after 9 days of growth) tumours and that DLDF can detect whether or not a tumour has been treated with chemotherapy. Our results also suggest that DLDF can detect localised changes in the underlying tumour microstructure, which are not evident using conventional measurements of the apparent diffusion coefficient (ADC). Tissue category maps generated by DLDF showed regions containing a mixture of normal brain and tumour cells, and in some cases evidence of tumour invasion across the corpus callosum, which were broadly consistent with histology. In conclusion, DLDF shows the potential for applying deep learning on a pixel-wise level, which reduces the need for vast training datasets and could easily be applied to other multi-dimensional imaging acquisitions.
doi:10.1101/193730 fatcat:7kqxvp7twjeglo3q2gh3adwmri

Acupuncture needling sensation: The neural correlates of deqi using fMRI

Aziz UR Asghar, Gary Green, Mark F. Lythgoe, George Lewith, Hugh MacPherson
2010 Brain Research  
Z (Gaussianized T/F) statistic within-group images were thresholded using clusters preselected by Z > 4.3 (significant activation) or Z < − 4.3 (significant deactivation) and a corrected cluster significance  ... 
doi:10.1016/j.brainres.2009.12.019 pmid:20025853 fatcat:tlrkwz35onh2lkhidjfyreowwm

Vagal determinants of exercise capacity

Asif Machhada, Stefan Trapp, Nephtali Marina, Robert C.M. Stephens, John Whittle, Mark F. Lythgoe, Sergey Kasparov, Gareth L. Ackland, Alexander V. Gourine
2017 Nature Communications  
F. References: References are appropriate. G. C larity and context: The text is clearly written and the figures nicely present the data.  ...  Figure 1d (right panel) clearly shows a marked increase (albeit slightly smaller than in the control animals) in heart rate during exercise in conditions of DVMN silencing.  ... 
doi:10.1038/ncomms15097 pmid:28516907 pmcid:PMC5454375 fatcat:ntpdcuywv5cjxfgdknwtptzdqe

Quantification of light attenuation in optically cleared mouse brains

Angela d'Esposito, Daniil Nikitichev, Adrien Desjardins, Simon Walker-Samuel, Mark F. Lythgoe
2015 Journal of Biomedical Optics  
Optical clearing, in combination with recently developed optical imaging techniques, enables visualization and acquisition of high-resolution, three-dimensional images of biological structures deep within the tissue. Many different approaches can be used to reduce light absorption and scattering within the tissue, but there is a paucity of research on the quantification of clearing efficacy. With the use of a custom-made spectroscopy system, we developed a way to quantify the quality of
more » ... in biological tissue and applied it to the mouse brain. Three clearing techniques were compared: BABB (1:2 mixture of benzyl alcohol and benzyl benzoate, also known as Murray's clear), pBABB (peroxide BABB, a modification of BABB which includes the use of hydrogen peroxide), and passive CLARITY. We found that BABB and pBABB produced the highest degree of optical clearing. Furthermore, the approach allows regional measurement of light attenuation to be performed, and our results show that light is most attenuated in regions with high lipid content. We provide a way to choose between the multiple clearing protocols available, and it could prove useful for evaluating images that are acquired with cleared tissues.
doi:10.1117/1.jbo.20.8.080503 pmid:26277988 pmcid:PMC4568291 fatcat:4pnpgnslpbf4bkkvgsp52zmnru

Origins of the vagal drive controlling left ventricular contractility

Asif Machhada, Nephtali Marina, Alla Korsak, Daniel J. Stuckey, Mark F. Lythgoe, Alexander V. Gourine
2016 Journal of Physiology  
Sites of microinjections were marked by fluorescent beads and were confirmed to lie within the targeted DVMN regions (Fig. 4B) .  ...  At resting heart rate conditions (prior to β-adrenoceptor blockade and spinal cord transection) microinjections of glutamate into the left caudal DVMN induced marked changes in heart rate and ABP, indicative  ... 
doi:10.1113/jp270984 pmid:26940639 pmcid:PMC4945717 fatcat:njdqf26nl5gexp5mndvhnwkyri

CO2 signalling mediates neurovascular coupling in the cerebral cortex [article]

Patrick S Hosford, Jack A Wells, Ivan Ruminot, Isabel N Christie, Shefeeq M Theparambil, Anna Hadjihambi, L. Felipe Barros, Mark F Lythgoe, Alexander V Gourine
2021 bioRxiv   pre-print
The BOLD response was reduced by 83% (0.33±0.2%, p=0.013) in conditions of 10% inspired CO2 (Figure 1c ,f).  ...  Yet, CO2 given in the inspired air still effectively blocked the neurovascular response in conditions of systemic acetazolamide action (Figure 1c ,e,f).  ... 
doi:10.1101/2020.12.31.424942 fatcat:7ha5jk5asbfibklaxe7qtsvx54

Chemically Treated 3D Printed Polymer Scaffolds for Biomineral Formation

Richard J. Jackson, P. Stephen Patrick, Kristopher Page, Michael J. Powell, Mark F. Lythgoe, Mark A. Miodownik, Ivan P. Parkin, Claire J. Carmalt, Tammy L. Kalber, Joseph C. Bear
2018 ACS Omega  
Figure 3 . 3 SLS-printed substrates: (a,b) spike arrays, (c) 96-well plate chamfered insert, (d) 2 mm thick plate, (e,f) human ear bones (ossicles, joined, 3× scale), and (g,h) hollow cube.  ...  nylon-12 mesh showing the fractured macroporous structure and 3D printed nylon-12 framework treated with (b) a TiO 2 sol, (c) titanium(IV) butoxide−TEOS mix, (d) titanium(IV) butoxide, (e) TEOS, and (f)  ... 
doi:10.1021/acsomega.8b00219 pmid:29732454 pmcid:PMC5928486 fatcat:zwnk7jsa5jgbzkdcn57wgcuynq

High-Fidelity Meshes from Tissue Samples for Diffusion MRI Simulations [chapter]

Eleftheria Panagiotaki, Matt G. Hall, Hui Zhang, Bernard Siow, Mark F. Lythgoe, Daniel C. Alexander
2010 Lecture Notes in Computer Science  
We pick the packing density so that the intra-capillary volume fraction is also f = 0.8 .  ...  To construct the extruded mesh we choose an image from the stack we used for the three-dimensional mesh model with f = 0.8 which is consistent with the three-dimensional model, replicate it to have the  ... 
doi:10.1007/978-3-642-15745-5_50 fatcat:chy76hth4fbu5pqxawwiu67aca

Vascular assessment of liver disease—towards a new frontier in MRI

Manil D Chouhan, Mark F Lythgoe, Rajeshwar P Mookerjee, Stuart A Taylor
2016 British Journal of Radiology  
Contrast agent concentration maps for a sample dataset are shown at (a) baseline, (b) 23, (c) 70, (d) 120, (e) 225 and (f) 302 s.  ...  Note the predominantly arterial phase enhancement (b), portal venous phase enhancement (c) and progressive parenchymal washout through to (f).  ... 
doi:10.1259/bjr.20150675 pmid:27115318 pmcid:PMC5124867 fatcat:55w4tmhvnbakvf7qjnav4ya5ia

Volumetric Spatial Correlations of Neurovascular Coupling Studied using Single Pulse Opto-fMRI

Isabel N. Christie, Jack A. Wells, Sergey Kasparov, Alexander V. Gourine, Mark F. Lythgoe
2017 Scientific Reports  
(f)-the individual subject data are shown inSupplementary Figure 1).  ...  With the increasing light intensity both the magnitude (Fig. 1e ,g) and spatial extent (Fig. 1d ,f) of the recorded BOLD signal increased.  ... 
doi:10.1038/srep41583 pmid:28176823 pmcid:PMC5296864 fatcat:e6myjkh6hjggdb7z6kwhs2yxxu

Magnetic Tagging Increases Delivery of Circulating Progenitors in Vascular Injury

Panagiotis G. Kyrtatos, Pauliina Lehtolainen, Manfred Junemann-Ramirez, Ana Garcia-Prieto, Anthony N. Price, John F. Martin, David G. Gadian, Quentin A. Pankhurst, Mark F. Lythgoe
2009 JACC: Cardiovascular Interventions  
Using in vitro MRI, cells were visible on T2*weighted images at dilutions as low as 25 cells/mm 2 and caused a marked reduction in T2* values from 8 cells/mm 2 (Fig. 2D) .  ...  These particles lead to a marked decrease in the magnetic resonance imaging (MRI) parameter T2* and the possibility of visualizing their localization noninvasively on T2*-weighted MRI (7) (8) (9) .  ... 
doi:10.1016/j.jcin.2009.05.014 pmid:19695550 fatcat:7jai5egzprczbciz6rvrr3fcpm

178 Application of cardiac mri to quantitatively assess myocardial damage in isoproterenol-induced heart failure

Xiao Xiao Han, Georgina Ellison, Mark F Lythgoe, Daniel J Stuckey
2017 Heart  
doi:10.1136/heartjnl-2017-311726.176 fatcat:asoieoeberb3vawtbw4shbfw6m

Investigating low-velocity fluid flow in tumours using convection-MRI [article]

Simon Walker-Samuel, Thomas A Roberts, Rajiv Ramasawmy, Jake Burrell, S Peter Johnson, Bernard Siow, Simon Richardson, Miguel Goncalves, Douglas Pendse, Simon P. Robinson, R, Barbara Pedley, Mark F. Lythgoe
2017 bioRxiv   pre-print
The total MR signal S was then given by ic ic ees ees v v S f S f S f S    [8] with 1    ic ees v f f f and Sic = 1. 1000 Monte Carlo iterations were performed, within each of which a different distribution  ...  Blood flow, F, in each vessel was calculated according to the Hagen-Poiseuille equation:   8 4 d P F   [3] from which blood velocity, vv, was given by vv = F / d 2 , where d is the vessel diameter.  ... 
doi:10.1101/200279 fatcat:42clfkwlkvfkrjvdkcocddezli

fMRI mapping of the visual system in the mouse brain with interleaved snapshot GE-EPI

Arun Niranjan, Isabel N. Christie, Samuel G. Solomon, Jack A. Wells, Mark F. Lythgoe
2016 NeuroImage  
for many future applications given the marked image distortion previously reported (Adamczak et al., 2010) ).  ...  We hypothesised positive BOLD responses in all three regions for all f. In addition, we expected positive trends in BOLD response magnitude with f in the LGd and SCs, and a negative trend in VISp.  ... 
doi:10.1016/j.neuroimage.2016.06.015 pmid:27296012 pmcid:PMC4988789 fatcat:khlxrm5ixzhezobb4b3khnl4cu
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