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Mapping axon conduction delays in vivo from microstructural MRI [article]

Mark Drakesmith, Derek K Jones
2018 bioRxiv   pre-print
R 2 RMSE k AIC BIC Rushton model 1.54 × 10 7 0.766 0.766 5.69 1 1.76 12.87 Linear outer diameter model 1.58 × 10 7 0.760 0.760 5.77 1 1.76 12.87 Polynomial expansion (full) 1.23 × 10  ...  resistivity Ω m 0.7 0.14 Peri-axonal resistivity Ω m 0.7 0.14 Myelin conductance mS cm −2 1 0.2 Fast Na+ conductance mS cm −2 30 6 Persistent Na+ conductance mS cm −2 0.05 0.01 Slow K+  ... 
doi:10.1101/503763 fatcat:uodgbj2janfazisoqmpbrvr5oi

Book Review: Algebra teaching around the world. Frederick K. S. Leung, Kyungmee Park, Derek Holton, & David Clarke (Eds.) (2014)

Ian Jones
2015 Educational Studies in Mathematics  
In Algebra Teaching around the World, 23 mathematics education researchers investigated the teaching and learning of algebra in eighth grade classrooms in various countries. The book comprises 13 chapters and an appendix. A key strength of the book is that the data were collected in a range of countries using identical methods, as part of the Learner's Perspective Study (LPS). Culture is included among the various influences on classroom practice and the book explores whether a division between
more » ... Confucian-Heritage and Western cultures provides a useful explanatory distinction. The teachers observed and interviewed were those considered effective within their own countries. In order to investigate teaching, learning, classroom culture, and wider contexts, multiple sources of evidence were collected, including videos and field notes of lessons, interviews with teachers and students, and documentary sources including student work and achievement data. Several chapters provide extensive detail about the local education context, for example by including detailed curricular specifications, and authors offer a detailed connection between the data and conclusions drawn, including substantial transcript excerpts and meticulous interpretation. Recurrent themes, such as within-country differences and the mismatch between stated and enacted curricula, ensure that the book contributes important and thought-provoking insights to the field. In this review I will focus on international differences, within-country differences, theoretical differences, and cultural differences, respectively.
doi:10.1007/s10649-015-9650-y fatcat:7niewkajrreevab7ohsotddpv4

Short Association Fibre Tractography [article]

Dmitri Shastin, Sila Genc, Greg D. Parker, Kristin Koller, Chantal M.W. Tax, John Evans, Khalid Hamandi, William P. Gray, Derek K. Jones, Maxime Chamberland
2021 bioRxiv   pre-print
Derek K. Jones: conceptualization, writing land: conceptualization, writing -original draft, writing -review & editing, visualization, supervision.  ...  K W , B W , C W , and E W L ), the average over all nodes was used.To compare surface seeding with ACT, a two-tailed paired sample t-test was used.  ... 
doi:10.1101/2021.05.07.443084 fatcat:nn2zlw2lwvhvlpqmifcbokg22a

Q-space quantitative diffusion MRI measures using a stretched-exponential representation [article]

Tomasz Pieciak, Maryam Afzali, Fabian Bogusz, Aja-Fernández, Derek K. Jones
2020 arXiv   pre-print
For the proposed methodology we fit the representation using k shells (k = 3, . . . , 8; similarly to the EAP-based methods) while calculate the measures using only one shell, i.e., b = 3000 s/mm 2 or  ...  ) RBF, (d) single-shell (b = 1000 s/mm 2 ), (e) single-shell (b = 3000 s/mm 2 ), (f) singleshell (b = 5000 s/mm 2 ), (g) 3D-SHORE, (h) MAP-MRI, (i) MAPL, (j) stretchedexponential (b = 1000 s/mm 2 ), (k)  ... 
arXiv:2009.07376v1 fatcat:uoth4fq2kzcfvn4pfgtxmph2o4

Perisylvian language networks of the human brain

Marco Catani, Derek K. Jones, Dominic H. ffytche
2004 Annals of Neurology  
Full details of the acquisition sequence are provided in Jones and colleagues. 22 After correction for the image distortions introduced by the application of the diffusion-encoding gradients, the diffusion  ... 
doi:10.1002/ana.20319 pmid:15597383 fatcat:yoqzldtco5dkhj3zcf6l5zhefq

Challenges and limitations of quantifying brain connectivityin vivowith diffusion MRI

Derek K Jones
2010 Imaging in Medicine  
Crick F, Jones E: The backwardness of human neuroanatomy.  ...  In a way, this article foretold the invention of diffusion MRI and tractography. 1 2 3 4 5 6 Indicates Jones DK (Ed.). Diffusion MRI: Theory, Methods, and Applications.  ... 
doi:10.2217/iim.10.21 fatcat:hjfoxhms4rautkiws5hxol634a

Nonivasive quantification of axon radii using diffusion MRI

Jelle Veraart, Daniel Nunes, Umesh Rudrapatna, Els Fieremans, Derek K Jones, Dmitry S Novikov, Noam Shemesh
2020 eLife  
., 1994; Jones, 2010; Beaulieu, 2002; Novikov et al., 2019) .  ...  In this study, we were not able to achieve a reproducible and precise estimate of D 0 and opted to use the longitudinal diffusivity D k a as a proxy for D 0 , with D k a D 0 .  ... 
doi:10.7554/elife.49855 pmid:32048987 pmcid:PMC7015669 fatcat:kq2vbqvsfbbvjadxlad4jvatwy

Imaging Microglia and Astrocytes non-invasively using Diffusion MRI [article]

Raquel Garcia-Hernandez, Alejandro Trouve Carpena, Mark Drakesmith, Kristen Koller, Derek K. Jones, Santiago Canals, Silvia De Santis
2020 bioRxiv   pre-print
K., Saijo, K., Winner, B., Marchetto, M. C., & Gage, F. H. Mechanisms Underlying Inflammation in Neurodegeneration. Cell 140, 918-934 (2010). 4. Yahfoufi, N., Matar, C. & Ismail, N.  ...  K. & Coles, J. P. Inter subject variability and reproducibility of diffusion tensor imaging within and between different imaging sessions. PLoS One 8, e65941 (2013) author/funder.  ... 
doi:10.1101/2020.02.07.938910 fatcat:o3gy7frhgbhrlji24qkbnqptzu

Optimization of graph construction can significantly increase the power of structural brain network studies [article]

Eirini Messaritaki, Stavros I Dimitriadis, Derek K Jones
2019 bioRxiv   pre-print
Structural brain networks derived from diffusion magnetic resonance imaging data have been used extensively to describe the human brain, and graph theory has allowed quantification of their network properties. Schemes used to construct the graphs that represent the structural brain networks differ in the metrics they use as edge weights and the algorithms they use to define the network topologies. In this work, twenty graph construction schemes were considered. The schemes use the number of
more » ... amlines, the fractional anisotropy, the mean diffusivity or other attributes of the tracts to define the edge weights, and either an absolute threshold or a data-driven algorithm to define the graph topology. The test-retest data of the Human Connectome Project were used to compare the reproducibility of the graphs and their various attributes (edges, topologies, graph theoretical metrics) derived through those schemes, for diffusion images acquired with three different diffusion weightings. The impact of the scheme on the statistical power of the study and on the number of participants required to detect a difference between populations or an effect of an intervention was also calculated. The reproducibility of the graphs and their attributes depended heavily on the graph construction scheme. Graph reproducibility was higher for schemes that used thresholding to define the graph topology, while data-driven schemes performed better at topology reproducibility. Additionally, schemes that used thresholding resulted in better reproducibility for local graph theoretical metrics, while data-driven schemes performed better for global metrics. Crucially, the number of participants required to detect a difference between populations or an effect of an intervention could change by a large factor depending on the scheme used, affecting the power of studies to reveal the effects of interest.
doi:10.1101/553743 fatcat:uo3t7z2mejgpphjxdz22ng3ije

Predicting MEG resting-state functional connectivity using microstructural information [article]

Eirini Messaritaki, Sonya Foley, Simona Schiavi, Lorenzo Magazzini, Bethany Routley, Derek K Jones, Krish D Singh
2020 biorxiv/medrxiv   pre-print
Understanding how human brain microstructure influences functional connectivity is an important endeavor. In this work, magnetic resonance imaging data from ninety healthy participants were used to calculate structural connectivity matrices using the streamline count, fractional anisotropy, radial diffusivity and a myelin measure (derived from multicomponent relaxometry) to assign connection strength. Unweighted binarized structural connectivity matrices were also constructed.
more » ... aphy resting-state data from those participants were used to calculate functional connectivity matrices, via correlations of the Hilbert envelopes of beamformer timeseries at four frequency bands: delta (1-4 Hz), theta (3-8 Hz), alpha (8-13 Hz) and beta (13-30 Hz). Non-negative matrix factorization was performed to identify the components of the functional connectivity. Shortest-path-length and search-information analyses of the structural connectomes were used to predict functional connectivity patterns for each participant. The microstructurally-informed algorithms predicted the components of the functional connectivity more accurately than they predicted the total functional connectivity. The shortest-path-length algorithm exhibited the highest prediction accuracy. Of the weights of the structural connectivity matrices, the streamline count and the myelin measure gave the most accurate predictions, while the fractional anisotropy performed poorly. Different structural metrics paint very different pictures of the structural connectome and its relationship to functional connectivity.
doi:10.1101/2020.09.15.298307 fatcat:ze2sahhztbey3plpcyxjikavwm

NMR methods to monitor the enzymatic depolymerization of heparin

John F. K. Limtiaco, Szabolcs Beni, Christopher J. Jones, Derek J. Langeslay, Cynthia K. Larive
2010 Analytical and Bioanalytical Chemistry  
Heparin and the related glycosaminoglycan, heparan sulfate, are polydisperse linear polysaccharides that mediate numerous biological processes due to their interaction with proteins. Because of the structural complexity and heterogeneity of heparin and heparan sulfate, digestion to produce smaller oligosaccharides is commonly performed prior to separation and analysis. Current techniques used to monitor the extent of heparin depolymerization include UV absorption to follow product formation and
more » ... size exclusion or strong anion exchange chromatography to monitor the size distribution of the components in the digest solution. In this study, we used 1 H nuclear magnetic resonance (NMR) survey spectra and NMR diffusion experiments in conjunction with UV absorption measurements to monitor heparin depolymerization using the enzyme heparinase I. Diffusion NMR does not require the physical separation of the components in the reaction mixture and instead can be used to monitor the reaction solution directly in the NMR tube. Using diffusion NMR, the enzymatic reaction can be stopped at the desired time point, maximizing the abundance of larger oligosaccharides for protein-binding studies or completion of the reaction if the goal of the study is exhaustive digestion for characterization of the disaccharide composition. In this study, porcine intestinal mucosa heparin was depolymerized using the enzyme heparinase I. The unsaturated bond formed by enzymatic cleavage serves as a UV chromophore that can be used to monitor the progress of the depolymerization and for the detection and quantification of oligosaccharides in subsequent separations. The double bond also introduces a unique multiplet with peaks at 5. 973, 5.981, 5.990, and 5.998 ppm in the 1 H-NMR spectrum downfield of the anomeric region. This multiplet is produced by the proton of the C-4 double bond of the non-reducing end uronic acid at the cleavage site. Changes in this resonance were used to monitor the progression of the enzymatic digestion and compared to the profile obtained from UV absorbance measurements. In addition, in situ NMR diffusion measurements were explored for their ability to profile the different-sized components generated over the course of the digestion.
doi:10.1007/s00216-010-4132-7 pmid:20814667 pmcid:PMC3015211 fatcat:lefn4xwjyncwngujd2gbqlmkjm

T 1 relaxometry of crossing fibres in the human brain

Silvia De Santis, Yaniv Assaf, Ben Jeurissen, Derek K Jones, Alard Roebroeck
2016 NeuroImage  
A B S T R A C T A comprehensive tract-based characterisation of white matter should include the ability to quantify myelin and axonal attributes irrespective of the complexity of fibre organisation within the voxel. Recently, a new experimental framework that combines inversion recovery and diffusion MRI, called inversion recovery diffusion tensor imaging (IR-DTI), was introduced and applied in an animal study. IR-DTI provides the ability to assign to each unique fibre population within a voxel
more » ... a specific value of the longitudinal relaxation time, T 1 , which is a proxy for myelin content. Here, we apply the IR-DTI approach to the human brain in vivo on 7 healthy subjects for the first time. We demonstrate that the approach is able to measure differential tract properties in crossing fibre areas, reflecting the different myelination of tracts. We also show that tract-specific T 1 has less inter-subject variability compared to conventional T 1 in areas of crossing fibres, suggesting increased specificity to distinct fibre populations. Finally we show in simulations that changes in myelination selectively affecting one fibre bundle in crossing fibre areas can potentially be detected earlier using IR-DTI.
doi:10.1016/j.neuroimage.2016.07.037 pmid:27444568 pmcid:PMC5035137 fatcat:5reh3kn6jreqrjrwyrgmc4vrzm

RESTORE: Robust estimation of tensors by outlier rejection

Lin-Ching Chang, Derek K. Jones, Carlo Pierpaoli
2005 Magnetic Resonance in Medicine  
A recent study by Jones (12) , however, showed that the variability of estimated tensor maps can depend on the number of unique gradient sampling orientations and that at least 30 unique sampling orientations  ... 
doi:10.1002/mrm.20426 pmid:15844157 fatcat:lsbmihcrcrhznjwvg6dccunrkm

Toward more robust and reproducible diffusion kurtosis imaging

Rafael N. Henriques, Sune N. Jespersen, Derek K. Jones, Jelle Veraart
2021 Magnetic Resonance in Medicine  
The similarity between K and K (or K (2) ) is high.  ...  (1) =K −Ψ, (5) Ψ = 2 5 D 2 11 + D 2 22 + D 2 33 + 2D 2 12 + 2D 2 13 + 2D 2 23 D 2 − 6 5 . (6) K (2) =K. (7) K (3) = N K , D, | N (8) = arg min ‖S − exp( − B )‖ 2 + ‖h( ) −K‖ 2 , | 1603 HENRIQUES Et al  ... 
doi:10.1002/mrm.28730 pmid:33829542 fatcat:czovfkde2ngj5b7gbutcr2vh3q

Impact of b-value on estimates of apparent fibre density [article]

Sila Genc, Chantal M.W. Tax, Erika P Raven, Maxime Chamberland, Greg D Parker, Derek K Jones
2020 biorxiv/medrxiv   pre-print
Leftlateralisation of language has been well documented (Catani, Jones, & ffytche, 2005) and related to microstructure (Lebel & Beaulieu, 2009 ).  ...  ., b = 1,000 s/mm 2 ) for diffusion tensor imaging (DTI) analyses (Jones, Horsfield, & Simmons, 1999; Landman et al., 2007) , or moderate-to-high b-values (e.g., b ≥ 3,000 s/mm 2 ) for probabilistic tractography  ... 
doi:10.1101/2020.01.15.905802 fatcat:qrlgrsjfiren3hzpw3xvaghb4i
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