Section on Tissue Biophysics and Biomimetics

Selected Articles

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2013

Özarslan E, Koay CG, Shepherd TM, Komlosh ME, Irfanoglu MO, Pierpaoli C, and Basser PJ. (2013) Mean Apparent Propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure. Neuroimage 78:16-32.
Komlosh ME, Özarslan E, Lizak MJ, Horkayne-Szakaly I, Freidlin RZ, Horkay F, and Basser PJ. Mapping average axon diameters in porcine spinal cord white matter and rat corpus callosum using d-PFG MRI. Neuroimage 78:210–216.
Basser PJ and Assaf Y. 2013. Non-invasive in vivo MRI axon diameter measurement methods. U.S. Patent 8,380,280, filed May 2, 2008, and issued February 19, 2013.
Albaugh M D, Ducharme S, Collins D L, Botteron K N, Althoff R R, Evans A C, Karama S, Hudziak J J, Evidence for a cerebral cortical thickness network anti-correlated with amygdalar volume in healthy youths: Implications for the neural substrates of emotion regulation. NeuroImage 71, 42 (May 1, 2013).
Eliav U, Komlosh ME, Basser PJ, and Navon G. (2013) Collagen Composition and Content-Dependent Contrast in Porcine Annulus Fibrosus Achieved by Using Double Quantum and Magnetization Transfer Filtered UTE MRI. Magn Reson Med. 2013 Feb 14. [Epub ahead of print]
Pajevic, S and Basser, PJ. (2013) An optimum principle predicts the distribution of axon diameters in normal white matter. PLoS ONE 8(1): e54095. Published: January 28, 2013.
E. Özarslan, C. G. Koay, P. J. Basser. (2013) Simple harmonic oscillator based reconstruction and estimation for one-dimensional q-space magnetic resonance (1D-SHORE). Excursions in Harmonic Analysis: The February Fourier Talks at the Norbert Wiener Center, ed. T. D. Andrews, R. Balan, J. J. Benedetto, W. Czaja, and K. A. Okoudjou, New York: Springer Science + Business Media, vol. 2, p. 373–400.
A.V. Avram, E. Özarslan, J.E. Sarlls, P.J. Basser. (2013) In vivo detection of microscopic anisotropy using quadruple pulsed-field gradient (qPFG) diffusion MRI on a clinical scanner. Neuroimage 64: 229–239.

2012

Ducharme S, Hudziak J J, Botteron K N, Albaugh M D, Nguyen T V, Karama S, Evans A C, Decreased regional cortical thickness and thinning rate are associated with inattention symptoms in healthy children. Journal of the American Academy of Child and Adolescent Psychiatry 51, 18 (Jan, 2012).
Waber D P, Forbes P W, Almli C R, Blood E A, Four-year longitudinal performance of a population-based sample of healthy children on a neuropsychological battery: the NIH MRI study of normal brain development. Journal of the International Neuropsychological Society: JINS 18, 179 (Mar, 2012).
Nguyen T V, McCracken J, Ducharme S, Botteron K N, Mahabir M, Johnson W, Israel M, Evans A C, Karama S, Testosterone-Related Cortical Maturation Across Childhood and Adolescence. Cereb Cortex, (May 22, 2012).
Khundrakpam B S, Reid A, Brauer J, Carbonell F, Lewis J, Ameis S, Karama S, Lee J, Chen Z, Das S, Evans A C, Developmental Changes in Organization of Structural Brain Networks. Cereb Cortex, (Jul 10, 2012).
Pasternak, O., Sochen, N., & Basser, P.J. (2012). Metric Selection and Diffusion Tensor Swelling. In D.H. Laidlaw & A. Vilanova (Eds.), New Developments in the Visualization and Processing of Tensor Fields (pp 323-336). Berlin: Springer Berlin Heidelberg.
Chandran PL, Horkay F. (2012) Aggrecan, an Unusual Polyelectrolyte: Review of Solution Behavior and Physiological Implications. Acta Biomaterialia 8(1):3-12.
Lorincz O, Toke ER, Somogyi E, Horkay F, Chandran PJ, Douglas JF, Szebeni J, Lisziewicz J. (2012) Structure and Biological Activity of Pathogen-like Synthetic Nanomedicines. Nanomedicine: Nanotechnology, Biology, and Medicine 8, 497–506.
Chandran PL, Dimitriadis EK, Horkay F. Probing DNA Assembly into Nanoparticles with Short DNA. In Gels and Biomedical Materials, Materials Research Society, Volume 1418, 27-33, Cambridge University Press, 2012.
Silva C, Horkayne-Szakaly I, Chandran PL, Dimitriadis EK, Papanicolas C, Basser PJ, Horkay F. Depth Dependent Osmotic and Swelling Properties of Cartilage. In Gels and Biomedical Materials, Materials Research Society, Volume 1418, 33-39, Cambridge University Press, 2012.
Horkay F. Interactions of Cartilage Extracellular Matrix Macromolecules. J. Polym. Sci., Part B: Polymer Physics, 1-7 (2012), DOI: 10.1002/polb.23191
Horkay F, Narayan R, Langrana N, Weiss R. et al. (eds) Gels and Biomedical Materials, Materials Research Society, Volume 1418, 1-253, Cambridge University Press, 2012.
R.Z. Freidlin, J.W. Kakareka, T.J. Pohida, M.E. Komlosh, P.J. Basser. (2012) A spin echo sequence with a single-sided bipolar diffusion gradient pulse to obtain snapshot diffusion weighted images in moving media. J Mag Res. 221:24–31.
Ferenc Horkay, Peter J. Basser, Anne-Marie Hecht, and Erik Geissler. (2012) Chondroitin Sulfate in Solution: Effects of Mono- and Divalent Salts. Macromolecules 45:2882−2890.
Brain Development Cooperative Group. (2012) Total and Regional Brain Volumes in a Population-Based Normative Sample from 4 to 18 Years: The NIH MRI Study of Normal Brain Development. Cerebral Cortex 22:1-12.
Eliav U, Komlosh M, Basser PJ, and Navon G. (2012) Characterization and mapping of dipolar interactions within macromolecules in tissues using a combination of DQF, MT and UTE MRI. NMR Biomed. 25: 1152–1159. doi: 10.1002/nbm.2784
Chang L-C, Walker L, and Pierpaoli C. (2012) Informed RESTORE: A Method for Robust Estimation of Diffusion Tensor from Low Redundancy Datasets in the Presence of Physiological Noise Artifacts. Magnetic Resonance in Medicine 68:1654–1663.
Walker L, Curry M, Nayak A, Lange N, Pierpaoli C, and the Brain Development Cooperative Group. (2012) A Framework for the Analysis of Phantom Data in Multicenter Diffusion Tensor Imaging Studies. Human Brain Mapping, Mar 28, 2012.
Irfanoglu MO, Walker L, Sarlls J, Marenco S, Pierpaoli C. (2012) Effects of image distortions originating from susceptibility variations and concomitant fields on diffusion MRI tractography results. Neuroimage 61(1):275-88.
Koay CG, Özarslan E, Johnson KM, and Meyerand ME. (2012) Sparse and optimal acquisition design for diffusion MRI and beyond. Med Phys 39:2499–2511.
Özarslan E, Shepherd TM, Koay CG, Blackband SJ, and Basser PJ. (2012) Temporal scaling characteristics of diffusion as a new MRI contrast: Findings in rat hippocampus. NeuroImage 60:1380–1393.
Shemesh N, Özarslan E, Basser PJ, and Cohen Y. (2012) Accurate noninvasive measurement of cell size and compartment shape anisotropy in yeast cells using double-pulsed field gradient MR. NMR Biomed 25:236–246.

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2011

Irfanoglu MO, Walker L, Sammet S, Pierpaoli C, Machiraju R., "Susceptibility distortion correction for echo planar images with non-uniform B-spline grid sampling: a diffusion tensor image study.", Med Image Comput Comput Assist Interv. 2011;14(Pt 2):174-81.
Ducharme S, Hudziak J J, Botteron K N, Ganjavi H, Lepage C, Collins D L, Albaugh M D, Evans A C, Karama S, Right anterior cingulate cortical thickness and bilateral striatal volume correlate with child behavior checklist aggressive behavior scores in healthy children. Biological Psychiatry 70, 283 (Aug 1, 2011).
Ganjavi H, Lewis J D, Bellec P, MacDonald P A, Waber D P, Evans A C, Karama S, Negative associations between corpus callosum midsagittal area and IQ in a representative sample of healthy children and adolescents. PloS One 6, e19698 (2011).
Karama S, Colom R, Johnson W, Deary I J, Haier R, Waber D P, Lepage C, Ganjavi H, Jung R, Evans A C, Cortical thickness correlates of specific cognitive performance accounted for by the general factor of intelligence in healthy children aged 6 to 18. NeuroImage 55, 1443 (Apr 15, 2011).
Basser PJ and Pierpaoli C. (2011) Recollections about our 1996 JMR paper on diffusion anisotropy. J Magn Reson 213:571–572.
Sarlls JE, Pierpaoli C, Talagala SL, and Luh W-M. (2011) Robust Fat Suppression at 3T in High-Resolution Diffusion-Weighted Single-Shot Echo-Planar Imaging of Human Brain. Magnetic Resonance in Medicine 66:1658–1665.
Özarslan E, Komlosh ME, Lizak MJ, Horkay F, and Basser PJ. (2011) Double pulsed field gradient (double-PFG) MR imaging (MRI) as a means to measure the size of plant cells. Magn Reson Chem 49:S79–S84.
Horkay F, Cho SH, Tathireddy P, Rieth L, Solzbacker F, and Magda J. (2011) Thermodynamic analysis of the selectivity enhancement obtained by using smart hydrogels that are zwitterionic when detecting glucose with boronic acid moieties. Sensors and Actuators B 160:1363–1371
Jiang FX, Lin DC, Horkay F, and Langrana NA. (2011) Probing Mechanical Adaptation of Neurite Outgrowth on a Hydrogel Material Using Atomic Force Microscopy. Annals of Biomedical Engineering 39(2):706–713.
Lőrincz O, Tőke ER, Somogyi E, Horkay F, Chandran PL, Douglas JF, Szebeni J, and Lisziewicz J. (2011) Structure and biological activity of pathogen-like synthetic nanomedicines. Nanomedicine: Nanotechnology, Biology, and Medicine, 8(4):497-506.
Horkay F, Basser PJ, Hecht A-M, and Geissler E. (2011) Hierarchical Organization of Cartilage Proteoglycans. Macromol. Symp. 306-307:11–17.
Salvador R, Silva S, Basser PJ, and Miranda PC. (2011) Determining which mechanisms lead to activation in the motor cortex: A modeling study of transcranial magnetic stimulation using realistic stimulus waveforms and sulcal geometry. Clinical Neurophysiology 122:748–758.
Komlosh ME, Özarslan E, Lizak MJ, Horkay F, Schram V, Shemesh N, Cohen Y, and Basser PJ. (2011) Pore diameter mapping using double pulsed-field gradient MRI and its validation using a novel glass capillary array phantom. J Magn Reson 208:128-135.
Özarslan E, Shemesh N, Koay CG, Cohen Y, and Basser PJ. (2011) Nuclear magnetic resonance characterization of general compartment size distributions. New J Phys 13:015010 (1-17).
Fonov V, Evans AC, Botteron K, Almli CR, McKinstry RC, Collins DL, and the Brain Development Cooperative Group. (2011) Unbiased average age-appropriate atlases for pediatric studies. NeuroImage 54(1):313-327.
Walker L, Chang L-C, Koay CG, Sharma N, Cohen L, Verma R, and Pierpaoli C. (2011) Effects of physiological noise in population analysis of diffusion tensor MRI data. NeuroImage 54(2):1168-77.

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2010

Lange N, Froimowitz M P, Bigler E D, Lainhart J E, Associations between IQ, total and regional brain volumes, and demography in a large normative sample of healthy children and adolescents. Developmental Neuropsychology 35, 296 (2010).
P.L. Chandran, E.K. Dimitriadis, P.J. Basser, and F. Horkay. (2010) Probing Aggrecan Interactions by Atomic Force Microscopy. In Journal of Polymer Science B 48(24): 2575-2581. PDF
Basser, PJ, & Özarslan, E. (2010). Anisotropic Diffusion: From the Apparent Diffusion Coefficient to the Apparent Diffusion Tensor. In Derek K. Jones (Ed.), Diffusion MRI: Theory, Methods, and Applications (pp. 79-91). New York, NY: Oxford University Press.
Koay, CG. (2010). Least Squares Approaches to Diffusion Tensor Estimation. In Derek K. Jones (Ed.), Diffusion MRI: Theory, Methods, and Applications (pp. 272-284). New York, NY: Oxford University Press.
Pierpaoli, C. (2010). Artifacts in Diffusion MRI. In Derek K. Jones (Ed.), Diffusion MRI: Theory, Methods, and Applications (pp. 303-318). New York, NY: Oxford University Press.
Basser, PJ. (2010). Invention and Development of Diffusion Tensor MRI (DT-MRI or DTI) at the NIH. In Derek K. Jones (Ed.), Diffusion MRI: Theory, Methods, and Applications (pp. 730-734). New York, NY: Oxford University Press.
Basser PJ, Özarslan E. (2010) Characterizing Compartment Distributions from Diffusion Weighted Magnetic Resonance (MR) Data. OTT Ref No: 2343.
Basser PJ, Assaf Y. Diffusion tensor and q-space MRI specimen characterization. #7,643,863; January 5, 2010.
Basser PJ, Pickalov V. Estimation of the average propagator from magnetic resonance data. #7,711,171; May 4, 2010.
Horkay, F.; Langrana, N.; Richtering. W. (eds.): Responsive Gels and Biopolymer Assemblies, MRS Symposium Series, 1234E, Warrendale, PA, 2010.
Horkay F, Falus P, Hecht A-M, and Geissler E. (2010) Length Scale Dependence of the Dynamic Properties of Hyaluronic Acid Solutions in the Presence of Salt. J. Phys. Chem. B 114:15445–15450.
Chandran PL, Dimitriadis EK, Basser PJ, and Horkay F. (2010) Probing interactions between aggrecan and mica surface by the atomic force microscopy. Journal of Polymer Science Part B: Polymer Physics 48(24): 2575-2581.
Nevo U, Özarslan E, Komlosh ME, Koay CG, Sarlls JE, and Basser, PJ. (2010) A system and mathematical framework to model shear flow effects in biomedical DW-imaging and spectroscopy. NMR in Biomedicine 23(7):734–744.
Shemesh N, Özarslan E, Komlosh ME, Basser PJ, and Cohen Y. (2010) From single-pulsed field gradient to double-pulsed field gradient MR: gleaning new microstructural information and developing new forms of contrast in MRI. NMR in Biomedicine 23(7):757–780.
Horkay F, Magda J, Alcoutlabi M, Atzet S, and Zarembinski T. (2010) Structural, mechanical and osmotic properties of injectable hyaluronan-based composite hydrogels. Polymer 51:4424—4430.
Horkay F, Basser PJ, Hecht A-M, and Geissler E. (2010) Counterion and pH-Mediated Structural Changes in Charged Biopolymer Gels. Macromol. Symp. 291–292:354–361.
Lin, DC, Douglas, JF, and Horkay F. (2010) Development of minimal models of the elastic properties of flexible and stiff polymer networks with permanent and thermoreversible cross-links. Soft Matter 6:3548–3561.
Geissler E, Hecht A-M, and Horkay F. (2010) Scaling Behavior of Hyaluronic Acid in Solution with Mono- and Divalent Ions. Macromol. Symp. 291–292:362–370.
Shemesh N, Özarslan E, Adiri T, Basser PJ, Cohen Y. (2010) Noninvasive bipolar double-pulsed-field-gradient NMR reveals signatures for pore size and shape in polydisperse, randomly oriented, inhomogeneous porous media. J Chem Phys 133:044705-1—044705-9.
Lange N, Froimowitz MP, Bigler ED, Lainhart JE, Brain Development Cooperative Group. (2010) Associations Between IQ, Total and Regional Brain Volumes and Demography in a Large Normative Sample of Healthy Children and Adolescents. Dev Neuropsychol. 35(3): 296–317.
Pasternak O, Sochen N, and Basser PJ. (2010) The effect of metric selection on the analysis of diffusion tensor MRI data. Neuroimage 49:2190–2204.
Shemesh N, Özarslan E, Basser PJ, and Cohen Y. (2010) Detecting diffusion-diffraction patterns in size distribution phantoms using double-pulsed field gradient NMR: Theory and experiments. J Chem Phys 132:034703-1—034703-12.

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2009

Leppert I R, Almli C R, McKinstry R C, Mulkern R V, Pierpaoli C, Rivkin M J, Pike G B, T(2) relaxometry of normal pediatric brain development. Journal of Magnetic Resonance Imaging: JMRI 29, 258 (Feb, 2009).
S. Karama, Y. Ad-Dab'bagh, R.J. Haier, I.J. Deary, O.C. Lyttelton, C. Lepage, A.C. Evans and the Brain Development Cooperative Group. Erratum to "Positive association between cognitive ability and cortical thickness in a representative US sample of healthy 6 to 18 year-olds." In Intelligence 2009 37:432–442. PDF
Sarlls JE and Pierpaoli C. (2009) In vivo diffusion tensor imaging of the human optic chiasm at sub-millimeter resolution. NeuroImage 47:1244–1251.
Basser PJ. (2009) Method And System For Measuring The Diffusion Tensor And For Diffusion Tensor Imaging. OTT Ref No: 301.
Horkay F, Basser PJ, Pierpaoli C. (2009) A Phantom for Diffusion MRI: A Method of Enhancing Performance and Reliability. OTT Ref No: 2034.
Basser PJ. (2009) Non-Invasive in vivo MRI Axon Diameter Measurement Methods. OTT Ref No: 1925.
Basser PJ, Özarslan E. (2009) Magnetic Resonance Specimen Evaluation Using Multiple Pulse Field Gradient Sequences. OTT Ref No: 1926.
Basser PJ. (2009) Diffusion Tensor and q-Space MRI Specimen Characterization. OTT Ref No: 906.
Yoon U, Fonov VS, Perusse D, Evans AC, Brain Development Cooperative Group. (2009) The effect of template choice on morphometric analysis of pediatric brain data. Neuroimage 45:769–777.
Jian B, Vemuri BC, E Özarslan. (2009) A Mixture of Wisharts (MOW) Model for Multifiber Reconstruction. In D. Laidlaw and J Weickert (Eds.), Visualization and Processing of Tensor Fields (pp. 38-56). Springer Berlin Heidelberg. View chapter on Google Books.
Horkay, F, Basser, PJ, Londono, DJ, Hecht, AM, Geissler, E. (2009) Ions in hyaluronic acid solutions. J Chem Phys 131:184902-1 - 184902-8.
Bencherif SA, Siegwart DJ, Srinivasan A, Horkay F, Hollinger JO, Washburn NR, and Matyjaszewski K. (2009) Nanostructured hybrid hydrogels prepared by a combination of atom transfer radical polymerization and free radical polymerization. Biomaterials 30:5270–5278.
Lin DC, Shreiber, DI, Dimitriadis EK, and Horkay F. (2009) Spherical indentation of soft matter beyond the Hertzian regime: numerical and experimental validation of hyperelastic models. Biomech Model Mechanobiol 8:345–358.
Horkay F, Lin DC. (2009) Mapping the Local Osmotic Modulus of Polymer Gels. Langmuir 25(15):8735–8741.
Irfanoglu MO, Koay CG, Pajevic S, Machiraju R, and Basser PJ. (2009) Diffusion Tensor Field Registration in the Presence of Uncertainty. MICCAI Part I, LNCS 5761:181–189
McGraw T, Vemuri BC, Özarslan E, Chen Y, and Mareci TH. (2009) Variational denoising of diffusion weighted MRI. Inverse Probl Imag 3:625-648.
Leppert IR, Almli CR, McKinstry RC, Mulkern RV, Pierpaoli C, Rivkin MJ, Pike GB, and The Brain Development Cooperative Group. (2009). Response to "T2 relaxometry of maturing brains." Journal of Magnetic Resonance Imaging 30:912.
Shemesh N., Özarslan E., Bar-Shir A., Basser P.J., and Cohen Y. (2009) Observation of restricted diffusion in the presence of a free diffusion compartment: Single- and double-PFG experiments. J Magn Reson 200:214-225.
Freidlin R.Z., Özarslan E., Assaf Y., Komlosh M.E., and Basser P.J. (2009) A multivariate hypothesis testing framework for tissue clustering and classification of DTI data. NMR Biomed 22(7):716-729.
Koay CG. On the six-dimensional orthogonal tensor representation of the rotation in three dimensions: A simplified approach. Mechanics of Materials. 2009; 41: 951-953.
Koay CG, Özarslan E and Pierpaoli C. Probabilistic Identification and Estimation of Noise (PIESNO): A self-consistent approach and its applications in MRI. J Magn Reson 2009; 199: 94-103. (Software URL: http://sites.google.com/site/hispeedpackets/)
Koay CG, Özarslan E and Basser PJ. A signal transformational framework for breaking the noise floor and its applications in MRI. J Magn Reson 2009; 197: 108-119. (Software URL: http://sites.google.com/site/hispeedpackets/)
Özarslan, E. (2009) Compartment shape anisotropy (CSA) revealed by double pulsed field gradient MR. J Magn Reson 199:56-67.
Basser, P.J., and Özarslan, E. (2009) Introduction to Diffusion MR. In Diffusion MRI: From Quantitative Measurement to In vivo Neuroanatomy. Heidi Johansen-Berg and Timothy E.J. Behrens, editors. Elsevier 1-9.
Leppert, I.R., Almli, C.R., McKinstry, R.C., Mulkern, R.V., Pierpaoli, C., Rivkin, M.J., Pike, G.B., and the Brain Development Cooperative Group. 2009. T-2 Relaxometry of Normal Pediatric Brain Development. Journal of Magnetic Resonance Imaging 29:258–267.
Karama, S., Ad-Dab'bagh, Y., Haier, R.J., Deary, I.J., Lyttelton, O.C., Lepage, C., Evans, A.C., and the Brain Development Cooperative Group. 2009. Positive association between cognitive ability and cortical thickness in a representative US sample of healthy 6 to 18 year-olds. Intelligence 37(2): 145–155.
Shemesh, N., Özarslan, E., Basser, P.J., and Cohen, Y 2009. Measuring small compartmental dimensions with low-q angular double-PGSE NMR: The effect of experimental parameters on signal decay. J Magn Reson 198:15-23.
Özarslan, E., Shemesh, N., and Basser, P.J. 2009. A general framework to quantify the effect of restricted diffusion on the NMR signal with applications to double pulsed field gradient NMR experiments. J Chem Phys 130:104702 (1-9). Erratum
Özarslan, E., Koay, C.G., and Basser, P.J. 2009. Remarks on q-space MR propagator in partially restricted, axially-symmetric, and isotropic environments. Magn Reson Imaging 27:834-844.
Barazany, D., Basser, P.J., and Assaf, Y. 2009. In vivo measurement of axon diameter distribution in the corpus callosum of rat brain. Brain 132(5):1210-1220.
Roth, B.J., and Basser, P.J. 2009. Mechanical Model of Neural Tissue Displacement During Lorentz Effect Imaging. Magnetic Resonance in Medicine 61:59–64.

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2008

Basser PJ, Pajevic S. (2008) Quantitative Assessment Of Changes In Tissue Status In Disease, Development, Aging, Or Degeneration Using Diffusion Tensor Magnetic Resonance Imaging. OTT Ref No: 410.
Horkay F, Basser PJ, Berman A. Method for tissue osmometry. #7,380,477; June 3, 2008.
Horkay, F., and Basser, P.J. 2008. Ionic and pH Effects on the Osmotic Properties and Structure of Polyelectrolyte Gels. Journal of Polymer Science: Part B: Polymer Physics 46: 2803–2810.
Yin, D.-W., Horkay, F., Douglas, J.F, and de Pablo, J.J. 2008. Molecular simulation of the swelling of polyelectrolyte gels by monovalent and divalent counterions. The Journal of Chemical Physics 129:154902-1 – 154902-11.
Tasaki, I. 2008. On the Reversible Abrupt Structural Changes in Nerve Fibers Underlying Their Excitation and Conduction Processes. In Phase Transitions in Cell Biology. G. H. Pollack, and W. C. Chin, editors. Springer Science+Business Media B.V. 1-21.
Horkay, F., A. Ryan, N. Langrana, and D. Londono, editors. 2008. Bioinspired Polymer Gels and Networks. MRS, Warrendale, PA.
Lin, D. C., E. K. Dimitriadis, and F. Horkay. 2008. Elasticity models for the spherical indentation of gels and soft biological tissues. In Bioinspired Polymer Gels and Networks. F. Horkay, A. Ryan, N. Langrana, and D. Londono, editors. MRS Symposium Series, Warrendale, PA. 1-6.
Horkay, F. (2008) Biopolymer Gels: Nanostructure and Macroscopic Properties. Progr Colloid Polym Sci 135:10–15.
Basser, P.J. (2008) Diffusion and Diffusion Tensor MR Imaging: Fundamentals. In Magnetic Resonance Imaging of the Brain and Spine. S. W. Atlas, editor. Lippincott Williams and Wilkins, Philadelphia.
Bar-Shir, A., Avram, L., Özarslan, E., Basser, P.J., and Cohen, Y. (2008) The effect of the diffusion time and pulse gradient duration ratio on the diffraction pattern and the structural information estimated from q-space diffusion MR: Experiments and simulations. Journal of Magnetic Resonance. 194(2):230-236.
Horkay, F., and Basser, P.J. (2008) Insensitivity to Salt of Assembly of a Rigid Biopolymer Aggrecan. Physical Review Letters 101:068301-1—068301-4.
Pasternak, O., Verma, R., Sochen, N., and Basser, P.J. (2008) On What Manifold Do Diffusion Tensors Live? IJ - 2008 MICCAI Workshop - Manifolds in Medical Imaging: Metrics, Learning and Beyond.
Silva, S., Basser, P.J., and Miranda, P.C. (2008) Elucidating the mechanisms and loci of neuronal excitation by transcranial magnetic stimulation using a finite element model of a cortical sulcus. Clinical Neurophysiology. (In Press)
Wu, M., Chang, L.-C., Walker, L., Lemaitre, H., Barnett, A.S., Marenco, S., and Pierpaoli, C. (2008) Comparison of EPI Distortion Correction Methods in Diffusion Tensor MRI Using a Novel Framework. MICCAI 2008, Part II, LNCS 5242, pp. 321-329.
Irfanoglu, M.O., Machiraju, R., Sammet, S., Pierpaoli, C., and Knopp, M.V. (2008) Automatic Deformable Diffusion Tensor Registration for Fiber Population Analysis. MICCAI 2008, Part II, LNCS 5242, pp. 1014-1022.
Chang, L-C., Koay, C.G., Basser, P.J., and Pierpaoli, C. (2008) Linear Least-Squares Method for Unbiased Estimation of T₁ From SPGR Signals. Magnetic Resonance in Medicine 60:496–501.
Sarlls, J.E. and Pierpaoli, C. (2008) Diffusion-Weighted Radial Fast Spin-Echo for High-Resolution Diffusion Tensor Imaging at 3T. Magnetic Resonance in Medicine 60:270–276.
Bencherif, S.A., Srinivasan, A., Horkay, F., Hollinger, J.O., Matyjaszewski, K., and Washburn, N.R. (2008) Influence of the degree of methacrylation on hyaluronic acid hydrogels properties. Biomaterials 29: 1739–1749.
Horkay, F. and Hammouda, B. (2008) Small-angle neutron scattering from typical synthetic and biopolymer solutions. Colloid Polym Sci 286:611–620.
Avram, L., Özarslan, E., Assaf, Y., Bar-Shir, A., Cohen, Y., Basser, P.J. (2008) Three-dimensional water diffusion in impermeable cylindrical tubes: theory versus experiments. NMR Biomed. 21: 888–898.
Kim, S., Barnett, A.S., Pierpaoli, C., and Chi-Fishman, G. (2008) Three-dimensional mapping of lingual myoarchitecture by diffusion tensor MRI. NMR Biomed. 21: 479–488.
Assaf, Y., Blumenfeld-Katzir, T., Yovel, Y., and Basser, P.J. (2008) AxCaliber: A Method for Measuring Axon Diameter Distribution from Diffusion MRI. Magnetic Resonance in Medicine 59:1347–1354.
Koay, C.G., Nevo, U., Chang, L.C., Pierpaoli, C., and Basser, P.J. (2008) The elliptical cone of uncertainty and its normalized measures in diffusion tensor imaging. IEEE Trans Med Imag 27(6): 834-846.
Lin, D.C. and Horkay, F. (2008) Nanomechanics of polymer gels and biological tissues: A critical review of analytical approaches in the Hertzian regime and beyond. Soft Matter 4:669-682.
Horkay, F., Basser, P.J., Hecht, A-M., and Geissler, E. (2008) Gel-like behavior in aggrecan assemblies. J Chem Phys 128:135103(1-7).
Özarslan, E. and Basser, P.J. (2008) Microscopic anisotropy revealed by NMR double pulsed field gradient experiments with arbitrary timing parameters. J Chem Phys 128:154511(1-11).
Komlosh, M.E., Lizak, M.J., Horkay, F., Freidlin, R.Z., and Basser, P.J. (2008) Observation of Microscopic Diffusion Anisotropy in the Spinal Cord Using Double-Pulsed Gradient Spin Echo MRI. Magnetic Resonance in Medicine 59:803–809.
Özarslan, E., Nevo, U. and Basser, P.J. (2008) Anisotropy induced by macroscopic boundaries: Surface normal mapping using diffusion-weighted imaging. Biophys J 94(7):2809-2818.

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2007

Liu, A.K., Marcus, K. J., Fischl, B., Grant, P.E., Poussaint, T.Y., Rivkin, M.J., Davis, P., Tarbell, N.J., and Yock, T. I. (2007) Changes in cerebral cortex of children treated for medulloblastoma. International Journal of Radiation Oncology, Biology, and Physics. Jul 15;68(4):992-8. Epub 2007 Mar 26. Abstract.
McMillan, K.M., Rogers, B.P., Koay, C.G., Laird, A.R., Price, R.R., and Meyerand, M.E. (2007) An objective method for combining multi-parametric MRI datasets to characterize malignant tumors. Med. Phys. 34:1053–1061.
Horkay, F., and McKenna, G.B. (2007) Polymer Networks and Gels. In Physical Properties of Polymers Handbook. James E. Mark, editor. Springer, New York.
Horkay, F., Basser, P.J., Hecht, A-M., and Geissler, E. (2007) Comparative study of scattering and osmotic properties of synthetic and biopolymer gels. Macromol. Symp. 256:80-87.
Geissler, E., Hecht, A-M., and Horkay, F. (2007) Scaling Equations for a Biopolymer in Salt Solution. Physical Review Letters 99: 267801-1 – 267801-4.
Silva, C.C., Lin, D.C., Horkayne-Szakaly, I., Basser, P.J., and Horkay, F. (2007) Novel Applications of the QCM Technique in Biomaterials Science. Bioinspired Polymer Gels and Networks, edited by F. Horkay, N.A. Langrana, A.J. Ryan, and J.D. Londono (Mater. Res. Soc. Symp. Proc. Volume 1060E, Warrendale, PA, 2007), 1060-LL03-06.
Boukari, H., Silva, C., Nossal, R., and Horkay, F. (2007) Monitoring nanoprobe diffusion in osmotically-stressed hydrogels. Bioinspired Polymer Gels and Networks, edited by F. Horkay, N.A. Langrana, A.J. Ryan, and J.D. Londono (Mater. Res. Soc. Symp. Proc. Volume 1060E, Warrendale, PA, 2007), 1060-LL07-03
Lin, D.C., Dimitriadis, E.K., and Horkay, F. (2007) Robust strategies for automated AFM force curve analysis - II. Adhesion-influenced indentation of soft, elastic materials. Journal of Biomechanical Engineering-Transactions of the ASME 129:904-912.
Lin, D.C., Dimitriadis, E.K., and Horkay, F. (2007) Elasticity of rubber-like materials measured by AFM nanoindentation. eXPRESS Polymer Letters 1:576-584.
Hauben, E., Roncarolo M,G., Draghici, E., Nevo, U. (2007) The role of tissue adaptation and graft size in immune tolerance. Transplant Immunology; 18(2):122-5.
Nevo, U., Hauben, E. (2007) Ecoimmunity: immune tolerance by symmetric co-evolution. Evolution and Development; 9(6):632-42.
Van Thienen, T.G., Horkay, F., Braeckmans, K., Stubbe, B.G., Demeester, J., and De Smedt, S.C (2007) Influence of free chains on the swelling pressure of PEG-HEMA and dex-HEMA hydrogels. International Journal of Pharmaceutics 337:31-39.
Lin, D.C., Dimitriadis, E.K., and Horkay, F. (2007) Robust strategies for automated AFM force curve analysis - I. Non-adhesive indentation of soft, inhomogeneous materials. Journal of Biomechanical Engineering-Transactions of the ASME 129: 430-440.
Michelman-Ribeiro, A., Horkay, F., Nossal, R., and Boukari, H. (2007) Probe diffusion in aqueous poly(vinyl alcohol) solutions studied by fluorescence correlation spectroscopy. Biomacromolecules 8: 1595-1600.
Basser, P.J. and Pajevic, S. (2007) Spectral decomposition of a 4th-order covariance tensor: Applications to diffusion tensor MRI. Signal Processing 87:220-236.
Chang, L-C., Koay, C.G., Pierpaoli, C., and Basser, P.J. (2007) Variance of estimated DTI-derived parameters via first-order perturbation methods. Magn Reson Med. 57:141-149.
Cheng Guan Koay, Lin-Ching Chang, Carlo Pierpaoli, Peter J. Basser. Error Propagation Framework for Diffusion Tensor Imaging via Diffusion Tensor Representations. IEEE Trans Med Imaging 26(8):1017-1034.
There are several unpleasant errors due to the IEEE production. A preprint is made available here that has correct layout of equations: download preprint. The erratum can be found here: download erratum
Cheng Guan Koay, Joelle E. Sarlls, Evren Özarslan. (2007) Three-dimensional analytical magnetic resonance imaging phantom in the Fourier domain. Magn Reson Med. 58: 430-436. [Download software]
Jian, B., Vemuri, B.C., Özarslan, E., Carney, P.R. and Mareci, T.H. (2007) A novel tensor distribution model for diffusion weighted MR signal. NeuroImage 37:164-176. Erratum.
Shepherd, T.M., Özarslan, E., Yachnis, A.T., King, M.A. and Blackband, S.J. (2007) Diffusion tensor microscopy indicates the cytoarchitectural basis for diffusion anisotropy in the human hippocampus. Am J Neuroradiol. 28:958-964.
Miranda, P.C., Correia, L., Salvador, R., and P.J. Basser. (2007) Tissue heterogeneity as a mechanism for localized neural stimulation by applied electric fields. Phys. Med. Biol. 52 5603-5617.
Özarslan, E., and Basser, P.J. (2007) MR diffusion-"diffraction" phenomenon in multi-pulse-field-gradient experiments. J Magn Reson 188:285-294.
Waber, D.P., De Moor, C., Forbes, P.W., Almli, C.R., Botteron, K.N., Leonard, G., Milovan, D., Paus, T., Rumsey, J., and the Brain Development Cooperative Group. (2007) The NIH MRI study of normal brain development: Performance of a population based sample of healthy children aged 6 to 18 years on a neuropsychological battery. Journal of the International Neuropsychological Society 13(5):729-46.
Almli, C.R., Rivkin, M.J., McKinstry, R.C., and the Brain Development Cooperative Group. (2007) The NIH MRI study of normal brain development (Objective-2): Newborns, infants, toddlers, and preschoolers. NeuroImage 35:308-325.
Marenco, S., Siuta, M.A., Kippenhan, J.S., Grodofsky, S., Chang, W., Kohn, P., Mervis, C.B., Morris, C.A., Weinberger, D.R., Meyer-Lindenberg, A., Pierpaoli, C., and Berman, K.F. (2007) Genetic contributions to white matter architecture revealed by diffusion tensor imaging in Williams syndrome. PNAS 38: 15117-15122.
Komlosh, M.E., Horkay, F., Freidlin, R.Z., Nevo, U., Assaf, Y., and Basser, P.J. (2007) Detection of microscopic anisotropy in gray matter and in a novel tissue phantom using double Pulsed Gradient Spin Echo MR. Journal of Magnetic Resonance 189:38-45.
R. Z. Freidlin, E. Özarslan, M. E. Komlosh, L.-C. Chang, C. G. Koay, D. K. Jones, and P. J. Basser. (2007) “Parsimonious model selection for tissue segmentation and classification applications: A study using simulated and experimental DTI data.” IEEE T Med Imaging 26(11):1576-1584.

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2006

Basser PJ, Pickalov V. (2006) In vivo Assessment of Tissue Microstructure and Microdynamics: Estimation of the Average Propagator from Magnetic Resonance Data. OTT Ref No: 1484.
Boukari, H., A. Michelman Ribeiro, R. Nossal, and F. Horkay. 2006. Fluorescence correlation spectroscopy study of TAMRA diffusion in poly(vinyl-alcohol) and Ficoll70 solutions. In Biomimetic Polymers and Gels. Mater. Res. Soc. Symp., Warrenton, PA. 1-6.
Marenco, S., R. Rawlings, G.K. Rohde, A.S. Barnett, R.A. Honea, C. Pierpaoli, and D.R. Weinberger. 2006. Regional distribution of measurement error in diffusion tensor imaging. Psychiatry Research 147:69-78.
Basser, P. J. (2006) Diffusion Tensor MR Imaging Fundamentals. In Clinical Magnetic Resonance Imaging. R. R. Edelman, J. Hesselink, M. Zlatkin, and J. V. C. III, editors. Saunders Elsevier, Philadelphia, 320-332.
Horkay, F., Hecht, A-M., and Geissler, E. (2006) Similarities between polyelectrolyte gels and biopolymer solutions. Journal of Polymer Science Part B-Polymer Physics 44: 3679-3686.
Horkay, F., Han, M-H., Han, I.S., Bang, I-S., Magda, J.J. (2006) Separation of the effects of pH and polymer concentration on the swelling pressure and elastic modulus of a pH-responsive hydrogel. Polymer 21: 7335-7338.
Assaf, Y., Ben-Sira, L., Constantini, S., Chang, L-C., and Beni-Adani, L. (2006) Diffusion tensor imaginig in hydrocephalus: Initial Experience. AJNR Am J Neuroradiol 27:1717-1724.
Carew, J.D., Koay, C.G., Wahba, G., Alexander, A.L., Meyerand, M.E., and Basser, P.J. (2006) The asymptotic behavior of the nonlinear estimators of the diffusion tensor and tensor-derived quantities with implications for group analysis.
Horkay, F., Hecht, A.M., Rochas, C., Basser, P.J., and Geissler, E. (2006) Anomalous small angle x-ray scattering determination of ion distribution around a polyelectrolyte biopolymer in salt solution. J. Chem. Phys. 125:234904.
Jones, D. K., Catani, M., Pierpaoli, C., Reeves, S. J. C., Shergill, S. S., O’Sullivan, M., Golesworthy, P., McGuire, P., Horsfield, M. A., Simmons, A., Williams, S. C. R., and Howard, R. J. (2006) Age Effects on Diffusion Tensor Magnetic Resonance Imaging Tractography Measures of Frontal Cortex Connections in Schizophrenia. Hum Brain Mapp 27:230-238.
Koay, C. G. and Basser, P. J. (2006) Analytically exact correction scheme for signal extraction from noisy magnitude MR signals. J Mag Res. 179:317-322.
Koay, C.G., Carew, J.D., Alexander, A.L., Basser, P.J., and Meyerand, M.E. (2006) Investigation of anomalous estimates of tensor-derived quantities in diffusion tensor imaging. Magn Reson Med. 55:930-936.
Koay, C.G., Chang, L-C., Carew, J.D., Pierpaoli, C., and Basser, P.J. (2006) A unifying theoretical and algorithmic framework for least squares methods of estimation in diffusion tensor imaging. J Magn Reson. 182:115-125. [For software request, please write to the corresponding author at guankoac@mail.nih.gov]
Lin, D.C., Dimitriadis, E.K., and Horkay, F. (2006) Advances in the mechanical characterization of soft materials by nanoindentation. In Recent Research Developments in Biophysics (Ed: Pandalai, S.G.), Vol. 5 Part II, pp. 333-370, Transworld Research Network, Kerala, India, 2006.
Özarslan, E., Basser, P.J., Shepherd, T.M., Thelwall, P.E., Vemuri, B.C., and Blackband, S.J. (2006) Observation of anomalous diffusion in excised tissue by characterizing the diffusion-time dependence of the MR signal. J Magn Reson. 183:315-323.
Özarslan, E., Shepherd, T.M., Vemuri, B.C., Blackband, S.J., and Mareci, T.H. (2006) Resolution of complex tissue microarchitecture using the diffusion orientation transform (DOT). NeuroImage 31:1086-1103.
Pajevic, S., Aldroubi, A., and Basser, P.J. (2006) Continuous Tensor Field Approximation of Diffusion Tensor MRI data. In J. Weickert & H. Hagen (Eds.), Visualization and Processing of Tensor Fields (299-314). Berlin Germany: Springer. Color Plates
Shepherd, T.M., Özarslan, E., King, M.A., Mareci, T.H. and Blackband, S.J. (2006) Structural insights from high-resolution diffusion tensor imaging and tractography of the isolated rat hippocampus. NeuroImage. 32:1499-1509.
Tasaki, I. (2006) A note on the local current associated with the rising phase of a propagating impulse in nonmyelinated nerve fibers. Bulletin Math Biol.
Evans, A.C., and the Brain Development Cooperative Group. (2006) The NIH MRI study of normal brain development. NeuroImage 30:184-202.

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2005

Basser PJ, Pajevic S. Determination of an empirical statistical distribution of the diffusion tensor in MRI. #6,845,342; January 18, 2005.
Horkay, F., Basser, P.J., Hecht, A-M., and Geissler, E. (2005) Effect of calcium ions on the structure of synthetic and biopolymer gels. Polymeric Materials: Scientific Engineering 93:105–106.
Horkay, F., and E. J. Amis, editors. 2005. Biological and Synthetic Polymer Networks and Gels. Wiley VCH, Weinheim.
Michelman-Ribeiro, A., H. Boukari, R. Nossal, and F. Horkay. 2005. Fluorescence Correlation Spectroscopy Study of Probe Diffusion in Poly(vinyl alcohol) Solutions and Gels. Macromol. Symp. 227:221-230.
Jones, D. K., Catani, M., Pierpaoli, C., Reeves, S. J.,Sukhwinder S. S., Sullivan, M. O., Maguire, P., Horsfield, M. A., Andrew Simmons, A., Williams, S.C.R., and Howard, R. J. (2005) A Diffusion TensorMagnetic Resonance Imaging Study of Frontal Cortex Connections in Very-Late-Onset Schizophrenia-Like Psychosis. Am J Geriatr Psychiatry 13:1092-1099.
Geissler, E., Hecht, A-M., and Horkay, F. (2005) Nanoscale inhomogeneities and thermodynamics of unfulfilled polymer gels. Journal of Macromolecular Science, Part B: Physics 44:873-880.
Lin-Gibson, S., Bencherif, S., Antonucci, J.M., Jones, R.L., and Horkay, F. (2005) Synthesis and characterization of poly(ethylene glycol) dimethacrylate hydrogels. Macromol. Symp. 227:243-254.
Hammouda, B., Horkay, F., and Becker, M.L. (2005) Clustering and Solvation in Poly(acrylic acid) Polyelectrolyte Solutions. Macromolecules 38:2019-2021.
Assaf, Y. and Basser, P.J. (2005) Composite hindered and restricted model of diffusion (CHARMED) MR imaging of the human brain. NeuroImage 27:48-58.
Basser, P. J. and Horkay, F. (2005) Toward a constitutive law of cartilage: A polymer physics perspective. Macromol. Symp. 227:53-64.
Boguñá, M., Pajevic, S., Basser, P.J., and Weiss, G.H. (2005) A model for noise effects on fibre tract trajectories in diffusion tensor imaging: theory and simulations. New Journal of Physics 7:1-7.
Chang, L.C., Jones, D.K., and Pierpaoli, C. (2005) RESTORE: Robust estimation of tensors by outlier rejection. Magn Reson Med. 53:1088-1095.
Geissler, E., Hecht, A.M, Rochas, C. Horkay, F. and Basser, P.J. (2005) Light, small angle neutron and X-Ray scattering from gels. Macromol, Symp 227:27-37.
Hauben, E., Roncarolo, M.G., Nevo, U., and Schwartz, M. (2005) Beneficial autoimmunity in Type 1 diabetes mellitus. Trends in Immunology 26:248-253.
Horkay, F., Basser, P.J., Hecht, A-M., and Geissler, E. (2005) Structural investigations of a neutralized polyelectrolyte gel and an associating neutral hydrogel. Polymer. 46:4242-4247.
Horkay, F., Horkayne-Szakaly, I., and Basser, P.J. (2005) Measurement of the osmotic properties of thin polymer films and biological tissue samples. Biomacromolecules 6:988-993.
Jones, D.K. and Pierpaoli, C. (2005) Confidence mapping in diffusion tensor magnetic resonance iImaging tractography using a bootstrap approach. Magn Reson Med. 53:1143-1149.
Jones, D.K., Travis, A.R., Eden, G., Pierpaoli, C., and Basser, P.J. (2005) PASTA: pointwise assessment of streamline tractography attributes. Magn Reson Med. 53:1462-1467.
Kim, S.,Chi-Fishman, G., Barnett,A. S., and Pierpaoli, C. (2005) Dependence on diffusion time of apparent diffusion tensor of ex vivo calf tongue and heart. Mag Res in Med 54:1387-1396.
Lin-Gibson, S., Jones, R.L., Washburn, N.R., and Horkay, F. (2005) Structure-property relationships of photopolymerizable poly(ethylene glycol) dimethacrylate hydrogels. Macromolecules 38: 897-2902.
Rohde, G.K., Barnett, A.S., Basser, P.J., and Pierpaoli, C. (2005) Estimating intensity variance due to noise in registered images: Applications to diffusion tensor MRI. NeuroImage 26:673-684.
Sen, P.N. and Basser, P.J. (2005) A model for diffusion in white matter in the brain. Biophysical Journal 89:2927-2938.
Sen, P.N. and Basser, P.J. (2005) Modeling diffusion in white matter in the brain: A composite porous medium. Magn Reson Imaging 23:215-220.
Tasaki, I. (2005) Reptitive abrupt structural changes in polyanionic gels: A comparison with analogous processses in nerve fibers. J. theor. Biol. 236:2-11.

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2004

Rohde, G.K., Pajevic, S., amd Pierpaoli, C. (2004) Multi-channel registration of diffusion-tensor images using directional information. 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano 712–715.
Lange, N., D.K. Jones, and C. Pierpaoli. (2004) A closed-form method for improving inter-subject coherence in diffusion tensor magnetic resonance imaging. In ISBI, Crystal City, VA. 1506-1509.
Michelman-Ribeiro, A., Boukari, H., Nossal, R., and Horkay, F. (2004) Structural Changes in Polymer Gels Probed by Fluorescence Correlation Spectroscopy. Macromolecules 37:10212-10214.
Amsden, B.G., Stubbe, B.G., Horkay, F., De Smedt, S.C., and Demeester, J. (2004) Modeling the swelling pressure of degrading hydroxyethylmethacrylate-grafted dextran hydrogels. J Polym Sci Part B: Polym Phys. 42:3397-3404.
Assaf, Y., Freidlin, R.Z., Rohde, G.K., and Basser, P.J. (2004) New modeling and experimental framework to characterize hindered and restricted water diffusion in brain white matter. Magn Reson Med. 52:965-978.
Basser, P.J. (2004) Scaling laws for myelinated axons derived from an electrotonic core-conductor model. Journal of Integrative Neuroscience 3(2):227-244.
Horkay, F. and Basser, P.J. (2004) Osmotic observations on chemically cross-linked DNA gels in physiological salt solutions. Biomacromolecules 5:232-237.
Jones, D.K. (2004) The effect of gradient sampling schemes on measures derived from diffusion tensor MRI: a Monte Carlo study. Magn Reson Med. 51:807-815.
Jones, D.K. and Basser, P.J. (2004) Squashing Peanuts and Smashing Pumpkins: How Noise Distorts Diffusion-Weighted MR Data. Magn Reson Med. 52:979-993.
Lin-Gibson, S., Bencherif, S., Cooper, J.A., Wetzel, S.J., Antonucci, J.M., Vogel, B.M., Horkay, F., and Washburn. N.R. (2004) Synthesis and characterization of PEG dimethacrylates and their hydrogels. Biomacromolecules 5:1280-1287.
Morfin, I., Horkay, F., Basser, P.J., Bley, F., Hecht, A., Rochas, C., and Geissler, E. (2004) Adsorption of Divalent Cations on DNA. Biophysical Journal 87:2897-2904.
Rohde, G.K., Barnett, A.S., Basser, P.J., Marenco, S., and Pierpaoli, C. (2004) Comprehensive approach for correction of motion and distortion in diffusion-weighted MRI. Magn Reson Med. 51:103-114.
Tasaki, I. (2004) On the conduction velocity of nonmyelinated nerve fibers. Journal of Integrative Neuroscience 3(2):115-124.
Washburn, N.R., Weir, M., Anderson, P., and Potter, K. (2004) Bone formation in polymeric scaffolds evaluated by proton magnetic resonance microscopy and x-ray microtomography. J Biomed Mater Res. 69A:738-747.

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2003

Jones, D.K. (2003) Determining and visualizing uncertainty in estimates of fiber orientation from diffusion tensor MRI. Magn Reson Med. 49: 7-12.
Basser, P.J. and Pajevic, S. (2003) A normal distribution for tensor-valued random variables: applications to diffusion tensor MRI. IEEE Trans Med Imaging 22:785-794.
Basser, P.J. and Pajevic, S. (2003) Dealing with uncertainty in diffusion tensor MR data. Israel Journal of Chemistry 43:129-144.
Horkay, F. and Basser, P.J. (2003) Osmotic properties of polyelectrolyte hydrogels in physiological salt solutions. Recent Res. Devel. Macromol. 7:293-313.
Horkay, F., Basser, P.J., Hecht, A.M., and Geissler, E. (2003) Calcium induced volume transition in polyelectrolyte gels. Macromol Symp. 200:21-30.
Miranda, P.C., Hallett, M., and Basser, P.J. (2003) The electric field induced in the brain by magnetic stimulation: a 3-D finite element analysis of the effect of tissue heterogeneity and anisotropy. IEEE Trans. Bio. Med. Eng. 50:1074-1085.
Morfin, I., Horkay, F., Basser, P.J., Bley, F., Ehrburger-Dolle, F., Hecht, A., and Geissler, E. (2003) Ion condensation in a polyelectrolyte gel. Macromol Symp. 200:227-233.
Pajevic, S. and Basser, P.J. (2003) Parametric and non-parametric statistical analysis of DT-MRI data. J Magn Reson. 161:1-14.
Rohde, G.K., Aldroubi, A., and Dawant, B.M. (2003) The adaptive bases algorithm for intensity-based nonrigid image registration. IEEE Trans Med Imaging 22:1470-1479.
Stubbe, B.G., Horkay, F., Amsden, B., Hennink, W.E., De Smedt, S.C., and Demeester, J. (2003) Tailoring the swelling pressure of degrading dextran hydroxyethyl methacrylate hydrogels. Biomacromolecules 4:691-695.

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2002

Horkay F, Basser PJ, Berman A. (2002) Tissue Microosmometer. OTT Ref No: 652.
Basser, P.J. (2002) Relationships between diffusion tensor and q-space MRI. Magn Reson Med. 47:392-397.
Basser, P.J. and Jones, D.K. (2002) Diffusion-tensor MRI: theory, experimental design and data analysis - a technical review. NMR Biomed. 15: 456-467.
Basser, P.J., Pajevic, S., et al. (2002) Fiber tract following in the human brain using DT-MRI data. IEICE Trans. Inf. & Syst. E85-D(1):15-21.
Dimitriadis, E.K., Horkay, F., Maresca, J., Kachar, B., and Chadwick, R.S. (2002) Determination of elastic moduli of thin layers of soft material using the atomic force microscope. Biophysical Journal 82:2798-2810.
Han, I.S., Han, M., Kim, J., Lew, S., Lee, Y.J., Horkay, F., and Magda, J.J. (2002) Constant-volume hydrogel osmometer: a new device concept for miniature biosensors. Biomacromolecules 3:1271-1275.
Hecht, A., Horkay, F., Schleger, P., and Geissler, E. (2002) Thermal fluctuations in polymer gels investigated by neutron spin echo and dynamic light scattering. Macromolecules 35:8552-8555.
Horkay, F., Basser, P.J., Hecht, A., and Geissler, E. (2002) Calcium-induced volume transition in polyacrylate hydrogels swollen in physiological salt solutions. Macromol. Biosci. 2:207-213.
Horkay, F., Hecht, A., Grillo, I., Basser, P.J., and Geissler, E, (2002) Experimental evidence for two thermodynamic length scales in neutralized polyacrylate gels. J Chem Phys. 117:9103-9106.
Pajevic, S., Aldroubi, A., and Basser, P.J. (2002) A continuous tensor field approximation of discrete DT-MRI data for extracting microstructural and architectural features of tissue. J of Magn Reson 154:85-100.
Pierpaoli, C. (2002) Inferring structural and architectural features of brain tissue from DT-MRI measurements. CNS Spectrums 7:510-515.
Potter, K., Leapman, R.D., Basser, P.J., and Landis, W.J. (2002) Cartilage calcification studied by proton nuclear magnetic resonance microscopy. J Bone Miner Res. 17: 652-660.
Smith, C. (2002) NIH commercializes new imaging technique. Nature Medicine 8(9): 906.
Stubbe, B.G., Braeckmans, K., Horkay, F., Hennink, W.E., De Smedt, S,C,, and Demeester, J. (2002) Swelling pressure observations on degrading Dex-HEMA hydrogels. Macromolecules 35:2501-2505.
Tasaki, I. (2002) Spread of discrete structural changes in synthetic polyanionic gel: a model of propagation of a nerve impulse. J. theor. Biol. 218:497-505.
Tasaki, I. and Matsumoto, G. (2002) On the cable theory of nerve conduction. Bulletin of Mathematical Biology 64:1069-1082.
Jones, D.K. (2002) Determining and visualizing uncertainty in estimates of fiber orientation from diffusion tensor MRI. Magnetic Resonance in Medicine 49:7-12.

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2001

Basser PJ, Maroudas A. Method for measuring mechanical properties of the collagen network in cartilage. #6,289,753; September 18, 2001.
Hasan, K.M., Basser, P.J., Parker, D.L., and Alexander, A.L. (2001) Analytical Computation of the Eigenvalues and Eigenvectors in DT-MRI. Journal of Magnetic Resonance 152:41-47.
Alexander, D.C., et al. (2001) Spatial transformations of diffusion tensor magnetic resonance images. IEEE Trans Med Imaging 20(11):1131-1139.
Hecht, A., Horkay, F., and Geissler, E. (2001) Neutron scattering investigations on a bimodal polymer gel. J Phys Chem. 105:5637-5642.
Hecht, A., Horkay, F., and Geissler, E. (2001) Structure of polymer solutions containing fumed silica. Phys Rev. 64:041402-1-041402-6.
Horkay, F., Hecht, A., et al. (2001) Comparison between neutral gels and neutralized polyelectrolyte gels in the presence of divalent cations. Macromolecules 34:4285-4287.
Horkay, F., Tasaki, I., and Basser, P.J. (2001) Effect of monovalent-divalent cation exchange on the swelling of polyacrylate hydrogels in physiological salt solutions. Biomacromolecules 2:195-199.
Pierpaoli, C., et al. (2001) Water diffusion changes in wallerian degeneration and their dependence on white matter architecture. NeuroImage 13:1174-1185.

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2000

Basser, P.J., Pajevic, S. (2000) Statistical artifacts in diffusion tensor MRI (DT-MRI) caused by background noise. Magn Reson Med. 44:41-50.
Basser, P.J., Pajevic, S., et al. (2000) In vivo fiber tractography using DT-MRI data. Magn Res Med 44:625-632.
Basser, P.J. and Roth, B.J. (2000) New currents in electrical stimulation of excitable tissues. Annu Rev Biomed Eng. 02:377-397.
Horkay, F., Basser, P.J., et al. (2000) Osmotic and SANS observations on sodium polyacrylate hydrogels in physiological salt solutions. Macromolecules 33:8329-8333.
Horkay, F., McKenna, G., et al. (2000) Neutron scattering properties of randomly cross-linked polyisoprene gels. Macromolecules 33:5215-5220.
Horkay, F., Tasaki, I., and Basser, P.J. (2000) Osmotic swelling of polyacrylate hydrogels in physiological salt solutions. Biomacromolecules 1:84-90.

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1999

Pierpaoli C, Basser PJ. (1999) Method to Reduce the Bias in the Mean and Variance of Indices of Water Diffusion Anisotropy as Measured by Diffusion Tensor MRI. OTT Ref No: 323.
Pierpaoli CM, Basser PJ. Method to significantly reduce bias and variance of diffusion anisotrophy measurements. #5,969,524; October 19, 1999.
Aldroubi, A. and Basser, P.J. (1999) Reconstruction of vector and tensor ﬁelds from sampled discrete data. Contemporary Mathematics 247:1-15.
Barratti, C., Barnett, A.S., and Pierpaoli, C. (1999) Comparative MR imaging study of brain maturation in kittens with T1, T2, and the trace of the diffusion tensor. Radiology 210:133-142.
Pajevic, S. and Pierpaoli, C. (1999) Color schemes to represent the orientation of anisotropic tissues from diffusion tensor data: application to white matter fiber tract mapping in the human brain. Magn Reson Med. 42:526-540.
Tasaki, I. (1999) Evidence for phase transition in nerve fibers, cells and synapses. Ferroelectrics 220:305-316.
Tasaki, I. (1999) Rapid structural changes in nerve fibers and cells associated with their excitation processes. Jap J Physiol. 49:125-138.
Virta, A., Barnett, A., and Pierpaoli, C. (1999) Visualizing and characterizing white matter fiber structure and architecture in the human pyramidal tract using diffusion tensor MRI. Magn Reson Imaging 17:1121-1133.

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1998

Basser, P.J. and Pierpaoli, C. (1998) A simplified method to measure the diffusion tensor from seven MR images. MRM 39:928-934.
Basser, P.J., Schneiderman, R., et al. (1998) Mechanical properties of the collagen network in human articular cartilage as measured by osmotic stress technique. Arch Biochem Biophys. 351(2):207-219.
Shrager, R.I. and Basser, P.J. (1998) Anisotropically weighted MRI. MRM 40:160-165.
Tasaki, I. (1998) Repetitive mechanical responses of the amphibian skin to adrenergic stimulation. Jap J Physiol. 48:297-300.

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1997

Basser, P.J. (1997) New histological and physiological stains derived from diffusion-tensor MR images. J. Ann NY Acad Sci. 820:123-138.
Mattiello, J., Basser, P.J., and LeBihan, D. (1997) The b matrix in diffusion tensor echo-planer imaging. Magn Reson Med. 37:292-300.
Tasaki, I. (1997) Rapid volume expansion in the torpedo electric organ associated with its postsynaptic potential. Biochem Biophys Res Comm. 233:305-308.

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1996

Basser PJ, Mattiello JH, and LeBihan D. Method and system for measuring the diffusion tensor and for diffusion tensor imaging. #5,539,310; July 23, 1996. PDF
Basser, P.J. and Pierpaoli, C. (1996) Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 111:209-219.
George, M.S., Wassermann, E.M., Williams, W.A., Steppel, J., Pascual-Leone, A., Basser, P.J., Hallett, M., and Post, R.M. (1996) Changes in mood and hormone levels after rapid-rate transcranial magnetic stimulation (rTMS) of the prefrontal cortex. The Journal of Neuropsychiatry and Clinical Neurosciences. 8:172-180.
Pierpaoli, C., Jezzard, P., Basser, P.J., Barnett, A., and Chiro, G. (1996) Diffusion tensor MR imaging of the human brain. Radiology 201:637-648.
Pierpaoli, C. and Basser, P.J. (1996) Toward a quantitative assessment of diffusion anisotropy. Magn Reson Med. 36:893-906.

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1995

Basser, P.J. (1995) Inferring microstructural features and the physiological state of tissue from diffusion weighted images. NMR Biomed. 8:333-344.
Basser, P.J., Mattiello, J., and Le Bihan, D. (1995) Anisotropic diffusion: MR diffusion tensor imaging. In D. Le Bihan (Ed.), Diffusion and Perfusion Magnetic Resonance Imaging. (pp. 140-149). New York: Raven Press, Ltd.
George, M.S., Wassermann, E.M., Williams, W.A., Callahan, A., Ketter, T.A., Basser, P.J., Hallett, M., and Post, R.M. (1995) Daily repetitive transcranial magnetic stimulation (rTMS) improves mood in depression. NeuroReport 6:1853-1856.
Le Bihan, D. and Basser, P.J. (1995) Molecular diffusion and nuclear magnetic resonance. In D. Le Bihan (Ed.), Diffusion and Perfusion Magnetic Resonance Imaging (pp. 5-17). New York: Raven Press, Ltd.
Mattiello, J., Basser, P.J., and Le Bihan, D. (1995) Analytical calculation of the b matrix in diffusion imaging. In D. Le Bihan (Ed.), Diffusion and Perfusion Magnetic Resonance Imaging. (pp. 77-99). New York: Raven Press, Ltd.

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1994

Basser, P.J. (1994) Focal magnetic stimulation of an axon. IEEE Transactions on Biomedical Engineering 41:601–606.
Basser, P.J., Mattiello, J., and LeBihan, D. (1994) Estimation of the effective self-diffusion tensor from the NMR spin echo. J Magn Reson B 103:247-254.
Basser, P.J., Mattiello, J., and LeBihan, D. (1994) MR diffusion tensor spectroscopy and imaging. Biophysical Journal 66:259-267.
Mattiello, J., Basser, P.J., and LeBihan, D. (1994) Analytical expressions for the b matrix in NMR diffusion imaging and spectroscopy. J Magn Reson A 108:131-141.
Roth, B.J., Basser, P.J., and Wikswo, J.P. (1994) A theoretical model for magneto-acoustic imaging of bioelectric currents. IEEE Trans. Bio. Med. Eng. 41:723-728.

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1993

Basser, P.J. (1993) Cable equation for a myelinated axon derived from its microstructure. Med. & Biol. Comput. 31:S87-S92.
Basser, P.J. and Grodzinsky, A.J. (1993) The Donnan model derived from microstructure. Biophysical Chemistry 46:57-68.

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1992

Basser PJ. Pressure sensor element and method to measure contact stress. #5,125,408; June 30, 1992.
Basser, P.J., Wijesinghe, R.S., and Roth, B.J. (1992) The activating function for magnetic stimulation derived from a three-dimensional volume conductor model. IEEE Transactions on Biomedical Engineering 39: 1207–1211.
Basser, P.J. (1992) Interstitial pressure, volume, and flow during infusion into brain tissue. Microvascular Research 44:143-165.

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1991

Basser, P.J. and Roth, B.J. (1991) Stimulation of a myelinated nerve axon by electromagnetic induction. Med. & Biol. Eng. & Comput. 29:261-268.

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1990

Basser PJ. Pressure sensor element to measure contact stress. #4,967,764; November 6, 1990.
Roth B.J. and Basser, P.J. (1990) A model of the stimulation of a nerve fiber by electromagnetic induction. IEEE Trans. Bio. Med. Eng. 37:588-597.

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