Structure and Measurement of the Brain

READING LIST -- Winter 2015


(1) Neurons


pdf -- Zigmond, M.J., F.E. Bloom, S.C. Landis, J.L. Roberts, and L.R. Squire eds. (1999) Fundamental Neuroscience, Academic Press, Chaps. 5, 6, and part of 7, pp. 107-165.

pdf -- Douglas, R., H. Markram, and K. Martin (2004) Neocortex. In G.M. Shepherd (ed.), Synaptic Organization In the Brain, Oxford, pp. 499-558.

Additional background, cellular physiology:

pdf -- Callaway, J.S. (1998) Local circuits in primary visual cortex of the macaque monkey. Annual Review of Neuroscience 21:47-74.

pdf -- Arieli, A., A. Sterkin, A. Grinvald, and A. Aertsen (1996) Dynamics of ongoing activity: explanation of the large variability in evoked cortical responses. Science 273:1868-1871.

pdf -- Larkum, M.E., J.J. Zhu, and B. Sakmann (1999) A new cellular mechanism for coupling inputs arriving at different cortical layers. Nature 398:338-341.

(2) Synaptic Plasticity, Models


pdf -- Dan, Y. and M.-M. Poo (2005) Spike timing-dependent plasticity: from synapse to perception. Physiological Reviews 86:1033-1048.

Additional background, neural models:

pdf -- Hopfield, J.J. (1984) Neurons with graded response have collective computational properties like those of two-state neurons. Proceedings of the National Academy of Science USA 81:3088-3092.

pdf -- Linsker, R. (1986a) From basic network principles to neural architecture: Emergence of spatial-opponent cells. Proceedings of the National Academy of Science USA 83:7508- 7512.

pdf -- Sereno, M.I. and M.E. Sereno (1991) Learning to see rotation and dilation with a Hebb rule. In R.P. Lippmann, J.E. Moody, and D.S. Touretzky (eds.), Advances in Neural Information Processing Systems 3. Morgan Kaufmann Publishers, pp. 320-326.

pdf -- Wilson, M.A. and J.M. Bower (1989) The simulation of large-scale neural networks. In C. Koch and I. Segev (eds.), Methods in Neuronal Modeling. MIT Press, pp. 291-331.

(2b Neural Development


pdf -- Sereno, M.I. (1991) The brain in two pages.

pdf -- Grove, E.A. and T. Fukuchi-Shimogori (2003) Generating the cerebral cortical area map. Annual Review of Neuroscience 26:335-380.

Additional background, development:

pdf -- O'Leary, D.D.M. (1989) Do cortical areas emerge from a protocortex? Trends in Neurosciences 12:400-406.

pdf -- McLaughlin, T. and D.M. O'Leary (2005) Molecular gradients and development of retinotopic maps. Annual Review of Neuroscience 28:327-355.

pdf -- Ghosh, A., A. Antonioni, S.K. McConnell, and C.J. Shatz (1990) Requirement for subplate neurons in the formation of thalamocortical connections. Nature 347:179-181.

pdf -- Hahm, J.-O, R.B. Langdon, and M. Sur (1991) Disruption of retinogeniculate afferent segregation by antagonists to NMDA receptors. Nature 351:568-570.

pdf -- Williams, R.W., D. Hogan and P.E. Garraghty (1994) Target recognition and visual maps in the thalamus of achiasmatic dogs. Nature 367:637-639.

pdf -- Brown, A., P.A. Yates, P. Burrola, D. Ortuno, A. Vaidya, T.H. Jessell, S.L. Pfaff, D.D.M. O'Leary, and G. Lemke (2000) Topographic mapping from the retina to the midbrain is controlled by relative but not absolute levels of EphA receptor signaling. Cell 102:77-88.

pdf -- Hatten, M.E. (1999) Central nervous system neuronal migration. Annual Review of Neurosciences 22:511-539.

pdf -- Rhinn, M. and M. Brand (2001) The midbrain-hindbrain boundary organizer. Current Opinion in Neurobiology 11:34-42.

pdf -- Rhinn, M., A. Picker, and M. Brand (2006) Global and local mechanisms of forebrain and midbrain patterning. Current Opinion in Neurobiology 16:5-12.

(3) Visual System I


pdf -- Callaway, E.M. (2005) Structure and function of parallel pathways in the primate early visual system Journal of Physiology 566:13-19.

pdf -- Tanaka, K. (1998) Representation of visual motion in the extrastriate visual cortex. In T. Watanabe (ed.), High-level motion processing. MIT Press, pp. 295-313.

Additional background, visual system:

pdf -- Sereno, M.I. (1988) The visual system. In W. von Seelen, G. Shaw, and U.M. Leinhos (eds.), Organization of Neural Networks. Weinheim: VCH Verlagsgesellschaft, pp. 167-184.

pdf -- Ohzawa, I. (1998) Mechanisms of stereoscopic vision: the disparity energy model. Current Opinion in Neurobiology 8:509-515.

pdf -- Sincich, L.C. and J.C. Horton (2005) The circuitry of V1 and V2 intergration of color, form, and motion. Annual Review of Neuroscience 28:303-326.

pdf -- Yabuta, N.H., A. Sawatari, and E.M. Callaway (2001) Two functional channels from primary visual cortex to dorsal visual cortical areas. Science 292:297-300.

(4) Visual System II

pdf -- Sereno, M.I. and J.M. Allman (1991) Cortical visual areas in mammals. In A.G. Leventhal (ed.), The Neural Basis of Visual Function. Macmillan, pp. 160-172.

pdf -- Colby, C.L. and M.E. Goldberg (1999) Space and attention in parietal cortex. Annual Review of Neurosciences 22:319-349.

Additional background, visual system:

pdf -- Sereno, M.I., C.T. McDonald, and J.M. Allman (1994) Analysis of retinotopic maps in extrastriate cortex. Cerebral Cortex 4:601-620.

pdf -- Felleman, D.J. and D.C. Van Essen (1991) Distributed hierarchical processing in the primate cerebral cortex. Cerebral Cortex 1:1-47.

pdf -- Haenny, P.E., J.H.R. Maunsell, and P.H. Schiller (1988) State dependent activity in monkey visual cortex. II. Retinal and extraretinal factors. Experimental Brain Research 69:245-259.

pdf -- Desimone, R. and J. Duncan (1995) Neural mechanisms of selective visual attention. Annual Review of Neuroscience 18:193-222.

pdf -- Sereno, A.B. and J.H.R. Maunsell (1998) Shape selectivity in primate lateral intraparietal cortex. Nature 395:500-503.

pdf -- Logothetis, N.K. and J. Pauls (1995) Psychophysical and physiological evidence for viewer-centered object representations in the primate. Cerebral Cortex 5:270-288.

pdf -- Wang, G., M. Tanifuji, and K. Tanaka (1998) Functional architecture in monkey inferotemporal cortex revealed by in vivo optical imaging. Neuroscience Research 32:33-46.

pdf -- Rolls, E.T., N.C. Aggelopoulos, and F. Zheng (2003) The receptive fields of inferior temporal cortex neurons in natural scenes. Journal of Neuroscience 23:339-348.

(5) Somatosensory System


pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System -- Somatosensory System. Springer-Verlag, pp. 149-164.

pdf -- Iwamura, Y. (1998) Hierarchical somatosensory processing. Current Opinion in Neurobiology 8:522-528.

pdf -- Kaas, J.H. (2000) The reorganization of sensory and motor maps after injury in adult mammals. In M.S. Gazzaniga, ed., The New Cognitive Neurosciences, MIT Press, pp. 223-236.

Additional background, somatosensory system:

pdf -- Pons, T.P., P.E. Garraghty, A.K. Ommaya, J.H. Kaas, E. Taub, and M. Mishkin (1991) Massive cortical reorganization after sensory deafferentation in adult macaques. Science 252: 1857-1860.

pdf -- Buonomano, D.V. and M.M. Merzenich (1998) Cortical plasticity: from synapses to maps. Annual Review of Neuroscience 21:149-186.

pdf -- D.R. Sengelaub, N. Muja, A.C. Mills, W.A. Myers, J.D. Churchill, and P.E. Garraghty (1997) Denervation-induced sprouting of intact peripheral afferents into the cuneate nucleus of adult rats. Brain Research 769:256-262.

pdf -- Calford, M.B., and R. Tweedale (1990) Interhemispheric transfer of plasticity in the cerebral cortex. Science 249:805-807.

(6) Auditory System


pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System -- Auditory System. Springer-Verlag, pp. 165-179.

pdf -- Suga, N. (1988) Auditory neuroethology and speech processing: complex-sound processing by combination-sensitive neurons. In G.M. Edelman, W.E. Gall, and W.M Cowan (eds.), Auditory Function: Neurobiological Bases of Hearing. John Wiley and Sons, pp. 679-720.

pdf -- Konishi, M., T.T. Takahashi, H. Wagner, W.E. Sullivan, and C.E. Carr (1988) Neurophysiological and anatomical substrates of sound localization in the the owl. In G.M. Edelman, W.E. Gall, and W.M Cowan (eds.), Auditory Function: Neurobiological Bases of Hearing. John Wiley and Sons, pp. 721-745.

Additional background, auditory system:

pdf -- Kulkarni, A. and H.S. Colburn (1998) Role of spectral detail in sound-source localization. Nature 396:747-749.

pdf -- McAlpine, D., D. Jiang, A.R. Palmer (2001) A neural code for low-frequency sound localization in mammals. Nature Neuroscience 4:396-401.

pdf -- Brand, A., O. Behrend, T. Marquardt, D. McAlpine, and B. Grothe (2002) Precise inhibition is essential for microsecond interaural time difference coding. Nature 417:543-547.

pdf -- Carr, C.E. and C. Koppl (2004) Coding interaural time differences at low best frequencies in the barn owl. Journal of Physiology - Paris 98:99-112.

pdf -- Rauschecker, J.P. (1998) Cortical processing of complex sounds. Current Opinion in Neurobiology 8:516-521.

pdf -- deCharms, R.C., D.T. Blake, and M.M. Merzenich (1998) Optimizing sound features for cortical neurons. Science 280:1439-1443.

(7) Motor System I (eye movements)


pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System. Springer-Verlag, pp. 247-278.

pdf -- Sparks, D.L. and R. Hartwich-Young (1989) The deep layers of the superior colliculus. In R.H. Wurtz and M.E. Goldberg (eds.) The Neurobiology of Saccadic Eye Movements. Elsevier, pp. 213-255.

pdf -- Sommer, M.A. and R.H. Wurtz (2006) Influence of the thalamus on spatial visual processing in frontal cortex. Nature 444:374-377.

Additional background, eye movements:

pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System. Springer-Verlag, pp. 185-196.

pdf -- Wurtz, R.H. and D.P. Munoz (1995) Role of monkeys superior colliculus in control of saccades and fixation. In M.S. Gazzaniga (ed.), The Cognitive Neurosciences, MIT Press, pp. 533-548.

pdf -- Rodgers, C., D.P. Munoz, S.H. Scott, and M. Pare (2006) Discharge properties of monkey tectoreticular neurons. Journal of Neurophysiology 95:3502-3511.

pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System. Springer-Verlag, pp. 221-236.

(8) Motor System II


pdf -- Thompson, R.F. and D.J. Krupa (1994) Organization of memory traces in the mammalian brain. Annual Review of Neuroscience 17:519-549.

Additional background, motor system:

pdf -- Hoover, J.E. and P.L. Strick (1993) Multiple output channels in the basal ganglia. Science 259:819-821.

pdf -- Hoover, J.E. and P.L. Strick (1999) The organization of cerebellar and basal ganglia outputs to primary motor cortex as revealed by retrograde transneuronal transport of Herpes Simplex Virus Type 1. Journal of Neuroscience 19:1446-1463.

pdf -- Clower, D.M., R.P. Dum, P.L. Strick (2005) Basal ganglia and cerebellar inputs to 'AIP'. Cerebral Cortex 15:913-920.

pdf -- Kaji, R., R. Urushihara, N. Murase, H. Shimazu, S. Goto (2005) bnormal sensory gating in basal ganglia disorders. Journal of Neurology 252 [Suppl 4]:IV/13-IV/16.

pdf -- Carpenter, A.F., A.P. Georgopoulos and G. Pellizzer (1999) Motor cortical encoding of serial order in a context-recall task. Science 283:1752-1757.

pdf -- Rizzolatti, G., L. Fogassi, and V. Gallese (2000) Cortical mechanisms subserving object grasping and action recognition: A new view on the cortical motor functions. In M.S. Gazzaniga, ed., The New Cognitive Neurosciences, MIT Press, pp. 539-552.

pdf -- Graziano, M. (2006) The organization of behavioral repertoire in motor cortex. Annual Review of Neuroscience 29:105-134.

(9) Limbic System


pdf -- Muller, R.U., J.B. Ranck, and J.S. Taube (1996) Head direction cells: properties and functional significance. Current Opinion in Neurobiology 6:196-206.

pdf -- Fyhn, M., S. Molden, M.P. Witter, E.I. Moser, and M.B. Moser (2004) Spatial representation in the entorhinal cortex. Science 305:1258-1264.

pdf -- Hafting, T.., Fyhn, S. Molden, M.-B. Moser, E.I. Moser (2005) Microstructure of a spatial map in the entorhinal cortex. Nature 436:801-806.

Additional background, limbic system:

pdf -- Nieuwenhuys, R., J. Voogd, and C. van Huizen (1988) The Human Central Nervous System. Springer-Verlag, pp. 293-309, 323-344.

pdf -- Muller, R.U., J.L. Kubie, and J.B. Ranck (1987) Spatial firing patterns of hippocampal complex-spike cells in a fixed environment. Journal of Neuroscience 7:1935-1950.

pdf -- Muller, R.U. and J.L. Kubie (1987) The effects of changes in the environment on the spatial firing of hippocampal complex-spike cells. Journal of Neuroscience 7:1951- 1968.

pdf -- Taube, J.S., R.U. Muller, and J.B. Ranck (1990) Head-direction cells recorded from the postsubiculum in freely moving rats. I. description and quantitative analysis. Journal of Neuroscience 10:420-435.

pdf -- Zugaro, M.B., A Berthoz, and S.I. Wiener (2001) Background, but not foreground, spatial cues are taken as references for head direction responses by rat anterodorsal thalamus neurons. Journal of Neuroscience 21:RC154.

pdf -- Yoganarasimha, D. and J.J. Knierim (2004) Coupling between place cells and head direction cells during relative translations and rotation of distal landmarks. Experimental Brain Research 160:344-359.

pdf -- Sargolini, F., M. Fyhn, T. Hafting, B.L. McNaughton, M.P. Witter, M.B. Moser, and E.I. Moser (2006) Conjunctive representation of position, direction, and velocity in entorhinal cortex. Science 312:758-762.

pdf -- Brivanlou, I.H., J.L.M. Dantzker, C.F. Stevens, and E.M. Callaway (2004) Topographic specificity of functional connections from hippocampal CA3 to CA1. Proceedings of the National Academcy of Science USA 101:2560-2565.

(10) MRI: Signals and Contrast, Image Formation


pdf -- Huettel, S.A, A.W.Song, and G. McCarthy (2004) Functional Magnetic Resonance Imaging, Chap. 4, pp. 75-97.

pdf -- precis of Sereno hand-written notes (PDF includes all links below)

[single page links]

Spin and Precession (p. 2)

Bloch Equation (p. 3)

Bloch Equation--Matrix Version, incl dot/cross/complex products (p. 4)

Saturation-Recovery Signal (p. 13)

Signal Equation (p. 6 -- for ref, we only covered in words)

Phase-Sensitive Detection (p. 7 -- for ref, we only covered in words)

Spin Echo (p. 9)

Gradient Echo (p. 12)

Frequency-Encoding--Avoid This Intuition (p. 28)

Frequency-Encoding--Correct Intuition (p. 29)

Spin Phase in Image Space--What Gradients Do (p. 34)

Complex Algebra (p. 20)

Fourier Transform (p. 21)

Aliasing and FOV (p. 37)

Additional background, MRI image formation:

pdf -- Full 63-page Sereno hand-written UCSD Neuroimaging class notes

simple matlab examples

Back to syllabus