Papers by Partha p. Mitra
Fee, Michale S., Partha P. Mitra, and David Kleinfeld. Central somatosensory (S1) cortex (Fabri a... more Fee, Michale S., Partha P. Mitra, and David Kleinfeld. Central somatosensory (S1) cortex (Fabri and Burton 1991; Izraeli versus peripheral determinants of patterned spike activity in rat and Porter 1995;; White and Deamicis vibrissa cortex during whisking. J. Neurophysiol. 78: 1144Neurophysiol. 78: -1149Neurophysiol. 78: , 1977 as well as central pathways at the level of brain stem 1997. We report on the relationship between single-unit activity nuclei (Erzurumlu and Killackey 1979).
We derive an expression for the magnetization M(k, t) in a pulsed field gradient spin echo (PFGSE... more We derive an expression for the magnetization M(k, t) in a pulsed field gradient spin echo (PFGSE) experiment for spins diffusing in a restricted geometry with relaxation at the pore walls. Exact solutions for a slab, and simple considerations for a periodic pore geometry show that the normalized amplitude M(k,t,p)/M(O,t,p) depends only weakly on the surface relaxivity p for small p. This suggests a 'factorization' that for small p, Mp (k, t) ~ Mp (0, t) Mp=0 (k, t). This factorization is useful in understanding PFGSE experiments, because Mp=0(k, t) is theoretically simpler to analyze, and is related to the structure of the pore space.
Proceedings of the National Academy of Sciences, 1997
The computations involved in the processing of a visual scene invariably involve the interactions... more The computations involved in the processing of a visual scene invariably involve the interactions among neurons throughout all of visual cortex. One hypothesis is that the timing of neuronal activity, as well as the amplitude of activity, provides a means to encode features of objects. The experimental data from studies on cat [Gray, C. M., Konig, P., Engel, A. K. & Singer, W. (1989) Nature (London) 338, 334-337] support a view in which only synchronous (no phase lags) activity carries information about the visual scene. In contrast, theoretical studies suggest, on the one hand, the utility of multiple phases within a population of neurons as a means to encode independent visual features and, on the other hand, the likely existence of timing differences solely on the basis of network dynamics. Here we use widefield imaging in conjunction with voltage-sensitive dyes to record electrical activity from the virtually intact, unanesthetized turtle brain. Our data consist of single-trial measurements. We analyze our data in the frequency domain to isolate coherent events that lie in different frequency bands. Low frequency oscillations (<5 Hz) are seen in both ongoing activity and activity induced by visual stimuli. These oscillations propagate parallel to the afferent input. Higher frequency activity, with spectral peaks near 10 and 20 Hz, is seen solely in response to stimulation. This activity consists of plane waves and spiral-like waves, as well as more complex patterns. The plane waves have an average phase gradient of Ϸ͞2 radians͞mm and propagate orthogonally to the low frequency waves. Our results show that large-scale differences in neuronal timing are present and persistent during visual processing.
Proceedings of the National Academy of Sciences, 1998
Cortical blood flow at the level of individual capillaries and the coupling of neuronal activity ... more Cortical blood flow at the level of individual capillaries and the coupling of neuronal activity to flow in capillaries are fundamental aspects of homeostasis in the normal and the diseased brain. To probe the dynamics of blood flow at this level, we used two-photon laser scanning microscopy to image the motion of red blood cells (RBCs) in individual capillaries that lie as far as 600 micrometers below the pia mater of primary somatosensory cortex in rat; this depth encompassed the cortical layers with the highest density of neurons and capillaries. We observed that the flow was quite variable and exhibited temporal fluctuations around 0.1 Hz, as well as prolonged stalls and occasional reversals of direction. On average, the speed and flux (cells per unit time) of RBCs covaried linearly at low values of flux, with a linear density of approximately 70 cells per mm, followed by a tendency for the speed to plateau at high values of flux. Thus, both the average velocity and density of RBCs are greater at high values of flux than at low values. Time-locked changes in flow, localized to the appropriate anatomical region of somatosensory cortex, were observed in response to stimulation of either multiple vibrissae or the hindlimb. Although we were able to detect stimulus-induced changes in the flux and speed of RBCs in some single trials, the amplitude of the stimulus-evoked changes in flow were largely masked by basal fluctuations. On average, the flux and the speed of RBCs increased transiently on stimulation, although the linear density of RBCs decreased slightly. These findings are consistent with a stimulus-induced decrease in capillary resistance to flow.
PLoS Computational Biology, 2009
In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly ... more In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.
Arxiv preprint q-bio/ …, Jan 1, 2000
Magnetic Resonance Imaging, 1994
gator of the molecules of a fluid diffusing in the pores of a porous medium. For small values of ... more gator of the molecules of a fluid diffusing in the pores of a porous medium. For small values of k = 'yg&, where g is the gradient strength, 6 is the duration of the gradient pulse, and y the gyromagnetic ratio, the PFGSE amplitude gives the diffusion coefficient o(t). The exact short-time diffusion coefficient, D(t)/&, = 1 -(4m,S)/ (9& &?) -D&L!V(12 5) + ptS/6Y,, provides an important method for determining the surface to pore-volume ratio S/V,. Here the mean surface curvature H = (l/R1 + l/R&. Combining early II(f) with the magnetization decay one obtains the surface relaxivity p. The long-time effective diffusion constant derived from PFGSE gives information on the tortuosity of the connected space. The diffusion coefficient measured by PFGSE equals that derived from electrical conductivity only when p = 0. Exact solutions with partially absorbing boundary conditions for a periodic structure are used to illustrate the influence of p on the diffusion coefficient. M(k,t) can be well represented by a convolution of the structure factor of the connected pore space with an appropriate Gaussian propagator. This ansatz provides a model-independent way of obtaining the structure factor. Kevwords: Restricted diffusion: Porous medium: NMR surface relaxation; NMR pulsed field gradient; Surfaceto-volume ratio; Formation factor. 12(2):279-284; 1994. Kleinberg, R.L. Pore-size distribution, pore coupling, and transverse relaxation spectra of porous rocks. Magn. Reson. Imaging 12(2):271-274; 1994. Callaghan, P.T.; MacGowan, D.; Packer, K.J.; Zelaya, F.O. Diffraction like effects in NMR diffusion studies of fluids in porous solids. Nature 351:467-468; 1991.
Journal of Neuroscience Methods - J NEUROSCI METH, 1997
The Publisher regrets that the paper was inadvertently printed without incorporating the correcti... more The Publisher regrets that the paper was inadvertently printed without incorporating the corrections to the page proofs. Note the following:
Journal of Neuroscience Methods, 1996
Neuronal noise sources and systematic variability in the shape of a spike limit the ability to so... more Neuronal noise sources and systematic variability in the shape of a spike limit the ability to sort multiple unit waveforms recorded from nervous tissue into their single neuron constituents. Here we present a procedure to efficiently sort spikes in the presence of noise that is anisotropic, i.e., dominated by particular frequencies, and whose amplitude distribution may be non-Gaussian, such as occurs when spike waveforms are a function of interspike interval. Our algorithm uses a hierarchical clustering scheme. First, multiple unit records are sorted into an overly large number of clusters by recursive bisection. Second, these clusters are progressively aggregated into a minimal set of putative single units based on both similarities of spike shape as well as the statistics of spike arrival times, such as imposed by the refractory period. We apply the algorithm to waveforms recorded with chronically implanted micro-wire stereotrodes from neocortex of behaving rat. Natural extensions of the algorithm may be used to cluster spike waveforms from records with many input channels, such as those obtained with tetrodes and multiple site optical techniques.
A major challenge in the histological sectioning of brain tissue is achieving accurate alignment ... more A major challenge in the histological sectioning of brain tissue is achieving accurate alignment in the standard coronal, horizontal, or sagittal planes. Correct alignment is desirable for ease of subsequent analysis and is a prerequisite for computational registration and algorithm-based quantification of experimental data. We have developed a simple and low-cost technique for whole-brain cryosectioning of rodent brains that reliably results in a precise alignment of stereotactic coordinates. The system utilises a 3-D printed model of a mouse brain to create a tailored cavity that is used to align and support the brain during freezing. The alignment of the frozen block is achieved in relation to the fixed edge of the mold. The system also allows for two brains to be frozen and sectioned simultaneously. System components, procedural steps, and examples of the end results are presented.
IEEE Transactions on Signal Processing, 2000
We develop the concept of joint time-frequency estimation of wireless channels. The motivation is... more We develop the concept of joint time-frequency estimation of wireless channels. The motivation is to optimize channel usage by increasing the signal-to-noise ratio (SNR) after demodulation while keeping training overhead at a moderate level. This issue is important for single-input single-output (SISO) and multipleinput multiple-output (MIMO) systems but particularly so for the latter. Linear operators offer a general mathematical framework for symbol modulation in channels that vary both temporally and spectrally within the duration and bandwidth of one symbol. In particular, we present a channel model that assumes first-order temporal and spectral fluctuations within one symbol or symbol block. Discrete prolate spheroidal sequences (Slepian sequences) are used as pulse-shaping functions. The channel operator in the Slepian basis is almost tridiagonal, and the simple intersymbol interference pattern can be exploited for efficient and fast decoding using Viterbi's algorithm. To prove the concept, we use the acoustic channel as a meaningful physical analogy to the radio channel. In acoustic 2 2 MIMO experiments, our method produced estimation results that are superior to first-order time-only, frequencyonly, and zeroth-order models by 7.0, 9.4, and 11.6 db. In computer simulations of cellular wireless channels with realistic temporal and spectral fluctuations, time-frequency estimation gains us 12 to 18 db over constant-only estimation in terms of received SNR when signal-to-receiver-noise is 10 to 20 db. The bit error rate (BER) decreases by a factor of two for a binary constellation.
2012 46th Annual Conference on Information Sciences and Systems (CISS), 2012
The three-dimensional data-driven Anatomic Gene Expression Atlas of the adult mouse brain consist... more The three-dimensional data-driven Anatomic Gene Expression Atlas of the adult mouse brain consists of numerized in situ hybridization data for thousands of genes, co-registered to the Allen Reference Atlas. We propose quantitative criteria to rank genes as markers of a brain region, based on the localization of the gene expression and on its functional fitting to the shape of the region. These criteria lead to natural generalizations to sets of genes. We find sets of genes weighted with coefficients of both signs with almost perfect localization in all major regions of the left hemisphere of the brain, except the pallidum. Generalization of the fitting criterion with positivity constraint provides a lesser improvement of the markers, but requires sparser sets of genes.
PLoS Computational Biology, 2009
In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly ... more In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.
Journal of Neuroscience Methods, 2010
In analyzing neurophysiologic data, individual experimental trials are usually assumed to be stat... more In analyzing neurophysiologic data, individual experimental trials are usually assumed to be statistically independent. However, many studies employing functional imaging and electrophysiology have shown that brain activity during behavioral tasks includes temporally correlated trial-to-trial fluctuations. This could lead to spurious results in statistical significance tests used to compare data from different interleaved behavioral conditions presented throughout an experiment. We characterize trialto-trial fluctuations in local field potentials recorded from the frontal cortex of a macaque monkey performing an oculomotor delayed response task. Our analysis identifies slow fluctuations (<0.1 Hz) of spectral power in 22/27 recording sessions. These trial-to-trial fluctuations are non-Gaussian, and call into question the statistical utility of standard trial shuffling. We compare our results with evidence for slow fluctuations in human functional imaging studies and other electrophysiologic studies in nonhuman primates.
IEEE Transactions on Information Theory, 2000
Significant volumes of knowledge have been accumulated in recent years linking subtle genetic var... more Significant volumes of knowledge have been accumulated in recent years linking subtle genetic variations to a wide variety of medical disorders from Cystic Fibrosis to mental retardation. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, largely due to the relatively tedious and expensive process of DNA sequencing. Since the genetic polymorphisms that underlie these disorders are relatively rare in the human population, the presence or absence of a disease-linked polymorphism can be thought of as a sparse signal. Using methods and ideas from compressed sensing and group testing, we have developed a cost-effective genotyping protocol. In particular, we have adapted our scheme to a recently developed class of high throughput DNA sequencing technologies, and assembled a mathematical framework that has some important distinctions from 'traditional' compressed sensing ideas in order to address different biological and technical constraints.
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Papers by Partha p. Mitra