Localization of sources of human evoked responses

The evoked response, a signal present in the electro-encephalogram when specific sense modalities are stimulated with brief sensory inputs, has not yet revealed as much about brain function as it apparently promised when first recorded in the late 1940's. One of the problems has been to record the responses at a large number of points on the surface of the head; thus in order to achieve greater spatial resolution than previously attained, a 50-channel recording system was designed to monitor experiments with human visually evoked responses.

Conventional voltage versus time plots of the responses were found inadequate as a means of making qualitative studies of such a large data space. This problem was solved by creating a graphical display of the responses in the form of equipotential maps of the activity at successive instants during the complete response. In order to ascertain the necessary complexity of any models of the responses, factor analytic procedures were used to show that models characterized by only five or six independent parameters could adequately represent the variability in all recording channels.

One type of equivalent source for the responses which meets these specifications is the electrostatic dipole. Two different dipole models were studied: the dipole in a homogeneous sphere and the dipole in a sphere comprised of two spherical shells (of different conductivities) concentric with and enclosing a homogeneous sphere of a third conductivity. These models were used to determine nonlinear least squares fits of dipole parameters to a given potential distribution on the surface of a spherical approximation to the head. Numerous tests of the procedures were conducted with problems having known solutions. After these theoretical studies demonstrated the applicability of the technique, the models were used to determine inverse solutions for the evoked response potentials at various times throughout the responses. It was found that reliable estimates of the location and strength of cortical activity were obtained, and that the two models differed only slightly in their inverse solutions. These techniques enabled information flow in the brain, as indicated by locations and strengths of active sites, to be followed throughout the evoked response.

The biological sense of smell: olfactory search behavior and a metabolic view for olfactory perception

Part I of the thesis describes the olfactory searching and scanning behaviors of rats in a wind tunnel, and a detailed movement analysis of terrestrial arthropod olfactory scanning behavior. Olfactory scanning behaviors in rats may be a behavioral correlate to hippocampal place cell activity.

Part II focuses on the organization of olfactory perception, what it suggests about a natural order for chemicals in the environment, and what this in tum suggests about the organization of the olfactory system. A model of odor quality space (analogous to the "color wheel") is presented. This model defines relationships between odor qualities perceived by human subjects based on a quantitative similarity measure. Compounds containing Carbon, Nitrogen, or Sulfur elicit odors that are contiguous in this odor representation, which thus allows one to predict the broad class of odor qualities a compound is likely to elicit. Based on these findings, a natural organization for olfactory stimuli is hypothesized: the order provided by the metabolic process. This hypothesis is tested by comparing compounds that are structurally similar, perceptually similar, and metabolically similar in a psychophysical cross-adaptation paradigm. Metabolically similar compounds consistently evoked shifts in odor quality and intensity under cross-adaptation, while compounds that were structurally similar or perceptually similar did not. This suggests that the olfactory system may process metabolically similar compounds using the same neural pathways, and that metabolic similarity may be the fundamental metric about which olfactory processing is organized. In other words, the olfactory system may be organized around a biological basis.

The idea of a biological basis for olfactory perception represents a shift in how olfaction is understood. The biological view has predictive power while the current chemical view does not, and the biological view provides explanations for some of the most basic questions in olfaction, that are unanswered in the chemical view. Existing data do not disprove a biological view, and are consistent with basic hypotheses that arise from this viewpoint.

Analysis of temporal structure in spike trains of visual cortical area MT

The temporal structure of neuronal spike trains in the visual cortex can provide detailed information about the stimulus and about the neuronal implementation of visual processing. Spike trains recorded from the macaque motion area MT in previous studies (Newsome et al., 1989a; Britten et al., 1992; Zohary et al., 1994) are analyzed here in the context of the dynamic random dot stimulus which was used to evoke them. If the stimulus is incoherent, the spike trains can be highly modulated and precisely locked in time to the stimulus. In contrast, the coherent motion stimulus creates little or no temporal modulation and allows us to study patterns in the spike train that may be intrinsic to the cortical circuitry in area MT. Long gaps in the spike train evoked by the preferred direction motion stimulus are found, and they appear to be symmetrical to bursts in the response to the anti-preferred direction of motion. A novel cross-correlation technique is used to establish that the gaps are correlated between pairs of neurons. Temporal modulation is also found in psychophysical experiments using a modified stimulus. A model is made that can account for the temporal modulation in terms of the computational theory of biological image motion processing. A frequency domain analysis of the stimulus reveals that it contains a repeated power spectrum that may account for psychophysical and electrophysiological observations.

Some neurons tend to fire bursts of action potentials while others avoid burst firing. Using numerical and analytical models of spike trains as Poisson processes with the addition of refractory periods and bursting, we are able to account for peaks in the power spectrum near 40 Hz without assuming the existence of an underlying oscillatory signal. A preliminary examination of the local field potential reveals that stimulus-locked oscillation appears briefly at the beginning of the trial.

The central nervous control of walking in the locust, Schistocerca Americana

Rhythmic motor behaviors in all animals appear to be under the control of "central pattern generator" circuits, neural circuits which can produce output patterns appropriate for behavior even when isolated from their normal peripheral inputs. Insects have been a useful model system in which to study the control of legged terrestrial locomotion. Much is known about walking in insects at the behavioral level, but to date there has been no clear demonstration that a central pattern generator for walking exists. The focus of this thesis is to explore the central neural basis for locomotion in the locust, Schistocerca americana.

Rhythmic motor patterns could be evoked in leg motor neurons of isolated thoracic ganglia of locusts by the muscarinic agonist pilocarpine. These motor patterns would be appropriate for the movement of single legs during walking. Rhythmic patterns could be evoked in all three thoracic ganglia, but the segmental rhythms differed in their sensitivities to pilocarpine, their frequencies, and the phase relationships of motor neuron antagonists. These different patterns could be generated by a simple adaptable model circuit, which was both simulated and implemented in VLSI hardware. The intersegmental coordination of leg motor rhythms was then examined in preparations of isolated chains of thoracic ganglia. Correlations between motor patterns in different thoracic ganglia indicated that central coupling between segmental pattern generators is likely to contribute to the coordination of the legs during walking.

The work described here clearly demonstrates that segmental pattern generators for walking exist in insects. The pattern generators produce motor outputs which are likely to contribute to the coordination of the joints of a limb, as well as the coordination of different limbs. These studies lay the groundwork for further studies to determine the relative contributions of central and sensory neural mechanisms to terrestrial walking.

Spinal cord injury therapy through active learning

Therapy employing epidural electrostimulation holds great potential for improving therapy for patients with spinal cord injury (SCI) (Harkema et al., 2011). Further promising results from combined therapies using electrostimulation have also been recently obtained (e.g., van den Brand et al., 2012). The devices being developed to deliver the stimulation are highly flexible, capable of delivering any individual stimulus among a combinatorially large set of stimuli (Gad et al., 2013). While this extreme flexibility is very useful for ensuring that the device can deliver an appropriate stimulus, the challenge of choosing good stimuli is quite substantial, even for expert human experimenters. To develop a fully implantable, autonomous device which can provide useful therapy, it is necessary to design an algorithmic method for choosing the stimulus parameters. Such a method can be used in a clinical setting, by caregivers who are not experts in the neurostimulator's use, and to allow the system to adapt autonomously between visits to the clinic. To create such an algorithm, this dissertation pursues the general class of active learning algorithms that includes Gaussian Process Upper Confidence Bound (GP-UCB, Srinivas et al., 2010), developing the Gaussian Process Batch Upper Confidence Bound (GP-BUCB, Desautels et al., 2012) and Gaussian Process Adaptive Upper Confidence Bound (GP-AUCB) algorithms. This dissertation develops new theoretical bounds for the performance of these and similar algorithms, empirically assesses these algorithms against a number of competitors in simulation, and applies a variant of the GP-BUCB algorithm in closed-loop to control SCI therapy via epidural electrostimulation in four live rats. The algorithm was tasked with maximizing the amplitude of evoked potentials in the rats' left tibialis anterior muscle. These experiments show that the algorithm is capable of directing these experiments sensibly, finding effective stimuli in all four animals. Further, in direct competition with an expert human experimenter, the algorithm produced superior performance in terms of average reward and comparable or superior performance in terms of maximum reward. These results indicate that variants of GP-BUCB may be suitable for autonomously directing SCI therapy.

Study of ion movements in isolated chicken retinas during spreading depression

Spreading depression (SD) is a phenomenon observed in several sections of vertebrate central nervous system. It can occur spontaneously or be evoked by a variety of stimuli, and consists of a wave of depression of the normal electrical activity of the nervous tissue which spreads slowly in all directions in the tissue. This wave of depression is accompanied by several concomitants including ion movements. All the concomitants of SD can be explained by an increase in the sodium permeability of the plasma membranes of cellular elements involved in this phenomenon.

In the chicken retina, SD is accompanied by a transparency change which can be detected with the naked eye. The isolated retina is a thin (0.1 mm) membrane in which the extracellular fluid quickly and completely equilibrates with the incubation solutions. This preparation was therefore used to study the ion movements during SD by measuring and comparing the ion contents and the extracellular space (ECS) of retinas incubated in various solutions of which some inhibited SD, whereas others allowed this phenomenon to occur.

The present study has shown that during SD there is a shift of extracellular sodium into the intracellular compartment of the retina, a release of intracellular K and a decrease in the magnitude of ECS. These results are in agreement with previous postulates about SD, although the in vitro experimental condition makes the ion movements appear larger and the loss of ECS smaller than observed in the intact cortical tissue. The movements of Na and K, in opposite directions, are reversible. The development and magnitudes of SD is very little affected by deprivation of the oxygen supply.

It was established that the inward sodium shift is not a consequence of an arrest of the Na-pump. It can be prevented, together with SD by the membrane stabilizers, magnesium and procaine. Spreading depression and the ion movements are incompletely inhibited by tetrodotoxin, which blocks the sodium influx into nerve fibers during the action potential. The replacement of Na in the bathing solution by Li does not prevent SD, which is accompanied by Li accumulation in the intracellular compartment. From these experiments and others it was concluded that the mechanism underlying SD and the ion shifts is an increase in the sodium permeability of cell membranes.

The ionic basis of frequency selectivity in hair cells of the bullfrog's sacculus

Hair cells from the bull frog's sacculus, a vestibular organ responding to substrate-borne vibration, possess electrically resonant membrane properties which maximize the sensitivity of each cell to a particular frequency of mechanical input. The electrical resonance of these cells and its underlying ionic basis were studied by applying gigohm-seal recording techniques to solitary hair cells enzymatically dissociated from the sacculus. The contribution of electrical resonance to frequency selectivity was assessed from microelectrode recordings from hair cells in an excised preparation of the sacculus.

Electrical resonance in the hair cell is demonstrated by damped membrane-potential oscillations in response to extrinsic current pulses applied through the recording pipette. This response is analyzed as that of a damped harmonic oscillator. Oscillation frequency rises with membrane depolarization, from 80-160 Hz at resting potential to asymptotic values of 200-250 Hz. The sharpness of electrical tuning, denoted by the electrical quality factor, Q_e, is a bell-shaped function of membrane voltage, reaching a maximum value around eight at a membrane potential slightly positive to the resting potential.

In whole cells, three time-variant ionic currents are activated at voltages more positive than -60 to -50 mV; these are identified as a voltage-dependent, non-inactivating Ca current (I_ca), a voltage-dependent, transient K current (I_a), and a Ca-dependent K current (I_c). The C channel is identified in excised, inside-out membrane patches on the basis of its large conductance (130-200 pS), its selective permeability to Kover Na or Cl, and its activation by internal Ca ions and membrane depolarization. Analysis of open- and closed-lifetime distributions suggests that the C channel can assume at least two open and three closed kinetic states.

Exposing hair cells to external solutions that inhibit the Ca or C conductances degrades the electrical resonance properties measured under current-clamp conditions, while blocking the A conductance has no significant effect, providing evidence that only the Ca and C conductances participate in the resonance mechanism. To test the sufficiency of these two conductances to account for electrical resonance, a mathematical model is developed that describes I_ca, I_c, and intracellular Ca concentration during voltage-clamp steps. I_ca activation is approximated by a third-order Hodgkin-Huxley kinetic scheme. Ca entering the cell is assumed to be confined to a small submembrane compartment which contains an excess of Ca buffer; Ca leaves this space with first-order kinetics. The Ca- and voltage-dependent activation of C channels is described by a five-state kinetic scheme suggested by the results of single-channel observations. Parameter values in the model are adjusted to fit the waveforms of I_ca and I_c evoked by a series of voltage-clamp steps in a single cell. Having been thus constrained, the model correctly predicts the character of voltage oscillations produced by current-clamp steps, including the dependencies of oscillation frequency and Q_e on membrane voltage. The model shows quantitatively how the Ca and C conductances interact, via changes in intracellular Ca concentration, to produce electrical resonance in a vertebrate hair cell.

Conditioned responses in the reticular formation

Unit activity was recorded from the midbrain and pons of 40 freely moving rats in an appetitive classical conditioning situation. Responses to auditory stimuli were observed from 100 units before and during a conditioning procedure in which presentation of food occurred 1 sec after the onset of the auditory stimulus. Conditioned unit responses (i.e., spike rate accelerations or decelerations) were considered to be positive when 1) no similar responses appeared prior to conditioning, and 2) latencies were equal to or less than those of sensory responses derived from the inferior colliculus. Such short latency conditioned unit responses were recorded from 11 probes located in the mid-lateral pert of the ventral region of the brain stem. This region was differentiated from paramedian, far lateral and dorsal parts of the brain stem reticular formation. Conditioned unit responses of considerably longer latencies were recorded from 76 probe located in these other regions. Among the longer latency responses interesting differences appeared in experiments conducted after the first conditioning series was completed. With additional training, units in the "reticular activating system" of midbrain and pons tended to yield stabilized responses in the early portion of the CS-US interval closely related in time to the orientation responses evoked by the CS. In contrast, the responses of units in the limbic midbrain tended to stabilize in the later part of the CS-US interval closely related in time to preparatory responses tied to the US. During extinction when the auditory stimulus was no longer followed by presentation of food, many of the responses were reduced to their pre-conditioning levels. However, there was a tendency for units which had displayed short latency responses on the first conditioning day to be more resistant to extinction than units which had displayed longer latency conditioned responses. The data were interpreted as indicating a local correlate of learning in the reticular formation of midbrain end pons and a separation of the midbrain system into at least two areas: 1) the classical "reticular activating system" related to orienting reactions, and 2) the limbic midbrain areas related to drives and rewards. Because the ventral and mid-lateral area with very short latency conditioned responses was not clearly tied to either of these; it was considered as possibly representing a third division.

Microscopic Origin of Macroscopic Strength in Granular Media: A Numerical and Analytical Approach

Constitutive modeling in granular materials has historically been based on macroscopic experimental observations that, while being usually effective at predicting the bulk behavior of these type of materials, suffer important limitations when it comes to understanding the physics behind grain-to-grain interactions that induce the material to macroscopically behave in a given way when subjected to certain boundary conditions.

The advent of the discrete element method (DEM) in the late 1970s helped scientists and engineers to gain a deeper insight into some of the most fundamental mechanisms furnishing the grain scale. However, one of the most critical limitations of classical DEM schemes has been their inability to account for complex grain morphologies. Instead, simplified geometries such as discs, spheres, and polyhedra have typically been used. Fortunately, in the last fifteen years, there has been an increasing development of new computational as well as experimental techniques, such as non-uniform rational basis splines (NURBS) and 3D X-ray Computed Tomography (3DXRCT), which are contributing to create new tools that enable the inclusion of complex grain morphologies into DEM schemes.

Yet, as the scientific community is still developing these new tools, there is still a gap in thoroughly understanding the physical relations connecting grain and continuum scales as well as in the development of discrete techniques that can predict the emergent behavior of granular materials without resorting to phenomenology, but rather can directly unravel the micro-mechanical origin of macroscopic behavior.

In order to contribute towards closing the aforementioned gap, we have developed a micro-mechanical analysis of macroscopic peak strength, critical state, and residual strength in two-dimensional non-cohesive granular media, where typical continuum constitutive quantities such as frictional strength and dilation angle are explicitly related to their corresponding grain-scale counterparts (e.g., inter-particle contact forces, fabric, particle displacements, and velocities), providing an across-the-scale basis for better understanding and modeling granular media.

In the same way, we utilize a new DEM scheme (LS-DEM) that takes advantage of a mathematical technique called level set (LS) to enable the inclusion of real grain shapes into a classical discrete element method. After calibrating LS-DEM with respect to real experimental results, we exploit part of its potential to study the dependency of critical state (CS) parameters such as the critical state line (CSL) slope, CSL intercept, and CS friction angle on the grain's morphology, i.e., sphericity, roundness, and regularity.

Finally, we introduce a first computational algorithm to ``clone'' the grain morphologies of a sample of real digital grains. This cloning algorithm allows us to generate an arbitrary number of cloned grains that satisfy the same morphological features (e.g., roundness and aspect ratio) displayed by their real parents and can be included into a DEM simulation of a given mechanical phenomenon. In turn, this will help with the development of discrete techniques that can directly predict the engineering scale behavior of granular media without resorting to phenomenology.

Understanding Micro- and Macro-Mechanics of Soil Liquefaction: A Necessary Step for Field-Scale Assessment

Liquefaction is a devastating instability associated with saturated, loose, and cohesionless soils. It poses a significant risk to distributed infrastructure systems that are vital for the security, economy, safety, health, and welfare of societies. In order to make our cities resilient to the effects of liquefaction, it is important to be able to identify areas that are most susceptible. Some of the prevalent methodologies employed to identify susceptible areas include conventional slope stability analysis and the use of so-called liquefaction charts. However, these methodologies have some limitations, which motivate our research objectives. In this dissertation, we investigate the mechanics of origin of liquefaction in a laboratory test using grain-scale simulations, which helps (i) understand why certain soils liquefy under certain conditions, and (ii) identify a necessary precursor for onset of flow liquefaction. Furthermore, we investigate the mechanics of liquefaction charts using a continuum plasticity model; this can help in modeling the surface hazards of liquefaction following an earthquake. Finally, we also investigate the microscopic definition of soil shear wave velocity, a soil property that is used as an index to quantify liquefaction resistance of soil. We show that anisotropy in fabric, or grain arrangement can be correlated with anisotropy in shear wave velocity. This has the potential to quantify the effects of sample disturbance when a soil specimen is extracted from the field. In conclusion, by developing a more fundamental understanding of soil liquefaction, this dissertation takes necessary steps for a more physical assessment of liquefaction susceptibility at the field-scale.