Peter C. Doerschuk

Upper Extremity Limb Function Discrimination Using EMG Signal Analysis

A signal analysis technique is developed for discriminating a set of lower arm and wrist functions using surface EMG signals. Data wete obtained from four electrodes placed around the proximal forearm. The functions analyzed included wrist flexion/extension, wrist abduction/adduction, and forearm pronation/supination. Multivariate autoregression models were derived for each function; discrimination was performed using a multiple-model hypothesis detection technique. This approach extends the work of Graupe and Cline [1] by including spatial correlations and by using a more generalized detection philosophy, based on analysis of the time history of all limb function probabilities. These probabilities are the sufficient statistics for the problem if the EMG data are stationary Gauss-Markov processes. Experimental results on-normal subjects are presented which demonstrate the advantages of using the spatial and time correlation of the signals. This technique should be useful in generating control signals for prosthetic devices.

In vivo two-photon excited fluorescence microscopy reveals cardiac- and respiration-dependent pulsatile blood flow in cortical blood vessels in mice

Subtle alterations in cerebral blood flow can impact the health and function of brain cells and are linked to cognitive decline and dementia. To understand hemodynamics in the three-dimensional vascular network of the cerebral cortex, we applied two-photon excited fluorescence microscopy to measure the motion of red blood cells (RBCs) in individual microvessels throughout the vascular hierarchy in anesthetized mice. To resolve heartbeat- and respiration-dependent flow dynamics, we simultaneously recorded the electrocardiogram and respiratory waveform. We found that centerline RBC speed decreased with decreasing vessel diameter in arterioles, slowed further through the capillary bed, and then increased with increasing vessel diameter in venules. RBC flow was pulsatile in nearly all cortical vessels, including capillaries and venules. Heartbeat-induced speed modulation decreased through the vascular network, while the delay between heartbeat and the time of maximum speed increased. Capillary tube hematocrit was 0.21 and did not vary with centerline RBC speed or topological position. Spatial RBC flow profiles in surface vessels were blunted compared with a parabola and could be measured at vascular junctions. Finally, we observed a transient decrease in RBC speed in surface vessels before inspiration. In conclusion, we developed an approach to study detailed characteristics of RBC flow in the three-dimensional cortical vasculature, including quantification of fluctuations in centerline RBC speed due to cardiac and respiratory rhythms and flow profile measurements. These methods and the quantitative data on basal cerebral hemodynamics open the door to studies of the normal and diseased-state cerebral microcirculation.

Ab initio reconstruction and experimental design for cryo electron microscopy

A statistical model for the object and the complete image formation process in the cryo electron microscopy of viruses is presented. Using this model, maximum-likelihood reconstructions of the three-dimensional (3-D) structure of viruses are computed using the expectation maximization algorithm, and alternative experimental designs are evaluated based on Cramer-Rao bounds. Numerical examples of the reconstructions and experimental design evaluations are provided based on Cowpea mosaic virus.

In Vivo Assembly of an Archaeal Virus Studied with Whole-Cell Electron Cryotomography

We applied whole-cell electron cryotomography to the archaeon Sulfolobus infected by Sulfolobus turreted icosahedral virus (STIV), which belongs to the PRD1-Adeno lineage of dsDNA viruses. STIV infection induced the formation of pyramid-like protrusions with sharply defined facets on the cell surface. They had a thicker cross-section than the cytoplasmic membrane and did not contain an exterior surface protein layer (S-layer). Intrapyramidal bodies often occupied the volume of the pyramids. Mature virions, procapsids without genome cores, and partially assembled particles were identified, suggesting that the capsid and inner membrane coassemble in the cytoplasm to form a procapsid. A two-class reconstruction using a maximum likelihood algorithm demonstrated that no dramatic capsid transformation occurred upon DNA packaging. Virions tended to form tightly packed clusters or quasicrystalline arrays while procapsids mostly scattered outside or on the edges of the clusters. The study revealed vivid images of STIV assembly, maturation, and particle distribution in cell.

Nonlinear modeling and processing of speech based on sums of AM-FM formant models

We describe a new statistical approach based on nonlinear filtering ideas for decomposing signals that are modeled as a sum of jointly amplitude- and frequency-modulated cosines, where each cosine has a slowly varying center frequency and the sum of terms is observed in additive noise. This is an alternative approach to methods based on deterministic models such as the Kaiser-Teager (see Proc. IEEE ICASSP-93, vol.III, p.149 and IEEE Trans. Acoust., Speech, Signal Processing, vol.28, no.5, pp. 599, 1980) energy operator. The Cramer-Rao bound for the resulting statistical estimation problem is computed. A practical nonlinear filter, an extended Kalman filter, is described. We demonstrate the ideas on a variety of speech problems.

Model‐based vehicle tracking from image sequences with an application to road surveillance

A model-based approach to vehicle tracking is proposed and applied to a highway traffic surveillance problem, which is motivated by current research in intelligent transportation systems. Systems for traffic management and traveler information services require accurate and wide-area estimates of vehicle velocity and traffic spatial and temporal densities. A detection and tracking algorithm is developed that achieves good performance with complexity low enough for real-time implementation using inexpensive microprocessors. Detection thresholds are computed based on a statistical model for vehicle and background, and the theoretical detector performance is derived. The tracking algorithm filters position estimates from the detection algorithm using a simple vehicle dynamic model and the Kalman filter. Data association is accomplished with a nearest neighbor filter coupled with a lane-change handling logic.

Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps.

CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. Regions of high variation in the data set are apparent in the image reconstruction due to the poor density that results from the lack of superposition of these regions. These observations are qualitative and, to date, only preliminary efforts have been made to quantitate the heterogeneity in the ensemble of particles that are individually imaged. We developed and tested a quantitative method for simultaneously computing a reconstruction of the particle and a map of the space-varying heterogeneity of the particle based on an entire data set. The method uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle. The result describes the heterogeneity of the particle as a variance to be plotted at every voxel of the reconstructed density. The test, employing time resolved data sets of virus maturation, not only recapitulated local variations obtained with difference map analysis, but revealed a remarkable time dependent reduction in the overall particle dynamics that was unobservable with classical methods of analysis.

Tree approximations to Markov random fields

Methods for approximately computing the marginal probability mass functions and means of a Markov random field (MRF) by approximating the lattice by a tree are described. Applied to the a posteriori MRF these methods solve Bayesian spatial pattern classification and image restoration problems. The methods are described, several theoretical results concerning fixed-point problems are proven, and four numerical examples are presented, including comparison with optimal estimators and the iterated conditional mode estimator and including two agricultural optical remote sensing problems. >

Determination of three-dimensional low-resolution viral structure from solution x-ray scattering data.

The capsid is modeled as a region of constant electron density located between inner and outer envelopes that exhibit icosahedral symmetry. For computational purposes the envelopes are represented as truncated sums of weighted icosahedral harmonics. Methods are described for estimating the weights from x-ray solution scattering patterns based on nonlinear least squares, and two examples of the procedure, for viruses with known atomic-resolution structures, are given.

Physiologically Based Pharmacokinetic (PBPK) Models for Ethanol

Physiologically based pharmacokinetic models have been used to describe the distribution and elimination of ethanol after intravenous administration. These models have been used to estimate the ethanol infusion profile that is sufficient for achieving a prescribed breath ethanol concentration time course in individuals, providing a useful platform for several pharmacokinetic and pharmacodynamic investigations. Mathematical foundations of these models are examined, including the derivation of an explicit set of governing equations in the form of a system of nonlinear ordinary differential equations. These equations can then be used to formulate and refine parameter identification and control strategies. Finally, a framework in which models related to this model can be constructed and analyzed is described.