Biomedical subjects

I W Hunter

Publications and source records attributed to I W Hunter.

At least 19 recordsLinked to original sources

PubMed2001

Parallel cascade identification and its application to protein family prediction.

Parallel cascade identification is a method for modeling dynamic systems with possibly high order nonlinearities and lengthy memory, given only input/output data for the system gathered in an experiment. While the method was originally proposed for nonlinear system identification, two recent papers have illustrated its utility for protein family prediction. One strength of this approach is the capability of training effective parallel cascade classifiers from very little training data. Indeed, when the amount of training exemplars is limited, and when distinctions between a small number of categories suffice, parallel cascade identification can outperform some state-of-the-art techniques. Moreover, the unusual approach taken by this method enables it to be effectively combined with other techniques to significantly improve accuracy. In this paper, parallel cascade identification is first reviewed, and its use in a variety of different fields is surveyed. Then protein family prediction via this method is considered in detail, and some particularly useful applications are pointed out.

Computational Biology↗

PubMed2000

Automatic classification of protein sequences into structure/function groups via parallel cascade identification: a feasibility study.

A recent paper introduced the approach of using nonlinear system identification as a means for automatically classifying protein sequences into their structure/function families. The particular technique utilized, known as parallel cascade identification (PCI), could train classifiers on a very limited set of exemplars from the protein families to be distinguished and still achieve impressively good two-way classifications. For the nonlinear system classifiers to have numerical inputs, each amino acid in the protein was mapped into a corresponding hydrophobicity value, and the resulting hydrophobicity profile was used in place of the primary amino acid sequence. While the ensuing classification accuracy was gratifying, the use of (Rose scale) hydrophobicity values had some disadvantages. These included representing multiple amino acids by the same value, weighting some amino acids more heavily than others, and covering a narrow numerical range, resulting in a poor input for system identification. This paper introduces binary and multilevel sequence codes to represent amino acids, for use in protein classification. The new binary and multilevel sequences, which are still able to encode information such as hydrophobicity, polarity, and charge, avoid the above disadvantages and increase classification accuracy. Indeed, over a much larger test set than in the original study, parallel cascade models using numerical profiles constructed with the new codes achieved slightly higher two-way classification rates than did hidden Markov models (HMMs) using the primary amino acid sequences, and combining PCI and HMM approaches increased accuracy.

Algorithms↗

PubMed2000

Design and characterization of a laser-based instrument with spectroscopic feedback control for treatment of vascular lesions: the "Smart Scalpel".

To improve the effectiveness of microsurgical techniques, we are developing a semi-autonomous robotic surgical tool (called the "Smart Scalpel") as an alternate approach to treatment of vascular lesions. The device employs optical reflectance spectroscopy as part of a line scan imaging system to identify and selectively target blood vessels in a vascular lesion for thermal treatment with a focused laser beam. Our proof-of-concept reported here presents the design and construction of a prototype instrument, initial quantification of imaging system resolution and contrast, and preliminary verification of the imaging and targeting strategies with standard targets and live dermal tissue.

Animals↗

PubMed2000

3D-1D threading methods for protein fold recognition.

The threading approach to protein fold recognition attempts to evaluate how well a query sequence fits into an already-solved fold. 3D-1D threaders rely on matching 1-dimensional strings of 3-dimensional information predicted from the query sequence with corresponding features of the target structure. In many cases this is combined with a sequence comparison. The combination of sequence and structure information has been shown to improve the accuracy of fold recognition, relative to the exclusive use of sequence or structure. In this paper, we review progress made since the introduction of threading methods a decade ago, highlighting recent advances. We focus on two emerging methods that are unconventional 3D-1D threaders: proximity correlation matrices and parallel cascade identification.

Animals↗

PubMed1999

Are there critical bands in kinesthesia?

The effect of changing the bandwidth of noise on the ability of human subjects to detect a 10-Hz sinusoidal movement signal was measured in two experiments. The objective of these studies was to investigate whether critical bands exist for the kinesthetic system, as has been demonstrated for the auditory and tactile systems. It was found that subjects' ability to detect a 10-Hz sinusoidal movement stimulus embedded in noise was not influenced by the bandwidth of the noise over a range of 4-10 Hz. These findings suggest that, if a critical filter does exist for this system, it would have to be greater than 10 Hz.

Auditory Perception↗

PubMed1996

Prospects for telediagnosis using ultrasound.

Ultrasound imaging is currently used as a primary diagnostic tool in cardiology, abdominal disorders, pulmonary medicine, trauma, and obstetrics. Because of its relatively low capital and operating costs as well as its growth potential, it represents one of the major diagnostic modalities of future health care. However, the use of ultrasonography as a mobile and powerful modality is controlled by the availability of a highly skilled technician to acquire the images and an experienced physician to interpret them. This paper discusses the technology required to increase the availability of a diagnosing physician by employing telerobotics. With this technology, the physician can guide the motion of the transducer by the technician from a remote location. Thus, the physician controls the examination and renders the diagnosis. It is shown that communication lines at 1.5 Mbits/s (T-1 speed) can, with appropriate compression, support both real-time viewing of the ultrasound images and telerobotic manipulation of the transducer. The incremental costs of telediagnosis for an examination are estimated to be a small fraction of the base charges and significantly less than the expense of bringing a physician to a remote location or transporting a patient to a regional medical center. Telediagnosis can, in addition, provide benefits from immediate interpretation and consultation that cannot be duplicated using store-and-forward scenarios.

Costs and Cost Analysis↗

PubMed1995

Ophthalmic microsurgical robot and associated virtual environment.

An ophthalmic virtual environment has been developed as part of a teleoperated microsurgical robot built to perform surgery on the eye. The virtual environment is unique in that it incorporates a detailed continuum model of the anatomical structures of the eye, its mechanics and optical properties, together with a less detailed geometric-mechanical model of the face. In addition to providing a realistic visual display of the eye being operated on, the virtual environment simulates tissue properties during manipulation and cutting and the forces involved are determined by solving a mechanical finite element model of the tissue. These forces are then fed back to the operator via a force reflecting master and so the surgeon can experience both the visual and mechanical sensations associated with performing surgery. The virtual environment can be used to enhance the images produced by the camera on the microsurgical slave robot during surgery and as a surgical simulator in which it replaces these images with computer graphics generated from the eye model.

Computer Graphics↗

PubMed1995

Analysis of short-latency reflexes in human elbow flexor muscles.

1. A motor and digital controller have been developed to apply rapid stretches to the human elbow joint. The digital controller returns the forearm to the initial position before the reflex contraction. Thus short-latency reflex responses can be cleanly separated in time from the mechanical effects of the stretch under a wide variety of loading conditions. 2. The reflex force varies linearly with the velocity of stretch over nearly 2 orders of magnitude. The reflex force also varies linearly with the tonic level of force over the entire range of forces studied (0-100 N). This contrasts sharply with, for example, the human ankle joint, which shows a very limited linear range. 3. As the digital controller is made more compliant (less stiff), reflex shortening increases dramatically and becomes more prolonged, whereas the reflex force becomes somewhat smaller and shorter. With compliant loads and the brief stretches we applied, the reflex shortening is approximately equal to the stretch that generated it. 4. Simulations of the results confirm that the dependence of reflex shortening and force on the stiffness of the load is mainly determined by the mechanics of the limb and muscles. The simulations also indicate that 1) the gain of the reflex is as high as it can be without causing instability and 2) the presence of a rectification nonlinearity (e.g., lengthening the muscle produces a reflex, but shortening the muscle does not) is mainly responsible for preserving the stability of the elbow system.

Adult↗

PubMed1993

Influence of the mechanical properties of a manipulandum on human operator dynamics. II. Viscosity.

The influence of the viscosity of a manipulandum used by a human operator in a position-control pursuit-tracking task was examined. An active servo-system was used to set the viscosity of a manipulandum (motor) connected to the forearm to one of seven levels ranging in a geometric series from 12 to 800 N.s/m. During each condition the viscosity of the motor was held constant by a computer while subjects tracked, by moving their forearm in the sagittal plane, a visually presented target whose position changed randomly every 1.5 s for 255 s. Nonparametric and parametric impulse response functions were calculated between the input (target) and output (position) in each tracking condition. Nonparametric analyses revealed that subjects became sluggish at higher viscosities (above 200 N.s/m) and took longer to reach the target. A second-order low-pass transfer function was found to provide a very good description of tracking performance at each viscous level. The gain and damping parameter of this transfer function were not affected by the manipulandum's viscosity, whereas both the pure delay and natural frequency of the human operator system decreased systematically with increasing manipulandum viscosity. These findings suggest that over the range of viscosities studied, there is no speed-accuracy trade-off in terms of determining an optimal level of manipulandum viscosity for a human operator, and that a less viscous interface will result in faster performance.

Adult↗

PubMed1993

A perceptual analysis of viscosity.

The perception of viscosity was studied using the contralateral limb-matching procedure in which subjects adjusted the viscosity of a motor connected to the wrist of one (matching) arm until it was perceived to be the same as that of the motor attached to the other (reference) arm. Two servo-controlled electromagnetic linear motors with computer-controlled viscosity were used to present viscosities ranging in amplitude from 2 to 1024 N.s/m to 11 subjects. Ten different viscosities were matched by subjects, and there were ten repetitions of each stimulus amplitude. The psychophysical function relating the reference to matching viscosity was linear (99% variance accounted for), and the accuracy with which the viscosities were matched (slope of 0.88) paralleled that reported previously for force, limb position and stiffness. The Weber fraction for viscosity was 0.34, which is 50% larger than that measured for stiffness and over twice that reported for force. An analysis of the movements and forces generated to perceive the reference viscosity revealed that subjects did not vary the amplitude of the movements and typically made very small excursions of the forearm, but that both the velocity of the movements and force changed significantly as a function of the reference viscosity. These findings were interpreted as indicating that the human proprioceptive system is capable of integrating information regarding force and movement velocity so as to perceive the viscosity of a mechanical system connected to the limbs, but that its sensitivity to changes in viscosity is much less than would be predicted from its capacity to detect variations in muscle force and limb movement.

Adult↗

PubMed1993

Nonparametric two-dimensional point spread function estimation for biomedical imaging.

The problem of identifying optical system point spread functions (PSFs) arises frequently in the area of image processing and restoration. The paper presents a method for determining two-dimensional PSFs from input/output image signals. The PSF of the system is determined from a set of linear equations involving elements of the input autocorrelation function and the input/output cross-correlation function. The resulting PSF is the one that minimises the sum of squares difference between the actual output image and the predicted one.

Diagnostic Imaging↗

PubMed1993

Quantitative analysis of four EMG amplifiers.

Four typical EMG amplifiers were tested quantitatively to observe the diversity and specificity of available equipment. Gain, phase, common mode rejection ratio (CMRR) and noise characteristics were measured for each device. Various gain and phase responses were observed, each best suited to specific application areas. For all amplifiers, the CMRR was shown to decrease dramatically in the presence of input impedance mismatches of more than 10 k omega between the two electrodes. Because such impedance mismatches are common on the skin surface, these results indicate that proper skin preparation is required to maximize the noise rejection capabilities of the tested amplifiers.

Amplifiers, Electronic↗

PubMed1992

Time-varying stiffness of human elbow joint during cyclic voluntary movement.

The objective of this study was to determine the extent to which subjects modulate their elbow joint mechanical properties during ongoing arm movement. Small pseudo-random force disturbances were applied to the wrist with an airjet actuator while subjects executed large (1 rad) elbow joint movements. Using a lumped parameter model of the muscle, tendon and proprioceptive feedback dynamics, a time-varying system identification technique was developed to analyze the phasic changes in the elbow joint's mechanical response. The mechanical properties were found to be time-varying, and well approximated by a quasi-linear second-order model. The stiffness of the arm was found to drop during movement. The arm was always underdamped, with the damping ratio changing during movement. Inertia estimates were constant and consistent with previous measurements. Overall, the moving arm was found to be very compliant, with a peak stiffness value less than the lowest value measured during posture, and a natural frequency of less than 3 Hz. Changing the speed of movement, or the load from gravity, changed the stiffness measured, but not in strict proportion to the change in net muscle torque.

Adult↗

PubMed1992

Changes in pinch force with bidirectional load forces.

The forces used to grasp an object were measured while positive (push) and negative (pull) load forces were applied to the hand under varying frictional conditions. Subjects held between the tips of their thumb and index finger a manipulandum composed of two symmetrically mounted disks. The manipulandum was connected to the stage of an electromagnetic linear motor that generated load forces under computer control. In the first experiment, subjects held the position of the manipulandum constant while the motor generated forces in first the positive and then the negative direction. The motor force at which the manipulandum slipped from the fingers was measured in the second experiment. In both experiments, friction was varied by changing the surface (sandpaper, suede, or plastic) of the manipulandum disks. The pinch forces produced by subjects were linearly related to changes in motor force in both the positive and negative directions, with the slope of this relation varying as a function of the surface properties of the manipulandum. The modulation of pinch force with motor force was influenced, however, by the direction of the load force; higher forces were produced in response to negative load forces. Slip forces varied as a function of pinch force and surface texture; higher forces were associated with materials with lower coefficients of friction. These findings suggest that the friction between the skin and an object being grasped changes as a function of the direction of force that the object applies to the skin, possibly due to the anisotropic nature of glabrous skin, and that this mechanical property contributes to variations in pinch force.

Journal Article↗

PubMed1992

Identification of time-varying biological systems from ensemble data.

The theory underlying a new method for the identification of time-varying systems is described. The method uses singular value decomposition to obtain least-squares estimates of time-varying impulse response functions from an ensemble of input-output realizations. No a priori assumptions regarding the system structure or form of the time-variation are required and there are few restrictions on the input signal. Simulation studies, using a model of time-varying joint dynamics, show that the method can track rapid changes in system dynamics accurately and is robust in the presence of output noise. An application of the method is demonstrated by using it to track dynamic ankle stiffness during a rapid, voluntary, isometric contraction. During the transient phase of the contraction, low-frequency ankle stiffness gain decreased in a manner which could not be described with the second-order model of joint dynamics often used under stationary conditions.

Adult↗

PubMed1992

Differential thresholds for limb movement measured using adaptive techniques.

Differential thresholds for limb movement were measured in 10 subjects, using the transformed up-down procedure. Subjects were required to indicate which of two random displacement perturbations delivered to their forearms had the larger standard deviation (SD). The SD of the reference signal was fixed for each experimental condition at one of seven values ranging from 0.05 to 3.2 mm. THe SD of the other signal varied depending on the subject's response. Using this procedure, the differential threshold for limb movement was calculated to be 8%, which is very similar to the thresholds estimated previously for changes in limb position (9%) and force (7%). The sensitivity of the human proprioceptive system to changes in limb displacement was much greater than anticipated, with subjects being able to resolve a 5-microns difference between two perturbations delivered to their arms.

Adult↗

PubMed1992

An anatomical heart model with applications to myocardial activation and ventricular mechanics.

A three-dimensional finite element model of the mechanical and electrical behavior of the heart is being developed in a collaboration among Auckland University, New Zealand; the University of California at San Diego, U.S.; and McGill University, Canada. The equations of continuum mechanics from the theory of finite deformation elasticity are formulated in a prolate spheroidal coordinate system and solved using a combination of Galerkin and collocation techniques. The finite element basis functions used for the dependent and independent variables range from linear Lagrange to cubic Hermite, depending on the degree of spatial variation and continuity required for each variable. Orthotropic constitutive equations derived from biaxial testing of myocardial sheets are defined with respect to the microstructural axes of the tissue at the Gaussian quadrature points of the model. In particular, we define the muscle fiber orientation and the newly identified myocardial sheet axis orientation throughout the myocardium using finite element fields with nodal parameters fitted by least-squares to comprehensive measurements of these variables. Electrical activation of the model is achieved by solving the FitzHugh-Nagumo equations with collocation at fixed material points of the anatomical finite element model. Electrical propagation relies on an orthotropic conductivity tensor defined with respect to the local material axes. The mechanical constitutive laws for the Galerkin continuum mechanics model are (1) an orthotropic "pole-zero" law for the passive mechanical properties of myocardium and (2) a Wiener cascade model of the active mechanical properties of the muscle fibers. This chapter concentrates on two aspects of the model: first, grid generation, including both the generation of nodal coordinates for the finite element mesh and the generation of orthotropic material axes at each computational point, and, second, the formulation of constitutive laws suitable for numerically intensive finite element computations. Extensions to this model and applications to the mechanical and electrical function of the heart are described in Chapter 16 by McCulloch and co-workers.

Animals↗

PubMed1991

An airjet actuator system for identification of the human arm joint mechanical properties.

A system is described for determining the mechanical properties of the human arm during unconstrained posture and movement. An airjet perturbation device is attached to the wrist with a special cuff, and provides high-frequency stochastic perturbations in potentially three orthogonal directions. The airjet operates as a fluidic flip-flop utilizing the Coanda effect, and generates binary force sequences with a steady-state thrust of 4 N, a flat frequency response to 75 Hz, usable thrust to 150 Hz, and a rise time of 1 ms, when the static pressure at the nozzle inlet is 5.5 x 10(5) Pa (80 psi). These operating characteristics are adequate to identify the arm's mechanical properties efficiently and robustly.

Air↗