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At least 1,081 records · Page 60Linked to original sources
PubMed2004

Optimization of a vector quantization codebook for objective evaluation of surgical skill.

Surgical robotic systems and virtual reality simulators have introduced an unprecedented precision of measurement for both tool-tissue and tool-surgeon interaction; thus holding promise for more objective analyses of surgical skill. Integrative or averaged metrics such as path length, time-to-task, success/failure percentages, etc., have often been employed towards this end but these fail to address the processes associated with a surgical task as a dynamic phenomena. Stochastic tools such as Markov modeling using a 'white-box' approach have proven amenable to this type of analysis. While such an approach reveals the internal structure of the of the surgical task as a process, it requires a task decomposition based on expert knowledge, which may result in a relatively large/complex model. In this work, a 'black box' approach is developed with generalized cross-procedural applications., the model is characterized by a compact topology, abstract state definitions, and optimized codebook size. Data sets of isolated tasks were extracted from the Blue DRAGON database consisting of 30 surgical subjects stratified into six training levels. Vector quantization (VQ) was employed on the entire database, thus synthesizing a lexicon of discrete, task-independent surgical tool/tissue interactions. VQ has successfully established a dictionary of 63 surgical code words and displayed non-temporal skill discrimination. VQ allows for a more cross-procedural analysis without relying on a thorough study of the procedure, links the results of the black-box approach to observable phenomena, and reduces the computational cost of the analysis by discretizing a complex, continuous data space.

Algorithms↗
PubMed1996

Energy functions that discriminate X-ray and near native folds from well-constructed decoys.

This study generates ensembles of decoy or test structures for eight small proteins with a variety of different folds. Between 35,000 and 200,000 decoys were generated for each protein using our four-state off-lattice model together with a novel relaxation method. These give compact self-avoiding conformations each constrained to have native secondary structure. Ensembles of these decoy conformations were used to test the ability of several types of empirical contact, surface area and distance-dependent energy functions to distinguish between correct and incorrect conformations. These tests have shown that none of the functions is able to distinguish consistently either the X-ray conformation or the near-native conformations from others which are incorrect. Certain combinations of two of these energy functions were able, however, consistently to identify X-ray structures from amongst the decoy conformations. These same combinations are better also at identifying near-native conformations, consistently finding them with a hundred-fold higher frequency than chance. The fact that these combination energy functions perform better than generally accepted energy functions suggests their future use in folding simulations and perhaps threading predictions.

Crystallography, X-Ray↗
PubMed2006

The effect of copolymer composition on the dynamics of random copolymers in a homopolymer matrix.

The effect of copolymer composition on the dynamics of random copolymers in a homopolymer matrix is studied using computer simulations within the framework of the bond-fluctuation model on blends containing low concentrations (10%) of A-B copolymers, where A and B are two different types of monomers, dispersed in a homopolymer matrix of chains with only A-type monomers. Four copolymer compositions were studied, phi(A)=0.33, phi(A)=0.5, phi(A)=0.66, and phi(A)=0.82, while maintaining a statistically random sequence distribution. For this study, we have only included intermolecular interactions between A and B monomers. Our results indicate, in agreement with experimental data, that copolymer composition has an impact on system dynamics. Analysis of the structure reveals that copolymers with majority A content are expanded in the homopolymer matrix, have fewer interchain copolymer-copolymer contacts, and are well dispersed in the homopolymer matrix. On the other hand, copolymers with lower A content form a more compact structure, have more interchain contacts, and form aggregates that are short lived. This in turn leads to slower system dynamics. Both the radius of gyration (Rg) and copolymer end-to-end vectors (Re) increase with increasing A content until phi(A)=0.66 and then decrease. Copolymers with lower A content form more compact structures as the repulsive interactions between unlike species are minimized by the copolymers folding back on themselves and forming aggregates of copolymer chains. Thus, these results provide insight into the variation of copolymer dynamics with composition in the system by documenting the correlation between the thermodynamics of this mixture, the conformation of a copolymer chain in a homopolymer matrix, and the dynamics of both components in this blend.

Journal Article↗
PubMed2006

Approximate Bayesian multibody tracking.

Visual tracking of multiple targets is a challenging problem, especially when efficiency is an issue. Occlusions, if not properly handled, are a major source of failure. Solutions supporting principled occlusion reasoning have been proposed but are yet unpractical for online applications. This paper presents a new solution which effectively manages the trade-off between reliable modeling and computational efficiency. The Hybrid Joint-Separable (HJS) filter is derived from a joint Bayesian formulation of the problem, and shown to be efficient while optimal in terms of compact belief representation. Computational efficiency is achieved by employing a Markov random field approximation to joint dynamics and an incremental algorithm for posterior update with an appearance likelihood that implements a physically-based model of the occlusion process. A particle filter implementation is proposed which achieves accurate tracking during partial occlusions, while in cases of complete occlusion, tracking hypotheses are bound to estimated occlusion volumes. Experiments show that the proposed algorithm is efficient, robust, and able to resolve long-term occlusions between targets with identical appearance.

Algorithms↗
PubMed2005

Particle selection and beam collimation system for laser-accelerated proton beam therapy.

In a laser-accelerated proton therapy system, the initial protons have broad energy and angular distributions, which are not suitable for direct therapeutic applications. A compact particle selection and collimation device is needed to deliver small pencil beams of protons with desired energy spectra. In this work, we characterize a superconducting magnet system that produces a desired magnetic field configuration to spread the protons with different energies and emitting angles for particle selection. Four magnets are set side by side along the beam axis; each is made of NbTi wires which carry a current density of approximately 10(5) A/cm2 at 4.2 K, and produces a magnetic field of approximately 4.4 T in the corresponding region. Collimation is applied to both the entrance and the exit of the particle selection system to generate a desired proton pencil beam. In the middle of the magnet system, where the magnetic field is close to zero, a particle selection collimator allows only the protons with desired energies to pass through for therapy. Simulations of proton transport in the presence of the magnetic field show that the selected protons have successfully refocused on the beam axis after passing through the magnetic field with the optimal magnet system. The energy spread for any given characteristic proton energy has been obtained. It is shown that the energy spread is a function of the magnetic field strength and collimator size and reaches the full width at half maximum of 25 MeV for 230 MeV protons. Dose distributions have also been calculated with the GEANT3 Monte Carlo code to study the dosimetric properties of the laser-accelerated proton beams for radiation therapy applications.

Body Burden↗
PubMed2002

Coupling analysis of a matched piezoelectric sensor and actuator pair for vibration control of a smart beam.

This paper presents a theoretical and experimental study of the in-plane and out-of-plane coupling of a matched piezoelectric sensor/actuator pair bonded on a beam. Both the sensor and actuator are triangularly shaped polyvinylidene fluoride (PVDF) transducers and are intended to provide a compact sensor/actuator system for beam vibration control. The measured sensor-actuator frequency response function has shown an unpredicted increase in magnitude with frequency, which was found, to be due to in-plane vibration coupling. An analytical model has been developed to decompose the sensor-actuator response function into an in-plane contribution and an out-of-plane contribution. This in-plane coupling can limit the feedback control gains when a direct velocity feedback control is applied. A method called the j omega s compensation method is proposed to identify the effect of the in-plane vibration coupling at low frequencies. Even after this compensation, however, there was unexpected strong out-of-plane coupling at even modes, which may have been caused by a lack of accuracy in the shaping of the PVDF sensor and actuator. Numerical simulations have confirmed the sensitivity of the matched sensor/actuator pair with shaping errors.

Journal Article↗
PubMed2006

Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: theory and applications.

We present, to our knowledge, a new theory that takes internal dynamics of proteins into account to describe forced-unfolding and force-quench refolding in single molecule experiments. In the current experimental setup (using either atomic force microscopy or laser optical tweezers) the distribution of unfolding times, P(t), is measured by applying a constant stretching force f(S) from which the apparent f(S)-dependent unfolding rate is obtained. To describe the complexity of the underlying energy landscape requires additional probes that can incorporate the dynamics of tension propagation and relaxation of the polypeptide chain upon force quench. We introduce a theory of force correlation spectroscopy to map the parameters of the energy landscape of proteins. In force correlation spectroscopy, the joint distribution P(T, t) of folding and unfolding times is constructed by repeated application of cycles of stretching at constant f(S) separated by release periods T during which the force is quenched to f(Q) < f(S). During the release period, the protein can collapse to a manifold of compact states or refold. We show that P(T, t) at various f(S) and f(Q) values can be used to resolve the kinetics of unfolding as well as formation of native contacts. We also present methods to extract the parameters of the energy landscape using chain extension as the reaction coordinate and P(T, t). The theory and a wormlike chain model for the unfolded states allows us to obtain the persistence length l(p) and the f(Q)-dependent relaxation time, giving us an estimate of collapse timescale at the single molecular level, in the coil states of the polypeptide chain. Thus, a more complete description of landscape of protein native interactions can be mapped out if unfolding time data are collected at several values of f(S) and f(Q). We illustrate the utility of the proposed formalism by analyzing simulations of unfolding-refolding trajectories of a coarse-grained protein (S1) with beta-sheet architecture for several values of f(S), T, and f(Q) = 0. The simulations of stretch-relax trajectories are used to map many of the parameters that characterize the energy landscape of S1.

Biomechanical Phenomena↗
PubMed1996

Restriction fragment length polymorphism (RFLP) analysis on DNA from human compact bone.

DNA typing techniques primarily identify specific genetic markers that are highly polymorphic within a population and have found great utility in forensic science. The established DNA identification protocol, termed restriction fragment length polymorphism (RFLP), has been admitted as physical evidence in the investigation of crimes such as assault, sexual assault, and homicide. The limitation associated with this procedure concerns the integrity of the genetic material. This study sought to evaluate human bone as a source material for DNA identification following exposure to common forensic field conditions. Often, with the onset of decomposition and eventual disarticulation of a body, soft tissues, hair and teeth may not be recovered. The significance of this study lies in the fact that, within forensic anthropology, human bone represents the most biologically stable evidence and is sometimes all that remains after periods of exposure. Genomic DNA was extracted from human bone following exposure to surface deposit, shallow burial, and fresh water immersion. Samples were collected over a three month time course and analyzed by spectrophotometry and agarose gel electrophoresis as well as RFLP analysis. The data suggest that high molecular weight DNA may indeed be extracted from human bone and typed by RFLP analysis for use in forensic identification. Under simulated forensic field conditions, the severity of DNA degradation was in the order of fresh water immersion > shallow burial > surface deposit. Genomic DNA from bone deposited on the desert surface for up to 4 weeks was detected by RFLP analysis. No spurious bands were detected in any specimens, and to the extent that bands were still present, the RFLP patterns matched. These findings demonstrate that human bone can be a reliable source of genomic DNA, and that bone recovered from surface deposit is the most desirable for use in forensic identification.

Bone and Bones↗
PubMed2003

Evaluation of 3D correspondence methods for model building.

The correspondence problem is of high relevance in the construction and use of statistical models. Statistical models are used for a variety of medical application, e.g. segmentation, registration and shape analysis. In this paper, we present comparative studies in three anatomical structures of four different correspondence establishing methods. The goal in all of the presented studies is a model-based application. We have analyzed both the direct correspondence via manually selected landmarks as well as the properties of the model implied by the correspondences, in regard to compactness, generalization and specificity. The studied methods include a manually initialized subdivision surface (MSS) method and three automatic methods that optimize the object parameterization: SPHARM, MDL and the covariance determinant (DetCov) method. In all studies, DetCov and MDL showed very similar results. The model properties of DetCov and MDL were better than SPHARM and MSS. The results suggest that for modeling purposes the best of the studied correspondence method are MDL and DetCov.

Algorithms↗
PubMed2004

Lattice Monte Carlo simulations of three-dimensional charged polymer chains.

The configurational properties of strongly charged polyelectrolytes accompanied by neutralizing counterions in dilute solutions are simulated using the cooperative motion algorithm on the face-centered-cubic lattice. The full Coulomb potential and the excluded volume condition between different ions/beads are taken into account and the reduced temperature T* is considered the main, variable parameter. The calculations that have been carried out for solutions of both single and several chains indicate a few regions of their behavior: (1) for T*--> infinity, it corresponds to that of neutral, self-avoiding polymers under good solvent conditions; (2) for T* approximately 1, due to the electrostatic interactions being effectively stronger, the chains are more outstretched compared to their size at other temperatures; (3) for T* well below one, the counterion condensation becomes more and more dominant, which gradually leads to strongly collapsed chains; and (4) at the lowest temperatures the chains and counterions assume low-energy configurations in the form of neutral, compact aggregates.

Journal Article↗
PubMed1989

DANTALE: a new Danish speech material.

A new Danish speech material (DANTALE) for clinical and experimental speech audiometry is digitally recorded on compact disc (CD). The speech material is designed to meet present audiological requirements at Danish hearing centres. One channel of the CD contains the speech signals and the other a masking noise. The CD also contains various calibration signals recorded on both channels at the end of the CD. The speech material compromises: 1) Digit triplets for the measurement of speech reception threshold (SRT). 2) Lists of monosyllabic words for the measurement of discrimination score (DS) for adults, children and small children. The word lists for the adults are equalized with regard to important phonetic and "visual" elements and the word lists for the children consist of minimal pairs. 3) Continuous speech for the measurement of the most comfortable loudness level (MCL), assessment of hearing aid fitting and the like. The masking noise is an amplitude-modulated, speech-shaped noise signal, which is designed to simulate a 4-person speech babble in order to assess both the frequency selectivity and the temporal resolution. The speech material is described and the long-term power spectra and modulation spectra are given.

Audiometry, Speech↗
PubMed1999

Residue 3 of beta2-microglobulin affects binding of class I MHC molecules by the W6/32 antibody.

Previous studies of class I MHC molecules have shown that the owl monkey (Aotus) possesses at least two variants of the beta2-microglobulin (beta2m) protein. These two variants have different isoelectric points, and exhibit differential reactivity with the monoclonal antibody W6/32. We report cDNA sequences of the B2m gene, from W6/32-positive and W6/32-negative Aotus cell lines. The two beta2m variants we identified exhibit a single amino acid difference at position three. An arginine residue at position 3 was correlated with W6/32 reactivity, whereas histidine was associated with non-reactivity. W6/32 reactivity was conferred to a W6/32-negative Aotus cell line when it was transfected with the B2m from the W6/32-positive cell line. Residue 3 of beta2m is located at the surface of the class I molecule. It is also close to position 121 of the MHC class I heavy chain, which has previously been shown to influence W6/32 antibody binding. We conclude that W6/32 binds a compact epitope on the class I molecule that includes both residue 3 of beta2m and residue 121 of the heavy chain. We examined the distribution of the two beta2m motifs in a sample Aotus population using an allele-specific polymerase chain reaction assay. The pattern of beta2m segregation we observed matches that which was defined previously by serology. Additionally, we identified laboratory-born hybrid animals who possess both variants of beta2m.

Alleles↗
PubMed1993

Modeling the alpha IIb beta 3 integrin solution conformation.

The alpha IIb beta 3 platelet integrin is the prototypical member of a widely distributed class of transmembrane receptors formed by the noncovalent association of alpha and beta subunits. Electron microscopic (EM) images of the alpha IIb beta 3 complex show an asymmetric particle with a globular domain from which two extended regions protrude to contact the lipid bilayer. Distance constraints provided by disulfide bond patterns, epitope mapping, and ligand mimetic cross-linking studies rather suggest a somewhat more compact conformation for the alpha IIb beta 3 complex. We have studied the shape of detergent-solubilized alpha IIb beta 3 by employing a low-resolution modeling procedure in which each polypeptide has been represented as an array of interconnected, nonoverlapping spheres (beads) of various sizes. The number, size, and three-dimensional relationships among the beads were defined either solely by dimensions obtained from published EM images of integrin receptors (EM models, 21 beads), or solely by interdomain constraints derived from published biochemical data (biochemical model, 37 beads). Interestingly, although no EM data were employed in its construction, the resulting overall shape of the biochemical model was still compatible with the EM data. Both kinds of models were then evaluated for their calculated solution properties. The more elongated EM models have diffusion and sedimentation coefficients that differ, at best, by +2% and -18% from the experimental values, determined, respectively, in octyl glucoside and Triton X-100. On the other hand, the parameters calculated for the more compact biochemical model showed a more consistent agreement with experimental values, differing by -7% (octyl glucoside) to -6% (Triton X-100). Thus, it appears that using the biochemical constraints as a starting point has resulted in not only a more detailed model of the detergent-solubilized alpha IIb beta 3 complex, where the relative spatial location of specific domains the size of 5-10 kDa can be tentatively mapped, but in a model that can also reconcile the electron microscopy with the biochemical and the solution data.

Amino Acid Sequence↗
PubMed2005

Titration of hydrophobic polyelectrolytes using Monte Carlo simulations.

The conformation and titration curves of weak (or annealed) hydrophobic polyelectrolytes have been examined using Monte Carlo simulations with screened Coulomb potentials in the grand canonical ensemble. The influence of the ionic concentration pH and presence of hydrophobic interactions has been systematically investigated. A large number of conformations such as extended, pearl-necklace, cigar-shape, and collapsed structures resulting from the subtle balance of short-range hydrophobic attractive interactions and long-range electrostatic repulsive interactions between the monomers have been observed. Titration curves were calculated by adjusting the pH-pK(0) values (pK(0) represents the intrinsic dissociation constant of an isolated monomer) and then calculating the ionization degree alpha of the polyelectrolyte. Important transitions related to cascades of conformational changes were observed in the titration curves, mainly at low ionic concentration and with the presence of strong hydrophobic interactions. We demonstrated that the presence of hydrophobic interactions plays an important role in the acid-base properties of a polyelectrolyte in promoting the formation of compact conformations and hence decreasing the polyelectrolyte degree of ionization for a given pH-pK(0) value.

Journal Article↗
PubMed1995

Computational analysis of binding affinity and neural response at the L-alanine receptor.

A model of analogue-receptor binding is developed for the L-alanine receptor in the channel catfish using the AM1-SM2 and ab initio SCRF computational methods. Besides interactions involving the zwitterionic moiety of the amino acid analogue and complementary subsites on the receptor, the model suggests the presence of a hydrophobic pocket with dispersion interactions between the receptor and the residue on the amino acid analogue. Conformational analysis suggests not only a small compact active site on the receptor, but also that the analogues with the highest affinity occupy nearly identical regions of space. Although the binding interaction is dominated by the ionic terms, AM1-SM2 calculations indicate that free energy terms associated with cavity formation, solvent reorganization, and dispersion interactions can be correlated to activation and neural response. From a consideration of this model, molecular features of the analogues that are important for binding and neural response were deduced and other analogues or ligands were developed and tested.

Alanine↗
PubMed1996

Tracking and motion analysis of the left ventricle with deformable superquadrics.

We present a new approach to analyse the deformation of the left ventricle of the heart based on a parametric model that gives a compact representation of a set of points in a 3-D image. We present a strategy for tracking surfaces in a sequence of 3-D cardiac images. Following tracking, we then infer quantitative parameters which characterize: left ventricle motion, volume of left ventricle, ejection fraction, amplitude and twist component of cardiac motion. We explain the computation of these parameters using our model. Experimental results are shown in time sequences of two modalities of medical images, nuclear medicine and X-ray computed tomography (CT). Video sequences presenting these results are on the CD-ROM.

Computer Simulation↗
PubMed2005

Exploring protein's optimal HP configurations by self-organizing mapping.

Self-organizing map (SOM) has been used in protein folding prediction when the HP model is employed. The existing work uses a square-like shape lattice with l = m x n points to represent the optimal compact structure of a sequence of l amino acids. In this paper, a general l'-size sequence of amino acids is self-organized in a two dimensional lattice with l (> l') points. The obtained minimum configuration then has a flexible shape, in contrast to the compact structure limited in the lattice. To fulfil this extension, a new self-organizing map (SOM) technique is proposed to deal with the difficulty of the unsymmetric input and output spaces. New competition rules in the training phase are introduced and a local search method is applied to overcome the multi-mapping phenomena. Several HP benchmark examples with up to 36 amino acids are tested to verify the effectiveness of the proposed approach in this paper.

Algorithms↗
PubMed2000

A new fold in the scorpion toxin family, associated with an activity on a ryanodine-sensitive calcium channel.

We determined the structure in solution by (1)H two-dimensional NMR of Maurocalcine from the venom of Scorpio maurus. This toxin has been demonstrated to be a potent effector of ryanodyne-sensitive calcium channel from skeletal muscles. This is the first description of a scorpion toxin which folds following the Inhibitor Cystine Knot fold (ICK) already described for numerous toxic and inhibitory peptides, as well as for various protease inhibitors. Its three dimensional structure consists of a compact disulfide-bonded core from which emerge loops and the N-terminus. A double-stranded antiparallel beta-sheet comprises residues 20-23 and 30-33. A third extended strand (residues 9-11) is perpendicular to the beta-sheet. Maurocalcine structure mimics the activating segment of the dihydropyridine receptor II-III loop and is therefore potentially useful for dihydropyridine receptor/ryanodine receptor interaction studies. Proteins 2000;40:436-442.

Amino Acid Sequence↗