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PubMed1992

New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking.

A novel algorithm is presented which models protein-protein interactions using surface complementarity. The method is applied to antibody-antigen docking. A steric scoring scheme, based upon a soft potential, is used to assess complementarity, and a simple electrostatic model is then used to remove infeasible interactions. The soft potential allows for structural changes that occur during docking. Biochemical knowledge is necessary to reduce the number of docking orientations produced by the method to a manageable size. The information used includes the known epitope residues and a single loose distance constraint. The method is applied to all three crystallographically determined antibody-lysozyme complexes, HyHEL-10, D1.3 and HyHEL-5. For the first time, a predicted antibody structure (that of D1.3) is used as a docking target. In the four systems modelled, the method identifies between 15 and 40 possible docking orientations. The root-mean-square (r.m.s.) deviation between these orientations and the relevant crystallographic complex is measured in the interface region. For all four complexes an orientation is found with r.m.s. deviation in the range 1.9 A and 4.8 A. The algorithm is implemented on a single instruction/multiple datastream (SI/MD) architecture computer. The use of a parallel architecture computer ensures detailed coverage of the search space, whilst still maintaining a search time of two days.

Algorithms↗
PubMed1989

Base-rate effects in category learning: a comparison of parallel network and memory storage-retrieval models.

Exemplar-memory and adaptive network models were compared in application to category learning data, with special attention to base rate effects on learning and transfer performance. Subjects classified symptom charts of hypothetical patients into disease categories, with informative feedback on learning trials and with the feedback either given or withheld on test trials that followed each fourth of the learning series. The network model proved notably accurate and uniformly superior to the exemplar model in accounting for the detailed course of learning; both the parallel, interactive aspect of the network model and its particular learning algorithm contribute to this superiority. During learning, subjects' performance reflected both category base rates and feature (symptom) probabilities in a nearly optimal manner, a result predicted by both models, though more accurately by the network model. However, under some test conditions, the data showed substantial base-rate neglect, in agreement with Gluck and Bower (1988b).

Adult↗
PubMed1979

Data collection for cross-sectional image reconstruction by a moving ring of positron annihilation detectors.

A ring of positron annihilation detectors capable of two independent motions in the plane of the ring is considered. It can rotate around its center, and the whole ring may move so that its center traces a circular path. Provided certain parameters are chosen according to given formulas, data collected by such a detector ring can be reorganized (rebinned), in a computationally very inexpensive fashion, so that the data items in each bin are measurements along parallel lines spaced at small equal intervals. Efficient high resolution reconstruction algorithms that assume such data organization can therefore be applied to data collected collected by a moving positron ring detector. The method is demonstrated on a realistic example.

Computers↗
PubMed1991

[Cardiac magnetic resonance. Optimization of the parameters in the evaluation of right and left ventricular function].

MR imaging is the only non-invasive tomographic imaging modality capable of imaging the heart along planes that are parallel to each other and in any desired direction. Such reconstruction algorithms can thus be applied to MR images as the Simpson's rule which allows volume estimation of all cardiac cavities, although very irregular in shape, like the right ventricle. The authors optimized the technical parameters to obtain a set of multiphase double-angulated images on both the short and the long axes of the heart, in about 1-hour time. This technique was used to examine 31 patients suffering from several cardiopathies. The images allowed both end-diastolic and end-systolic volumes to be estimated, as well as the ejection fractions of both ventricles. In the left ventricle the area-length method and the Simpson's rule were applied, whereas only the latter was employed in the right ventricle. The correlation coefficients of US and MR data were, for the 3 parameters, r = 0.813, r = 0.920, and r = 0.879, respectively, in the first case, and r = 0.905, r = 0.923, and r = 0.890 in the second one. The time required to analyze the obtained data, which is done manually, is still considerably long.

Cardiac Volume↗
PubMed1990

Generalized gradient schemes for the measurement of two-dimensional image motion.

This paper describes a procedure for recovering the global velocity of an image by incorporating spatial filtering, and optionally, temporal filtering, into a scheme that employs a generalized version of the gradient algorithm of motion detection. Motion within a patch is analysed by six parallel channels, each incorporating a different spatiotemporal filter. Advantageous features of this scheme are: (a) global velocity is derived directly, without first computing local velocity at a number of image locations; (b) the filters compute first derivatives rather than second derivatives, making the scheme potentially more resistant to noise than certain other schemes; (c) two of the six filters can be chosen almost completely arbitrarily, and can therefore be tailored to maximize signal reliability, and (d) the measurement of velocity can be made as local or as global as desired by altering the size of the patch that is viewed by the filters. An analogous scheme is derived for the measurement of rotation as well as expansion or contraction of the image.

Animals↗
PubMed1992

Computer-assisted 3D-reconstruction and statistics of the limbic system. 2. Spatial statistics of the hippocampal formation, the fornix, and the mammillary bodies.

A statistical method is described to show the distribution of neuroanatomical structures within a Cartesian coordinate system from any given number of examinations. The algorithm is based on polygons derived from the outlines of neuroanatomical structures in parallel canthomeatal-orientated cutting planes. These polygons are transformed in virtual voxels, rotated into the bicommissural coordinate system, and projected onto the three main planes of this coordinate system. Areas with the same probability for the structures examined are given in these planes. As an example this method is applied to the hippocampal formation and the results attained are shown.

Hippocampus↗
PubMed1990

Modulation of muscle and pulmonary O2 uptakes by circulatory dynamics during exercise.

The effect of cardiovascular adjustments on the coupling of cellular to pulmonary gas exchange during unsteady states of exercise remains controversial. Computer simulations were performed to assess these influences on O2 delivery and pulmonary O2 uptake (pVO2). Algorithms were developed representing muscle and "rest-of-body" compartments, connected in parallel by arterial and venous circulations to a pump-and-lungs compartment. Exercise-induced increases in VO2 and cardiac output went to the muscle compartment. Model parameters [e.g., time constants for blood flow and muscle O2 uptake (mVO2)] could be varied independently. Simulation results demonstrated that 1) the rise in pVO2 during exercise contains three phases; 2) the contribution of changes in venous O2 stores to pVO2 kinetics and the O2 deficit occur almost entirely in phase 1; 3) under a wide variety of manipulations, the kinetics of pVO2 in phase 2 were within a couple of seconds of that assigned to mVO2 (i.e., there is not an obligatory slowing of VO2 kinetics at the lungs relative to those at the muscles; 4) by use of available estimates of blood flow adjustment, O2 delivery would not limit mVO2 after exercise onset; and 5) blood flow could limit O2 delivery in recovery, if blood flow returned to base-line levels at rates similar to those during the on-transient phase.

Cardiac Output↗
PubMed1991

Isotropic connections generate functional asymmetrical behavior in visual cortical cells.

1. We study the relationship between structure and function in inhibitory long-range interactions in visual cortex. The sharpening of orientation tuning with "cross-orientation inhibition" is used as an example to discuss anisotropies that are generated by long-range connections. 2. In this study, as opposed to the detailed cortex model described in a previous report, a model of the cortical orientation column structure is proposed in which cortical cells are described only by their orientation preference. 3. We present results using different geometric arrangements of orientation columns. In the simplest case, straight parallel orientation columns were used. We also utilized more realistic, curved columns generated by a simple algorithm. The results were confirmed by the study of a patch of real column structure, determined experimentally by Swindale et al. 4. A given cell receives functionally defined cross-orientation inhibition if the cell receives inhibitory input that is strongest along its nonpreferred orientation. On the other hand, a cell is said to receive structurally defined cross-orientation inhibition if the inhibition arises from source cells with an orientation preference orthogonal to that of the target cell. Even though those definitions seem to describe similar situations, we show that, in the general case, structurally defined cross-orientation inhibition does not efficiently sharpen orientation selectivity. In particular, for straight and parallel columns, structurally defined cross-orientation inhibition results in unequal amounts of inhibition for whole cell populations with different preferred orientations. 5. In more realistic column structures, we studied the question of whether structural cross-orientation inhibition could be implemented in a more efficient way. However, for the majority of cells, it is demonstrated that their nonpreferred stimulus will not preferably excite "cross-oriented" cells. Thus structural cross-orientation inhibition is not efficient in real cortical columns. 6. We propose a new mechanism called circular inhibition. In this connection scheme, a target cell receives inhibitory input from source cells that are located at a given distance (the same for all cells) from the target cell. Circular inhibition can be regarded as two-dimensional long-range lateral inhibition. As opposed to structural cross-orientation inhibition, this mechanism does not introduce unwanted anisotropies in the orientation tuning of the target cells. It is also conceptually much simpler and developmentally advantageous. It is shown that this connection scheme results in a net functional cross-orientation inhibition in all realistic column geometries. The inhibitory tuning strength obtained with circular inhibition is weak and similar to that measured in reality.(ABSTRACT TRUNCATED AT 400 WORDS)

Algorithms↗
PubMed1992

The two polypeptide chains in fibronectin are joined in antiparallel fashion: NMR structural characterization.

The fibronectin C-terminal interchain disulfide-linked heptapeptide dimer (Val-Asn-Cys-Pro-Ile-Glu-Cys)2 has been investigated via 1H NMR spectroscopy in both water and dimethyl sulfoxide (DMSO) solutions. Proton Overhauser experiments in DMSO indicate unambiguously that the two fibronectin polypeptide chains are linked head-to-tail (N-terminus to C-terminus), in an antiparallel fashion. It is found that the structure of the peptide is extended. From the 1H NMR interproton distance and angle constraints, the preferred mean (time-averaged) conformations in both H2O and DMSO were derived using distance geometry and molecular mechanics algorithms. The two conformations, although significantly dissimilar, exhibit the common feature of a structurally parallel (as opposed to chemically antiparallel) fibronectin alpha/beta chain array.

Amino Acid Sequence↗
PubMed1991

[Response analysis for an approximate 3-D image reconstruction in cone-beam SPECT].

Cone-beam Single Photon Emission Computed Tomography (SPECT) offers the potential for a large increase in sensitivity as compared with parallel hole or fan-beam collimation. Three-dimensional image reconstruction was approximately accomplished by backprojecting filtered projections using a two-dimensional fan-beam algorithm. The cone-beam projection data were formed from mathematical phantoms as analytically derived line integrals of the density. In order to reduce the processing time, the filtered projections were backprojected into each planes parallel to the circle on which the focal point moved. Discrepancy of source position and degradation of resolution were investigated by computer simulation in three-dimensional image space. The obtained results suggest that, the nearer to the central plane or the axis of rotation, the less image degradation is performed. By introducing a parameter of angular difference between the focal point and fixed point in the image space during rotation, degradation of the reconstructed image can be estimated for any cone-beam SPECT system.

Algorithms↗
PubMed1989

The clinical utility of renal concentrating capacity in polycystic kidney disease.

We studied 177 adult nonazotemic subjects with autosomal dominant polycystic kidney disease (ADPKD) and 123 unaffected family members (NADPKD). In order to assess the factors influencing renal concentrating capacity maximal urinary osmolality (UOsm) after overnight water deprivation and vasopressin was measured. UOsm was reduced in ADPKD (680 +/- 14) compared to NADPKD subjects (812 +/- 13 mOsm/kg). A greater severity of the architectural abnormality as assessed by cyst number and size and remaining volume of normal parenchyma was associated with a greater impairment of renal concentrating capacity. The concentrating defect was present in the youngest ADPKD subjects and the rate of decline of concentrating capacity with age in ADPKD paralleled that in NADPKD subjects. Based on the initial 135 subjects studied, we developed an algorithm for diagnostic screening for ADPKD utilizing blood pressure, serum creatinine and UOsm designed to maximize sensitivity. When applied to a subsequent population of 165 adults, 121 with ADPKD and 44 unaffected relatives, this algorithm would have spared 20% of unaffected subjects from the cost of ultrasound while failing to detect less than 2% of affected subjects. This simple protocol thus offers a rapid and inexpensive way to screen for ADPKD.

Adult↗
PubMed1991

Sample size estimation for comparing two or more treatment groups in clinical trials.

Methods for estimating required sample size for comparing two population means have been published. Most involve the use of complicated formulae and tables. These methods are limited to comparing two groups. Although techniques exist to determine sample sizes for comparing more than two groups, they are intrinsically far more complicated. A simple linear nomogram is proposed as a solution to these problems, and its use is illustrated with examples of parallel group, ordered parallel group and factorial designs.

Algorithms↗
PubMed1991

Asymmetric Boltzmann machines.

We study asymmetric stochastic networks from two points of view: combinatorial optimization and learning algorithms based on relative entropy minimization. We show that there are non trivial classes of asymmetric networks which admit a Lyapunov function L under deterministic parallel evolution and prove that the stochastic augmentation of such networks amounts to a stochastic search for global minima of L. The problem of minimizing L for a totally antisymmetric parallel network is shown to be associated to an NP-complete decision problem. The study of entropic learning for general asymmetric networks, performed in the non equilibrium, time dependent formalism, leads to a Hebbian rule based on time averages over the past history of the system. The general algorithm for asymmetric networks is tested on a feed-forward architecture.

Algorithms↗
PubMed1989

A two-dimensional pencil-beam algorithm for calculation of arc electron dose distributions.

A two-dimensional pencil-beam algorithm is presented for the calculation of arc electron dose distributions in any plane that is perpendicular to the axis of rotation. The dose distributions are calculated by modelling the arced beam as a single broad beam defined by the irradiated surface of the patient. The algorithm is two-dimensional in that the anatomical cross section of the patient and the skin collimators are assumed identical in parallel planes outside the plane of calculation. The broad beam is modelled as a collection of strip beams, each strip beam being characterised by its planar fluence, mean projected angular direction and a root-mean-square spread about the mean direction. Using these parameters, the dose distribution is calculated using pencil-beam theory. Examples of strip-beam parameters and resulting dose distributions for patient geometries are presented. Features of the algorithm, which include (1) incorporation of pencil-beam theory for the calculation of dose in heterogeneous tissue, (2) run times of only about twice that of comparable-sized fixed electron fields and (3) the input requirement of only a single depth dose and four off-axis dose profiles of measured data, make the algorithm practical for clinical use.

Algorithms↗
PubMed1992

Deblurring of 3-dimensional patterns of evoked rat cerebellar cortical activity: a study using voltage-sensitive dyes and optical sectioning.

One of the benefits of imaging neuronal activity is the capability of resolving spatial patterns in the x-y plane. With optical sectioning microscopy, the 3-dimensional (3-D) structure may also be studied without physical deformation by serially moving the focal plane of the microscope through the volume of interest along the focal axis. However, each image is blurred by contributions from neighboring planes. This degradation is most severe for low numerical aperture lenses and large amounts of defocus. In this study, an image restoration method using the optical properties of an aberration-free, defocused optical system has been developed for improving optical signals from voltage-sensitive dyes. Deblurring based on the optical transfer function (OTF) of the system was applied on two test sets of serially sectioned images: (1) fluorescent beads and (2) in vivo rat cerebellar cortex stained with the voltage-sensitive dye RH795. This method was shown to reduce significantly the out-of-focus contribution to the images, improving the spatial resolution not only in the x-y plane, but also the z axis. The algorithms were then applied to optical signals obtained by stimulation of the cerebellar surface. Optical signals having a distinct beam-like pattern were evoked and recorded over depths ranging from 0 to 300 microns prior to deblurring. Application of the deblurring algorithm reduced the depth of cerebellar cortex over which the optical signals were observed. In agreement, field potential recordings of the evoked parallel fiber volley and post-synaptic components were restricted to a narrow range of depths similar to the deblurred optical images. Removal of out-of-focus information is an essential step in the serial sectioning of central nervous system structures for neuronal imaging and 3-D reconstruction.

Algorithms↗
PubMed1990

PR interval behavior during exercise: implications for physiological pacemakers.

The relationship between heart rate response and the dynamic changes in the PR interval was assessed in 631 patients undergoing routine cardiac exercise tests for a variety of clinical indications. Patients were stratified into four subsets: nonmedicated normals (n = 437), patients on beta-antagonist agents (n = 118), those on antiarrhythmic agents alone (n = 61) and those with a clinical diagnosis of advanced (New York Heart Association [NYHA] Class III or IV) congestive heart failure. All patients were in stable sinus rhythm throughout the test. PR intervals were measured at rest, at mid-exercise and at peak exercise. Mean PR intervals shortened to a statistically significant degree in most subgroups. This effect was predominantly observed in the earlier stages of exercise. In patients with advanced heart failure, there was no statistically significant shortening of exercise PR intervals later in exercise, demonstrating a parallel with their relatively blunted heart rate response. These changes in exercise PR intervals suggest that implanted pacemaker algorithms may be constructed to maximize hemodynamic benefit in patients requiring physiological pacemakers.

Adolescent↗
PubMedDate not supplied

A multiple projection method for digital tomosynthesis.

A new method of optimized efficiency for the retrospective reconstruction of tomograms is presented. The method has been developed for use with isocentric fluoroscopic units and is capable of performing digital tomosynthesis of anatomical planes of user selected orientation and distance from the isocenter. Optimization of efficiency has been achieved by segmenting the reconstruction process into discrete transformations that are specific to groups of pixels, rather than performing pixel by pixel operations. These involve a number of projections of the acquired image matrices as well as parallel translations and summing. Application of this method has resulted in a significant reduction of computing time. The proposed algorithm has been experimentally tested on a radiotherapy simulator unit with the use of a phantom and the obtained results are reported and discussed.

Algorithms↗