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At least 127 records · Page 7Linked to original sources
PubMed1987

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase.

The crystal structure of M4 apo-lactate dehydrogenase from the spiny dogfish (Squalus acanthius) was initially refined by a constrained-restrained, and subsequently restrained, least-squares technique. The final structure contained 286 water molecules and two sulfate ions per subunit and gave an R-factor of 0.202 for difraction data between 8.0 and 2.0 A resolution. The upper limit for the co-ordinate accuracy of the atoms was estimated to be 0.25 A. The elements of secondary structure of the refined protein have not changed from those described previously, except for the appearance of a one-and-a-half turn 3(10) helix immediately after beta J. There is also a short segment of 3(10) helix between beta C and beta D in the part of the chain that connects the two beta alpha beta alpha beta units of the six-stranded parallel sheet (residues Tyr83 to Ala87). Examination of the interactions among the different elements of secondary structure by means of a surface accessibility algorithm supports the four structural clusters in the subunit. The first of the two sulfate ions is in the active site and occupies a cavity near the essential His195. Its nearest protein ligands are Arg171, Asp168 and Asn140. The second sulfate ion is located near the P-axis subunit interface. It is liganded by His188 and Arg173. These two residues are conserved in bacterial lactate dehydrogenase and form part of the fructose 1,6-bisphosphate effector binding site. Two other data sets in which one (collected at pH 7.8) or both (collected at pH 6.0) sulfate ions were replaced by citrate ions were also analyzed. Five cycles of refinement with respect to the pH 6.0 data (25 to 2.8 A resolution) resulted in an R value of 0.191. Only water molecules occupy the subunit boundary anion binding site at pH 7.8. The amino acid sequence was found to be in poor agreement with (2Fobs-Fcalc) electron density maps for the peptide between residues 207 and 211. The original sequence WNALKE was replaced by NVASIK. The essential His195 is hydrogen bonded to Asp168 on one side and Asn140 on the other. The latter residue is part of a turn that contains the only cis peptide bond of the structure at Pro141. The "flexible loop" (residues 97 to 123), which folds down over the active center in ternary complexes of the enzyme with substrate and coenzyme, has a well-defined structure. Analysis of the environment of Tyr237 suggests how its chemical modification inhibits the enzyme.

Amino Acid Sequence↗
PubMed1989

Nuclear medicine in the 1990s: a quantitative physiological approach.

This paper describes the potential advantages to medical diagnosis and treatment that might be obtained from the wider application of positron emission tomography as a clinical tool. Developments along the lines suggested here will require a radical change in thinking from both clinicians and the medically related scientific community in the UK and some enlightened and resourceful funding from a mixture of charitable, industrial and government sources. If these ideas are to be pursued successfully, then the work must start now on a much wider scale than is presently perceived in the UK, and close collaboration between physicists, engineers, chemists, biochemists, clinicians and industrialists is needed. Furthermore, it is imperative that the scientific developments now underway in silicon technology, parallel data processors, biochemical and pharmacological processes and even high-temperature superconductors be kept under close and constant review by those associated with the technological advancements of medicine, so that the value of such developments is rapidly transferred to applications to medicine. This must include closer relationships between academic medicine and science than is the general rule in the UK at present. In conclusion, the scenario presented here includes the installation of regional cyclotron facilities to provide a large number of institutions in the UK with positron-emitter labelled radiopharmaceuticals. Additionally, agents labelled with radionuclides from in-house generators and other already existing higher-energy cyclotrons will provide a versatile and valuable range of radiopharmaceuticals for the study of human disease. These developments must be supported by the manufacture of lower-cost positron camera systems, as suggested here, connected to high-data-rate parallel processors to provide images of body function and to determine the effects brought about by disease. These images may then be processed using algorithms based on kinetic models of the body systems to provide information about the basic biochemical and physiological processes of the body. Such a development could have a profound effect on our knowledge of human disease and on our ability to control and treat it successfully.

Forecasting↗
PubMed1991

Parallel simulated annealing for emission tomography.

A method for implementing simulated annealing in parallel to speed up the execution of emission tomography (ET) image reconstruction is presented. A high degree of parallelism can be attained by using a parallel-acceptance partitioning strategy, in which perturbations to subsets of the estimate are evaluated in parallel. However because the point spread function in ET imaging systems is globally dependent, processors cannot update the current estimate independently. Consequently, processors must be synchronized each time a perturbation is accepted to avoid introducing error. This can produce excessive communications overhead, especially when the acceptance rate is high. In this paper an energy function is constructed to reduce the synchronization requirements by using a reformulation of the log-likelihood function from the expectation maximization (EM) algorithm. The approach is to change the global dependence in the energy function from the current estimate to the estimate generated during the last iteration. The synchronization requirements for guaranteed convergence are then significantly reduced from once per acceptance to once per iteration. This parallel implementation on 54 Inmos T800 transputers connected in a ring topology resulted in execution times that were almost 50 times faster than on a VAX 8600.

Algorithms↗
PubMed1989

A low-cost single-board solution for real-time, unsupervised waveform classification of multineuron recordings.

We describe a low-cost single-board system for unsupervised, real-time spike sorting of recordings from a number of neurons on a single microelectrode. The maximum number of spike classes depends on the quality of the recording; it will typically be between 2 and 5. The spike sorter communicates with a conventional microcomputer through a standard serial port (RS232). For typical firing rates as measured in the mammalian central nervous system, this set-up will accommodate up to some 10 parallel spike sorters for as many separate microelectrodes.

Algorithms↗
PubMed1988

Refined evaluation of the exponential curve parameters and initial exchange rate constant for 22Na+ washout in cultured human skin fibroblasts.

A technique is proposed to evaluate the exponential curve parameters and the initial exchange rate constant (kie) for 22Na+ washout from cultured human skin fibroblasts. After loading with the isotope, the cells were subjected to cold washing and warming steps. A desaturation curve for 22Na+ washout was developed including the activity in the warming medium that corresponded to t = 0 min. Using nonlinear regression analysis, a general three exponential function adequately described the 22Na+ washout in the time interval of 0-70 min. A back extrapolation was performed to estimate the initial time (ti; a negative number) when the total activity was present in the cells. The ti was substituted into the first derivative function of the three exponents to yield the kie. Calculated from the equilibrium distribution of 22Na+ and the specific activity of the medium, the concentration of Na+ (in mM; mean +/- SD) for fibroblasts of two individuals were 13.3 +/- 2.3, n = 3, and 19.0 +/- 5.2, n = 4. This indicates that the washout originated mainly or exclusively from the cellular milieu. Therefore, the kie represents the equilibrium exchange rate constant for Na+ washout from an inhomogeneous cell-related space. Multiple experiments demonstrated that the kie value for the two subjects were significantly higher than the initial slopes of the washout curves (kA), a commonly used parameter to characterize Na+ washout, and significantly lower than the slopes of the fastest exponential components (k3): kie = 0.531 +/- 0.017, kA = 0.502 +/- 0.019, and k3 = 0.557 +/- 0.017 min-1 (n = 3) for one subject, and kie = 0.567 +/- 0.065, kA = 0.479 +/- 0.031, and k3 = 0.667 +/- 0.094 min-1 (n = 6) for the other subject. The respective equilibrium exchange rates for these cells, namely the products of kie and cellular Na+ contents, were 1.10 +/- 0.16 and 1.19 +/- 0.24 nmole/10(5) cells. Using the exponential curve parameters, analytical solutions of a serial model and a parallel model with three compartments were performed. According to these analyses the major portion of the cellular Na+ comprises a fast exchangeable cellular compartment. The relative size of this compartment (expressed as a fraction of total cellular Na+ content) for fibroblasts of the two subjects was 96.2 and 89.2% for the serial model and 96.1 and 89.3% according to the parallel model.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed1990

Evaluation of a human immunodeficiency virus test algorithm utilizing a recombinant protein enzyme immunoassay.

Many truly human immunodeficiency virus (HIV) antibody-negative serum samples may be unnecessarily subjected to costly and time-consuming Western blots (immunoblots). An investigation was undertaken to evaluate the efficiency of using a recombinant protein-based enzyme immunosorbent assay (EIA; Cambridge BioScience [CBC] Recombigen HIV EIA) as an adjunct to whole viral lysate EIA. A total of 2,212 serum samples which had been screened by viral lysate EIA were tested by CBC EIA in parallel with the Western blot. The sensitivity and specificity of the CBC kit were 99.9 and 99.7%, respectively. Positive and negative predictive values were 99.7 and 99.9%, respectively. The high sensitivity of this kit and its high negative predictive value make it an attractive addition to an HIV testing algorithm by reducing the number of Western blot tests on truly antibody negative serum samples.

Acquired Immunodeficiency Syndrome↗
PubMedDate not supplied

Calculation of the uncertainty in the dose delivered during radiation therapy.

There is, inevitably, uncertainty in our knowledge of the dose at any point within an irradiated patient. A technique is presented for estimating this uncertainty by performing three parallel calculations, one using nominal values and the others extreme values of the parameters upon which the dose depends. Such calculations can be made with almost any algorithm for calculating dose. They result in an estimate, at some specified confidence level which is determined by the data used, of the range of dose likely at any point. Such calculations should help therapists to avert over- or underdosage which might not be evident in conventional calculations of the nominal dose.

Humans↗
PubMed1992

Effect of the signal-to-noise ratio on the quality of linear estimation reconstructions of distributed current sources.

Currently, linear estimation reconstruction is the only feasible method for extracting information about spatially distributed current sources from measurements of neural magnetic fields. We present the results of a systematic study of the effect of the signal-to-noise ratio on the imaging quality of one such algorithm in over-as well as undetermined circumstances. In particular, we will discuss the necessary trade-off between the contradictory goals of a minimum norm of the reconstructed current density distribution and of a minimal deviation of the reconstructed fields from the measured fields. As an example, we show the reconstruction of a simple arrangement of two nearly parallel dipoles in two different depths inside a spherical volume conductor, discussing the differences between the computer simulation without noise and simulation with a realistic noise level.

Algorithms↗
PubMed1990

Order-disorder phenomena in myelinated nerve sheaths. I. A physical model and its parametrization: exact and approximate determination of the parameters.

An algorithm is developed for the analysis of the X-ray scattering spectra of lamellar systems, by reference to a precise physical model. The model consists of identical planar lamellae (the motif), all parallel and stacked in a one-dimensional crystal with four types of defect: stacking disorder, finite size of the crystallites, and presence of diffuse and blank scattering. In addition, the spectra are distorted by collimation aberrations. In order to evaluate the effects of these distortions, the following assumptions are made: (1) beyond some point Slimit the intensity curve can be expressed as a function of a (small) number of parameters; (2) the blank scattering, restricted to very small angles, can be identified and eliminated; and (3) the diffuse scattering is entirely defined by the values of idiff(h/D) at the lattice Sh = h/D (h is a positive integer less than or equal to DSlimit). These assumptions lead to an expression of the whole of the intensity curve as a function of a finite number of parameters: the average D and the variance sigma 2D of the repeat distance, the average number [N] of lamellae per crystallite, the set [idiff(h/D)] and the set [imotif(k/2D)] (where k is a positive integer), which defines the structure of the motif. An algorithm is proposed to determine the value of the various parameters. The derivation of the algorithm involves several operations: construction in real space of periodic functions whose motifs are step-sections of the autocorrelation function; expression in reciprocal space, and in terms of the experimental scattering curves, of the Fourier transform of those periodic functions; analysis of the properties of the two functions. The algorithm is tested using a variety of simulated scattering curves whose parameters [imotif(k/2D)], [idiff(2/D)], D, sigma D, [N] (and collimation distortions) are within the range commonly encountered in experimental conditions. The results show that the values of the parameters retrieved by the algorithms are very close to those used in the simulation. The calculations are fast and easy to implement on a computer. The main virtues of the algorithm are (1) to determine the values of all the parameters at once, eliminating most of the intermediate (and questionable) manipulations (separation of signal from noise, discrimination of overlapping reflections, integration of the intensities) and (2) to yield the continuous intensity curve of a single motif.

Algorithms↗
PubMed1987

Arbitrary oblique image sections for 3-D radiation treatment planning.

Methods for selecting and computing arbitrary image sections for displaying anatomic and isodose information for three-dimensional treatment planning are investigated. Selection of the desired plane may be made by defining a plane that is perpendicular to an existing image section (called the base image) and passing through a line on the base image. Alternatively, the anatomic structures displayed perspectively in three dimensions as a series of contours that can be rotated and translated may be used to define an arbitrary plane for image reconstruction. The viewing screen is considered to be the plane of interest. As a typical three-dimensional image of 30 to 60 sections requires considerable computer storage (on the order of 25 megabytes), a reconstruction algorithm may need extensive memory space or CPU and disk I/O time. Of the schemes examined, we believe the following is the most efficient. One pair of images is read from the disk at a time in sequence and intersections of the rows of the cutting plane with the box formed by the consecutive images are computed. Pixel values of all points between the given images are computed by interpolation. Special cases, such as the cutting plane being parallel to or coincident with an existing image, must be considered separately.

Algorithms↗
PubMed1979

A computerized rotating laminar radionuclide camera.

We have constructed a radionuclide camera that embodies a unique detector-collimator concept and provides a radically new approach to imaging. The heart of the instrument is a linear array of semiconductor detectors separated by thin tungsten plates that confine the field of view of each detector to one dimension. This collimator design has a higher collection efficiency than the standard parallel-hole collimator but cannot directly produce a two-dimensional image. When multiple measurements are taken as the array rotates through 180 degrees, a computerized image restoration algorithm can then produce two-dimensional images with resolution determined by the width of the detectors. A small prototype camera has produced images with resolution superior to conventional Anger cameras.

Computers↗
PubMed1991

Dose in bone and tissue near bone-tissue interface from electron beam.

This work has quantitatively studied the variation of dose both within bone and in unit density tissue near bone-tissue interfaces. Dose upstream of a bone-tissue interface is increased because of an increase in the backscattered electrons from the bone. The magnitude of this effect was measured using a thin parallel-plate ionization chamber upstream of a polymethyl methacrylate (PMMA)-hard bone interface. The electron backscatter factor (EBF) increased rapidly with bone thickness until a full EBF was achieved. This occurred at approximately 3.5 mm at 2 MeV and 6 mm at 13.1 MeV. The full EBF at the interface ranged from approximately 1.018 at 13.1 MeV to 1.05 at 2 MeV. It was also observed that the EBF had a dependence on the energy spectrum at the interface. The penetration of the backscattered electrons in the upstream direction of PMMA was also measured. The dose penetration fell off rapidly in the upstream direction of the interface. Dose enhancement to unit density tissue in bone was measured for an electron beam by placing thermoluminescent dosimeters (TLDs) in a PMMA-bone-PMMA phantom. The maximum dose enhancement in bone was approximately 7% of the maximum dose in water. However, the pencil-beam algorithm of Hogstrom et al. predicted an increase of only 1%, primarily owing to the inverse-square correction. Film was also used to measure the dose enhancement in bone. The film plane was aligned either perpendicular or parallel to the central axis of the beam. The film data indicated that the maximum dose enhancement in bone was approximately 8% for the former film alignment (which was similarly predicted by the TLD measurements) and 13% for the latter film alignment. These results confirm that the X ray film is not suitable to be irritated "edge on" in an inhomogeneous phantom without making perturbation corrections resulting from the film acting as a long narrow inhomogeneous cavity within the bone. In addition, the results give the radiotherapist a basis for clinical judgment when electron beams are used to treat lesions behind bone or near bony structures. We feel these data enhance the ability to recognize the shortcomings of the current dose calculation algorithm used clinically.

Bone and Bones↗
PubMed1988

Tracking multiple independent targets: evidence for a parallel tracking mechanism.

There is considerable evidence that visual attention is concentrated at a single locus in the visual field, and that this locus can be moved independent of eye movements. Two studies are reported which suggest that, while certain aspects of attention require that locations be scanned serially, at least one operation may be carried out in parallel across several independent loci in the visual field. That is the operation of indexing features and tracking their identity. The studies show that: (a) subjects are able to track a subset of up to 5 objects in a field of 10 identical randomly-moving objects in order to distinguish a change in a target from a change in a distractor; and (b) when the speed and distance parameters of the display are designed so that, on the basis of some very conservative assumptions about the speed of attention movement and encoding times, the predicted performance of a serial scanning and updating algorithm would not exceed about 40% accuracy, subjects still manage to do the task with 87% accuracy. These findings are discussed in relation to an earlier, and independently motivated model of feature-binding--called the FINST model--which posits a primitive identity maintenance mechanism that indexes and tracks a limited number of visual objects in parallel. These indexes are hypothesized to serve the function of binding visual features prior to subsequent pattern recognition.

Algorithms↗
PubMed1992

Segmentation, modelling and reconstruction of arterial bifurcations in digital angiography.

The paper presents a method to model an arterial bifurcation from a pair of X-ray angiographic images. It is the initial step of a reconstruction process aiming at detecting and quantifying abnormal sites located on bifurcations. The method proposed consists of two steps. First, each image is independently segmented to extract the vessels in the images. The algorithm uses dynamic programming first to find the bifurcation centrelines from the original images, and secondly to extract vessel edges from the morphological gradient images, under a constraint of parallelism with the previously detected centrelines. Then, a three-dimensional bifurcation model is built by adapting cylinders around the three-dimensional bifurcation centrelines. These cylinders are obtained as a stack of binary orientable ellipses fitted to the projection densities in the corresponding cross-sections. Results obtained on simulated data, phantom and femoral bifurcations are displayed.

Angiography, Digital Subtraction↗
PubMed2025

PRISM: privacy-preserving rare disease analysis using fully homomorphic encryption.

MOTIVATION: Rare diseases affect millions of people worldwide, yet their genomic foundations remain poorly understood due to limited patient data and strict privacy regulations, such as the General Data Protection Regulation (GDPR) (https://gdpr.eu/tag/gdpr/) in March 2025. These restrictions can hinder the collaborative analysis of genomic data necessary for uncovering disease-causing variants. RESULTS: We present PRISM, a novel privacy-preserving framework based on fully homomorphic encryption (FHE) that facilitates rare disease variant analysis across multiple institutions without exposing sensitive genomic information. To address the challenges of centralized trust, PRISM is built upon a Threshold FHE scheme. This approach decentralizes key management across participating institutions and ensures no single entity can unilaterally decrypt sensitive data. Our method filters disease-causing variants under recessive, dominant, and de novo inheritance models entirely on encrypted data. We propose two algorithmic variants: a multiplication-intensive (MUL-IN) approach and an addition-intensive (ADD-IN) approach. The ADD-IN algorithms minimize the number of costly multiplication operations, enabling up to a 17× improvement in runtime for recessive/dominant filtering and 22× for de novo filtering, compared to MUL-IN methods. While ADD-IN produces larger ciphertexts, efficient parallelization via SIMD and multithreading allows it to handle millions of variants in reasonable time. To the best of our knowledge, this is the first study that utilizes FHE for privacy-preserving rare disease analysis across multiple inheritance models, demonstrating its practicality and scalability in a single-cloud setting. AVAILABILITY AND IMPLEMENTATION: The source code and the data used in this work can be found in https://github.com/mdppml/PRISM.git.

Computer Security↗
PubMed1991

Cone-beam transmission computed tomography for nonuniform attenuation compensation of SPECT images.

This paper develops and tests cone-beam transmission computed tomography (CB-CT) for attenuation compensation of SPECT images. CB-CT was implemented on a rotating gamma camera with a point source (1-2 mCi) of 99mTc, and a light-weight aluminum source holder. A cone-beam collimator may be used but is not required. Since the point source is either located at the collimator focal point, or the camera is uncollimated, CB-CT has excellent sensitivity (at least 150 times that of a parallel-hole, high-resolution collimator). The predicted resolution is equal to the intrinsic gamma camera resolution (3-4 mm), which is much higher than for a high-resolution, parallel-hole collimator (10-20 mm). In the present study, CB-CT provided low noise, high-resolution attenuation maps for use in a nonuniform attenuation-weighted backprojection algorithm. The attenuation compensation accuracy was tested using basic geometries of line sources and nonuniform density models. For the appropriate scaling of the attenuation map, the attenuation compensation was accurate and removed the SPECT image distortion associated with nonuniform attenuation. Attenuation maps acquired either with cone beam collimator or without any collimator were both successful. Using CB-CT, SPECT can thus be made much more accurate without adding unduly to the imaging time, complexity, or cost.

Algorithms↗
PubMed2026

An automated geometric modeling framework in GATE for the design and optimization of high-sensitivity converging-beam SPECT collimators.

Objective.The trade-off between detection sensitivity and spatial resolution is a fundamental challenge in designing organ-dedicated Single-photon emission computed tomography (SPECT) collimators. While converging-hole geometries offer a solution, their optimization is often hindered by the lack of flexible computational tools capable of modeling large-scale, non-parallel hole arrays. This study aims to develop an automated geometric modeling framework to facilitate the design and evaluation of complex converging- and diverging-hole collimators within standard Monte Carlo environments.Approach.We developed a specialized modeling framework by implementing custom C++ classes and a vector-based alignment algorithm within GATE. This platform enables automated, orientation-consistent construction of large-scale converging arrays not natively supported by standard implementations. A high-sensitivity pure cone-beam collimator (CBC) was designed using this framework. The evaluation used hot-rod, disc, and Jaszczak phantoms for physical characterization, while XCAT and dedicated brain models were employed for clinical tasks, including cardiac, brain perfusion, and DaTscan SPECT simulations.Main results.The CBC achieved a nearly fourfold sensitivity increase compared to a conventional low-energy high-resolution parallel-hole collimator at a 20 cm radius of rotation, while maintaining comparable spatial resolution. Despite a 52.3% field of view reduction, the CBC yielded a 2.2-fold noise reduction (CV: 11.7% vs 25.9%) and mitigated partial volume effects via geometric magnification. XCAT and brain phantom simulations confirmed enhanced anatomical definition and contrast recovery in cardiac, perfusion, and DaTscan tasks.Significance.This work provides an efficient computational tool for rapid design space exploration of advanced collimator geometries. The results demonstrate that the proposed CBC design offers a significant sensitivity advantage, making it highly suitable for high-performance, small-volume clinical applications such as brain and cardiac molecular imaging.

Tomography, Emission-Computed, Single-Photon↗
PubMed1991

Clustering a large number of compounds. 2. Using the Connection Machine.

About 230,000 compounds in the National Cancer Institute Repository are available for screening under a new protocol. This paper is the second on an project to extract a representative sample of these compounds by clustering. The clustering program was implemented on the Connection Machine, a massively parallel computer with 16K processing elements. This implementation reduced a formidable task to a relatively routine run.

Algorithms↗