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PubMed1986

Interactive display of three-dimensional radionuclide distributions.

Tomographic images of three-dimensional radionuclide distributions are usually presented as a set of parallel planar slices. A technique has been developed to enable the observer to perceive directly the three-dimensional morphology of the activity distribution by displaying iso-count surfaces. Computer graphics techniques have been used to present shaded surface images using a conventional nuclear medicine computer system. Because of the relatively coarse spatial sampling of radionuclide tomograms, a smooth shading algorithm based on a local polynomial fit procedure was developed. By using a simple solid model approach for data storage the program executes interactively, allowing the observer to view the reconstructed activity distribution from any aspect. The technique has been successfully applied to radionuclide tomograms of several organs, and promises to be particularly useful for the display or cardiac blood pool data.

Algorithms↗
PubMed2004

DMLC leaf-pair optimal control of IMRT delivery for a moving rigid target.

In dynamic multileaf collimation (DMLC), pairs of servo-controlled leaves sweep across the target to deliver the modulated radiation intensity map while the beam is on continuously. The mathematical model for dynamic, optimal control of a single leaf pair has been developed for the case of a rigid target, translating parallel to the leaf trajectories. This mathematical model ensures delivery of the modulated intensity map while minimizing beam-on time. Numerical solutions of the model are presented here for optimal IMRT delivery for stationary and oscillating targets, together with a discussion of the results. Comparisons between solutions for stationary and mobile targets, as well as comparisons between optimal and suboptimal algorithms, are provided. These comparisons allow us to estimate potential gains in the effectiveness of DMLC IMRT delivery when it is based on optimal algorithms.

Algorithms↗
PubMed2006

Respiratory-triggered MRCP applying parallel acquisition techniques.

PURPOSE: To evaluate the influence of parallel imaging on the image quality of respiratory triggered magnetic resonance cholangiopancreatography (MRCP). MATERIALS AND METHODS: A total of 30 consecutive patients underwent MRCP applying a respiratory triggered T2-weighted (T2w) turbo spin-echo (TSE) sequence without and with parallel imaging (acceleration factor of 2). Acquisition times of both sequences were recorded. Quantitative evaluation included measurement of a contour sharpness index of two segments of the pancreaticobiliary tree as well as calculation of the relative contrast between ductal structures and organ parenchyma at four different segments. The qualitative evaluation was performed by two independent radiologists who graded overall image quality, depiction of eight segments of the pancreaticobiliary tree, and the frequency of artifacts. RESULTS: The application of parallel imaging significantly (P<0.05) reduced the acquisition time of the respiratory triggered MRCP sequence by 37.7% (six minutes and two seconds+/-one minute and 26 seconds vs. three minutes and 46 seconds+/-58 seconds). The quantitative and qualitative evaluation revealed no statistically significant differences between the two sequences (P>0.05). The frequency of artifacts was at the same level for both sequences as well. CONCLUSION: The application of parallel imaging for respiratory triggered MRCP significantly reduces the acquisition time without relevant influence on image quality.

Adult↗
PubMed2004

Parallel excitation with an array of transmit coils.

Theoretical and experimental results are presented that establish the value of parallel excitation with a transmit coil array in accelerating excitation and managing RF power deposition. While a 2D or 3D excitation pulse can be used to induce a multidimensional transverse magnetization pattern for a variety of applications (e.g., a 2D localized pattern for accelerating spatial encoding during signal acquisition), it often involves the use of prolonged RF and gradient pulses. Given a parallel system that is composed of multiple transmit coils with corresponding RF pulse synthesizers and amplifiers, the results suggest that by exploiting the localization characteristics of the coils, an orchestrated play of shorter RF pulses can achieve desired excitation profiles faster without adding strains to gradients. A closed-form design for accelerated multidimensional excitations is described for the small-tip-angle regime, and its suppression of interfering aliasing lobes from coarse excitation k-space sampling is interpreted based on an analogy to sensitivity encoding (SENSE). With or without acceleration, the results also suggest that by taking advantage of the extra degrees of freedom inherent in a parallel system, parallel excitation provides better management of RF power deposition while facilitating the faithful production of desired excitation profiles. Sample accelerated and specific absorption rate (SAR)-reduced excitation pulses were designed in this study, and evaluated in experiments.

Absorption↗
PubMed1994

Estimating heading during eye movements.

In eight experiments, we examined the ability to judge heading during tracking eye movements. To assess the use of retinal-image and extra-retinal information in this task, we compared heading judgments with executed as opposed to simulated eye movements. In general, judgments were much more accurate during executed eye movements. Observers in the simulated eye movement condition misperceived their self-motion as curvilinear translation rather than the linear translation plus eye rotation that was simulated. There were some experimental conditions in which observers could judge heading reasonably accurately during simulated eye movements; these included conditions in which eye movement velocities were 1 deg/sec or less and conditions which made available a horizon cue that exists for locomotion parallel to a ground plane with a visible horizon. Overall, our results imply that extra-retinal, eye-velocity signals are used in determining heading under many, perhaps most, viewing conditions.

Algorithms↗
PubMed2006

Dynamic lung mechanics in late-stage emphysema before and after lung volume reduction surgery.

This study evaluated the effects of lung volume reduction surgery (LVRS) on the heterogeneity of lung function in awake, late-stage emphysema patients with measurements taken before and after full recovery from LVRS. We assessed standard clinical measures of lung function and functional heterogeneity in six awake, late-stage emphysema patients before and 6 months after LVRS. Functional heterogeneity was quantified by measuring dynamic inspiratory resistance (R(L)(insp)) and elastance (E(L)(insp)) over a frequency range that included normal breathing ( approximately 0.33-8 Hz). Since LVRS involves targeted resection of emphysematous regions of the lung, we hypothesized that emphysema patients would be functionally more homogeneous post-LVRS. We also compared our measures of functional heterogeneity with indices of anatomic heterogeneity and severity using high-resolution computed tomography (HRCT). After LVRS, 6 min walk distance increased by 22% (940+/-91 versus 1158+/-299, p=0.031) and recoil pressure at TLC increased (9.0+/-2.0 versus 14+/-5, p=0.031), but changes in R(L)(insp) and E(L)(insp) varied greatly between subjects. A measure of anatomic severity quantified using HRCT positively correlated with airway resistance (r(s)=0.89, p=0.048). These results suggest that subjects with more severe disease as assessed by HRCT criteria had reduced overall effective airway caliber consequent to active airway constriction, reduced parenchymal tethering, and/or loss of parallel lung units. Furthermore, LVRS may not necessarily improve lung function via a substantial reduction in mechanical heterogeneity.

Adolescent↗
PubMedDate not supplied

[The interaction between two charged rods in an electrolyte solution].

A problem on the electrostatic interaction of two homogeneously charged macromolecular rods of a finite length, submerged into an electrolyte solution was considered. An explicit expression for the energy of interaction and rotational moment as a function of the angle of rotation between the long axes of the molecules was obtained. At small angles of rotation, the expression for energy turns into the corresponding formula for parallel rods, and the rotational moment tends to zero, as it follows from geometrical considerations. The possibility is discussed whether the study is applicable to real biological systems, including liquid-crystalline dispersions of DNA.

Algorithms↗
PubMed2003

Selection criteria for drug-like compounds.

The fast identification of quality lead compounds in the pharmaceutical industry through a combination of high throughput synthesis and screening has become more challenging in recent years. Although the number of available compounds for high throughput screening (HTS) has dramatically increased, large-scale random combinatorial libraries have contributed proportionally less to identify novel leads for drug discovery projects. Therefore, the concept of 'drug-likeness' of compound selections has become a focus in recent years. In parallel, the low success rate of converting lead compounds into drugs often due to unfavorable pharmacokinetic parameters has sparked a renewed interest in understanding more clearly what makes a compound drug-like. Various approaches have been devised to address the drug-likeness of molecules employing retrospective analyses of known drug collections as well as attempting to capture 'chemical wisdom' in algorithms. For example, simple property counting schemes, machine learning methods, regression models, and clustering methods have been employed to distinguish between drugs and non-drugs. Here we review computational techniques to address the drug-likeness of compound selections and offer an outlook for the further development of the field.

Algorithms↗
PubMed1986

Modelling of the control of heart rate by breathing using a kernel method.

The process of the breathing (input) to the heart rate (output) of man is considered for system identification by the input-output relationship, using a mathematical model expressed as integral equations. The integral equation is considered and fixed so that the identification method reduces to the determination of the values within the integral, called kernels, resulting in an integral equation whose input-output behaviour is nearly identical to that of the system. This paper uses an algorithm of kernel identification of the Volterra series which greatly reduces the computational burden and eliminates the restriction of using white Gaussian input as a test signal. A second-order model is the most appropriate for a good estimate of the system dynamics. The model contains the linear part (first-order kernel) and quadratic part (second-order kernel) in parallel, and so allows for the possibility of separation between the linear and non-linear elements of the process. The response of the linear term exhibits the oscillatory input and underdamped nature of the system. The application of breathing as input to the system produces an oscillatory term which may be attributed to the nature of sinus node of the heart being sensitive to the modulating signal the breathing wave. The negative-on diagonal seems to cause the dynamic asymmetry of the total response of the system which opposes the oscillatory nature of the first kernel related to the restraining force present in the respiratory heart rate system. The presence of the positive-off diagonal of the second-order kernel of respiratory control of heart rate is an indication of an escape-like phenomenon in the system.

Heart Rate↗
PubMed2002

Determination and refinement of disordered crystal structures using evolutionary algorithms in combination with Monte Carlo methods.

An evolutionary algorithm called 'differential evolution' is combined with Monte Carlo simulation to determine and optimize models of disordered crystal structures. Requirements for successfully finding the parameters describing disorder from diffuse scattering data are discussed and the algorithm is applied to resolving the racemic and associated displacive disorder of the host substructure in a perhydrotriphenylene inclusion compound. Refinement resulted in a very good visual agreement between observed and calculated intensities and in a relatively low value of R(diffuse) = 0.148 (3). The computations for determining and refining the structure took 29 d with five to ten workstations running in parallel. Analysis of the progress of the structure determination shows that the essential information can be obtained within a few hours. Limits of the technique and strategies to optimize the procedure are discussed.

Journal Article↗
PubMed1996

Short-term control of cardiovascular function: estimation of control parameters in healthy humans.

In a previous study, we recorded short-term cardiovascular responses after a steep increase in arterial pressure in healthy humans [Am. J. Physiol. 266 (Heart Circ. Physiol. 35): H199-H211, 1994]. The aim of the present study was to develop a mathematical model of the baroreflex control of arterial pressure, to use this model with the previously recorded data to estimate unknown parameters in the reflex control loop, and then to analyze the overall open- and closed-loop performance of the system by model simulations with use of individual sets of optimal parameters. The mathematical model consists of a heart, a linear elastic arterial reservoir, and two parallel resistive vascular beds. The arterial baroreflex loop is modeled by two separate time domain processing objects, each with its own gain, time constant, and delay, to simulate the action of a sympathetic signal to the peripheral vascular bed and a parasympathetic signal to the heart. In repeated model simulations, the control parameters in the model were systematically adjusted by an automated algorithm that minimized the deviations between the time courses of the cardiovascular variables simulated by the model and the previously recorded responses in each individual. In all 10 subjects, the short-term cardiovascular responses were adequately simulated by using individual sets of parameters in the model. Open-loop transfer functions for arterial pressure control were obtained by using the individual sets of optimal model parameters in new simulation runs. Open-loop gain for arterial pressure control at nearly zero frequency (steady state) was between 0.9 and 4. Model simulations also indicated an underdampened response at 0.05-0.07 Hz in the closed-loop situation in four subjects, corresponding to peaks in the mean arterial pressor power spectra obtained from separate recordings of spontaneous variations in the resting situation.

Baroreflex↗
PubMed2006

Computational intelligence for the detection and classification of malignant lesions in screening mammography.

This report deals with the discussion of the findings obtained from the application of two computational intelligence methodologies for the detection of microcalcifications in screening mammography data. Genetic programming and inductive machine learning have been applied, in order to produce meaningful diagnostic rules for the medical staff. The data used in the experiments correspond to information acquired from two images of each breast of the patient, along with some associated patient information such as the age at time of study. Similar datasets have been previously used in an attempt to facilitate the development of computer algorithms to aid screening. Experienced screening radiologists have double-read the screening mammograms, they have weighted the malignancy ratings and averaged out the levels of suspiciousness assigned to each finding in the screenings. The diagnostic rules which were obtained from both genetic programming and machine learning have been evaluated in detail and then analyzed and discussed by collaborative medical experts, in parallel to findings from related literature. Results seem encouraging for further use and analysis by medical staff specializing in screening mammography.

Artificial Intelligence↗
PubMed2006

Configuration of the electron transport algorithm of PENELOPE to simulate ion chambers.

The stability of the electron transport algorithm implemented in the Monte Carlo code PENELOPE with respect to variations of its step length is analysed in the context of the simulation of ion chambers used in photon and electron dosimetry. More precisely, the degree of violation of the Fano theorem is quantified (to the 0.1% level) as a function of the simulation parameters that determine the step size. To meet the premises of the theorem, we define an infinite graphite phantom with a cavity delimited by two parallel planes (i.e., a slab) and filled with a 'gas' that has the same composition as graphite but a mass density a thousand-fold smaller. The cavity walls and the gas have identical cross sections, including the density effect associated with inelastic collisions. Electrons with initial kinetic energies equal to 0.01, 0.1, 1, 10 or 20 MeV are generated in the wall and in the gas with a uniform intensity per unit mass. Two configurations, motivated by the design of pancake- and thimble-type chambers, are considered, namely, with the initial direction of emission perpendicular or parallel to the gas-wall interface. This version of the Fano test avoids the need of photon regeneration and the calculation of photon energy absorption coefficients, two ingredients that are common to some alternative definitions of equivalent tests. In order to reduce the number of variables in the analysis, a global new simulation parameter, called the speedup parameter (a), is introduced. It is shown that setting a = 0.2, corresponding to values of the usual PENELOPE parameters of C1 = C2 = 0.02 and values of WCC and WCR that depend on the initial and absorption energies, is appropriate for maximum tolerances of the order of 0.2% with respect to an analogue, i.e., interaction-by-interaction, simulation of the same problem. The precise values of WCC and WCR do not seem to be critical to achieve this level of accuracy. The step-size dependence of the absorbed dose is explained in the light of the properties of PENELOPE's transport mechanics. This work is intended to help users to adopt an optimal configuration that guarantees both a high-accuracy calculation of the absorbed dose and a reasonably short computing time.

Algorithms↗
PubMed2004

OrthoDisease: a database of human disease orthologs.

One of the greatest promises of genome sequencing projects is to further the understanding of human diseases and to develop new therapies. Model organism genomes have been sequenced in parallel to human genomes to provide effective tools for the investigation of human gene function. Many of their genes share a common ancestry and function with human genes, and this is particularly true for orthologous genes. Here we present OrthoDisease, a comprehensive database of model organism genes that are orthologous to human disease genes. OrthoDisease was constructed by applying the Inparanoid ortholog detection algorithm to disease genes derived from the Online Mendelian Inheritance in Man database (OMIM). Pairwise whole genome/proteome comparisons between Homo sapiens and six other organisms were performed to identify ortholog clusters. OMIM numbers were extracted from the OMIM Morbid Map and were converted to gene sequences using the Locuslink mim2loc and loc2acc tables. These were mapped to Inparanoid ortholog clusters using Blast. The number of ortholog clusters in OrthoDisease with each respective species is currently: M. musculus, 1,354; D. melanogaster, 724; C. elegans, 533; A. thaliana, 398; S. cerevisiae, 290; and E. coli, 153. The database is accessible online at http://orthodisease.cgb.ki.se, and can be searched with disease or protein names. The web interface presents all ortholog clusters that include a selected disease gene. A capability to download the entire dataset is also provided.

Animals↗
PubMed2002

Generalized autocalibrating partially parallel acquisitions (GRAPPA).

In this study, a novel partially parallel acquisition (PPA) method is presented which can be used to accelerate image acquisition using an RF coil array for spatial encoding. This technique, GeneRalized Autocalibrating Partially Parallel Acquisitions (GRAPPA) is an extension of both the PILS and VD-AUTO-SMASH reconstruction techniques. As in those previous methods, a detailed, highly accurate RF field map is not needed prior to reconstruction in GRAPPA. This information is obtained from several k-space lines which are acquired in addition to the normal image acquisition. As in PILS, the GRAPPA reconstruction algorithm provides unaliased images from each component coil prior to image combination. This results in even higher SNR and better image quality since the steps of image reconstruction and image combination are performed in separate steps. After introducing the GRAPPA technique, primary focus is given to issues related to the practical implementation of GRAPPA, including the reconstruction algorithm as well as analysis of SNR in the resulting images. Finally, in vivo GRAPPA images are shown which demonstrate the utility of the technique.

Algorithms↗
PubMed2003

CASP5 assessment of fold recognition target predictions.

We present an overview of the fifth round of Critical Assessment of Protein Structure Prediction (CASP5) fold recognition category. Prediction models were evaluated by using six different structural measures and four different alignment measures, and these scores were compared to those assigned manually over a diverse subset of target domains. Scores were combined to compare overall performance of participating groups and to estimate rank significance. The methods used by a few groups outperformed all other methods in terms of the evaluated criteria and could be considered state-of-the-art in structure prediction. We discuss a few examples of difficult fold recognition targets to highlight the progress of ab initio-type methods on difficult structure analogs and the difficulties of predicting multidomain targets and selecting prediction models. We also compared the results of manual groups to those of automatic servers evaluated in parallel by CAFASP, showing that the top performing automated server structure predictions approached those of the best manual predictors.

Algorithms↗
PubMed2002

Progenesis in Eunicida ("Polychaeta," Annelida)--separate evolutionary events? Evidence from molecular data.

The Eunicida are a well-defined annelid taxon currently comprising Dorvilleidae, Lumbrineridae, Eunicidae, Onuphidae, and Hartmanniellidae. Especially the Dorvilleidae include several species of small body size and apparently simple organisation, resembling larvae and juveniles of larger species. One hypothesis to explain the evolution of such species is progenesis. By this criterion the Dinophilidae were included in this group as well. Although their overall similarity suggests monophyly, parallel evolution of such progenetic taxa cannot be excluded. To infer the phylogeny of Eunicida and their presumed relationship to Dinophilidae and progenetic dorvilleids, 18S rDNA sequences from various Dinophilidae, Dorvilleidae, and members of other Eunicida were determined. The data matrix were extended by adding sequences from several annelid and molluscan species and analysed with maximum-parsimony, distance, and maximum-likelihood algorithms. Highly significant bootstrap-values support monophyly of the Dinophilidae, of a clade enclosing the Eunicidae and the Onuphidae, and of a dorvilleid group comprising six species including the presumed progenetic Parapodrilus psammophilus. The position of the Dinophilidae remains unresolved, so that their inclusion within the Eunicida can neither be corroborated nor rejected. However, a constraint monophyly of Dinophilidae and P. psammophilus is rejected by several tests, substantiating the hypothesis of separate progenetic evolutionary events. Furthermore, the molecular data indicate polyphyly of the Dorvilleidae.

Animals↗
PubMed1988

Three-dimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations.

Distance constraints from two-dimensional NMR cross-relaxation data are used to derive a three-dimensional structure for acyl carrier protein from Escherichia coli. Several approaches to structure determination are explored. The most successful proves to be an approach that combines the early stages of a distance geometry program with energy minimization in the presence of NMR constraints represented as pseudopotentials. Approximately 450 proton to proton distance constraints including 50 long-range constraints were included in these programs. Starting structures were generated at random by the distance geometry program and energies minimized by a molecular mechanics module to give final structures. Seven of the structures were deemed acceptable on the basis of agreement with experimentally determined distances. Root-mean-square deviations from the mean of these structures for backbone atoms range from 2 to 3 A. All structures show three roughly parallel helices with hydrophobic residues facing inward and hydrophilic residues facing outward. A hydrophobic cleft is recognizable and is identified as a likely site for acyl chain binding.

Acyl Carrier Protein↗