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PubMed2001

Collaborative interventional and surgical strategies in the management of congenital heart lesions.

In the last 15 years the development of catheter-directed percutaneous therapies have improved the delivery of care to children with congenital heart lesions. Paralleling these advances, enhanced surgical techniques are now applied to complex cardiac lesions previously thought to be inoperable. This chapter outlines several treatment strategies which utilize surgical and catheter-based algorithms to address congenital heart disorders.

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↗
PubMed1997

Adaptive control of arterial blood pressure with a learning controller based on multilayer neural networks.

We discuss a two-model multilayer neural network controller for adaptive control of mean arterial blood pressure (MABP) using sodium nitroprusside. A model with an autoregressive moving average (ARMA), representing the dynamics of the system, and a modified back-propagation training algorithm are used to design the control system to meet specified objectives of design (settling time and undershoot/overshoot) and clinical constraints. The controller is associated with a weighting-determinant unit (WDU) to determine and update the output weighting factor of the parallel two-model neural network for adequate control action and a control-signal modification unit (CMU) to comply with clinical constraints and to suppress the effect of adverse noise and to improve the WDU performance. Extensive computer simulations indicate satisfactory performance and robustness of the proposed controller in the presence of much noise, over the full range of plant parameters, uncertainties, and large variations of parameters.

Adaptation, Physiological↗
PubMed2002

Comparison of pulmonary arterial thermodilution and arterial pulse contour analysis: evaluation of a new algorithm.

STUDY OBJECTIVE: To compare cardiac index (CI) measurement by arterial pulse contour analysis using two different algorithms (CI(PC), CI(PCnew)) with pulmonary arterial thermodilution values (CI(PA)) so as to evaluate the difference between the conventional algorithm, CI(PC), and a new algorithm, CI(PCnew), that accounts for patients' individual aortic compliance. DESIGN: Prospective, clinical study. SETTING: Intensive care unit of a university hospital. PATIENTS: 20 ASA physical status II and III patients following elective cardiac surgery. MEASUREMENTS AND MAIN RESULTS: 360 parallel triplicate determinations of CI (CI(PA), CI(PC), CI(PCnew)) were performed within a 90-minute period during the immediate postoperative period. Prior to the start of the study period, CI(PC) as well as CI(PCnew) were calibrated by triplicate femoral arterial thermodilution measurements. Regression analysis of CI(PA) and CI(PC), as well as CI(PA) and CI(PCnew), revealed r = 0.89, p < 0.001, and r = 0.93, p < 0.001, respectively. Bland-Altman analysis was used for determining the accuracy and precision of CI(PC) and CI(PCnew) compared with CI(PA). The mean differences (m) and standard deviation (SD) between CI(PA) and CI(PC,) as well as CI(PA) and CI(PCnew), resulted in m = -0.312 L/min/m(2), SD = 0.456 L/min/m(2), and m = - 0.140 L/min/m(2), SD = 0.328 L/min/m(2), respectively. CONCLUSION: Arterial pulse contour analysis measurement of CI using either algorithm correlates well with CI values derived by pulmonary arterial thermodilution. However, the algorithm introduced in this study proved to be a more accurate predictor of values as derived by pulmonary artery catheter.

Algorithms↗
PubMed2007

Improved cine displacement-encoded MRI using balanced steady-state free precession and time-adaptive sensitivity encoding parallel imaging at 3 T.

Cine displacement-encoded MRI is a promising modality for quantifying regional myocardial function. However, it has two major limitations: low signal-to-noise ratio (SNR) and data acquisition efficiency. The purpose of this study was to incrementally improve the SNR and the data acquisition efficiency of cine displacement-encoded MRI through the combined use of balanced steady-state free precession (b-SSFP) imaging, 3T imaging, echo-combination image reconstruction, and time-adaptive sensitivity encoding (TSENSE) parallel imaging. Phantom experiments were performed to empirically determine the optimal excitation angle (alpha) and to estimate the measurement errors in the presence of 130 Hz peak-to-peak static magnetic field (B0) variation. The optimal alpha was determined to be 20 degrees . The intrinsic phase correction in the echo-combination effectively reduced the phase error, which produced small displacement errors (0.11 versus 0.11 mm) and negligible strain errors (-0.001 versus -0.002). Six healthy volunteers were imaged in three short-axis levels of the heart to evaluate the SNR and the relative accuracy of strain calculations. Compared with the 24-heartbeat cine echo-planar imaging acquisition, the 24-heartbeat non-accelerated b-SSFP acquisition yielded approximately 65% higher SNR, and the 12-heartbeat twofold accelerated b-SSFP acquisition yielded approximately 28% higher SNR. The 12-heartbeat twofold accelerated b-SSFP acquisition yielded functional maps with spatial resolution of 3.6 x 3.6 mm, temporal resolution of 35 ms, and relatively high SNR (31.2 +/- 5.4 at end diastole; 19.9 +/- 3.6 at end systole; 10.3 +/- 1.1 at late diastole; mean +/- SD). The left ventricular strain values between the non-accelerated and twofold accelerated b-SSFP acquisitions correlated strongly (slope = 0.99; bias = 0.00; R2 = 0.91) and were in excellent agreement. The combined implementation of b-SSFP imaging, 3T imaging, echo-combination image reconstruction, and TSENSE parallel imaging can be used to incrementally improve the cine displacement-encoded MRI pulse sequence.

Adult↗
PubMed2004

[Molecular classification in leukemias using gene expression profiling].

A comprehensive approach to the diagnosis in leukemias relies on cytomorphology, cytochemistry, cytogenetics, fluorescence in situ hybridization, multiparameter flow cytometry, and molecular methods. Recently, gene expression profiling using microarrays was invented to measure the expression of thousands of genes in one step. A specific signature stands for the molecular fingerprint of a tumor sample. Therefore, gene expression profiling may lead to a better molecular classification of leukemias and insights into pathophysiology. Furthermore, gene expression profiling may lead to new targeted therapies and can detect genes to be used for minimal residual disease studies. Very recent studies point also to the possibility to use gene expression profiling for prognostication. In conclusion, microarrays may lead to a single platform approach in leukemia diagnosis with quick and very robust results. This new technique should be further validated in parallel to the standard work-flow and has to be proven before substituting other methods in the future.

Algorithms↗
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↗
PubMed2001

Hitch-hiking: a parallel heuristic search strategy, applied to the phylogeny problem.

The article introduces a parallel heuristic search strategy ("Hitch-hiking") which can be used in conjunction with other random-walk heuristic search strategies. It is applied to an artificial phylogeny problem, in which character sequences are evolved using pseudo-random numbers from a hypothetical ancestral sequence. The objective function to be minimized is the minimum number of character-state changes required on a binary tree that could account for the sequences observed at the tips (leaves) of the tree -- the Maximum Parsimony criterion. The Hitch-hiking strategy is shown to be useful in that it is robust and that on average the solutions found using the strategy are better than those found without. Also the strategy can dynamically provide information on the characteristics of the landscape of the problem. I argue that Hitch-hiking as a scheme for parallelization of existing heuristic search strategies is of potentially very general use, in many areas of combinatorial optimization.

Algorithms↗
PubMed2003

Primer-design for multiplexed genotyping.

Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Mutation analysis by polymerase-mediated single-base primer extension (minisequencing) can be massively parallelized using DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5' end of the minisequencing primer and attaching the complementary antitag to the array or bead surface, the assay can be 'demultiplexed'. Such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. We present a computer program to automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/antitag system is generated, and the pairing of primers and DNA tags is automatically done in a way to avoid any crossreactivity. We report results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping. The software is available to academic users on request.

Algorithms↗
PubMed1998

Projection space image reconstruction using strip functions to calculate pixels more "natural" for modeling the geometric response of the SPECT collimator.

The spatially varying geometric response of the collimator-detector system in single photon emission computed tomography (SPECT) causes loss in resolution, shape distortions, reconstructed density nonuniformity, and quantitative inaccuracies. A projection space image reconstruction algorithm is used to correct these reconstruction artifacts. The projectors F use strip functions to calculate pixels more "natural" for modeling the two-dimensional (2-D) geometric response of the SPECT collimator transaxially to the axis of rotation. These projectors are defined by summing the intersection of an array of multiple strips rotated at equal angles to approximate the ideal system geometric response of the collimator. Two projection models were evaluated for modeling the system geometric response function. For one projector each strip is of equal weight, for the other projector a Gaussian weighting is used. Parallel beam and fan beam projections of a physical three-dimensional (3-D) Hoffman brain phantom and a Jaszczak cold rod phantom were used to evaluate the geometric response correction. Reconstructions were obtained by using the singular value decomposition (SVD) method and the iterative conjugate gradient algorithm to solve for q in the imaging equation FGq = p, where p is the projection measurement. The projector F included the new models for the geometric response, whereas, the backprojector G did not always model the geometric response in order to increase the computational speed. The final reconstruction was obtained by sampling the backprojection Gq at a discrete array of points. Reconstructions produced by the two proposed projectors showed improved resolution when compared against a unit-strip "natural" pixel model, the conventional image pixelized model with ray tracing to calculate the geometric response, and the filtered backprojection algorithm. When the reconstruction is displayed on fine grid points, the continuity and resolution of the image is preserved without the ring artifacts seen in the unit-strip "natural" pixel model. With present computing power, the geometric response correction using the proposed projection space reconstruction approach is not yet feasible for routine clinical use.

Algorithms↗
PubMed2002

Underdosage of the upper-airway mucosa for small fields as used in intensity-modulated radiation therapy: a comparison between radiochromic film measurements, Monte Carlo simulations, and collapsed cone convolution calculations.

Head-and-neck tumors are often situated at an air-tissue interface what may result in an underdosage of part of the tumor in radiotherapy treatments using megavoltage photons, especially for small fields. In addition to effects of transient electronic disequilibrium, for these small fields, an increased lateral electron range in air will result in an important extra reduction of the central axis dose beyond the cavity. Therefore dose calculation algorithms need to model electron transport accurately. We simulated the trachea by a 2 cm diameter cylindrical air cavity with the rim situated 2 cm beneath the phantom surface. A 6 MV photon beam from an Elekta SLiplus linear accelerator, equipped with the standard multileaf collimator (MLC), was assessed. A 10 x 2 cm2 and a 10 x 1 cm2 field, both widthwise collimated by the MLC, were applied with their long side parallel to the cylinder axis. Central axis dose rebuild-up was studied. Radiochromic film measurements were performed in an in-house manufactured polystyrene phantom with the films oriented either along or perpendicular to the beam axis. Monte Carlo simulations were performed with BEAM and EGSnrc. Calculations were also performed using the pencil beam (PB) algorithm and the collapsed cone convolution (CCC) algorithm of Helax-TMS (MDS Nordion, Kanata, Cahada) version 6.0.2 and using the CCC algorithm of Pinnacle (ADAC Laboratories, Milpitas, CA, USA) version 4.2. A very good agreement between the film measurements and the Monte Carlo simulations was found. The CCC algorithms were not able to predict the interface dose accurately when lateral electronic disequilibrium occurs, but were shown to be a considerable improvement compared to the PB algorithm. The CCC algorithms overestimate the dose in the rebuild-up region. The interface dose was overestimated by a maximum of 31% or 54%, depending on the implementation of the CCC algorithm. At a depth of 1 mm, the maximum dose overestimation was 14% or 24%.

Air↗
PubMedDate not supplied

Localization of fluorescence spots with space-space MUSIC for mammographylike measurement systems.

Breast cancer diagnosis may be improved by optical fluorescence imaging techniques in the near-infrared wavelength range. We have shown that the recently proposed space-space MUSIC (multiple signal classification) algorithm allows the 3-D localization of focal fluorophore-tagged lesions in a turbid medium from 2-D fluorescence data obtained from laser excitations at different positions. The data are assumed to be measured with two parallel planar sensor arrays on the top and bottom of the medium. The laser sources are integrated at different positions in one of the planes. The space-space data are arranged into an MxN matrix (M, number of sensors; N, number of excitation sources). A singular-value decomposition (SVD) of this matrix yields the detectable number of spot regions with linearly independent behavior with respect to the laser excitation positions and thus allows definition of a signal subspace. Matches between this signal subspace and data from model spots are tested at scanned points in a model medium viewed as the breast region under study. The locations of best matches are then considered the centers of gravity of focal lesions. The optical model used was unbounded and optically homogeneous. Nevertheless, simulated spots in bounded, inhomogeneous media modeling the breast could be localized accurately.

Algorithms↗
PubMed2004

A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions.

A new grid-cell algorithm is presented that permits the fast construction of cutoff-based nonbonded pairlists in molecular simulations under periodic boundary conditions based on an arbitrary box shape. The key features of the method are (1) the use of a one-dimensional mask array (to determine which grid cells contain interacting atoms) that incorporates the effect of periodicity, and (2) the grouping of adjacent interacting cells of the mask array into stripes, which permits the handling of empty cells with a very low computational overhead. Testing of the algorithm on water systems of different sizes (containing about 2000 to 11,000 molecules) shows that the method (1) is about an order of magnitude more efficient compared to a standard (double-loop) algorithm, (2) achieves quasi-linear scaling in the number of atoms, (3) is weakly sensitive in terms of efficiency to the chosen number of grid cells, and (4) can be easily parallelized.

Journal Article↗
PubMed2005

3D needle-tissue interaction simulation for prostate brachytherapy.

This paper presents a needle-tissue interaction model that is a 3D extension of a prior work based on the finite element method. The model is also adapted to accommodate arbitrary meshes so that the anatomy can effectively be meshed using third-party algorithms. Using this model a prostate brachytherapy simulator is designed to help medical residents acquire needle steering skills. This simulation uses a prostate mesh generated from clinical data segmented as contours on parallel slices. Node repositioning and addition, which are methods for achieving needle-tissue coupling, are discussed. In order to achieve realtime haptic rates, computational approaches to these methods are compared. Specifically, the benefit of using the Woodbury formula (matrix inversion lemma) is studied. Our simulation of needle insertion into a prostate is shown to run faster than 1 kHz.

Brachytherapy↗
PubMed2002

A knowledge-driven agent-centred framework for data mining in EMG.

In this paper, we present a multi-agent framework for data mining in electromyography. This application, based on a web interface, provides a set of functionalities allowing to manipulate 1000 medical cases and more than 25,000 neurological tests stored in a medical database. The aim is to extract medical information using data mining algorithms and to supply a knowledge base with pertinent information. The multi-agent platform gives the possibility to distribute the data management process between several autonomous entities. This framework provides a parallel and flexible data manipulation.

Data Collection↗
PubMed2006

3000 years of solitude: extreme differentiation in the island isolates of Dalmatia, Croatia.

Communities with increased shared ancestry represent invaluable tools for genetic studies of complex traits. "1001 Dalmatians" research program collects biomedical information for genetic epidemiological research from multiple small isolated populations ('metapopulation') in the islands of Dalmatia, Croatia. Random samples of 100 individuals from 10 small island settlements (n<2000 inhabitants) were collected in 2002 and 2003. These island communities were carefully chosen to represent a wide range of distinct and well-documented demographic histories. Here, we analysed their genetic make-up using 26 short tandem repeat (STR) markers, at least 5 cM apart. We found a very high level of differentiation between most of these island communities based on Wright's fixation indexes, even within the same island. The model-based clustering algorithm, implemented in STRUCTURE, defined six clusters with very distinct genetic signatures, four of which corresponded to single villages. The extent of background LD, assessed with eight linked markers on Xq13-21, paralleled the extent of differentiation and was also very high in most of the populations under study. For each population, demographic history was characterised and 12 "demographic history" variables were tentatively defined. Following stepwise regression, the demographic history variable that most significantly predicted the extent of LD was the proportion of locally born grandparents. Strong isolation and endogamy are likely to be the main forces maintaining this highly structured overall population.

Cluster Analysis↗
PubMed2004

Quick and simple: quality control of microarray data.

MOTIVATION: Microarrays are high-throughput tools for parallel miniaturized detection of biomolecules. In contrast to experiments using ratios of signals in two channels, experiments with only one fluorescent dye cause special problems for data analysis. The present work compares algorithms for quality filtering on spot level as well as array/slide level. RESULTS: Methods for quantitative spot filtering are discussed and new sets of quality scores for data preprocessing are designed. As measures of spot quality also reflect the quality of protocols, they were employed to find the optimal print buffer in an optimization experiment. In order to determine problematic arrays within a set of replicates we tested methods of outlier detection which can suitably replace the visual inspection of slides. CONTACT: Ursula.Sauer@arcs.ac.at.

Algorithms↗
PubMed1993

Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids.

We present a method to determine the location and extent of protein binding regions in nucleic acids by computer-assisted analysis of sequence data. The program ConsIndex establishes a library of consensus descriptions based on sequence sets containing known regulatory elements. These defined consensus descriptions are used by the program ConsInspector to predict binding sites in new sequences. We show the programs to correctly determine the significant regions involved in transcriptional control of seven sequence elements. The internal profile of relative variability of individual nucleotide positions within these regions paralleled experimental profiles of biological significance. Consensus descriptions are determined by employing an anchored alignment scheme, the results of which are then evaluated by a novel method which is superior to cluster algorithms. The alignment procedure is able to include several closely related sequences without biasing the consensus description. Moreover, the algorithm detects additional elements on the basis of a moderate distance correlation and is capable of discriminating between real binding sites and false positive matches. The software is well suited to cope with the frequent phenomenon of optional elements present in a subset of functionally similar sequences, while taking maximal advantage of the existing sequence data base. Since it requires only a minimum of seven sequences for a single element, it is applicable to a wide range of binding sites.

Algorithms↗