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PubMed2001

Visual search: efficiency continuum or distinct processes?

Whether visual search involves two distinct processes--traditionally referred to as serial and parallel--or a single process operating on a continuum of efficiency or speed, is an issue with a long history in the study of attention. On the basis of the unimodality of search slope distributions in a very large data set, Wolfe (1998) argued for a continuum model. Reanalysis of this data set using statistical procedures more appropriate for adjudicating between continuous and discontinuous models supports the existence of two distinct processes.

Algorithms↗
PubMed1994

An evaluation of lesion detectability with cone-beam, fanbeam and parallel-beam collimation in SPECT by continuous ROC study.

UNLABELLED: To evaluate lesion detectability for clinical evaluation of cone-beam (CB), fanbeam (FB) and parallel-beam (PB) collimator sensitivity, experimentally acquired phantom data were used to assess the advantage of CB collimation over conventional collimation. METHODS: Lesion detectability with CB, FB and PB collimation in SPECT was compared using a three-dimensional brain phantom and continuous receiver operating characteristic (CROC) analysis. A simulated cold lesion was located near the posterior portion of the thalamus. High count density scans of this phantom were acquired with CB, FB and PB collimators with similar resolution. These projections were scaled to count levels which reflected the measured sensitivities of the three collimators. Computer-generated Poisson noise was added to the projections to produce uncorrelated data sets. Images were reconstructed using a filtered backprojection algorithm. All reconstructions used a Hann filter with multiplicative attenuation correction. Each of seven trained observers viewed 288 sets of images and indicated the certainty of perceiving a cold lesion at a specified location by a rating of 0-100. Each image set contained four adjacent slices centered on the lesion to minimize partial volume effects. The program LABROC4 was used to fit CROC curves to individual observers' ratings. A t-test for paired data was performed on the individual areas. RESULTS: The average areas (standard deviations) under CROC curves for CB, FB and PB were 0.89 (0.03), 0.83 (0.05) and 0.76 (0.04), respectively. The differences of the areas were statistically significant with all two-tailed p values < 0.02. CONCLUSION: These results demonstrate that cold lesions in the posterior portion of the thalamus are best detected by images obtained using CB followed by FB and PB collimation.

Brain↗
PubMedDate not supplied

3D base: a geometrical data base system for the analysis and visualisation of 3D-shapes obtained from parallel serial sections including three different geometrical representations.

In this paper we discuss a geometrical data base that includes three different geometrical representations of one and the same reconstructed 3D shape: the contour-pile, the voxel enumeration, and the triangulation of a surface. The data base is tailored for 3D shapes obtained from plan-parallel serial sections. It is explained how this geometrical data base is useful with the different processing approaches of a 3D shape, such as analysis and visualisation. Methods of conversion between the geometrical representations are discussed. Examples of the operation of the data base as it is embedded in a data base management system are given by illustrations of retrieval of geometrical information.

Algorithms↗
PubMed2006

Factors limiting the application of electrical impedance tomography for identification of regional conductivity changes using scalp electrodes during epileptic seizures in humans.

Electrical impedance tomography (EIT) has the potential to produce images during epileptic seizures. This might improve the accuracy of the localization of epileptic foci in patients undergoing presurgical assessment for curative neurosurgery. It has already been shown that impedance increases by up to 22% during induced epileptic seizures in animal models, using cortical or implanted electrodes in controlled experiments. The purpose of this study was to determine if reproducible raw impedance changes and EIT images could be collected during epileptic seizures in patients who were undergoing observation with video-electroencephalography (EEG) telemetry as part of evaluation prior to neurosurgery to resect the region of brain causing the epilepsy. A secondary purpose was to develop an objective method for processing and evaluating data, as seizures arose at unpredictable times from a noisy baseline. Four-terminal impedance measurements from 258 combinations were collected continuously using 32 EEG scalp electrodes in 22 seizure episodes from 7 patients during their presurgical assessment together with the standard EEG recordings. A reliable method for defining the pre-seizure baseline and recording impedance data and EIT images was developed, in which EIT and EEG could be acquired simultaneously after filtering of EIT artefact from the EEG signal. Fluctuations of several per cent over minutes were observed in the baseline between seizures. During seizures, boundary voltage changes diverged with a standard deviation of 1-54% from the baseline. No reproducible changes with the expected time course of some tens of seconds and magnitude of about 0.1% could be reliably measured. This demonstrates that it is feasible to acquire EIT images in parallel with standard EEG during presurgical assessment but, unfortunately, expected EIT changes on the scalp of about 0.1% are swamped by much larger movement and systematic artefact. Nevertheless, EIT has the unique potential to provide invaluable neuroimaging data for this purpose and may still become possible with improvements in electrode design and instrumentation.

Adult↗
PubMed1995

Recognition of Telugu characters using neural networks.

The aim of the present work is to recognize printed and handwritten Telugu characters using artificial neural networks (ANNs). Earlier work on recognition of Telugu characters has been done using conventional pattern recognition techniques. We make an initial attempt here of using neural networks for recognition with the aim of improving upon earlier methods which do not perform effectively in the presence of noise and distortion in the characters. The Hopfield model of neural network working as an associative memory is chosen for recognition purposes initially. Due to limitation in the capacity of the Hopfield neural network, we propose a new scheme named here as the Multiple Neural Network Associative Memory (MNNAM). The limitation in storage capacity has been overcome by combining multiple neural networks which work in parallel. It is also demonstrated that the Hopfield network is suitable for recognizing noisy printed characters as well as handwritten characters written by different "hands" in a variety of styles. Detailed experiments have been carried out using several learning strategies and results are reported. It is shown here that satisfactory recognition is possible using the proposed strategy. A detailed preprocessing scheme of the Telugu characters from digitized documents is also described.

Algorithms↗
PubMed2006

Characteristics of pixel arrangements in various rhombuses for full-parallax three-dimensional image generation.

In full-parallax three-dimensional (3-D) imaging systems, the pixel cells often have the shape of a rhombus. Proper arrangement of pixels in these rhombic-shaped cells is important to maximize the quality of displayable 3-D images with a given display panel. The possible number of pixel arrangements in a rhombic cell with a definite dimension is found by considering the number of possible crossings between parallel line families forming the pixel cells, when the slopes of the lines are approximated by the ratio between the number of pixels in the vertical and horizontal directions. To make the rhombic cell have a uniquely defined pixel arrangement, its horizontal and vertical dimensions should be equal to the even multiple of the pixel dimension in their corresponding direction.

Algorithms↗
PubMed1990

Calculation of site affinity constants and cooperativity coefficients for binding of ligands and/or protons to macromolecules. I. Generation of partition functions and mass balance equations.

The thermodynamics of binding of a ligand A and/or proton H to a macromolecule M is treated by the partition function method. In complex systems, the representation of the equilibria by means of cumulative constants beta PQR used as coefficients in partition functions ZM, ZA, and ZH is ill-suited to least-squares refinement procedures because the cumulative constants are interrelated by common cooperativity functions gamma j(i) and common site affinity constants kappa j. There is therefore the need to express ZM, ZA, ZH as functions of site constants kappa j and cooperativity coefficients bj. This is done by developing an algebra of partition functions based on the following concepts: (i) factorability of partition functions; (ii) binary generating function Jj = (1 + kappa j[Y])i tau for each class j of sites, represented by column (Jj) and row (Jj) vectors; (iii) cooperativity between sites of one class described by functions gamma j(i), represented by diagonal matrices gamma j; (iv) probability of finding microspecies represented by elements of tensor product matrix Ll = (J1)[J2]; (v) statistical factors mij obtained from Newton polynomials, Jj; (vi) power operators Oi', O(i-l)', and O(i tau-l)', transforming vectors Jj; and (vii) operators Oi or O(i-l) indicating tensor products of i or (i-l) vectors Jj. Vectors Jj combined in tensors Ll give rise to both an affinity/cooperativity space and a parallel index space. The partition functions ZM, ZA, and ZH and the total amounts TM, TA, and TH can be obtained as an appropriate sum of elements of matrices Ll, each of which is represented in an index space by a combination p1, p2,...q1, q2,...r1, r2,... of indices ij. From these indices the contribution of that element to partition function ZM, ZA, or ZH and to total amount TM, TA, or TH is calculated in the affinity/cooperativity space as product of factors: [i tau !/i !(i tau-i)!]kappa ij(exp[bj (i-1)i])[X]i, i being any index p, q, r and X any component M, A, or H. Future applications of this algorithm to practical problems of macromolecule-ligand-proton equilibria are outlined.

Binding Sites↗
PubMed2006

High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis.

Expression microarrays hybridized with RNA can simultaneously provide both phenotypic (gene expression) and genotypic (marker) data. We developed two types of genetic markers from Affymetrix GeneChip expression data to generate detailed haplotypes for 148 recombinant inbred lines (RILs) derived from Arabidopsis thaliana accessions Bayreuth and Shahdara. Gene expression markers (GEMs) are based on differences in transcript levels that exhibit bimodal distributions in segregating progeny, while single feature polymorphism (SFP) markers rely on differences in hybridization to individual oligonucleotide probes. Unlike SFPs, GEMs can be derived from any type of DNA-based expression microarray. Our method identifies SFPs independent of a gene's expression level. Alleles for each GEM and SFP marker were ascertained with GeneChip data from parental accessions as well as RILs; a novel algorithm for allele determination using RIL distributions capitalized on the high level of genetic replication per locus. GEMs and SFP markers provided robust markers in 187 and 968 genes, respectively, which allowed estimation of gene order consistent with that predicted from the Col-0 genomic sequence. Using microarrays on a population to simultaneously measure gene expression variation and obtain genotypic data for a linkage map will facilitate expression QTL analyses without the need for separate genotyping. We have demonstrated that gene expression measurements from microarrays can be leveraged to identify polymorphisms across the genome and can be efficiently developed into genetic markers that are verifiable in a large segregating RIL population. Both marker types also offer opportunities for massively parallel mapping in unsequenced and less studied species.

Arabidopsis↗
PubMed2004

3-D simulation of the St. Jude Medical bileaflet valve opening process: fluid-structure interaction study and experimental validation.

BACKGROUND AND AIM OF THE STUDY: Simulation of the opening and closure dynamics of a mechanical valve through a moving deforming mesh algorithm presents a challenge because of the large rotations of the leaflet and of the small gaps between the housing and the leaflets, which make remeshing a critical issue. The present study offers a computational approach to the simulation of valve leaflet motion during the opening process, together with an experimental set-up for validation of the model. METHODS: A fully 3-D simulation of the 27 mm St. Jude Medical Hemodynamic Plus mechanical valve was performed using the computational code, Fluent. Interaction between the leaflet and fluid was simulated through customized user subroutines which, according to a weakly coupled approach, update the leaflet velocities through subsequent time steps by means of an under-relaxation procedure. A parallel, experimental test was defined to collect data for the set-up of simulations and for validation purposes. RESULTS: The computed leaflet velocity and angular displacement compared well with experimental data. The model captured the main features of the opening process, and did so also from a quantitative viewpoint. Nonetheless, some discrepancies were observed, including a delay of approximately 7 ms in the computed leaflet displacement and an underestimation by approximately 7% of the maximum computed leaflet velocity. CONCLUSION: The weakly coupled approach adopted here limited computational costs, thus allowing the simulation of a fully 3-D realistic mechanical valve within 154 CPU hours at minimal computational costs. No significant drawbacks were raised in comparison with the fully coupled approach. The opening process delay was similar to that reported previously, and cannot be ascribed to the weakly coupled approach adopted here.

Biomechanical Phenomena↗
PubMed1997

Densitometric and chromatin texture parameters of hepatocyte nuclei during controlled autolysis.

OBJECTIVE: To determine the extent of the effect of autolytic changes in hepatocyte nuclei on the results of measurements of integrated optical density (IOD) of nuclei stained by the Feulgen method and its possible relationship with changes in chromatin texture. STUDY DESIGN: Cytologic smears obtained from five pig livers by means of fine needle biopsy were fixed in 10% formalin at six time points after slaughtering (0-18 hours) and stained per Feulgen. In the hepatocyte nuclei IOD measurements were performed and supplemented with quantitative texture analysis. Texture analysis was carried out with our own algorithm, based on the movement of global gravity centers of heterochromatin granules during two-level, iteratively changed, grey thresholding. RESULTS: The variability coefficients of IOD of diploid hepatocytes during autolysis increased from 0.061 (0 hours) to 0.363 (18 hours), and the ploidy histograms became aneuploid. The texture of chromatin became more homogeneous, but other features of the texture did not indicate a significant correlation with the duration of autolysis. CONCLUSION: Autolysis is an important factor, which may influence the accuracy of DNA content and shape of ploidy diagrams. Changes in the morphologic pattern of heterochromatin may play a role in this, but the study was not conclusive because only one of six texture parameters (number of granules) changed parallel to mean IOD and autolysis time.

Animals↗
PubMed1993

Higher-order structure in regularity detection.

In three experiments a simple Euclidean transformation (reflection, translation, rotation) was applied to collections of twelve dots in such a way that they contained equal lower-order structure, defined on the pairwise grouping of elements with their partner following transformation (e.g. parallel virtual lines), but differed in the presence vs absence of higher-order structure, defined on pairs of pairwise groupings (e.g. virtual quadrangles with correlated angles). Based on the much better performance levels (d') in the case of additional higher-order structure, we conclude that global regularities are easier to detect when the local correspondences are supported by higher-order ones formed between them. These enable the lower-order groupings to spread out across the whole pattern very rapidly (called bootstrapping). As a preliminary attempt to specify these principles, we proposed a working model with two basic components: first, a function expressing the cost of a perceptual grouping or the lack of regularity, and, secondly, an algorithm based on simulated annealing to minimize the cost function. The simulation results obtained with our current implementation of these principles showed satisfactory qualitative agreement with human regularity detection performance. Finally, the theory was shown to capture the essence of a large number of grouping phenomena taken from diverse domains such as detection of symmetry in dot patterns, global structure in Glass and vector patterns, correspondence in stereoscopic transparency and apparent motion. Therefore, we are convinced that, in principle, the mechanism used by the human visual system to detect regularity incorporates something like bootstrapping based on higher-order structure. We regard this as a promising step towards unraveling the intriguing mechanisms of classic Gestalt phenomena.

Cues↗
PubMed2000

The role of proton therapy in the treatment of large irradiation volumes: a comparative planning study of pancreatic and biliary tumors.

PURPOSE: The purpose of this study was to examine the potential benefit of proton therapy for abdominal tumors. Extensive comparative planning was conducted investigating the most up-to-date photon and proton irradiation technologies. METHODS AND MATERIALS: A number of rival plans were generated for four patients: two inoperable pancreatic tumors, one inoperable and one postoperative biliary duct tumor. The dose prescription goal for these large targets was 50 Gy, followed by a boost dose up to 20 Gy to a smaller planning target volume (PTV). Photon plans were developed using "forward" planning of coplanar and noncoplanar conformal fields and "inverse" planning of intensity-modulated (IM) fields. Proton planning was simulated as administered using the so called spot-scanning technique. Plans were evaluated on the basis of normal tissues' dose-volume constraints (Emami B, Lyman J, Brown A, et al. Tolerance of normal tissue to therapeutic irradiation. Int J Radiat Oncol Biol Phys 1990;21:109-122) and coverage of treatment volumes with prescribed doses. RESULTS: For all cases, none of the forward calculated photon plans was able to deliver 50 Gy to large PTVs at the same time respecting the dose-volume constraints on all critical organs. Nine evenly spaced IM fields achieved or nearly achieved all maximum dose constraints to critical structures for two out of three inoperable patients. IM plans also obtained good results for the postoperative patient, even though the dose to the liver was very close to the maximum allowed. In all cases, photon irradiation of large PTV1s to 50 Gy followed by a 20 Gy boost entailed a risk very close to or higher than 5% for serious complications to the kidneys, liver, or bowel. Simple arrangements of 2, 3, and 4 proton fields obtained better dose conformation to the target, allowing the delivery of planned doses including the boost to all patients, without excessive risk of morbidity. Dose homogeneity inside the targets was also superior with protons. CONCLUSION: For the irradiation of large PTVs located in the abdominal cavity, where multiple, parallel structured organs surround the target volumes, proton therapy, delivered with a sophisticated isocentric technique, has the potential to achieve superior dose distributions compared with state-of-the-art photon irradiation techniques. IM photon plans obtain better results in the postoperative case, because the reduced volume lessens the effect of the unavoidable increase of integral dose to surrounding tissues.

Algorithms↗
PubMed2006

Mobility of a particle immersed in a liquid film between two fluids.

The mobility of a particle immersed in a liquid film between two viscous fluids is calculated in point approximation. The mobility in the direction parallel to the film diverges logarithmically as the ratio of the sum of outside viscosities to the film viscosity tends to zero, as in the [Saffman-Delbruck, Proc. Natl. Acad. Sci. U.S.A. 72, 3111 (1975)] expression for the mobility of a particle embedded in a membrane. A simple expression for the limiting behavior is derived. For any values of the parameters the mobility tensor can be evaluated by numerical quadrature of two one-dimensional integrals.

Algorithms↗
PubMed1995

Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer.

Rapid growth of protein structures database in recent years requires an effective approach for objective comparison and classification of deposited protein structures. We describe a novel method for structure comparison and classification based on the alignment of one-dimensional structure profiles. These profiles are obtained by calculating the OCCO pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups of consecutive amino acid residues) from protein three-dimensional coordinates. These angle measurements are then converted into a 24 letter alphabet, and the protein structures are represented by sequences of letter from this alphabet. The BioSCAN parallel computer, designed for primary sequence alignment, is used to rapidly align and classify these one-dimensional structure profiles. We have developed and implemented weighted scoring matrix to identify structural classes based on commonly found structural motifs. The results of our experiments are in good agreement with the traditional protein structure classification schemes. One-dimensional structure profiles significantly improve efficiency of structure comparison and classification.

Algorithms↗
PubMed1996

ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool.

Many advanced software tools fail to reach a wide audience because they require specialized hardware, installation expertise, or an abundance of CPU cycles. The worldwide web offers a new opportunity for distributing such systems. One such program, MEME, discovers repeated patterns, called motifs, in sets of DNA or protein sequences. This tool is now available to biologists over the worldwide web, using an asynchronous, single-program multiple-data version of the program called ParaMEME that runs on an Intel Paragon XP/S parallel computer at the San Diego Super-computer Center. ParaMEME scales gracefully to 64 nodes on the Paragon with efficiencies > 72% for large data sets. The worldwide web interface to ParaMEME accepts a set of sequences interactively from a user, submits the sequences to the Paragon for analysis, and e-mails the results back to the user. ParaMEME is available for free public use at http://@www.sdsc.edu/CompSci/Biomed/ MEME.

Algorithms↗
PubMed2006

Data consistency based translational motion artifact reduction in fan-beam CT.

A basic assumption in the classic computed tomography (CT) theory is that an object remains stationary in an entire scan. In biomedical CT/micro-CT, this assumption is often violated. To produce high-resolution images, such as for our recently proposed clinical micro-CT (CMCT) prototype, it is desirable to develop a precise motion estimation and image reconstruction scheme. In this paper, we first extend the Helgason-Ludwig consistency condition (HLCC) from parallel-beam to fan-beam geometry when an object is subject to a translation. Then, we propose a novel method to estimate the motion parameters only from sinograms based on the HLCC. To reconstruct the moving object, we formulate two generalized fan-beam reconstruction methods, which are in filtered backprojection and backprojection filtering formats, respectively. Furthermore, we present numerical simulation results to show that our approach is accurate and robust.

Algorithms↗
PubMed1997

NIR reflection measurements of hemoglobin and cytochrome aa3 in healthy tissue and tumors. Correlations to oxygen consumption: preclinical and clinical data.

OBJECTIVES: A new near infrared reflectance spectroscopy based technology (MULTISCAN OS 10/30) for non-invasive measurements of tissue oxygenation allows detection of absolute tissue hemoglobin concentration and saturation values in real time. METHODS: MULTISCAN OS 10/30 scans a tissue sector of defined geometry at 400 to 1200 nm wavelength with 0.3 nm intervals at a scan rate of up to 400 Hz in reflection mode. The newly developed algorithms are based on the entropy pattern of photons and allow the detection of absolute values of total hemoglobin (tHb), deoxy- (Hb) and oxy-hemoglobin (HbO2) in mg/ml tissue as well as tissue oxygen (saturation = tiSO2) in the range of 0 to 100% in real time. Cytochrome aa3 (Cyt) can be monitored simultaneously. RESULTS: Physiological Stimulation. Clamping experiments at the finger of volunteers, in the intestine of a pig, in the kidney of mice and rats showed a very fast, sensitive and tissue specific reaction. Changes in breathing and/or anesthesia conditions were immediately followed by corresponding changes of tissue oxygenation (brain, finger, skin). Simultaneous measurements of oxygen (HbO2), and cytochrome showed a strong correlation between both parameters. For validation purposes parallel polarographic measurements (pO2 measurements) were performed in mice. Furthermore angiographic data of patients as well as NMR/I data were compared with the NIR spectroscopy findings. Tumor Measurements. Patients with tumors of different origins showed significantly different oxygen values. The lowest level was found in glioblastoma (< 10% sat, < 1.0 mg/ml tHb), whereas renal carcinoma showed tremendously increased values (> 90% sat, > 5.0 mg/ml tHb). In contrast the surrounding healthy kidney tissue was significantly less oxygenated and perfused compared to the tumors. Oxygen Consumption Measurements. Oxygen consumption was measured in 16 patients after ligation of the blood supply (A. and V. renalis) to the kidney affected by tumor. All tumors showed a significantly lower consumption rate compared to the healthy tissue. These findings were controlled by animal experiments of human renal carcinomas on nude mice. The same results were obtained under these experimental conditions. CONCLUSION: MULTISCAN OS 10/30 is a new and useful tool for in vivo characterization of oxygen and cytochrome in healthy and tumor tissues. In many clinically relevant situations oxygen measurements can be helpful and support the clinical routine diagnostics.

Adult↗
PubMed2006

Use of a neural mass model for the analysis of effective connectivity among cortical regions based on high resolution EEG recordings.

Assessment of brain connectivity among different brain areas during cognitive or motor tasks is a crucial problem in neuroscience today. Aim of this work is to use a neural mass model to assess the effect of various connectivity patterns in cortical electroencephalogram (EEG) power spectral density, and investigate the possibility to derive connectivity circuits from EEG data. To this end, a model of an individual region of interest (ROI) has been built as the parallel arrangement of three populations, each described as in Wendling et al. (Eur J Neurosci 15:1499-1508, 2002). Connectivity among ROIs includes three parameters, which specify the strength of connection in the different frequency bands. The following main steps have been followed: (1) we analyzed how the power spectral density (PSD) is significantly modified by the kind of coupling hypothesized among the ROIs; (2) with the model, and using an automatic fitting procedure, we looked for a simple connectivity circuit able to reproduce PSD of cortical EEG in three ROIs during a finger-movement task. The estimated parameters represent the strength of connections among the ROIs in the different frequency bands. Cortical EEGs were computed with an inverse propagation algorithm, starting from measurement performed with 96 electrodes on the scalp. The present study suggests that the model can be used as a simulation tool, able to mimic the effect of connectivity on EEG. Moreover, it can be used to look for simple connectivity circuits, able to explain the main features of observed cortical PSD. These results may open new prospectives in the use of neurophysiological models, instead of empirical models, to assess effective connectivity from neuroimaging information.

Brain Mapping↗