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PubMedDate not supplied

Stratigraphic control of flow and transport characteristics.

Ground water flow and travel time are dependent on stratigraphic architecture, which is governed by competing processes that control the spatial and temporal distribution of accommodation and sediment supply. Accommodation is the amount of space in which sediment may accumulate as defined by the difference between the energy gradient and the topographic surface. The temporal and spatial distribution of accommodation is affected by processes that change the distribution of energy (e.g., sea level or subsidence). Fluvial stratigraphic units, generated by FLUVSIM (a stratigraphic simulator based on accommodation and sediment supply), with varying magnitudes and causes of accommodation, were incorporated into a hydraulic regime using MODFLOW (a ground water flow simulator), and particles were tracked using MODPATH (a particle-tracking algorithm). These experiments illustrate that the dominant type of accommodation process influences the degree of continuity of stratigraphic units and thus affects ground water flow and transport. When the hydraulic gradient is parallel to the axis of the fluvial system in the depositional environment, shorter travel times occur in low-total accommodation environments and longer travel times in high-total accommodation environments. Given the same total accommodation, travel times are longer when sea-level change is the dominant process than those in systems dominated by subsidence.

Models, Theoretical↗
PubMed1995

A transmission-map-based scatter correction technique for SPECT in inhomogeneous media.

In this paper a method of modeling the distribution of scattered events in emission projection data is developed and applied. This method is based on the use of a transmission map to define the inhomogeneous scattering object. The key point is the use of the set of line integrals calculated as part of the attenuation correction technique, as the basis of a model of the distribution of scattered events. The probability of a photon being scattered through a given angle and being detected in the emission energy window is approximated using a Gaussian function. The parameters of this Gaussian are determined using Monte Carlo generated parallel-beam scatter line spread functions from a nonuniformly attenuating phantom. The model is incorporated into a two-dimensional projector-backprojector and used with the Expectation-Maximization-Maximum-Likelihood algorithm for the reconstruction of fan-beam phantom data. The correction is shown to perform well for a phantom that varies slowly in the axial direction. For the more clinically realistic situation of a torso phantom, the method produces improvements in terms of blood pool to myocardium contrast, but does not restore the contrast to the level exhibited in a reconstruction from "scatter free" data.

Humans↗
PubMed2003

Guided wave helical ultrasonic tomography of pipes.

Ultrasonic guided waves have been used for a wide variety of ultrasonic inspection techniques. We describe here a new variation called helical ultrasound tomography (HUT) that uses guided ultrasonic waves along with tomographic reconstruction algorithms that have been developed by seismologists for what they call "cross borehole" tomography. In HUT, the Lamb-like guided waves travel the various helical criss-cross paths between two parallel circumferential transducer arrays instead of the planar criss-cross seismic paths between two boreholes. Although the measurement itself is fairly complicated, the output of the tomographic reconstruction is a readily interpretable map of a quantity of interest such as pipe wall thickness. In this paper we demonstrate HUT via laboratory scans on steel pipe segments into which controlled thinnings have been introduced.

Models, Theoretical↗
PubMed1986

[SPECT images using a multislice fan beam collimator].

Several methods to improve the image resolution of single photon emission computed tomography (SPECT) occur to us. It is one method to use multislice fan beam collimators which have the parallel collimation along the cephalic-caudul axis of a patient and the conversing collimation within planes parpendicular to that axis. It is impossible to obtain corrective image when we used the algorithm which is commonly used for reconstruction of SPECT images. We proposed a reconstruction algorithm for multislice fan beam collimator in this paper. An interpolation method developed for fan beam type X-ray CT was modified to reconstruct images from SPECT with multislice fan beam collimator. This algorithm was confirmed by means of computer simulation studies. Beside improving the system resolution by effectively reducing the intrinsic resolution of the cameras, this collimator also increases the system sensitivity by utilizing a large fraction of the crystal area. We have thought that to use multislice fan beam collimator is beneficial for SPECT images.

Tomography, Emission-Computed↗
PubMed1996

Transmission-based scatter correction of 180 degrees myocardial single-photon emission tomographic studies.

Meaningful comparison of single-photon emission tomographic (SPET) reconstructions for data acquired over 180 degrees or 360 degrees can only be performed if both attenuation and scatter correction are applied. Convolution subtraction has appeal as a practical method for scatter correction; however, it is limited to data acquired over 360 degrees. A new algorithm is proposed which can be applied equally well to data acquired over 180 degrees or 360 degrees. The method involves estimating scatter based on knowledge of reconstructed transmission data in combination with a reconstructed estimate of the activity distribution, obtained using attenuation correction with broad beam attenuation coefficients. Processing is implemented for planes of activity parallel to the projection images for which a simplified model for the scatter distribution may be applied, based on the measured attenuation. The appropriate broad beam (effective) attenuation coefficients were determined by considering the scatter buildup equation. It was demonstrated that narrow beam attenuation coefficients should be scaled by 0.75 and 0.65 to provide broad beam attenuation coefficients for technetium-99m and thallium-201 respectively. Using a thorax phantom, quantitative accuracy of the new algorithm was compared with conventional transmission-based convolution subtraction (TDCS) for 360 degrees data. Similar heart to lung contrasts were achieved and correction of 180 degrees data yielded a 10.4% error for cardiac activity compared to 5.2% for TDCS. Contrast for myocardium to ventricular cavity was similarly good for scatter-corrected 180 degrees and 360 degrees data, in contrast to attenuation-corrected data, where contrast was significantly reduced. The new algorithm provides a practical method for correction of scatter applicable to 180 degrees myocardial SPET.

Algorithms↗
PubMedDate not supplied

Faster linkage analysis computations for pedigrees with loops or unused alleles.

There seems to be no limit to the complexity of computations that genetic linkage analysts want to do. Two primary factors that increase the length of computations are pedigree loops and unknown genotypes. I describe the implementation in FASTLINK of some algorithmic improvements to partly address the problems of pedigree loops and unknown genotypes. LINKAGE is by far the most popular software package to do lod score computations on disease pedigrees. FASTLINK is derived from LINKAGE 5.1 and compatible with it. In contrast to LINKAGE, FASTLINK has the virtues that it is faster sequentially, runs well in parallel, is more robust against errors, and includes substantial new documentation. One of the new improvements allows the detection of violation of mendelian rules of inheritance in input pedigree files with loops. This error-detection capability was not provided in any previous version of LINKAGE or FASTLINK.

Algorithms↗
PubMed2006

Second derivatives in generalized Born theory.

Generalized Born solvation models offer a popular method of including electrostatic aspects of solvation free energies within an analytical model that depends only upon atomic coordinates, charges, and dielectric radii. Here, we describe how second derivatives with respect to Cartesian coordinates can be computed in an efficient manner that can be distributed over multiple processors. This approach makes possible a variety of new methods of analysis for these implicit solvation models. We illustrate three of these methods here: the use of Newton-Raphson optimization to obtain precise minima in solution; normal mode analysis to compute solvation effects on the mechanical properties of DNA; and the calculation of configurational entropies in the MM/GBSA model. An implementation of these ideas, using the Amber generalized Born model, is available in the nucleic acid builder (NAB) code, and we present examples for proteins with up to 45,000 atoms. The code has been implemented for parallel computers using both the OpenMP and MPI environments, and good parallel scaling is seen with as many as 144 OpenMP processing threads or MPI processing tasks.

Algorithms↗
PubMed2006

Advantages of parallel imaging in conjunction with hyperpolarized helium--a new approach to MRI of the lung.

Hyperpolarized helium (3He) gas MRI has the potential to assess pulmonary function. The non-equilibrium state of hyperpolarized 3He results in the continual depletion of the signal level over the course of excitations. Under non-equilibrium conditions the relationship between the signal-to-noise ratio (SNR) and the number of excitations significantly deviates from that established in the equilibrium state. In many circumstances the SNR increases or remains the same when the number of data acquisitions decreases. This provides a unique opportunity for performing parallel MRI in such a way that both the temporal and spatial resolution will increase without the conventional decrease in the SNR. In this study an analytical relationship between the SNR and the number of excitations for any flip angle was developed. Second, the point-spread function (PSF) was utilized to quantitatively demonstrate the unconventional SNR behavior for parallel imaging in hyperpolarized gas MRI. Third, a 24-channel (24ch) receive and two-channel (2ch) transmit phased-array system was developed to experimentally prove the theoretical predictions with 3He MRI. The in vivo experimental results prove that significant temporal resolution can be gained without the usual SNR loss in an equilibrium system, and that the entire lung can be scanned within one breath-hold (approximately 13 s) by applying parallel imaging to 3D data acquisition.

Administration, Inhalation↗
PubMed1999

Amplitude of human head movements associated with horizontal saccades.

Human saccades may or may not be associated with head movements. To date, little attention has been devoted to the mechanisms determining head movement recruitment and scaling. Normal human subjects made horizontal, centrifugal saccades along an encircling array of light-emitting diodes. Measurements of gaze, head, and eye-in-head angle were made at the conclusion of the head movement (or at the end of the eye movement in eye-only saccades). We found that head movement amplitude (deltaH) related in a simple fashion to the eye eccentricity that would have resulted if the gaze shift had been performed without a head movement. Plots of deltaH vs this predicted eye eccentricity (E(PRED)) had a central flat region in which gaze shifts were unaccompanied by head movements (the eye-only range) and two flanking lobes in which deltaH was a linear function of E(PRED) (the eye-head ranges). DeltaH correlated with EPRED better than with gaze shift amplitude, as would be expected if head movements were controlled so as to keep eye eccentricity within a particular range. Head movement tendencies were quantified by the width of the eye-only range, the slope of the eye-head range, and the width of the region within which the eye was likely to be found at the conclusion of the completed gaze-shifting behavior (the customary ocular motor range). The measures ranged widely in these normal subjects: 35.8+/-31.9 degrees for the eye-only range (mean+/-SD), 0.77+/-0.16 for the slope of the eye-head range, and 44.0+/-23.8 degrees for the customary ocular motor range. Yet for a given subject, the measurements were reproducible across experimental sessions, with the customary ocular motor range being the most consistent measure of the three. The form of the deltaH vs E(PRED) plots suggests that the neural circuitry underlying eye-head coordination carries out two distinct functions--gating the head movement and scaling the head movement. The reason for the large intersubject variability of head movement tendencies is unknown. It does not parallel intersubject differences in full-scale eye (in orbit) range or full-scale neck range.

Adult↗
PubMedDate not supplied

Parallel computation of simple arithmetic using peptide-antibody interactions.

We propose a theoretical model for representing and manipulating binary numbers using peptide-antibody interactions. In particular, we present models to solve simple binary arithmetical problems like addition and subtraction. As the interactions can take place in parallel we show that the number of steps is independent of the size (bits) of the numbers.

Algorithms↗
PubMed2004

Analysis of perfect mappings of the stimuli through neural temporal sequences.

The analysis of an optimal neural system that maps stimuli into unique sequences of activations of fundamental atoms or functional clusters (FCs) is carried out. We say that it is perfect because the system maps with an injective function every stimulus in minimum time with the least number of FCs, such that every FC is activated only once. The neural system has the possibility to sustain several sequences in parallel. In this framework, we study the capacity achievable by the system, minimal completion time and complexity in terms of the number of parallel sequences. We show that the maximum capacity of the system is achieved without using parallel sequences at the expense of long completion times. However, when the capacity value is fixed, the largest possible number of parallel sequences is optimal because it requires short completion times. The complexity measure adds to important points: (i) the largest complexity of the system is achieved without parallel sequences, and (ii) the capacity estimation is a good estimation of the complexity of the system.

Algorithms↗
PubMedDate not supplied

Optimal design of protein production plants with time and size factor process models.

In this work we propose an optimization model for the design of a biotechnological multiproduct batch plant. A first level of detail posynomial model is constructed for each unit, as well as decisions regarding the structural optimization of the plant. A particular feature of this model is that it contains composite units in which semicontinuous items operate on the material contained by batch items. This occurs in the purification steps, in particular with the microfilters operating between retentate and permeate vessels, and with the homogenizer and ultrafilters operating on the material contained in a batch holding vessel. Also, the unit models rely on batch operating time expressions that depend on both the batch size and the size of semicontinuous items. The model takes into account all of the available options to increase the efficiency of the batch plant design: unit duplication in-phase and out-of-phase and intermediate storage tanks. The resulting mathematical model for the minimization of the plant capital cost is a mixed integer non-linear program (MINLP), which is solved to global optimality with an implementation of the outer approximation/ equality relaxation/ augmented penalty (OA/ER/AP) method. A plant that produces four recombinant proteins in eight processing stages is used to illustrate the proposed approach. An interesting feature of this example is that it represents an attempt to standardize a plant for the production of both therapeutic and nontherapeutic proteins; the model applied is generic and can thus be applied to any such modular plant. Results indicate that the best solution in terms of minimal capital cost contains no units in parallel and with intermediate storage tank allocation.

Algorithms↗
PubMed2002

Characterization of dose distributions through the max and mean dose concept.

A new approach for the determination of the equivalent uniform dose (EUD) for inhomogeneously irradiated normal organs is developed and tested. The EUD is calculated as a linear combination of the maximum and the mean dose: EUD = alphaDmax + (1 - alpha)D. We call this the max & mean model. The values of alpha are determined by a fit to the Emami tables for complication levels of 5% and 50%. The predictions of the max & mean model are compared with the Emami tables for different treatment volume fractions. The quality of the fit is also compared with the well-known power-law EUD model. The max & mean model makes it possible to make useful predictions of the EUD for organs having an organization anywhere between serial and parallel. The model can be fitted to the Emami tables within the same error range as the widely used power-law model (about 10%) and can be integrated into linear multicriteria optimization algorithms for planning of intensity-modulated radiotherapy.

Dose Fractionation, Radiation↗
PubMed2006

Optimal crossover designs for logistic regression models in pharmacodynamics.

Pharmacodynamics (PD) is the study of the biochemical and physiological effects of drugs. The construction of optimal designs for dose-ranging trials with multiple periods is considered in this paper, where the outcome of the trial (the effect of the drug) is considered to be a binary response: the success or failure of a drug to bring about a particular change in the subject after a given amount of time. The carryover effect of each dose from one period to the next is assumed to be proportional to the direct effect. It is shown for a logistic regression model that the efficiency of optimal parallel (single-period) or crossover (two-period) design is substantially greater than a balanced design. The optimal designs are also shown to be robust to misspecification of the value of the parameters. Finally, the parallel and crossover designs are combined to provide the experimenter with greater flexibility.

Algorithms↗
PubMed2007

Construction of the electroencephalogram player: a device to present electroencephalogram data to electroencephalogram-based anesthesia monitors.

BACKGROUND: Recently, an increasing number of electroencephalogram (EEG)-based monitors of the hypnotic component of anesthesia has become available. Most of these monitors calculate a numerical index reflecting the hypnotic component of anesthesia. Most of the underlying algorithms are proprietary. Therefore, a quality check or comparison of different indices is very complex. METHODS: Because there is limited information about the algorithms used for index calculation of the different monitors, a reliable comparison or test of the monitors is possible only if the same set of EEG data are presented to each monitor. RESULTS: Parallel EEG monitoring during surgery is limited to two or three monitors because the space for electrode placement on the head is limited. This problem can be solved by using the EEG player to play back recorded EEG data to different monitors. CONCLUSIONS: The output of the player corresponds to the original EEG signal. A comparison of different indices based on identical EEGs is therefore possible. The index reproducibility can also be checked, if the same signal is presented to different monitors.

Anesthesia↗
PubMed2005

Growth hormone therapy for children born small for gestational age: height gain is less dose dependent over the long term than over the short term.

BACKGROUND: Approximately 3% of children are born small for gestational age (SGA), and approximately 10% of SGA children maintain a small body size throughout childhood and often into adult life. Among short SGA children, growth hormone (GH) therapy increases short-term growth in a dose-dependent manner; experience with long-term therapy is limited. OBJECTIVE: To delineate the dose dependency of long-term height gain among short SGA children receiving GH therapy. METHODS: We performed an epianalysis of the first adult height data for SGA children (n = 28) enrolled in 3 randomized trials comparing the growth-promoting efficacy of 2 continuous GH regimens (33 or 67 microg/kg per day for approximately 10 years, starting at approximately 5 years of age); in addition, we performed a meta-analysis of the adult height results published previously and those presented here. RESULTS: Epianalysis outcomes (n = 28) suggested that adult height increased more with a higher-dose regimen than with a lower-dose regimen. In the meta-analysis (n = 82), the higher-dose regimen was found to elicit a long-term height gain superior to that achieved with the lower-dose regimen by a mean of 0.4 SD (approximately 1 inch). Children who were shorter at the start of therapy experienced more long-term height gain. CONCLUSIONS: These findings confirm GH therapy as an effective and safe approach to reduce the adult height deficit that short SGA children otherwise face. In addition, the first meta-analysis indicated that height gain is less dose dependent over the long term than over the short term, at least within the dose range explored to date. For SGA children whose stature is not extremely short, current data support the use of a GH dose of approximately 33 microg/kg per day from start to adult height, particularly if treatment starts at a young age; shorter children (for example, height below -3 SD) might benefit from an approach in which short-term catch-up growth is achieved with a higher dose (> or =50 microg/kg per day) and long-term growth to adult height is ensured with a GH dose of approximately 33 mug/kg per day. Because GH-induced accelerations of height and weight gain evolve in parallel, the dose tapering from > or =50 microg/kg to approximately 33 microg/kg can be accomplished by simply maintaining the absolute GH dose (in micrograms) while the child gains weight (in kilograms). With this algorithm, more growth-responsive children taper their GH dose down to approximately 33 microg/kg per day more quickly.

Adult↗
PubMed1994

[Parallel processing of dose calculation for external photon beam therapy].

We implemented external photon beam dose calculation programs into a parallel processor system consisting of Transputers, 32-bit processors especially suitable for multi-processor configuration. Two network conformations, binary-tree and pipeline, were evaluated for rectangular and irregular field dose calculation algorithms. Although computation speed increased in proportion to the number of CPU, substantial overhead caused by inter-processor communication occurred when a smaller computation load was delivered to each processor. On the other hand, for irregular field calculation, which requires more computation capability for each calculation point, the communication overhead was still less even when more than 50 processors were involved. Real-time responses could be expected for more complex algorithms by increasing the number of processors.

Mathematical Computing↗
PubMed2002

Modeling a parallel L4 neuron array of the fly (Musca domestica) vision system with a sequential processor.

At RMBS 2001 Olson presented a novel approach to image edge detection based on the vision system of the common house fly, Musca domestica [1]. Biologically based vision systems are inherently parallel and the vision related cells form a self-contained cartridge, ommatidium, which is duplicated across the surface of the fly's eye. Histological evidence provides the interconnection both within the vision cartridge and the connections to adjacent cartridges. Due to the parallel nature of biologically inspired vision systems, they outperform computer based digital vision systems in speed performance and memory requirements. Olson provided a model of the cartridge with its intra- and inter-connections. This model, rendered in MATLAB and Excel, demonstrated the feasibility of edge detection in the first several synaptic cellular connections within the cartridge. His results demonstrated how edge detection and object movements are easily obtained using a biologically based vision model. He demonstrated the model using simple rectangular and circular objects. We term this work Olson's Algorithm. We have extended Olson's Algorithm into a high-resolution model using a standard off-the-shelf frame grabber. Although, the frame grabber is a digitally based instrument, its image planes are used to model the photoreceptor layer (R1-R6), the L1, L2 monopolar cell layer, and also the monopolar L4 cell layer. The connections between these cells are programmed in "C". The high-resolution model demonstrates the feasibility of using a biologically based vision system in a real world application. Furthermore, it allows object segmentation, movement, and tracking to be modeled prior to implementation in parallel analog hardware.

Algorithms↗