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PubMed1988

[Enhancement of the information value of kidney scintigraphy using 99m Tc-DMSA].

A method of high frequency image filtration improving the quality of imaging, and more precise renometry with measurement of the total count and the level of RP kidney accumulation were used for raising the informative value of the results of renal scintigraphy with 99m Tc-DMSA. 54 patients with unilateral pyelonephritis, 46--with bilateral pyelonephritis, 15--with nephroptosis, and 10 healthy persons were examined. Informative values were calculated on the basis of the results of these investigations. The sensitivity of routine renometry was 0.88, its specificity--0.27 and precision--0.78; the same indices for routine static scintigraphy were 0.88; 0.4 and 0.84; for modified renal investigations--0.98; 0.77 and 0.96, respectively. The results of the investigations have shown that the use of scintigraphy with improved quality of kidney images in parallel with modified renometry raises the informative value of renal studies with 99m Tc-DMSA and precision of diagnosis of renal parenchymal lesions.

Algorithms↗
PubMed2006

A generic 3-dimensional system to mimic trabecular bone surface adaptation.

The paper presents the structure optimizing system based on surface remodelling. The grounds for algorithm formulation are given by the bone remodelling phenomenon leading to optimization of trabecular network in the bone. The assumptions, algorithms and limitations of the own mesh generator Cosmoprojector are described. Unlike other approaches, the system is able to mimic real bone evolution including tissue consolidation and separation. The article presents a closed system consisting of finite element mesh generation, decision criteria for structure adaptation and finite element analysis in parallel environment. It also provides some computation results obtained by using specially designed software.

Adaptation, Physiological↗
PubMed2006

Multiplicative optical tomography of cardiac electrical activity.

Cardiac electrical activity can be mapped today through the response of voltage-sensitive dyes; but poor transparency of muscle tissue has enforced shallow-depth imaging. We present a three-dimensional (3D) reconstruction method for electrical activity deep inside the myocardial wall. Our approach is nonlinear and differs substantially from standard diffusive optical tomography. It does not require matrix inversion, data regularization or a priori information concerning the original object. Opposite sides of a slab-shaped preparation are scanned in parallel by detection and illumination points with a constant vector offset between illumination and detection axes (biaxial scanning). Scanning is performed in two perpendicular directions. In each direction, a pair of 2D images is obtained under offsets of opposite signs. These two pairs are the input for a multiplicative reconstruction algorithm, whose output is a 3D image. The overall procedure was successfully tested on computer-generated sources that include points, lines and hemispheres, patterned after actual electrophysiological excitations. The algorithm is computationally efficient and stable with respect to varying noise levels in the raw data.

Algorithms↗
PubMed2003

Effectiveness of compensating filters in the presence of tissue inhomogeneities.

CT based 3D treatment planning systems (3DTPS) can be used to design compensating filters that, in addition to missing tissue compensation, can account for tissue inhomogeneities. The use of computer-driven systems provides a practical, convenient, and accurate method of fabricating compensating filters. In this work, we have evaluated a commercially available PAR Scientific DIGIMILL milling machine linked with FOCUS 3DTPS. Compensating filters were fabricated using refined gypsum material with no additives. Thus, filters were of manageable dimensions and were not sensitive to common machining errors. Compensating filters were evaluated using a homogeneous step phantom and step phantoms containing various internal inhomogeneities (air, cork, and bone). The accuracy of two planning algorithms used to design filters was experimentally evaluated. The superposition algorithm was found to produce better agreement with measurements than the Clarkson algorithm. Phantom measurements have demonstrated that compensating filters were able to produce a uniform dose distribution along the compensation plane in the presence of tissue inhomogeneity. However, the dose variation was greatly amplified in planes located beyond the inhomogeneity when a single compensated beam was used. The use of parallel-opposed compensated beams eliminated this problem. Both lateral and depth-dose uniformity was achieved throughout the target volume.

Biophysics↗
PubMed1996

The effects of air cavities on X-ray dose distribution at 6 and 25 MV.

Three different air channels were constructed in solid water. These resemble upper respiratory and larynx geometry. Central-axis depth-dose distributions were measured on and beyond the distal surface of the air cavities. The measurements were made with a parallel-plate Markus ionisation chamber and TLDs for 6 and 25 MV X-ray beams of field sizes 4 cm x 4 cm and 4 cm x 7 cm. Measured dose was then compared to calculated dose for the Clarkson Scatter Integration and Equivalent Tissue-air Ratio (ETAR) algorithms. Both algorithms show errors in dose calculation at the distal surface of air cavities mainly because they fail to account for the effect of electronic disequilibrium. The magnitude of prediction error is found to depend on energy, field size and cavity geometry. For a 4 cm x 4 cm field at 6 MV the dose difference between the calculated value and the measured value, at the distal surface of square cavity is 8.2% and 13.7% for the ETAR and Clarkson algorithm respectively while that for a 4 cm x 7 cm field, the dose difference is reduced to 1.4% and 7.1% respectively. In general the ETAR algorithm shows better performance than the Clarkson algorithm because the Clarkson method calculates scatter dose assuming a homogeneous water medium while the ETAR uses a weighted sum of scatter components which is density dependent. The measured data can be used as benchmark data in the development and testing of new photon dose calculation algorithms.

Air↗
PubMed2005

Cell wall extension results in the coordinate separation of parallel microfibrils: evidence from scanning electron microscopy and atomic force microscopy.

Enlargement of the cell wall requires separation of cellulose microfibrils, mediated by proteins such as expansin; according to the multi-net growth hypothesis, enlargement passively reorients microfibrils. However, at the molecular scale, little is known about the specific movement of microfibrils. To find out, we examined directly changes in microfibril orientation when walls were extended slowly in vitro under constant load (creep). Frozen-thawed cucumber hypocotyl segments were strained by 20-30% by incubation in pH 4.5 buffer or by incubation of heat-inactivated segments in alpha-expansin or a fungal endoglucanase (Cel12A). Subsequently, the innermost layer of the cell wall was imaged, with neither extraction nor homogenization, by field-emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM). AFM images revealed that sample preparation for FESEM did not appreciably alter cell wall ultrastructure. In both FESEM and AFM, images from extended and non-extended samples appeared indistinguishable. To quantify orientational order, we used a novel algorithm to characterize the fast Fourier transform of the image as a function of spatial frequency. For both FESEM and AFM images, the transforms of non-extended samples were indistinguishable from those of samples extended by alpha-expansin or Cel12A, as were AFM images of samples extended by acidic buffer. We conclude that cell walls in vitro can extend slowly by a creep mechanism without passive reorientation of innermost microfibrils, implying that wall loosening agents act selectively on the cross-linking polymers between parallel microfibrils, rather than more generally on the wall matrix.

Cell Wall↗
PubMed2001

The dielectrophoretic levitation and separation of latex beads in microchips.

A linear travelling wave dielectrophoretic (twDEP) microchip was fabricated and used to investigate both the levitation and the twDEP motion of latex beads as a function of applied potential and frequency, suspending medium conductivity, bead size, and surface characteristics. The surface conductance of the latex beads was characterised by measurement of the dielectrophoretic (DEP) crossover frequency. Collection of sample prior to initiation of twDEP was achieved using positive DEP forces generated by an integrated pair of parallel electrodes positioned in front of the twDEP array within the microfluidic channel. The principle of linear twDEP separation is shown using latex beads and rabbit heart cells.

Algorithms↗
PubMed2006

The present values of delayed rewards are approximately additive.

In two experiments, human subjects were asked to estimate their present values of single delayed rewards and their present values of temporal sequences of three rewards. Present values were solicited by asking subjects to indicate an amount of money v for which they would be indifferent between receiving v at the end of the session and receiving the delayed reward(s). A procedure was used for which responding the true value of v was the optimal strategy, and the actual payoff that each subject received was determined by one randomly selected trial. In Experiment 1 (n=29) each delayed reward was 9.90 dollars in cash. In Experiment 2 (n=19) the delayed rewards were dated 15 dollars gift certificates to a local restaurant. In both experiments, the present values of the sequences were approximately equal to the sums of the present values of their component rewards. The presence of outliers suggests that a few subjects may have valued sequences less than the sums of their single rewards. Effects of a preference for uniform sequences, if any, were too small to be detected. Discounting of sequences was well fit by a parallel hyperbolic discounting equation, consistent with Mazur's [Mazur, J.E., 1986. Choice between single and multiple delayed reinforcers. J. Exp. Anal. Behav. 46 (1), 67-77] results using multiple reinforcers.

Adult↗
PubMed2001

Parallel synthesis of a vitamin D(3) library in the solid-phase.

A highly efficient synthesis of the vitamin D(3) system on solid support is described. Two synthetic strategies for the solid-phase synthesis of vitamin D(3) were developed. One is for 11-hydroxy analogues, and the other is for most other synthetic analogues. In the latter strategy, the sulfonate-linked CD-ring 58 was initially immobilized on PS-DES resin to give solid-supported CD-ring 63 (Scheme 10). Similarly, solid-supported CD-ring 63 was prepared by attachment of the CD-ring 10 to the chlorosulfonate resin 64. The vitamin D(3) system was synthesized by Horner-Wadsworth-Emmons reaction of the A-ring phosphine oxide to a solid-supported CD-ring, followed by simultaneous introduction of the side chain and cleavage from resin with a Cu(I)-catalyzed Grignard reagent. Parallel synthesis of the vitamin D(3) analogues was accomplished by a split and pool methodology utilizing radio frequency encoded combinatorial chemistry, and a manual parallel synthesizer for side chain diversification and deprotection. Additionally, we demonstrated the synthesis of various A-rings in a similar protocol for efficient preparation of building blocks.

Algorithms↗
PubMed2000

Ant-like task allocation and recruitment in cooperative robots.

One of the greatest challenges in robotics is to create machines that are able to interact with unpredictable environments in real time. A possible solution may be to use swarms of robots behaving in a self-organized manner, similar to workers in an ant colony. Efficient mechanisms of division of labour, in particular series-parallel operation and transfer of information among group members, are key components of the tremendous ecological success of ants. Here we show that the general principles regulating division of labour in ant colonies indeed allow the design of flexible, robust and effective robotic systems. Groups of robots using ant-inspired algorithms of decentralized control techniques foraged more efficiently and maintained higher levels of group energy than single robots. But the benefits of group living decreased in larger groups, most probably because of interference during foraging. Intriguingly, a similar relationship between group size and efficiency has been documented in social insects. Moreover, when food items were clustered, groups where robots could recruit other robots in an ant-like manner were more efficient than groups without information transfer, suggesting that group dynamics of swarms of robots may follow rules similar to those governing social insects.

Algorithms↗
PubMed2006

Finite-particle tracking reveals submicroscopic-size changes of mitochondria during transport in mitral cell dendrites.

The mechanisms of molecular motor regulation during bidirectional organelle transport are still uncertain. There is, for instance, the unsettled question of whether opposing motor proteins can be engaged in a tug-of-war. Clearly, any non-synchronous activation of the molecular motors of one cargo can principally lead to changes in the cargo's shape and size; the cargo's size and shape parameters would certainly be observables of such changes. We therefore set out to measure position, shape and size parameters of fluorescent mitochondria (during their transport) in dendrites of cultured neurons using a finite-particle tracking algorithm. Our data clearly show transport-related submicroscopic-size changes of mitochondria. The observed displacements of the mitochondrial front and rear ends are consistent with a model in which microtubule plus- and minus-end-directed motor proteins or motors of the same type but moving along anti-parallel microtubules are often out-of-phase and occasionally engaged in a tug-of-war. Mostly the leading and trailing ends of mitochondria undergo similar characteristic movements but with a substantial time delay between the displacements of both ends, a feature reminiscent of an inchworm-like motility mechanism. More generally, we demonstrate that observing the position, shape and size of actively transported finite objects such as mitochondria can yield information on organelle transport that is generally not accessible by tracking the organelles' centroid alone.

Animals↗
PubMed1988

Intracellular pH in frog skin: effects of Na+, volume, and cAMP.

Single skins were analyzed by 31P-nuclear magnetic resonance (NMR) spectroscopy during alternate perfusion with control and experimental solutions. Intracellular (pHc) and extracellular (pHo) pH were monitored by measuring the spectral frequencies of intracellular Pi and external methylphosphonate, respectively. Base-line pHc was 7.20 +/- 0.02 (SE) when pHo was 6.99 +/- 0.02. A 4-acetamido-4'-isothiocyanostilbene-2,2'-disulfonic acid (SITS)-inhibitable, HCO3--dependent alkaline shift in pHc can be elicited by replacing external Cl- by gluconate or sulfate. We now report that this effect is observed even in sodium-free media. The substitution of gluconate for external Cl- has also been reported to shrink cell volume. This shrinkage can be minimized by replacing Cl- with gluconate during perfusion with hypotonic, rather than isotonic, media. Conducted in this manner, the anionic substitution produces a much smaller alkaline shift in pHc. Replacement of external NaCl with N-methyl-D-glucamine chloride acidified the cells reversibly by 0.22 +/- 0.02. In the presence of the Na-H antiport blocker 5-(N-methyl-N-isobutyl)amiloride (MIA), restoration of external Na+ did not increase pHc. Separate addition of MIA acidified the cells by 0.18 +/- 0.03. Adenosine 3',5'-cyclic monophosphate (cAMP) also alters pHc. Addition of 1 mM 8(4-chlorophenylthio)cAMP or 100 mU/ml vasopressin acidified the cells by 0.22 +/- 0.03 and by 0.14 +/- 0.04, respectively. The data suggest that frog skin regulates pHc by the parallel operation of Na-H and Na+-independent Cl-HCO3 antiports. Cell volume and cAMP may play regulating roles in this epithelium.

Algorithms↗
PubMed2005

ParPEST: a pipeline for EST data analysis based on parallel computing.

BACKGROUND: Expressed Sequence Tags (ESTs) are short and error-prone DNA sequences generated from the 5' and 3' ends of randomly selected cDNA clones. They provide an important resource for comparative and functional genomic studies and, moreover, represent a reliable information for the annotation of genomic sequences. Because of the advances in biotechnologies, ESTs are daily determined in the form of large datasets. Therefore, suitable and efficient bioinformatic approaches are necessary to organize data related information content for further investigations. RESULTS: We implemented ParPEST (Parallel Processing of ESTs), a pipeline based on parallel computing for EST analysis. The results are organized in a suitable data warehouse to provide a starting point to mine expressed sequence datasets. The collected information is useful for investigations on data quality and on data information content, enriched also by a preliminary functional annotation. CONCLUSION: The pipeline presented here has been developed to perform an exhaustive and reliable analysis on EST data and to provide a curated set of information based on a relational database. Moreover, it is designed to reduce execution time of the specific steps required for a complete analysis using distributed processes and parallelized software. It is conceived to run on low requiring hardware components, to fulfill increasing demand, typical of the data used, and scalability at affordable costs.

Algorithms↗
PubMed2002

Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis.

BACKGROUND: Oligonucleotide microarrays measure the relative transcript abundance of thousands of mRNAs in parallel. A large number of procedures for normalization and detection of differentially expressed genes have been proposed. However, the relative impact of these methods on the detection of differentially expressed genes remains to be determined. RESULTS: We have employed four different normalization methods and all possible combinations with three different statistical algorithms for detection of differentially expressed genes on a prototype dataset. The number of genes detected as differentially expressed differs by a factor of about three. Analysis of lists of genes detected as differentially expressed, and rank correlation coefficients for probability of differential expression shows that a high concordance between different methods can only be achieved by using the same normalization procedure. CONCLUSIONS: Normalization has a profound influence of detection of differentially expressed genes. This influence is higher than that of three subsequent statistical analysis procedures examined. Algorithms incorporating more array-derived information than gene-expression values alone are urgently needed.

Animals↗
PubMed1996

Physical and clinical evaluation of high-resolution thyroid pinhole tomography.

UNLABELLED: High-resolution pinhole-SPECT (PSPECT) is a new method for examining the thyroid gland. METHODS: The camera is tilted slightly so that it is as close to the thyroid as possible. Patients are injected with 185-260 MBq (5-7 mCi) of [99mTc]pertechnetate and examined for 20 min. The reconstruction algorithm is based on filtered back-projection. RESULTS: We performed static scintigraphy on the thyroids of 114 patients, followed by PSPECT. The major advantage of P SPECT is high resolution. Three- and 4-mm-pinholes produce resolutions of 6 mm and 7 mm, respectively, while resolutions obtained with a parallel collimator are always above 15 mm. The second advantage associated with this method is the good visualization of the cold nodules surrounded by higher activity. Finally, the reconstruction program provides exact sizes of thyroids. CONCLUSION: SPECT is a powerful tool for examining the thyroid.

Adolescent↗
PubMed2005

Birefringence of the primate retinal nerve fiber layer.

The purpose of this study was to measure the peripapillary retinal nerve fiber layer (RNFL) thickness, phase retardation (PR), and depth-resolved birefringence (Deltan) of the normal primate eye using Enhanced Polarization-Sensitivity Optical Coherence Tomography (EPS-OCT). Both eyes of two rhesus monkeys were imaged with EPS-OCT. A multiple incident polarization state nonlinear fitting algorithm was used to determine RNFL phase retardation. RNFL thickness (RNFLT) was determined from the corresponding EPS-OCT intensity image and phase retardation per unit depth (PR/UD, proportional to Deltan) was calculated by dividing PR by RNFLT. Peripapillary area maps consisting of pixels uniformly distributed along a radius from 0.8 to 1.8 mm from the center of the optic nervehead were constructed for RNFLT, PR, and PR/UD. Average PR/UD in the superior and inferior quadrants was 18 degrees /100 mivrom (Deltan=4.2 x 10(-4)) and average PR/UD in the nasal and temporal quadrants was 6.3 degrees /100 microm (Deltan=1.5 x 10(-4)). Relative magnitude of PR radial gradient is similar to that of RNFLT radial gradient and no radial gradient was observed for PR/UD. Polarization-dependent amplitude attenuation per unit depth (PDAA/UD) was 0.02 rad/100 microm in thick RNFL regions. RNFL birefringence was higher in the arcuate bundles compared to nasal and temporal fibers (P=0.001). Birefringence was nearly equal in nasal and temporal quadrants. No statistically significant (P=0.01) radial gradient of birefringence was observed in any quadrant. RNFL birefringence is believed to originate from anisotropic structures within the cytoskeleton of the parallel axons. Birefringence differences presented in this study cannot be explained by the known axon diameter distribution around the optic nervehead and suggest other sources of the birefringence signal including neurotubules and neurofilaments.

Algorithms↗
PubMed1980

Analysis and prediction of protein beta-sheet structures by a combinatorial approach.

Analysis of beta-sheet sandwiches (for example immunoglobulin domains) suggests an algorithm that successfully predicts the tertiary fold of these proteins from their sequence and secondary structure. We propose tertiary structures for beta 2-microglobulin and an HLA-B7 antigen fragment. Topological rules are presented that markedly reduce the number of folds for proteins in which a-helices pack against a parallel beta-sheet.

Biological Evolution↗
PubMedDate not supplied

Cone beam collimation for single photon emission computed tomography: analysis, simulation, and image reconstruction using filtered backprojection.

This paper presents an analysis of two cone beam configurations (having focal lengths of 40 and 60 cm) for the acquisition of single photon emission computed tomography (SPECT) projection data. A three-dimensional filtered backprojection algorithm is used to reconstruct SPECT images of cone beam projection data obtained using Monte Carlo simulations. The mathematical analysis resulted in on-axis point source sensitivities (calculated for a distance of 15 cm from the collimator surface) for cone beam configurations that were 1.4-3 times the sensitivities of parallel-hole and fan beam geometries having similar geometric resolutions. Cone beam collimation offers the potential for improved sensitivity for SPECT devices using large-field-of-view scintillation cameras.

Humans↗