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The electrochemistry of ubiquinone-10 in a phospholipid model membrane.

The electrochemistry of ubiquinone-10, UQ, incorporated over a phospholipid layer adsorbed on a mercury drop electrode has been investigated over a wide pH range. It is shown that the position of the quinone headgroup in relation to the lipid determines the reversibility of the redox chemistry. For pH <7, the reaction follows a disproportionation route involving the ubiquione radical. There is evidence for the presence of a parallel reaction sequence. The bifurcation point appears to occur for the UQ molecule, which disproportionates after protonation and reduction, in parallel with direct electron transfer to yield the UQ--radical anion. The incorporation of UQ in a lipid monolayer makes its reduction very irreversible for pH > 7.

Algorithms↗

Assembly of fingerprint contigs: parallelized FPC.

SUMMARY: One of the more common uses of the program FingerPrint Contigs (FPC) is to assemble random restriction digest 'fingerprints' of overlapping genomic clones into contigs. To improve the rate of assembling contigs from large fingerprint databases we have adapted FPC so that it can be run in parallel on multiple processors and servers. The current version of 'parallelized FPC' has been used in our laboratory to assemble mammalian BAC fingerprint databases, each containing more than 300000 BAC fingerprints. AVAILABILITY: This parallelized version of FPC is available under the GNU GPL licence, and can be downloaded from ftp://ftp.bcgsc.bc.ca/pub/fpcd.

Algorithms↗

The concentration-effect relationship of the respiratory depressant effects of alfentanil and fentanyl.

UNLABELLED: The relative potencies of fentanyl and alfentanil for respiratory depression were determined in eight healthy male volunteers in a double-blinded, randomized study with a cross-over design. The drugs were delivered by computer-driven infusion with logarithmically ascending plasma concentrations until the respiratory rate reached 2/min and/or oxygen saturation decreased below 85% with subjects breathing room air. Ventilation was measured with respiratory inductive plethysmography, indirect calorimetry, and arterial blood gas analysis, and plasma drug concentrations were determined. Pharmacodynamic modeling was performed using a fractional E(max) model for minute volume and respiratory rate and the concentrations producing 50% depression (i.e., apparent 50% effective concentration [EC(50)] values) were determined. Both drugs decreased ventilation in a similar manner, and drug infusions were terminated at mean +/- SD measured plasma concentrations of 254 +/- 88 ng/mL and 5.1 +/- 1.7 ng/mL for alfentanil and fentanyl, respectively. Alfentanil decreased minute volume from baseline by 54% +/- 19% and respiratory rate by 40% +/- 11% with EC(50) values of 234 +/- 57 ng/mL and 195 +/- 101 ng/mL. The respective decreases for fentanyl were 50% +/- 11%, 41% +/- 15%, and the estimated EC(50) values were 6.1 +/- 1.4 ng/mL and 3.5 +/- 1.4 ng/mL, respectively. Using the apparent EC(50) values, the calculated potency ratio for alfentanil:fentanyl was (mean and 95% confidence interval) 1:39 (1:31-1:46) for minute volume and 1:51 (1:34-1:68) for respiratory rate. This is analogous to the analgesic effect studied earlier. The findings support the notion of parallel analgesic and respiratory depressant effects of alfentanil and fentanyl. Therefore equianalgesic concentrations of both drugs will lead to equally pronounced respiratory depression. IMPLICATIONS: This double-blinded, randomized study evaluated the potency ratio of alfentanil and fentanyl-induced respiratory depression. The findings support the notion of parallel analgesic and respiratory depressant effects of alfentanil and fentanyl. Therefore equianalgesic concentrations of both drugs will lead to equally pronounced respiratory depression.

Adult↗

[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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

[Trans-thoracic 3D echocardiography reconstruction for left ventricular volume determination].

2D-echocardiography is a safe and inexpensive method for accurate left ventricular volume quantification. However, accuracy of measurements is limited by the requirement of geometric assumptions and volume computation algorithms. Reproducibility is diminished by erroneous image plane positioning, which is due to the necessity of standardized reference images. The degree of variation can influence clinical decision making. 3D-echocardiography has overcome those problems. Volume quantitation is performed without the need of geometric assumptions, computation algorithms or reference images. The shape of a ventricle is defined by acquired data, not by calculated data. Since the recent development of sophisticated hardware- and software techniques the method can be utilized under clinical circumstances. For data acquisition tomographic planes are acquired either in a random or in a sequential order. For random acquisition the transducer is positioned at various acoustic windows at the thoracic wall and spatial orientation of the corresponding plane is localized by a spark gap device. By this way various, non-parallel cross-sectional images of the left ventricle are acquired. The spatial position of the planes is displayed by lines in a parasternal longitudinal view, each representing a "line of intersection". When tomographic planes are acquired in a sequential manner, mostly rotational scanning is utilized. Here, multiple apical views of the left ventricle are acquired during ECG- and respiration gated rotation of the transducer over a span of 180 degrees.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

An automated multi well cell track system to study leukocyte migration.

Design of automated image processing systems to determine migration characteristics of individual cells is not trivial. Every test sample requires separate recording and the analysis of individual cell tracks in two- or three-dimensional migration systems by time-lapse microscopy is extremely laborious. Here, we describe a new Automated Cell Track System (ACTS). In addition to contrast differences, which are used by existing analysis systems, the ACTS algorithms recognize cells on the basis of morphological similarities in successive images and adapt to the continuous shape changes of individual cells during migration. The system facilitates simultaneous analysis of multiple cells and the measurement of multiple wells in one single experiment. We validated the system studying HSB-2 T cell migration in standard 96-well microtiter plates coated with ICAM-1-Fc protein or control CD14-Fc protein. Migration of HSB-2 T cells on ICAM-1-Fc is Leukocyte Function-associated Antigen-1 (LFA-1)-mediated and both the number and the speed of migrating cells depend on the ICAM-1-Fc concentration. We show that automated analysis of the migration data yields similar results as manual analysis, but in a fraction of the time. We conclude that this system is extremely well suited to precisely monitor the migratory behavior of individual cells. The analysis of multiple wells in parallel makes this set-up appropriate in high throughput screening in which multiple components are simultaneously tested for their effect on cell migration.

Algorithms↗

A nonlinear regression analysis of nonlinear, passive-deflation flow-volume plots.

When studying lung mechanics of intubated premature infants, by the passive-deflation technique we noted that in many flow-volume plots the descending limb was curvilinear with a convexity toward the volume axis. By conventional linear analysis lung mechanics of these patients did not change after the administration of terbutaline, but Mead's tangent-chord slope ratio method for quantifying the amount of curvature showed that the shape of the flow-volume plots did change. Because of the limitations of this method, we developed a microcomputer-based, reiterative regression algorithm which optimizes a nonlinear function for the best fit to any given set of data. We then studied six very low birth weight infants with clinical evidence of pulmonary gas trapping (weight at study, 1.22 +/- 0.29 kg; age, 26 +/- 16 days). We measured respiratory system resistance (Rrs), compliance (Crs), and expiratory time constants (TCrs) by the passive deflation technique before and after subcutaneous administration of 0.02 mg/kg of terbutaline. No effect of terbutaline in a dose sufficient to increase heart rate > 25 beats/min was observed. The same data analyzed using the nonlinear regression technique with a function based upon a two compartment model of parallel inhomogeneities revealed one compartment with relatively normal Rrs, Crs, and TCrs values, and a second compartment with a very high Rrs. The latter fell by 50% after terbutaline. These data suggest that abnormalities of airway resistance in ventilated preterm infants are not easily identifiable by classic linear analysis of lung mechanics.(ABSTRACT TRUNCATED AT 250 WORDS)

Airway Resistance↗

Allosteric voltage gating of potassium channels II. Mslo channel gating charge movement in the absence of Ca(2+).

Large-conductance Ca(2+)-activated K(+) channels can be activated by membrane voltage in the absence of Ca(2+) binding, indicating that these channels contain an intrinsic voltage sensor. The properties of this voltage sensor and its relationship to channel activation were examined by studying gating charge movement from mSlo Ca(2+)-activated K(+) channels in the virtual absence of Ca(2+) (<1 nM). Charge movement was measured in response to voltage steps or sinusoidal voltage commands. The charge-voltage relationship (Q-V) is shallower and shifted to more negative voltages than the voltage-dependent open probability (G-V). Both ON and OFF gating currents evoked by brief (0.5-ms) voltage pulses appear to decay rapidly (tau(ON) = 60 microseconds at +200 mV, tau(OFF) = 16 microseconds at -80 mV). However, Q(OFF) increases slowly with pulse duration, indicating that a large fraction of ON charge develops with a time course comparable to that of I(K) activation. The slow onset of this gating charge prevents its detection as a component of I(gON), although it represents approximately 40% of the total charge moved at +140 mV. The decay of I(gOFF) is slowed after depolarizations that open mSlo channels. Yet, the majority of open channel charge relaxation is too rapid to be limited by channel closing. These results can be understood in terms of the allosteric voltage-gating scheme developed in the preceding paper (Horrigan, F.T., J. Cui, and R.W. Aldrich. 1999. J. Gen. Physiol. 114:277-304). The model contains five open (O) and five closed (C) states arranged in parallel, and the kinetic and steady-state properties of mSlo gating currents exhibit multiple components associated with C-C, O-O, and C-O transitions.

Algorithms↗