PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Computers, Hybrid”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources
PubMed1989

Indexes to the reassociation and stability of solution DNA hybrids.

The computation, assumptions, and properties of DNA-hybrid stability and reassociation indexes were reviewed. Different methods of computing the same index typically yielded similar values. However, because dissociation curves change from asymmetric to symmetric as increasingly divergent DNAs are compared, adequate determination of mode required fitting a complex function. Delta Tm, delta mode, and delta T50H correlated well up to ca. 12, and all were found to be useful indexes of genomic similarity in that range. They also exhibited similar levels of error, even though T50H comprises a percent reassociation component with relatively large variance. At greater distances, the delta Tm scale became markedly compressed because of the boundary imposed by the temperature of hybrid formation (incubation temperature). Though not compressed or technically limited by it, delta mode and delta T50H could not be extrapolated with certainty below the incubation temperature. Among theoretical problems discussed: Tm and mode index an increasingly small percentage of the genome as the extent of reassociation decreases, and they may compare different genomic segments as DNAs become highly diverged. T50H relies upon the assumptions that all sequences evolve at a constant rate and that reassociation behavior is the same among all sequences regardless of their extent of divergence. Tm and T50H may be biased by self-hybridization of repetitive elements or cross-hybridization of paralogous sequences. Delta mode is free of such biases as long as the genomes under comparison are not too diverged. No index was found to be best in all circumstances.

Algorithms↗
PubMed2002

Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations.

Collagen-like peptides of the type (Pro-Pro-Gly)(10) fold into stable triple helices. An electron-withdrawing substituent at the H(gamma)(3) ring position of the second proline residue stabilizes these triple helices. The aim of this study was to reveal the structural and energetic origins of this effect. The approach was to obtain experimental NMR data on model systems and to use these results to validate computational chemical analyses of these systems. The most striking effects of an electron-withdrawing substituent are on the ring pucker of the substituted proline (Pro(i)) and on the trans/cis ratio of the Xaa(i-1)-Pro(i) peptide bond. NMR experiments demonstrated that N-acetylproline methyl ester (AcProOMe) exists in both the C(gamma)-endo and C(gamma)-exo conformations (with the endo conformation slightly preferred), N-acetyl-4(R)-fluoroproline methyl ester (Ac-4R-FlpOMe) exists almost exclusively in the C(gamma)-exo conformation, and N-acetyl-4(S)-fluoroproline methyl ester (Ac-4S-FlpOMe) exists almost exclusively in the C(gamma)-endo conformation. In dioxane, the K(trans/cis) values for AcProOMe, Ac-4R-FlpOMe, and Ac-4S-FlpOMe are 3.0, 4.0, and 1.2, respectively. Density functional theory (DFT) calculations with the (hybrid) B3LYP method were in good agreement with the experimental data. Computational analysis with the natural bond orbital (NBO) paradigm shows that the pucker preference of the substituted prolyl ring is due to the gauche effect. The backbone torsional angles, phi and psi, were shown to correlate with ring pucker, which in turn correlates with the known phi and psi angles in collagen-like peptides. The difference in K(trans/cis) between AcProOMe and Ac-4R-FlpOMe is due to an n-->pi interaction associated with the Bürg-Dunitz trajectory. The decrease in K(trans/cis) for Ac-4S-FlpOMe can be explained by destabilization of the trans isomer because of unfavorable electronic and steric interactions. Analysis of the results herein along with the structures of collagen-like peptides has led to a theory that links collagen stability to the interplay between the pyrrolidine ring pucker, phi and psi torsional angles, and peptide bond trans/cis ratio of substituted proline residues.

Collagen↗
PubMed1993

Single-exposure conventional and computed radiography. The hybrid cassette revisited.

RATIONALE AND OBJECTIVES: The authors constructed and evaluated a hybrid cassette for single-exposure extremity imaging with storage-phosphor plates and conventional radiographic film. METHODS: A hybrid cassette was constructed using a fine radiographic screen and a storage-phosphor plate. Exposures of a Lucite step wedge and a line pair gauge were made with the hybrid cassette, a conventional radiographic cassette, and a storage-phosphor cassette. The spatial resolution and imaging speeds of the hybrid and standard systems were compared. RESULTS: Spatial resolution loss was less than 0.5 line pairs per mm with the hybrid cassette. Speed loss was characteristic of the hybrid cassette, requiring approximately 40% greater exposure to produce the same film density as standard cassettes. CONCLUSIONS: The speed difference between this and a previous study is probably due to differences in film-screen choice, kilovolt peak, and storage-phosphor plate generations. The sensitivity spectrum of our film and the emission spectrum of our screens were more closely matched than were the spectra in the previous study; we used lower kilovolt peak, and our storage-phosphor plates were a later, more efficient, generation. Despite slight speed losses, the hybrid cassette appears to be a better choice for obtaining matched images for clinical trials than the alternative of two separate exposures.

Extremities↗
PubMedDate not supplied

Hybrid reconstruction algorithm for x-ray computed tomography.

A hybrid reconstruction algorithm (HRA) is derived for fan beam geometry for use with systems utilizing a linear array of detectors. The algorithm uses fan beam geometry with a modified parallel beam reconstruction formula. The parallel beam algorithm is used with fan beam geometry by a simple geometric conversion and a different back projection formula. Correction for center of rotation shift is done during the back projection. Computer simulations are shown, both with the center of rotation shift uncorrected and corrected.

Algorithms↗
PubMedDate not supplied

A hybrid method to compute accurate efficiencies for volume samples in gamma-ray spectrometry.

In recent years, Monte Carlo (MC) methods have been increasingly applied to cope with variability in photopeak efficiencies due to matrix effects. But to obtain proper results only by numerical simulation, especially at low energies, sample bulk density and chemical composition must be well characterized. In this paper, we propose a method that combines both experimental measurements and MC simulations, being applicable to matrices of unknown composition. A transmission measurement of a 210Pb point source through the sample allows one to compute accurately its photopeak efficiencies at energies above 46.5 keV. The method is validated for several inorganic and organic matrices measured in Petri dishes geometry.

Algorithms↗
PubMed2001

An improved surface-based method for DNA computation.

DNA computing is a novel method for solving a class of intractable computational problems, in which the computing time can grow exponentially with problem size. Up to now, many accomplishments have been achieved to improve its performance and increase its reliability, among which a surface-based method is an efficient candidate. In this paper, the surface-based approach proposed by Liu, Q., Wang, L., Frutos, A.G., Condon, A.E., Corn, R.M., and Smith, L.M., 2000, DNA computing on surfaces. Nature 403, 175-179 is analyzed and an improved surface-based method for DNA computation (i.e. the hybrid DNA/optical computing method) is proposed. Compared with Liu et al.'s approach, our method has some significant advantages such as low cost, short operating time, reusable surface and simple experimental steps. Moreover, the concept of combining easily patterned DNA computing steps with equally parallel, but generally uniform and not easily patterned optical computing steps is an important new direction.

Computing Methodologies↗
PubMed2005

A hybrid approach to reducing computed tomography metal artifacts in intracavitary brachytherapy.

PURPOSE: To develop a hybrid approach to reduce computed tomography (CT) metal artifacts caused by the Fletcher-Suit applicator. METHODS AND MATERIALS: Using the acquired raw projection data, the hybrid algorithm determines the separate contributions from the metal and non-metal objects. Next, reconstructions of metal and non-metal images are separately obtained from their estimated projections. A final image is formed by appropriately combining the individual images. Phantom and patient data are used to evaluate the performance of this method. RESULTS: CT images reconstructed by use of the standard filtered-backprojection (FBP) algorithm contain significant artifacts even for small metal objects. However, images reconstructed using the hybrid algorithm contain virtually no artifacts. For metal objects with complex structures, the hybrid algorithm can also yield images containing fewer severe streak artifacts than those reconstructed using the FBP algorithm alone. CONCLUSIONS: These studies demonstrate that the hybrid approach can effectively reduce CT metal artifacts caused by the Fletcher-Suit applicator.

Algorithms↗
PubMed2006

[Screening and their anti-tumor activity of antisense oligodeoxynucleotides targeting KDR mRNA in breast cancer MCF-7 cells].

OBJECTIVE: To screen the antisense oligodeoxynucleotides (asONs) which could hybridize with KDR (kinase insert domain-containing receptor) mRNA in an effective and specific way and to explore their anti-tumor effects on breast cancer MCF-7 cell line in vitro. METHODS: The asONs were firstly selected using oligodeoxynucleotides library hybridization or computer prediction, then their hybridization ability with KDR mRNA was further tested with oligonucleotide microarray. The asONs with strong hybridization intensity were selected. Their inhibitory effects on MCF-7 cells proliferation and KDR expression were assayed by MTT, RT-PCR and Western blotting assay, respectively. RESULTS: In 13 asONs selected with oligodeoxynucleotides library hybridization, 8 (8/13, 61.5%) showed strong hybridization signals, while such was only 1 in 17 asONs designed by computer prediction. 9 asONs with strong hybridization intensity were selected and synthesized with phosphorothioated modification. All these asONs inhibited the MCF-7 cells proliferation in a dose-dependent manner, in which asON4 and asON7 screened by oligodeoxynucleotides library in combination with oligonucleotide microarray were the most effective, with inhibitory rates of 51.6% and 62.2% at 0.8 micromol/L, respectively. The KDR expression at mRNA and protein levels was reduced by both the two asONs, in a dose-dependent manner. CONCLUSION: asONs screened by oligodeoxynucleotides library hybridization are well consistent with that chosen with oligonucleotide microarray. The combination of oligodeoxynucleotides library with oligonucleotide microarray is an effective approach of asONs screening. The asONs targeting KDR mRNA showed prominent anti-tumor activity on breast cancer MCF-7 cells.

Breast Neoplasms↗
PubMed1989

A quantitative 'in-situ' hybridization method using computer-assisted image analysis. Validation and measurement of atrial-natriuretic-factor mRNA in the rat heart.

We have validated a quantitative 'in-situ' hybridization method and computer-assisted image analysis of autoradiographs as a technique for measuring atrial-natriuretic-factor (ANF) mRNA in tissue sections of rat heart by: (i) producing radioactive standards to calibrate the autoradiograms and (ii) assessing: (a) specificity (through RNAase A background subtraction, comparison of ANF mRNA and non-ANF mRNA probe binding to sections, Northern analysis and section-thickness titration curves); (b) sensitivity (by calculating the limit of detection for ventricular levels of ANF mRNA); (c) precision [inter-assay CV (coefficient of variation) less than 10%; intra-assay CV 6-7%]; and (d) accuracy. We have found with this technique that deoxycortone and saline treatment of rats elevates ANF mRNA to a larger extent in the ventricles than in the atria and that, in neonatal-rat hearts, ANF mRNA is elevated in all cardiac chambers relative to adult levels.

Animals↗
PubMed2003

A hybrid numerical method to compute erythrocyte TMP in low-frequency electric fields.

This paper presents a coupling method of the finite element method and the boundary element method to compute the transmembrane potential (TMP) of an erythrocyte in a low-frequency electric field. We compute an in vitro erythrocyte's TMP induced by external electric fields by this hybrid method. It takes advantage of the homogeneous characteristics from both intracellular region and extracellular region. Moreover, we may use a fine three-dimensional (3-D) mesh around the thin membrane and avoid 3-D meshes in other regions. Numerical results of a spherical cell show that the hybrid method is accurate. The computed threshold of the applied electric field for membrane electric breakdown agrees well with those experimental results. Numerical results can also guide us to locate the maximum induced TMP on the erythrocyte membrane in various electric fields. Some further applications of the hybrid method are also discussed.

Algorithms↗
PubMed1995

Rapid physical mapping of the human trk protooncogene (NTRK1) to human chromosome 1q21-q22 by P1 clone selection, fluorescence in situ hybridization (FISH), and computer-assisted microscopy.

Physical mapping of small genomic DNA fragments or expressed sequences by in situ hybridization is typically limited by the size of the target DNA sequence. Isolation of large insert DNA clones from libraries containing the target DNA sequence facilitates physical mapping by fluorescence in situ hybridization and allows rapid assignment of genes to cytogenetic bands. Here, we demonstrate the scheme by mapping the human protooncogene trk (NTRK1), a tyrosine kinase receptor type I gene that has earlier been assigned to two different cytogenetic loci. Large DNA insert library screening was carried out by in vitro DNA amplification using oligonucleotide primers flanking exon 4 of trk. The scheme presented here can easily be generalized to map physically very small nonrepetitive genomic DNA fragments or incomplete cDNAs.

Bacteriophage P1↗
PubMed2004

Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-Notch protein signalling.

Hybrid automata are an eminently suitable modelling framework for biological protein regulatory networks, as the protein concentration dynamics inside each biological cell are modelled using linear differential equations; inputs activate or deactivate these continuous dynamics through discrete switches, which themselves are controlled by protein concentrations reaching given thresholds. This paper proposes an iterative refinement algorithm for computing discrete abstractions of a class of hybrid automata with piecewise affine continuous dynamics and forced discrete transitions, defined completely in terms of symbolic variables and parameters. Furthermore, these discrete abstractions are utilised to compute symbolic parametric backward reachable sets from the equilibria of the hybrid automata, that are guaranteed to be exact or conservative under-approximations. The algorithm is then implemented using MATLAB and QEPCAD, to compute reachable sets for the biologically observed equilibria of the multiple cell Delta-Notch protein signalling automaton with symbolic parameters. The results are analysed to show that novel, non-intuitive, and biologically interesting properties can be deduced from the reachability computation, thus demonstrating the utility of the algorithm.

Algorithms↗