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Biomedical subjects

R P Millane

Publications and source records attributed to R P Millane.

16 recordsLinked to original sources
PubMed2003

Fluorescence optical diffusion tomography.

A nonlinear, Bayesian optimization scheme is presented for reconstructing fluorescent yield and lifetime, the absorption coefficient, and the diffusion coefficient in turbid media, such as biological tissue. The method utilizes measurements at both the excitation and the emission wavelengths to reconstruct all unknown parameters. The effectiveness of the reconstruction algorithm is demonstrated by simulation and by application to experimental data from a tissue phantom containing the fluorescent agent Indocyanine Green.

Bayes Theorem↗
PubMed2003

Efficient frequency-domain sample selection for recovering limited-support images.

An image whose region of support is smaller than its bounding rectangle can, in principle, be reconstructed from a subset of the Nyquist samples. However, determining such a sampling set that gives a stable reconstruction is a difficult and computationally intensive problem. An algorithm is developed for determining periodic nonuniform sampling patterns that is orders of magnitude faster than existing algorithms. The speedup is achieved by using a sequential selection algorithm and heuristic metrics for the quality of sampling sets that are fast to compute, as opposed to the more rigorous linear algebraic metrics that have been used previously. Simulations show that the sampling sets determined using the new algorithm give image reconstructions that are of accuracy comparable with those determined by other slower algorithms.

Journal Article↗
PubMed2003

On apparent counterexamples to phase dominance.

Phase dominance refers to the observation that the phase of the Fourier transform of an image carries more information than does the amplitude. We show that apparent counterexamples to phase dominance are not in fact counterexamples since the phase functions used are not independent of the true phase function. Phase dominance appears to be a general phenomenon.

Journal Article↗
PubMed2002

Source-detector calibration in three-dimensional Bayesian optical diffusion tomography.

Optical diffusion tomography is a method for reconstructing three-dimensional optical properties from light that passes through a highly scattering medium. Computing reconstructions from such data requires the solution of a nonlinear inverse problem. The situation is further complicated by the fact that while reconstruction algorithms typically assume exact knowledge of the optical source and detector coupling coefficients, these coupling coefficients are generally not available in practical measurement systems. A new method for estimating these unknown coupling coefficients in the three-dimensional reconstruction process is described. The joint problem of coefficient estimation and three-dimensional reconstruction is formulated in a Bayesian framework, and the resulting estimates are computed by using a variation of iterative coordinate descent optimization that is adapted for this problem. Simulations show that this approach is an accurate and efficient method for simultaneous reconstruction of absorption and diffusion coefficients as well as the coupling coefficients. A simple experimental result validates the approach.

Bayes Theorem↗
PubMed2001

Diffraction by the ideal paracrystal.

A detailed analysis is made of the statistics and diffraction by a general, finite, two-dimensional ideal paracrystal. The statistics of the diagonal chain through the ideal paracrystal are derived, and the special cases of square and hexagonal ideal paracrystals are considered. Expressions for the diffraction are derived and characteristics of diffraction patterns are discussed in terms of the different parameters of the model for square and hexagonal ideal paracrystals. The variation of peak widths with scattering angle along different directions in reciprocal space is examined.

Journal Article↗
PubMed2000

The crystallite size-disorder relationship based on the spiral paracrystal.

A simple physical model of the relationship between crystallite size and disorder for paracrystalline materials is presented, based on the spiral paracrystal and distortion of the lattice cells. Simulations show that the model leads to relationships similar to the alpha* rule. Average crystallite sizes predicted by the model are in agreement with experimental data and also allow crystallite-size distributions to be proposed. The model provides a more satisfactory and complete explanation of this relationship than do current descriptions.

Carbohydrate Conformation↗
PubMed1991

Ordered water in hydrated solid-state polysaccharide systems.

Water molecules within a monolayer or so of macromolecular surfaces are often located in well-defined positions and have restricted mobility. These ordered water molecules play a role in stabilizing polysaccharide ordered structures and intermolecular interactions that are the basis of the rheological properties utilized in food systems. X-ray fiber diffraction can be used to determine the three-dimensional structures of polysaccharides in solid, but well-hydrated, polycrystalline fibers. In favorable cases, difference Fourier synthesis can be used to locate ordered water molecules in these systems, allowing one to visualize their functionally important interactions. These studies provide relevant evidence regarding water interactions in more hydrated systems and in solution. The functionality of ordered water in some polysaccharides used in food systems, as well as in some connective tissue glycosaminoglycans where the ordered water has been defined in considerable detail, as determined by fiber diffraction, is described in this chapter. These structures allow one to derive some general features of the role of ordered water in such systems.

Carbohydrate Sequence↗
PubMed1991

Effects of disorder on fibre diffraction patterns.

Diffraction patterns from oriented polycrystalline specimens of fibrous polymers sometimes contain features indicating that the constituent microcrystallites are disordered. Such disorder affects the relationship between the crystal structure and the diffracted intensities. Therefore, the effects of disorder must be considered when determining structures from fibre diffraction data. Theory is developed here that describes the intensities diffracted by disordered polycrystalline fibres, and is used to calculate diffraction patterns from stimulated specimens with various kinds of disorder. The results show how Bragg and continuous diffraction are distributed on such diffraction patterns, and implications for structure determination are discussed.

Crystallization↗
PubMed1991

A model of atrioventricular nodal conduction.

A model of cardiac impulse propagation through the atrioventricular node is described. The model is based on a synthesis of various experimentally determined characteristics of atrioventricular nodal conduction. The model can be set up to mimic a particular patient's atrioventricular node, by using data collected during routine electrophysiological studies. It can also be used as a component in a larger model of the cardiac conduction system, to simulate cardiac arrhythmias.

Arrhythmias, Cardiac↗
PubMed1989

A re-examination of the crystal structure of A-DNA using fiber diffraction data.

Classical A-DNA helices with h = 0.25 nm may represent the greatest mass per unit length attainable by polynucleotide duplexes. The X-ray diffraction pattern from polycrystalline and well-oriented fibers of calf thymus DNA in its A-form has been carefully re-examined. Indexing on the basis of a C-face-centered monoclinic unit cell of dimensions a = 2.170 nm, b = 3.990 nm, c = 2.803 nm and beta = 96.82 degrees is superior to alternatives that have been proposed. Two right-handed. Watson-Crick base-paired, helical DNA chains with 2 X 11 nucleotides per 2.803 nm pitch, each carrying C3'-endo furanose rings, pass through the unit cell. The crystallography requires the two chains in the duplex to be antiparallel and conformationally identical but the 11 nucleotides in each pitch may be distinct. However, a secondary structure with a mononucleotide asymmetric unit provides as good an X-ray agreement as one with 11 distinct nucleotides. This relative lack of variability is quite different from what is observed in fibrous B-DNAs.

Animals↗
PubMed1987

Structure of the alpha-form of poly[d(A)].poly[d(T)] and related polynucleotide duplexes.

The alpha-form of poly[d(A)].poly[d(T)], observed in fibers at high (greater than 80%) relative humidity, is a 10-fold double-helical structure of pitch 3.2 nm. This new X-ray analysis shows that the two strands of the double helix are of the same kind conformationally and both B-like in containing C-2'-endo-puckered deoxyribose rings. Nevertheless, the two strands are different enough for the overall morphology of the duplex to resemble that of the heteromerous model for the drier (beta) form of poly[d(A)].poly[d(T)] in which one strand has C-2'-endo rings and the other C-3'-endo. Since the orientations of the bases in poly[d(A)].poly[d(T)] are persistently different from those of classical B-DNA it is likely that there will be local bending (about 10 degrees) at the junctions between general sequence tracts and the oligo[d(A)].oligo[d(T)] tracts that occur in some native DNAs. The conclusions about the structure of alpha-poly[d(A)].poly[d(T)] are reinforced by independent analyses of similar X-ray diffraction patterns from poly[d(A)].poly[d(U)] and poly[d(A-I)].poly[d(C-T)].

Models, Molecular↗
PubMed1986

DNA-RNA hybrid secondary structures.

DNA-RNA and DNA-DNA duplexes are even more polymorphic than observed previously. DNA-RNA hybrids can have secondary structures like A-DNA or A-RNA, but double helices of the synthetic DNA-RNA hybrids poly(dA) X poly(rU) and poly(dI) X poly(rC), respectively, form 11-fold and 10-fold double-helical structures in which the two chains have quite different conformations. Extensive X-ray fiber diffraction analyses show that in both structures the DNA chains have C-2'-endo-puckered furanose rings, while the anti-parallel RNA chains have C-3'-endo-puckered rings. The bidirectional properties of such duplexes may be important in the transfer of biological information from nucleic acids.

Base Composition↗
PubMed1984

Structure of a pleiomeric form of poly d(AT):poly d(AT).

A chemically simple polynucleotide duplex, poly d(AT):poly d(AT), has been trapped in a fibrous form with a complex helical secondary structure with a large (7.4 nm) axial repeat 24 nucleotides long. The motif which is repeated by the symmetry elements is a hexanucleotide in which two residues (both TpA) have the less common gauche minus conformation at C3'-O3' and consequently distinctive phosphate orientations. This reinforces earlier conclusions that PypPu nucleotides tend to have different shapes from PupPy nucleotides and that DNA surfaces may signal what base sequences lie beneath them. The morphological differences between this pleiomeric DNA polymer and closely-related, but more symmetrical allomorphs are just as great as those observed in short DNA fragments in crystals.

Base Sequence↗
PubMed1983

Chondroitin 4-sulfate: comparison of the structures of the potassium and sodium salts.

Analysis of the X-ray diffraction pattern from an oriented, polycrystalline fiber of a potassium chondroitin 4-sulfate proteoglycan shows that the polysaccharide chains have a left-handed 3-fold helical secondary structure stabilized by intra- and intermolecular hydrogen bonds. Two antiparallel chains pass through each trigonal unit cell, which has dimensions a = b = 1.385 nm, c = 2.776 nm and space group symmetry P3(2)21. The cations and water molecules in the crystals are not all periodic and only one potassium ion and four water molecules per disaccharide were located by difference Fourier methods. Sodium chondroitin 4-sulfate forms an analogous structure with polyanions of similar geometry. However, the packing arrangements in the two salts are quite different, presumably because of the different co-ordination preference of K+ and Na+. Thus the relatively small differences between these two cations are greatly amplified by the idiosyncratic polymer networks they promote.

Animals↗
PubMed1981

Stereochemical details of the side-by-side model for DNA.

Coordinates are presented for a refined model of the side-by-side (SBS) structure for the in vivo B-form of duplex DNA. Bond lengths and bond angles are within 0.025A and 2.0 degrees of standard values and there are no non-bonded intramolecular contacts shorter than 2.75 A. These and other details of the refined model indicate that the SBS proposal is stereochemically viable.

Base Composition↗