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PubMed2006

Assessment of imaging studies used with radiosurgery: a volumetric algorithm and an estimation of its error. Technical note.

The Gamma Knife has played an increasingly important role in the neurosurgical treatment of patients. Intracranial lesions are not removed by radiosurgery. Rather, the goal of treatment is to induce tumor control. During planning, the creation of dose-volume histograms requires an accurate volumetric analysis of intracranial lesions selected for radiosurgery. In addition, an accurate follow-up imaging analysis of tumor volume is essential for assessing the results of radiosurgery. Nevertheless, sources of volumetric error and their expected magnitudes must be properly understood so that the operator may correctly interpret apparent changes in tumor volume. In this paper, the authors examine the often-neglected contributions of imaging geometry (principally image slice thickness and separation) to overall volumetric error. One of the fundamental sources of volumetric error is that resulting from the geometry of the acquisition protocol. The authors consider the image sampling geometry of tomographic modalities and its contribution to volumetric error through a simulation framework in which a synthetic digital tumor is taken as the primary model. Because the exact volume of the digital phantom can be computed, the volume estimates derived from tomographic "slicing" can be directly compared precisely and independently from other error sources. In addition to providing empirical bounds on volumetric error, this approach provides a tool for guiding the specification of imaging protocols when a specific volumetric accuracy, or volume change sensitivity, for particular structures is sought a priori. Using computational geometry techniques, the volumetric error associated with image acquisition geometry was shown to be dependent on the number of slices through the region of interest (ROI) and the lesion volume. With a minimum of five slices through the ROI, the volume of a compact lesion could be calculated accurately with less than 10% error, which was the predetermined goal for the purposes of computing accurate dose-volume histograms and determining follow-up changes in tumor volume. Accurate dose-volume histograms can be generated and follow-up volumetric assessments performed, assuming accurate lesion delineation, when the object is visualized on at least five axial slices. Volumetric analysis based on fewer than five slices yields unacceptably larger errors (that is, > 10%). These volumetric findings are particularly relevant for radiosurgical treatment planning and follow-up analysis. Through the application of this volumetric methodology and a greater understanding of the error associated with it, neurosurgeons can better perform radiosurgery and assess its outcome.

Algorithms↗
PubMed1994

Refined molecular structure of pig pancreatic alpha-amylase at 2.1 A resolution.

The structure of pig pancreatic alpha-amylase has been determined by X-ray diffraction analysis using multiple isomorphous replacement in a crystal of space group P2(1)2(1)2(1) (a = 70.6 A, b = 114.8 A, c = 118.8 A) containing nearly 75% solvent. The structure was refined by simulated annealing and Powell minimization, as monitored by 2Fo-Fc difference Fourier syntheses, to a conventional R of 0.168 at 2.1 A resolution. The final model consists of all 496 amino acid residues, a chloride and a calcium ion, 145 water molecules and an endogenous disaccharide molecule that contiguously links protein molecules related by the 2(1) crystallographic operator along x. The protein is composed of a large domain (amino acid residues 1 to 403) featuring a central alpha ta-barrel of eight parallel strands and connecting helices with a prominent excursion between strand beta 3 and helix alpha 3 (amino acid residues 100 to 168). The final 93 amino acid residues at the carboxyl terminus form a second small domain consisting of a compact Greek key beta-barrel. The domains are tightly associated through hydrophobic interfaces. The beta 3/alpha 3 excursion and portions of the central alpha/beta-barrel provide four protein ligands to the tightly bound Ca ion; three water molecules complete the coordination. The Cl- ion is bound within one end of the alpha/beta-barrel by two arginine residues in a manner suggesting a plausible mechanism for its allosteric activation of the enzyme. A crystalline complex of the pancreatic alpha-amylase with alpha-cyclodextrin, a cyclic substrate analog of six glucose residues, reveals, in difference Fourier maps, three unique binding sites. One of the alpha-cyclodextrin sites is near the center of the long polysaccharide binding cleft that traverses one end of the alpha/beta-barrel, another is at the extreme of this cleft. By symmetry this can also be considered as two half sites located at the extremes of the active site cleft. This latter alpha-cyclodextrin displaces the endogenous disaccharide when it binds and, along with the first sugar ring, delineates the extended starch binding site. The third alpha-cyclodextrin binds at an "accessory site" near the edge of the protein and is quite distant from the polysaccharide binding cleft. Its presence explains the multivalency of alpha-amylase binding to dextrins in solution. The extended active site cleft is formed by large, sweeping, connecting loops at one end of the alpha/beta-barrel. These include three sequence segments that are highly conserved among alpha-amylases.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2000

On a classical limit for electronic degrees of freedom that satisfies the Pauli exclusion principle.

Fermions need to satisfy the Pauli exclusion principle: no two can be in the same state. This restriction is most compactly expressed in a second quantization formalism by the requirement that the creation and annihilation operators of the electrons satisfy anticommutation relations. The usual classical limit of quantum mechanics corresponds to creation and annihilation operators that satisfy commutation relations, as for a harmonic oscillator. We discuss a simple classical limit for Fermions. This limit is shown to correspond to an anharmonic oscillator, with just one bound excited state. The vibrational quantum number of this anharmonic oscillator, which is therefore limited to the range 0 to 1, is the classical analog of the quantum mechanical occupancy. This interpretation is also true for Bosons, except that they correspond to a harmonic oscillator so that the occupancy is from 0 up. The formalism is intended to be useful for simulating the behavior of highly correlated Fermionic systems, so the extension to many electron states is also discussed.

Journal Article↗
PubMed2004

A molecular mechanism for autoinhibition of the tandem SH3 domains of p47phox, the regulatory subunit of the phagocyte NADPH oxidase.

The phagocyte NADPH oxidase is a multisubunit enzyme responsible for the production of reactive oxygen species. p47(phox) is a cytosolic component of the NADPH oxidase and plays an important role in the assembly of the activated complex. The structural determination of the tandem SH3 domains of p47(phox) is crucial for elucidation of the molecular mechanism of the activation of p47(phox). We determined the X-ray crystal structure of the tandem SH3 domains with the polybasic/autoinhibitory region (PBR/AIR) of p47(phox). The GAPPR sequence involved in PBR/AIR forms a left-handed polyproline type-II helix (PPII) and interacts with the conserved SH3 binding surfaces of the SH3 domains simultaneously. These SH3 domains are related by a 2-fold pseudosymmetry axis at the centre of the binding groove and interact with the single PPII helix formed by the GAPPR sequence with opposite orientation. In addition, a number of intra-molecular interactions among the SH3 domains, PBR/AIR and the linker tightly hold the architecture of the tandem SH3 domains into the compact structure and stabilize the autoinhibited form synergistically. Phosphorylation of the serine residues in PBR/AIR could destabilize and successively release the intra-molecular interactions. Thus, the overall structure could be rearranged from the autoinhibitory conformation to the active conformation and the PPII ligand binding surfaces on the SH3 domains are now unmasked, which enables their interaction with the target sequence in p22(phox).

Amino Acid Sequence↗
PubMed2005

Comparison of ultrastructural cytotoxic effects of carbon and carbon/iron particulates on human monocyte-derived macrophages.

In this study, we tested the hypothesis that the presence of iron in carbon particulates enhances ultrastructural perturbation in human monocyte-derived macrophages (MDMs) after phagocytosis. We used 1-microm synthetic carbon-based particulates, designed to simulate environmental particulates of mass median aerodynamic diameter < or = 2.5 microm (PM2.5). Cultures of human MDMs or T-lymphocytes (as a nonphagocytic control) were exposed to carbon or carbon/iron particulates for various time periods and examined by transmission electron microscopy for ultrastructural changes. T-cells failed to internalize either of the particulates and showed no organelle or nuclear changes. Conversely, MDMs avidly phagocytized the particulates. MDMs treated with C particulates exhibited morphologic evidence of macrophage activation but no evidence of lysis of organelles. In contrast, MDMs treated with C/Fe particulates exhibited coalescence of particulate-containing lysosomes. This phenomenon was not observed in the case of C particulates. By 24 hr there was a tendency of the C/Fe particulates to agglomerate into loose or compact clusters. Surrounding the compact C/Fe agglomerates was a uniform zone of nearly total organelle lysis. The lytic changes diminished in proportion to the distance from the agglomerate. In such cells, the nucleus showed loss of chromatin. Although C particles induced no detectable oxidative burst on treated MDMs, C/Fe particles induced a nearly 5-fold increase in the extracellular oxidative burst by treated MDMs compared with untreated controls. Iron bound to C particles catalyzed the decomposition of hydrogen peroxide to generate hydroxyl radicals. Results of these studies suggest that, among particulates of similar size, biologic activity can vary profoundly as a function of particulate physicochemical properties.

Air Pollutants↗
PubMed2001

Investigations of ash topography/morphology and their relationship with heavy metals leachability.

The leachability of heavy metals such as chromium (Cr), lead (Pb) and cadmium (Cd) from the ash material obtained from waste combustion was studied. The effects of ash surface topography and morphology on the leachability of these elements were examined using atomic force microscopy (AFM) and scanning electron microscopy (SEM). The AFM (scan size 10 x 10 microns) and SEM images of the simulated ash pellet obtained at various operating temperatures (1000, 1400 and 1500 degrees C) showed significant microstructural and topographical changes. Ash pellets treated at 1000 degrees C contain porous and non-continuous surface. On the other hand, the ash pellet obtained at higher temperature (1500 degrees C) was found to contain a smooth, continuous and non-porous surface. The AFM height profile studies indicated that the top surface variation of the ash pellet at 1000, 1400 and 1500 degrees C were found to be -40.0 to 25.5, -3.7 to 4.7 and -0.10 to 0.66 nm respectively. The SEM analyses also confirmed the presence of smooth, non-porous outer surface of ash formed at 1500 degrees C. In addition, it also showed the presence of compact and rigid interior for the same ash pellet. The leachability of the heavy metals was determined using standard toxicity characteristic leaching procedure (TCLP) test and the samples were analysed using atomic absorption spectroscopy. The results showed that the TCLP leaching ratios of the heavy metals were Cr = 0.30, Pb = 0.05 and Cd = 0.09 at 1000 degrees C. However, the ash obtained at 1400 degrees C showed negligible heavy metals leaching ratio while at 1500 degrees C no leachability was detected (TCLP concentration dropped to nondetectable levels). The use of high temperature treatment enabled the immobilization of heavy metals in the ash preventing their leaching. Such ash can be considered as a non-hazardous material for reuse or safe disposal.

Environmental Pollutants↗
PubMed1992

The compact domain conformation of human Glu-plasminogen in solution.

A complete understanding of the accelerating mechanisms of plasminogen activation and fibrinolysis necessarily requires structural information on the conformational forms of plasminogen. Given the absence of high-resolution structural data on plasminogen the use of lower resolution approaches has been adopted. Two such approaches have previously indicated a compact conformation of Glu-plasminogen (Tranqui, L., Prandini, M., and Chapel, A. (1979) Biol. Cellulaire, 34, 39-42; Bányai, L. and Patthy, L. (1985) Biochim. Biophys. Acta, 832, 224-227) whereas a third has suggested a fairly extended conformation (Mangel, W., Lin, B. and Ramakrishnan, V. (1990) Science, 248, 69-73). Native Glu-plasminogen has been investigated using small-angle X-ray scattering (SAXS) experiments. It is concluded that this molecule in solution is compact (radius of gyration, RG 3.05 +/- 0.02 nm and maximum intramolecular distance, Im 9.1 +/- 0.3 nm) and that the data are consistent with the right-handed spiral structure observed using electron microscopy by Tranqui et al. (1979). A spiral structure of native plasminogen would have important implications for the conformational response of plasminogen to fibrin and concomitant stimulation of plasminogen activation.

Computer Simulation↗
PubMed2006

Phosphate closes the solution structure of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Mycobacterium tuberculosis.

The 5-enolpyruvylshikimate-3-phosphate synthase catalyses the sixth step of the shikimate pathway that is responsible for synthesizing aromatic compounds and is absent in mammals, which makes it a potential target for drugs development against microbial diseases. Here, we report the phosphate binding effects at the structure of the 5-enolpyruvylshikimate-3-phosphate synthase from Mycobacterium tuberculosis. This enzyme is formed by two similar domains that close on each other induced by ligand binding, showing the occurrence of a large conformation change. We have monitored the phosphate binding effects using analytical ultracentrifugation, small angle X-ray scattering and, circular dichroism techniques. The low resolution results showed that the enzyme in the presence of phosphate clearly presented a more compact structure. Thermal-induced unfolding experiments followed by circular dichroism suggested that phosphate rigidified the enzyme. Summarizing, these data suggested that the phosphate itself is able to induce conformational change resulting in the closure movement in the M. tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗
PubMed2002

First-principles study of aqueous hydroxide solutions.

Car-Parrinello molecular dynamics simulations have been carried out for aqueous NaOH and KOH solutions under ambient conditions over a wide range of concentrations. From these simulations, we have observed a continuous change of the water structure with added hydroxide, characterized by a significant shift of the second peak of the OO radial distribution functions to shorter distances. At the highest concentration investigated, the normal tetrahedral coordination of pure water is completely missing, a result that is consistent with a recent neutron diffraction experiment. The added hydroxide also gives rise to some unique spectroscopic features, including a "free" O-H stretch, a broadening of the normal water OH stretching band, and a large blue shift of both the librational band and the low-frequency translation. These results are in good agreement with the experimental data. Finally, it was demonstrated that the structural and dynamical behavior is inextricably linked to the formation of compact hydroxide-water complexes.

Journal Article↗
PubMed1989

Refolding of denatured ribonuclease observed by size exclusion chromatography.

The unfolding and refolding of pancreatic ribonuclease have been observed by absorbance, fluorescence, and size exclusion chromatographic measurements in solutions of guanidinium chloride continuously maintained at pH 6.0 and 4 degrees C. The spectral measurements were fitted with a minimal number of kinetic phases while the chromatographic measurements were simulated from an explicit mechanism. All of the measurements are consistent with a minimal mechanism involving seven components. The folded components include the native protein and two transiently stable intermediates each having the same hydrodynamic volume. The intermediate having all native peptide isomers has an unfolding midpoint in 3.8 M denaturant while the intermediate having one nonnative peptide isomer has an unfolding midpoint in 1.3 M denaturant. The unfolded protein is distributed among four components having the same hydrodynamic volume but differing peptide isomers. At equilibrium, 10% of the denatured protein has all native isomers, 60% has one nonnative isomer, 5% has a different nonnative isomer, and 25% has both nonnative isomers. In low denaturant concentrations, the dominant component with one nonnative isomer can refold to transiently populate the compact intermediate with the same nonnative isomer.

Animals↗
PubMed2001

Effect of genotype, sex and rearing temperature on carcase and meat quality of guinea fowl.

1. The aim of our study was to analyse the effect of genotype (label and standard), sex and rearing temperature (simulating daily outdoor in the summer or winter) on the carcase and meat quality of guinea fowl. Using 20 animals per treatment, slaughtered at 96 d of age we measured the breast angle and the thickness of the skin on the wing membrane. Carcases were weighed and cut into parts according to a standardised procedure to determine the percentages of abdominal fat, breasts, wings and thighs with shanks. 2. At slaughter, standard guinea fowl were heavier than label guinea fowl and for both genotypes, the females were heavier than the males (+5.6%). The mean value of breast angle was 85 degrees. This value was significantly higher for the standard guinea fowls and for the females of both genotypes compared with males. Thus, female carcases, particularly standard females, were more compact. The skin was thicker for the standard guinea fowls (0.84 mm vs 0.77 mm) which could be due to more subcutaneous fat. 3. Carcase yield was higher for the males (68.7% vs 68.2%). The percentage of abdominal fat was higher for the standard guinea fowls (2.8% vs 2.4%) and for the females of both genotypes compared with males. The label guinea fowls had higher yields of breasts and thighs with shanks. For both lines, the breast and thigh meat of females was judged more tender and less stringy. 4. Low rearing temperature decreased growth performance but had no significant effect on carcase quality.

Abdomen↗
PubMed2004

Search for lesions in mammograms: statistical characterization of observer responses.

We investigate human performance for visually detecting simulated microcalcifications and tumors embedded in x-ray mammograms as a function of signal contrast and the number of possible signal locations. Our results show that performance degradation with an increasing number of locations is well approximated by signal detection theory (SDT) with the usual Gaussian assumption. However, more stringent statistical analysis finds a departure from Gaussian assumptions for the detection of microcalcifications. We investigated whether these departures from the SDT Gaussian model could be accounted for by an increase in human internal response correlations arising from the image-pixel correlations present in 1/f spectrum backgrounds and/or observer internal response distributions that departed from the Gaussian assumption. Results were consistent with a departure from the Gaussian response distributions and suggested that the human observer internal responses were more compact than the Gaussian distribution. Finally, we conducted a free search experiment where the signal could appear anywhere within the image. Results show that human performance in a multiple-alternative forced-choice experiment can be used to predict performance in the clinically realistic free search experiment when the investigator takes into account the search area and the observers' inherent spatial imprecision to localize the targets.

Female↗
PubMed2004

Computational fluid dynamics modeling of the paddle dissolution apparatus: agitation rate, mixing patterns, and fluid velocities.

The purpose of this research was to further investigate the hydrodynamics of the United States Pharmacopeia (USP) paddle dissolution apparatus using a previously generated computational fluid dynamics (CFD) model. The influence of paddle rotational speed on the hydrodynamics in the dissolution vessel was simulated. The maximum velocity magnitude for axial and tangential velocities at different locations in the vessel was found to increase linearly with the paddle rotational speed. Path-lines of fluid mixing, which were examined from a central region at the base of the vessel, did not reveal a region of poor mixing between the upper cylindrical and lower hemispherical volumes, as previously speculated. Considerable differences in the resulting flow patterns were observed for paddle rotational speeds between 25 and 150 rpm. The approximate time required to achieve complete mixing varied between 2 to 5 seconds at 150 rpm and 40 to 60 seconds at 25 rpm, although complete mixing was achievable for each speed examined. An analysis of CFD-generated velocities above the top surface of a cylindrical compact positioned at the base of the vessel, below the center of the rotating paddle, revealed that the fluid in this region was undergoing solid body rotation. An examination of the velocity boundary layers adjacent to the curved surface of the compact revealed large peaks in the shear rates for a region within ~3 mm from the base of the compact, consistent with a "grooving" effect, which had been previously seen on the surface of compacts following dissolution, associated with a higher dissolution rate in this region.

Models, Chemical↗
PubMed2006

Relativistic correlating basis sets for lanthanide atoms from Ce to Lu.

Contracted Gaussian-type function (CGTF) sets for the description of the 4f subshell correlation and of the 6s and 5d subshell correlation are developed for lanthanide atoms from Ce to Yb. Also prepared are basis sets for the 5d orbitals, which are vacant in the ground states of most lanthanide atoms but are essential in molecular environments. In addition, correlating CGTF sets for the 4f subshell correlation are supplemented for the Lu atom. A segmented contraction scheme is employed for their compactness and efficiency. Contraction coefficients and exponents are determined by minimizing the deviation from accurate natural orbitals generated from configuration interaction calculations that include relativistic effects through the third-order Douglas-Kroll approximation. All-electron and model core potential calculations with the present correlating sets are performed on the ground state of the diatomic CeO molecule. The calculated spectroscopic constants are in good agreement with experimental values.

Algorithms↗
PubMed2001

Periodic and quasi-periodic behavior in resource-dependent age structured population models.

To describe the dynamics of a resource-dependent age structured population, a general non-linear Leslie type model is derived. The dependence on the resources is introduced through the death rates of the reproductive age classes. The conditions assumed in the derivation of the model are regularity and plausible limiting behaviors of the functions in the model. It is shown that the model dynamics restricted to its omega-limit sets is a diffeomorphism of a compact set, and the period-1 fixed points of the model are structurally stable. The loss of stability of the non-zero steady state occurs by a discrete Hopf bifurcation. Under general conditions, and after the loss of stability of the structurally stable steady states, the time evolution of population numbers is periodic or quasi-periodic. Numerical analysis with prototype functions has been performed, and the conditions leading to chaotic behavior in time are discussed.

Age Distribution↗
PubMed2004

Small angle x-ray scattering from lipid-bound myelin basic protein in solution.

The structure of myelin basic protein (MBP), purified from the myelin sheath in both lipid-free (LF-MBP) and lipid-bound (LB-MBP) forms, was investigated in solution by small angle x-ray scattering. The water-soluble LF-MBP, extracted at pH < 3.0 from defatted brain, is the classical preparation of MBP, commonly regarded as an intrinsically unfolded protein. LB-MBP is a lipoprotein-detergent complex extracted from myelin with its native lipidic environment at pH > 7.0. Under all conditions, the scattering from the two protein forms was different, indicating different molecular shapes. For the LB-MBP, well-defined scattering curves were obtained, suggesting that the protein had a unique, compact (but not globular) structure. Furthermore, these data were compatible with earlier results from molecular modeling calculations on the MBP structure which have been refined by us. In contrast, the LF-MBP data were in accordance with the expected open-coil conformation. The results represent the first direct structural information from x-ray scattering measurements on MBP in its native lipidic environment in solution.

Computer Simulation↗
PubMed2003

A model for frequency dependence of conductivities of the live human skull.

A mathematical model (sigma(omega) approximately equal to A omega alpha, where, sigma is identical with conductivity, omega = 2 pi f is identical with applied frequency (Hz), A (amplitude) and alpha (unit less) is identical with search parameters) was used to fit the frequency dependence of electrical conductivities of compact, spongiosum, and bulk layers of the live and, subsequently, dead human skull samples. The results indicate that the fit of this model to the experimental data is excellent. The ranges of values of A and alpha were, spongiform (12.0-36.5, 0.0083-0.0549), the top compact (5.02-7.76, -0.137-0.0144), the lower compact (2.31-10.6, 0.0267-0.0452), and the bulk (7.46-10.6, 0.0133-0.0239). The respective values A and alpha for the respective layers of the dead skull samples were (40.1-89.7, -0.0017-0.0287), (5.53-14.5, -0.0296 - -0.0061), (4.58-15.9, -0.0226-0.0268), and (12.7-25.3, -0.0158-0.0132).

Algorithms↗
PubMed2005

Unusual compactness of a polyproline type II structure.

Polyproline type II (PPII) helix has emerged recently as the dominant paradigm for describing the conformation of unfolded polypeptides. However, most experimental observables used to characterize unfolded proteins typically provide only short-range, sequence-local structural information that is both time- and ensemble-averaged, giving limited detail about the long-range structure of the chain. Here, we report a study of a long-range property: the radius of gyration of an alanine-based peptide, Ace-(diaminobutyric acid)2-(Ala)7-(ornithine)2-NH2. This molecule has previously been studied as a model for the unfolded state of proteins under folding conditions and is believed to adopt a PPII fold based on short-range techniques such as NMR and CD. By using synchrotron radiation and small-angle x-ray scattering, we have determined the radius of gyration of this peptide to be 7.4 +/- 0.5 angstroms, which is significantly less than the value expected from an ideal PPII helix in solution (13.1 angstroms). To further study this contradiction, we have used molecular dynamics simulations using six variants of the AMBER force field and the GROMOS 53A6 force field. However, in all cases, the simulated ensembles underestimate the PPII content while overestimating the experimental radius of gyration. The conformational model that we propose, based on our small angle x-ray scattering results and what is known about this molecule from before, is that of a very flexible, fluctuating structure that on the level of individual residues explores a wide basin around the ideal PPII geometry but is never, or only rarely, in the ideal extended PPII helical conformation.

Circular Dichroism↗