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PubMed2006

On-line content uniformity determination of tablets using low-resolution Raman spectroscopy.

Analytical techniques for rapid and nondestructive content uniformity determination of pharmaceutical solid dosage forms have been studied for several years in an effort to replace the traditional wet chemistry procedures, which are labor intensive and time consuming. Both Raman spectroscopy and near-infrared spectroscopy have been used for this purpose, and predictability errors are approaching those of the traditional techniques. In this study, a low-resolution Raman spectrometer was utilized to demonstrate the feasibility of both rapid at-line and on-line determination of tablet content uniformity. Additionally, sampling statistics were reviewed in an effort to determine how many tablets should be assayed for specific batch sizes. A good correlation was observed between assay values determined by high-performance liquid chromatography and Raman analysis. Due to rapid acquisition times for the Raman data, it was possible to analyze far more samples than with wet chemistry methods, leading to a better statistical description of variation within the batch. For at-line experiments, the sampling volume was increased by rotating the laser beam during the acquisition period. For the on-line experiments, the sampling volume was increased by sampling from a stream of tablets moving underneath the Raman probe on a conveyor system. Finally, an approach is proposed for monitoring content uniformity immediately following the compaction process. In conclusion, Raman spectroscopy has potential as a rapid, nondestructive technique for at- or on-line determination of tablet content uniformity.

Algorithms↗

PubMed1999

Solution structure by NMR of circulin A: a macrocyclic knotted peptide having anti-HIV activity.

The three-dimensional solution structure of circulin A, a 30 residue polypeptide from the African plant Chassalia parvifolia, has been determined using two-dimensional 1H-NMR spectroscopy. Circulin A was originally identified based upon its inhibition of the cytopathic effects and replication of the human immunodeficiency virus. Structural restraints consisting of 369 interproton distances inferred from nuclear Overhauser effects, and 21 backbone dihedral and nine chi1 angle restraints from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimisation in the program X-PLOR. The final set of 12 structures had mean pairwise rms differences over the whole molecule of 0.91 A for the backbone atom, and 1.68 A for all heavy atoms. For the well-defined region encompassing residues 2-12 and 18-27, the corresponding values were 0.71 and 1.66 A, respectively. Circulin A adopts a compact structure consisting of beta-turns and a distorted segment of triple-stranded beta-sheet. Fluorescence spectroscopy provided additional evidence for a solvent-exposed Trp residue. The molecule is stabilised by three disulfide bonds, two of which form an embedded loop completed by the backbone fragments connecting the cysteine residues. A third disulfide bond threads through the centre of this loop to form a "cystine-knot" motif. This motif is present in a range of other biologically active proteins, including omega-contoxin GVIA and Cucurbita maxima trypsin inhibitor. Circulin A belongs to a novel class of macrocyclic peptides which have been isolated from plants in the Rubiaceae family. The global fold of circulin A is similar to kalata B1, the only member of this class for which a structure has previously been determined.

Amino Acid Sequence↗

PubMed2001

Zipping and collapse of diblock copolymers.

Using exact enumeration methods and Monte Carlo simulations, we study the phase diagram relative to the conformational transitions of a diblock copolymer in two dimensions. The polymer is made of two homogeneous strands of monomers of different species which are joined to each other at one end. We find that, depending on the values of the energy parameters in the model, there is either a first order collapse from a swollen phase to a compact phase of spiral type, or a continuous transition to an intermediate zipped phase followed by a first order collapse at lower temperatures. Critical exponents of the zipping transition are computed, and their exact values are conjectured on the basis of a mapping onto percolation geometry, thanks to recent results on path-crossing probabilities.

Journal Article↗

PubMed2000

Phenomenological glass model for vibratory granular compaction

A model for weakly excited granular media is derived by combining the free volume argument of Nowak et al. [Phys. Rev. E 57, 1971 (1998)] and the phenomenological model for supercooled liquids of Adam and Gibbs [J. Chem. Phys. 43, 139 (1965)]. This is made possible by relating the granular excitation parameter Gamma, defined as the peak acceleration of the driving pulse scaled by gravity, to a temperaturelike parameter eta(Gamma). The resulting master equation is formally identical to that of Bouchaud's trap model for glasses [J. Phys. I 2, 1705 (1992)]. Analytic and simulation results are shown to compare favorably with a range of known experimental behavior. This includes the logarithmic densification and power spectrum of fluctuations under constant eta, the annealing curve when eta is varied cyclically in time, and memory effects observed for a discontinuous shift in eta. Finally, we discuss the physical interpretation of the model parameters and suggest further experiments for this class of systems.

Journal Article↗

PubMed2005

The effect of membrane potential on the development of chemical osmotic pressure in compacted clay.

When clay soils are subjected to salt concentration gradients, various interrelated processes come into play. It is known that chemical osmosis induces a water flow and that a membrane potential difference develops that counteracts diffusive flow of solutes and osmotic flow of water. In this paper, we present the results of experiments on the influence of membrane potential on chemical osmotic flow and diffusion of solutes and we show how we are able to derive the membrane potential value from theory. Moreover, the simultaneous development of water pressure, salt concentration and membrane potential difference are simulated using a model for combined chemico-electroosmosis in clays. A new method for short-circuiting the clay sample is employed to assess the influence of electrical effects on flow of water and transport of solutes.

Journal Article↗

PubMed2003

MD simulations of anthrax edema factor: calmodulin complexes with mutations in the edema factor "switch a" region and docking of 3'-deoxy ATP into the adenylyl cyclase active site of wild-type and mutant edema factor variants.

Bacillus anthracis, a spore-forming infectious bacterium, produces an exotoxin, called the edema factor (EF), that functions in part by disrupting internal signalling pathways. When complexed with human host cell calmodulin (CaM), EF becomes an active adenylyl cyclase, producing the internal signal substance cyclic-AMP in an uncontrolled fashion. Recently, the crystal structures for uncomplexed EF and EF:CaM complexes in the presence and absence of a substrate analog (3'-deoxy-ATP), were reported. EF mutational studies have implicated a number of residues important in CaM binding and/or in the generation of the adenylyl cyclase active site, formed by the movements of the EF switch A, B and C regions upon CaM binding. Here we report on the results of molecular dynamics (MD) simulations on two EF:CaM complexes, one containing wild-type EF and the other containing EF in which a cluster of residues in the switch A region (L523, K525, Q526 and V529) have been mutated to alanine. The switch A mutations cause a large increase in the flexibility of the switch C region, the rupture of a number of EF-CaM interactions, an expansion of the carboxyl-terminal domain of CaM, and a change in the Ca(2+) ion binding abilities of the CaM that is in complex with EF. The results indicate the importance of the mutated switch A residues in maintaining a compact EF:CaM complex that appears to be a prerequisite for the generation of a fully-functional adenylyl cyclase active site. The effects of mutating key residues (K346, K353, H577, E588, D590 and N639) in the active site region of EF (to alanine) on the ability of EF to bind the 3'-deoxy-ATP substrate analog were also examined. Active-site residue substitutions at positions 583 (N583A) and 577 (H577A) were found to be particularly disruptive for the placement of the adenine ring moiety into the position found in the x-ray crystal structure of the ligand-protein complex.

Adenylyl Cyclases↗

PubMed2026

Dual solvent cavities and hydrogen-bond networks define the chromophore environment in a far-red/orange-sensing cyanobacteriochrome.

Cyanobacteriochromes (CBCRs) are bilin-binding photoreceptors that exhibit remarkable spectral diversity and mediate light-dependent signaling in cyanobacteria. Far-red/orange-sensing CBCRs (froCBCRs) have attracted interest because of their unusually red-shifted absorption properties, yet structural information for their illuminated states has been lacking. Here, we report the first high-resolution (1.8 Å) crystal structure of the orange-absorbing (Po) state of the froCBCR ToFrO from Tolypothrix sp. PCC 7910. The structure reveals a compact, cyclic bilin configuration and water-mediated hydrogen-bonding networks within two solvent-accessible cavities. Within the GAF domain, the D-ring remains nearly perpendicular to the planar A-to-C ring system through interactions involving a flexible loop region. Comparative analyses of cryogenic synchrotron and room-temperature X-ray free-electron laser (XFEL) structures, together with molecular dynamics (MD) simulations, revealed alternative Met636 conformations associated with dynamic water exchange through the solvent-accessible cavity. Site-directed mutagenesis of cavity-lining and water-interacting residues resulted in modest spectral shifts. By contrast, mutations of two Trp residues, participating in π-π stacking with the D-ring and likely imposing a steric constraint near the A-ring, resulted in substantial blue and red shifts in the dark and illuminated states, respectively. Together with the observed chromophore geometry, these findings indicate that the spectral properties of ToFrO are governed by chromophore conformation and its direct interaction with surrounding residues through hydrogen-bonding, electrostatic, and π-π interactions. These results further suggest that cavity-mediated solvent organization contributes to stabilizing the local structural environment surrounding the chromophore and adjacent protein backbone. Collectively, these findings elucidate the structural basis for photoconversion and spectral tuning in froCBCRs.

Cyanobacteria↗

PubMed2000

Effect of fluid flow on smooth muscle cells in a 3-dimensional collagen gel model.

A 3D collagen gel model was developed to simulate interstitial fluid flow and to assess the importance of this flow on the biochemical production rates of vascular smooth muscle cells (SMCs). Rat aortic SMCs were suspended in type I collagen, and the gel was supported by nylon fibers that allowed a 9-cm length of the SMC-gel model to withstand 90 cm H(2)O differential pressure over a 6-hour period without significant compaction. Up to 1 dyne/cm(2) shear stress on the suspended SMCs could be induced by the pressure-driven interstitial flow. The suspended SMCs were globular, had a diameter of approximately 10 microm, and were distributed uniformly throughout the gel. The collagen fibers formed a network that was connected randomly with the surface of SMCs and nylon fibers. The diameter of the collagen fibers was approximately 100 nm, and the concentration of collagen was 2.5 mg/mL. Using these parameters, fiber matrix theory predicted a Darcy permeability coefficient (K:(p)) of 1.22x10(-)(8) cm(2), which was close to the measured value of K:(p). The production rates of prostaglandin (PG) I(2) and PGE(2) were used as markers of biochemical responsiveness of SMCs to fluid shear stress. Both PGI(2) and PGE(2) production rates under 1 dyne/cm(2) shear stress were significantly elevated relative to static (no-flow) controls. The production rates, however, were approximately 10 times lower than observed when the same cells were plated on collagen-treated glass slides (2D model) and exposed to the same level of shear stress by use of a rotating disk apparatus. The results indicate that interstitial flow can affect SMC biology and that SMCs are more quiescent in 3D cultures than in 2D cultures. The 3D collagen gel model should be useful for future studies of interstitial flow effects on SMC function.

Animals↗

PubMed2002

Numerical analysis of dipole sound source around high speed trains.

As the maximum speed of high speed trains increases, the effect of aeroacoustic noise on the sound level on the ground becomes increasingly important. In this paper, the distribution of dipole sound sources at the bogie section of high speed trains is predicted numerically. The three-dimensional unsteady flow around a train is solved by the large eddy simulation technique. The time history of vortices shows that unstable shear layer separation at the leading edge of the bogie section sheds vortices periodically. These vortices travel downstream while growing to finally impinge upon the trailing edge of the section. The wavelength of sound produced by these vortices is large compared to the representative length of the bogie section, so that the source region can be regarded as acoustically compact. Thus a compact Green's function adapted to the shape can be used to determine the sound. By coupling the instantaneous flow properties with the compact Green's function, the distribution of dipole sources is obtained. The results reveal a strong dipole source at the trailing edge of the bogie section where the shape changes greatly and the variation of flow with time is also great. On the other hand, the bottom of the bogie section where the shape does not change, or the leading edge and boundary layer where the variation of flow with time is small, cannot generate a strong dipole source.

Journal Article↗

PubMed1994

Electrotonic profiles of interneurons in stratum pyramidale of the CA1 region of rat hippocampus.

1. Whole-cell recordings have been made from interneurons located in stratum pyramidale in the CA1 region of the hippocampus. The responses of these interneurons to brief current pulses were recorded; the neurons were filled with biocytin and their morphology was reconstructed. 2. The interneurons were identified as basket cells on the basis of the regional distribution of their axon collateral network and their location in stratum pyramidale. 3. A compartmental model of the reconstructed neuron was made, and the specific membrane resistivity (Rm), specific cytoplasmic resistivity (Ri), and somatic shunt leakage resistance (Rs) determined by adjusting these parameters until an optimal fit was obtained between the compartmental model's current pulse response and the recorded current pulse response of the neuron. 4. This procedure was successful for six neurons, giving Rm from 7 to 66 k omega cm2, Ri from 52 to 484 omega cm, and Rs from 84 M omega to infinity. The specific membrane capacitance was assumed to be 1 microF/cm2. The electrotonic length of the apical dendrites was 1.06 +/- 0.4, and for the basal dendrites it was 0.51 +/- 0.26 (mean +/- SD). 5. Although the total surface area of the interneurons and the physical length of their dendrites was much smaller than for CA1 pyramidal neurons, their electrotonic profiles were similar. Neurons with small physical profiles cannot be assumed to be more electrotonically compact than larger neurons, especially if the dendrites of the smaller neurons have a proportional reduction in diameter. 6. Two neurons did not require a somatic leakage conductance in their electrical representation. This suggests that when a somatic leakage conductance is required, it is an artifact resulting from electrode damage, rather than a requirement caused by a lower resistivity of the somatic membrane compared with the dendritic membrane. 7. Simulations of synaptic currents evoked in the dendrites of these interneurons while the soma is voltage clamped indicate large errors will occur in the time course measurements and amplitude of these currents. Also the ratio of N-methyl-D-aspartate:alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (NMDA:AMPA) currents at these synapses calculated from currents recorded at the soma will be in error because of the differential attenuation of the faster AMPA currents compared with the NMDA currents.

Animals↗

PubMedDate not supplied

Determining the number of centroids for CMLP network.

In our recent studies we have proposed and investigated a centroid-based multilayer perceptron (CMLP) network architecture for modelling purposes. In the CMLP network the first hidden layer is a centroid layer. We have found that the proposed hybrid can provide significant advantages over standard multilayer perceptron networks in terms of fast and efficient learning, and compact network structure in complex classification problems. Previously the number of units for the centroid layer had been determined empiricially. Here we extend our work by introducing a method for determining the minimal number of centroid units for a given problem. The proposed scheme also enables efficient initialization of the centroids units. In addition, we also propose an initialization scheme for the MLP part of the CMLP network. Our benchmark simulations show that the proposed methods significantly improve the CMLP scheme.

Computer Simulation↗

PubMed2006

Failure process of a bundle of plastic fibers.

We present an extension of fiber bundle models considering that failed fibers still carry a fraction 0 < or = alpha < or = 1 of their failure load. The value of alpha interpolates between the perfectly brittle failure (alpha = 0) and perfectly plastic behavior (alpha = 1) of fibers. We show that the finite load bearing capacity of broken fibers has a substantial effect on the failure process of the bundle. In the case of global load sharing it is found that for alpha --> 1 the macroscopic response of the bundle becomes perfectly plastic with a yield stress equal to the average fiber strength. On the microlevel, the size distribution of avalanches has a crossover from a power law of exponent approximately 2.5 to a faster exponential decay. For localized load sharing, computer simulations revealed a sharp transition at a well-defined value alpha(c) from a phase where macroscopic failure occurs due to localization as a consequence of local stress enhancements, to another one where the disordered fiber strength dominates the damage process. Analyzing the microstructure of damage, the transition proved to be analogous to percolation. At the critical point alpha(c), the spanning cluster of damage is found to be compact with a fractal boundary. The distribution of bursts of fiber breakings shows a power-law behavior with a universal exponent approximately 1.5 equal to the mean-field exponent of fiber bundles of critical strength distributions. The model can be relevant to understand the shear failure of glued interfaces where failed regions can still transmit load by remaining in contact.

Journal Article↗

PubMed2000

Role of the beta-strand insert in the central domain of the fibrinogen gamma-module.

The crystal structure of the fibrinogen gamma-module (residues gamma143-411) [Yee, V. C., et al. (1997) Structure 5, 125-138] revealed an unusual feature. Namely, residues gamma381-390 in the functionally important COOH-terminal region form a beta-strand that is inserted into an antiparallel beta-sheet of the central domain (gamma192-286), while the rest (gamma393-411) seems to be flexible. To clarify the structural and functional importance of this beta-strand insert, we analyzed the folding status of the plasmin-derived fibrinogen fragment D(3) and several truncated variants of the gamma-module expressed in Escherichia coli. It was found that D(3), in which most of the COOH-terminal domain of the gamma-module (gamma287-379) is removed proteolytically, retains a gamma374-405 peptide that seems to be associated noncovalently with the bulk of the molecule via its beta-strand insert region. A study of the denaturation-renaturation process of D(3) suggested that without this peptide its truncated gamma-module remains folded but is destabilized. This was confirmed directly with the truncated recombinant variants of the gamma-module, including residues gamma148-392, gamma148-373, and gamma148-286. They all were folded, but those devoid of the beta-strand insert were destabilized. The results indicate that although the beta-strand insert contributes to the stabilization of the gamma-module, it can be removed without destroying the compact structure of the latter. On the basis of this finding and some other observations, we propose a mechanism for the function-related conformational changes in the fibrin(ogen) gamma-modules.

Calorimetry, Differential Scanning↗

PubMed2003

Variable-angle total internal reflection fluorescence microscopy (VA-TIRFM): realization and application of a compact illumination device.

A novel compact illumination device in variable-angle total internal reflection fluorescence microscopy (VA-TIRFM) is described. This device replaces the standard condensor of an upright microscope. Light from different laser sources is delivered via a monomode fibre and focused onto identical parts of a sample under variable angles of total internal reflection. Thus, fluorophores in close proximity to a cell-substrate interface are excited by an evanescent wave with variable penetration depth, and localized with high (nanometre) axial resolution. In addition to quantitative measurements in solution, fluorescence markers of the cytoplasm and the plasma membrane, i.e. calcein and laurdan, were examined using cultivated endothelial cells. Distances between the glass substrate and the plasma membrane were determined using the mathematical algorithm of a four-layer model, as well as a Gaussian-shaped intensity profile of the illumination spot on the samples. Distances between 0 and 30 nm in focal contacts and between 100 and 300 nm in other parts of the cell were thus determined. In addition to measurements of cell-substrate topology, the illumination device appears appropriate for numerous applications in which high axial resolution is required, e.g. experiments on endocytosis or exocytosis, as well as measurements of ion concentrations proximal to the plasma membrane. The compact illumination device is also suitable for combining TIRFM with further innovative techniques, e.g. time-resolved fluorescence spectroscopy, fluorescence lifetime imaging (FLIM) or fluorescence resonance energy transfer (FRET).

2-Naphthylamine↗

PubMed2001

Rapid gastric fluid digestion and biochemical characterization of engineered proteins enriched in essential amino acids.

The barley high lysine (BHL) proteins are nutritionally enhanced derivatives of barley chymotrypsin inhibitor-2 (CI-2). A compactly folded new CI-2 derivative, BHL9, was engineered with the highest content of threonine, tryptophan, and isoleucine yet achieved in this protein family (15.1, 9.4, and 12.1 wt %, respectively). BHL9 had an unfolding midpoint of 5.5 M guanidinium chloride, significantly greater than values for wild type (3.9 M) or for the previously most stable BHL protein, BHL8 (3.6 M). BHL9 and all other derivatives were digested within 15 s in simulated gastric fluid (SGF), suggesting nutritional availability upon ingestion. Denaturation of the proteins in SGF minus pepsin was revealed by changes in their fluorescence emission spectra and/or far UV circular dichroism spectra. The proteins lack homology to known allergens. Significantly, the BHL8 and BHL9 proteins were stable to proteases at pH 7.5 or 8.0, attesting to their potential for high expression in plants.

Amino Acids, Essential↗

PubMed2025

An electrostatic repulsion model of centromere organisation.

During cell division, chromosomes reorganise into compact bodies in which centromeres localise precisely at the chromatin surface1-4 to enable kinetochore-microtubule interactions essential for genome segregation5-8. The physical principles guiding this centromere positioning remain unknown. Here, we reveal that human core centromeres are directed to the chromatin surface by repulsion of centromere-associated proteins - independent of condensin-mediated loop extrusion and microtubule engagement. Using cellular perturbations, biochemical reconstitution, and multiscale molecular dynamics simulations, we show that chromatin surface localisation emerges from repulsion between condensed chromatin and both the kinetochore and the highly negatively charged centromere protein, CENP-B. Together, these elements form a centromeric region composed of two domains with opposing affinities, one favouring integration within the mitotic chromosome and the other favouring exposure to the surrounding cytoplasm, thereby driving surface positioning. Tethering synthetic negatively charged proteins to chromatin was sufficient to recapitulate this surface localisation in cells and in vitro, indicating that electrostatic repulsion is a key determinant of surface localisation. These findings demonstrate that centromere layering is not hardwired by chromatin folding patterns but instead emerges from phase separation in chromatin. Our work uncovers electrostatic polarity as a general and programmable mechanism to spatially organise chromatin.

Journal Article↗

PubMed2007

Influence of oxide-based sintering additives on densification and mechanical behavior of tricalcium phosphate (TCP).

In this research, we studied and analyzed the effects of four different oxide-based sintering additives on densification, mechanical behavior, biodegradation and biocompatibility of tricalcium phosphate (TCP) bioceramics. Selective sintering additives were introduced into pure TCP ceramics, in small quantities, through homogeneous mixing, using a mortar and pestle. The consequent powders of different compositions were pressed into cylindrical compacts, uniaxially and sintered at elevated temperatures, 1150 degrees C and 1250 degrees C, separately in a muffle furnace. X-ray powder diffraction technique was used to analyze the phase-purity of TCP after sintering. Hardness of these sintered specimens was evaluated using a Vickers hardness tester. Sintered cylindrical samples were tested under uniaxial compressive loading, as a function of composition to determine their failure strength. Biodegradation studies conducted using simulated body fluid under dynamic environment, revealed that these additives could control the rate of resorption and hardness degradation of TCP ceramics.

Absorbable Implants↗

PubMed1994

A three-dimensional representation of an athletic female knee joint using magnetic resonance imaging.

Intense interest in knee joint mechanics has resulted in the development of numerous models to predict forces acting at the knee. However, few models have accounted for the unique geometric characteristics of the knee joint's articular surfaces when predicting the mechanical response of the joint. The purpose of this study was to stimulate accurately the complex geometric characteristics of the tibiofemoral joint for input into a finite element model representing the knee joint of athletic females. The right knee of an athletic female with no history of knee joint trauma was imaged using a 0.5 T magnetic resonance imaging (MRI) unit. Twelve cross-sectional slices of the knee were scanned in each of three orthogonal planes (coronal, sagittal and axial) at slice intervals of 6 mm, 7 m, and 8 mm respectively. A scan plan (two coronal images and an axial image) was also generated to enable calculation of the orthogonal scans with respect to one another. Select anatomical reference points representing cancellous and compact bone, major ligament attachment areas, and articular cartilage of the distal femur and proximal tibia were digitized from the processed shadowgraphs. The processed digitized data were input into a computer graphics program which was the pre- and post-processing software for the finite element analysis package. Contours of the cancellous and compact bone of the tibial and femoral condyles were generated using beta and cubic spline curves. Bezier quadratic and cubic polynomials were used to reconstruct the tibial and femoral shafts.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗