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PubMed2006

Global attraction and stability for Cohen-Grossberg neural networks with delays.

We consider a class of Cohen-Grossberg neural networks with delays. We prove the existence and global asymptotic stability of an equilibrium point and estimate the region of existence. Furthermore, we show that the trajectories of the neural networks with positive initial data will stay in the positive region if the amplification function satisfies a divergent condition. We also establish the existence of a globally attracting compact set for more general networks. We estimate this compact set explicitly in terms of the network parameters from physiological and biological models. Our results can be applied to neural networks with a wide range of activation functions which are neither bounded nor globally Lipschitz continuous such as the Lotka-Volterra model. We also give some examples and simulations.

Animals↗

PubMed1998

Portfolio: a prototype workstation for development and evaluation of tools for analysis and management of digital portal images.

PURPOSE: The purpose of this investigation was to design and implement a prototype physician workstation, called PortFolio, as a platform for developing and evaluating, by means of controlled observer studies, user interfaces and interactive tools for analyzing and managing digital portal images. The first observer study was designed to measure physician acceptance of workstation technology, as an alternative to a view box, for inspection and analysis of portal images for detection of treatment setup errors. METHODS AND MATERIALS: The observer study was conducted in a controlled experimental setting to evaluate physician acceptance of the prototype workstation technology exemplified by PortFolio. PortFolio incorporates a windows user interface, a compact kit of carefully selected image analysis tools, and an object-oriented data base infrastructure. The kit evaluated in the observer study included tools for contrast enhancement, registration, and multimodal image visualization. Acceptance was measured in the context of performing portal image analysis in a structured protocol designed to simulate clinical practice. The acceptability and usage patterns were measured from semistructured questionnaires and logs of user interactions. RESULTS: Radiation oncologists, the subjects for this study, perceived the tools in PortFolio to be acceptable clinical aids. Concerns were expressed regarding user efficiency, particularly with respect to the image registration tools. CONCLUSIONS: The results of our observer study indicate that workstation technology is acceptable to radiation oncologists as an alternative to a view box for clinical detection of setup errors from digital portal images. Improvements in implementation, including more tools and a greater degree of automation in the image analysis tasks, are needed to make PortFolio more clinically practical.

Algorithms↗

PubMed1996

The folding mechanism of larger model proteins: role of native structure.

The folding mechanism of a 125-bead heteropolymer model for proteins is investigated with Monte Carlo simulations on a cubic lattice. Sequences that do and do not fold in a reasonable time are compared. The overall folding behavior is found to be more complex than that of models for smaller proteins. Folding begins with a rapid collapse followed by a slow search through the semi-compact globule for a sequence-dependent stable core with about 30 out of 176 native contacts which serves as the transition state for folding to a near-native structure. Efficient search for the core is dependent on structural features of the native state. Sequences that fold have large amounts of stable, cooperative structure that is accessible through short-range initiation sites, such as those in anti-parallel sheets connected by turns. Before folding is completed, the system can encounter a second bottleneck, involving the condensation and rearrangement of surface residues. Overly stable local structure of the surface residues slows this stage of the folding process. The relation of the results from the 125-mer model studies to the folding of real proteins is discussed.

Models, Theoretical↗

PubMed1999

Spatial correlations of mobility and immobility in a glass-forming Lennard-Jones liquid.

Using extensive molecular dynamics simulations of an equilibrium, glass-forming Lennard-Jones mixture, we characterize in detail the local atomic motions. We show that spatial correlations exist among particles undergoing extremely large ("mobile") or extremely small ("immobile") displacements over a suitably chosen time interval. The immobile particles form the cores of relatively compact clusters, while the mobile particles move cooperatively and form quasi-one-dimensional, stringlike clusters. The strength and length scale of the correlations between mobile particles are found to grow strongly with decreasing temperature, and the mean cluster size appears to diverge near the mode-coupling critical temperature. We show that these correlations in the particle displacements are related to equilibrium fluctuations in the local potential energy and local composition.

Journal Article↗

PubMed2003

Growth behavior of helical cellular automata.

A helical cellular automata (HCA) model constructed on a two-dimensional grid of cells with a helical structure is presented and the pattern formation of this model studied by numerous computer simulations. It is found that the evolutions of the HCA are sensitive to the circumference of the helix p. With various p, the initial growth of the model generates various patterns ranging from Sierpinski triangle gasket, complex textured pattern, to lateral quasiperiodic structure. A sudden transition from regular fractal to compact pattern occurs near the point where p is equal to a positive integer power of 2. With increasing height of the patterns (increasing growth time), the model also exhibits different growth behaviors in the vertical direction for various p, including the formation of regular periodic patterns and the evolution from initial regular patterns to eventual random structures. Fractal dimension analysis is used to characterize these different evolution processes quantitatively.

Journal Article↗

PubMed1992

Crystal structure of recombinant human interleukin-4.

The crystal structure of recombinant human interleukin-4 (rhuIL-4) was initially determined at 3.5-A resolution by multiple isomorphous replacement techniques and subsequently refined to a resolution of 2.35 A by simulated annealing. The final crystallographic R-factor, based on all data in the range 6.0-2.35 A (7470 reflections), is 0.232. Bond lengths and bond angles in the molecule have root mean square deviations from ideal values of 0.016 A and 2.4 degrees, respectively. The overall structure is highly compact and globular with a predominantly hydrophobic core. The main structural feature of rhuIL-4 is a four alpha-helix bundle, which composes approximately 58% of the structure. The helices are arranged in a left-handed antiparallel bundle with two overhand connections. Within these connections is a two-stranded antiparallel beta-sheet. Both the tertiary and secondary structures of rhuIL-4 are similar to those of human granulocyte-macrophage colony-stimulating factor. Critical regions for receptor binding are proposed.

Amino Acid Sequence↗

PubMed2003

Image-based computational simulation of flow dynamics in a giant intracranial aneurysm.

BACKGROUND AND PURPOSE: Blood flow dynamics are thought to play an important role in the pathogenesis and treatment of intracranial aneurysms; however, hemodynamic quantities of interest are difficult to measure in vivo. This study shows that computational fluid dynamics (CFD) combined with computed rotational angiography can provide such hemodynamic information in a patient-specific and prospective manner. METHODS: A 58-year-old woman presented with partial right IIIrd cranial nerve palsy due to a giant carotid-posterior communicating artery aneurysm that was subsequently coiled. Computed rotational angiography provided high resolution volumetric image data from which the lumen geometry was extracted. This and a representative flow rate waveform were provided as boundary conditions for finite element CFD simulation of the 3D pulsatile velocity field. RESULTS: CFD analysis revealed high speed flow entering the aneurysm at the proximal and distal ends of the neck, promoting the formation of both persistent and transient vortices within the aneurysm sac. This produced dynamic patterns of elevated and oscillatory wall shear stresses distal to the neck and along the sidewalls of the aneurysm. These hemodynamic features were consistent with patterns of contrast agent wash-in during cine angiography and with the configuration of coil compaction observed at 6-month follow-up. CONCLUSION: Anatomic realism of lumen geometry and flow pulsatility is essential for elucidating the patient-specific nature of aneurysm hemodynamics. Such image-based CFD analysis may be used to provide key hemodynamic information for prospective studies of aneurysm growth and rupture or to predict the response of an individual aneurysm to therapeutic options.

Blood Flow Velocity↗

PubMed2003

Spiral versus J-shaped coils for neurovascular embolisation-an in-vitro study.

Our purpose was to compare the characteristics of J-shaped detachable platinum coils with those of spiral coils in in-vitro vascular models. J-shaped coils consist of distal semicircular and proximal straight segments, the latter extending for most of the length of the coil. Spiral coils have a helical shape memory and are thus limited in expansion. In in-vitro silicone vascular models simulating intracranial aneurysms and dural arteriovenous fistulae, we compared J-shaped and spiral coils with regard to ease of delivery, anchoring and folding patterns, and stability in various types of vascular lumen. Delivery and retrieval were comparable. In large and irregular aneurysms and venous sinuses, J-shaped coils could form a more complex basket which conformed to the shape of the vascular cavity. The J-shaped coil was always in contact with the vessel wall. In wide-necked aneurysms, coil protrusion was more frequent with J-shaped coils, while spiral coils tended to stay compact and circular. Arteries were occluded in a shorter segment with spiral coils. J-shaped coils were safe and superior for large and irregular aneurysms or sinuses. Spiral coils were preferable for spherical aneurysms and segmental occlusion of arteries.

Angiography↗

PubMed1996

The influence of external fixators on fracture motion during simulated walking.

This experimental study examines the relative influence of five unilateral external fixators on tibial fracture stability during simulated walking. Stability during routine patient activity is important, because cyclic inter fragmentary motion, or strain, has been shown to affect fracture healing. In model stable fractures simulating early healing (six weeks), it was found that fixators do little to constrain against axial inter fragmentary strains as great as 100% at only nominal weight-bearing (6.0 kg). These strains may occur repeatably at peak amplitudes of motion during walking. Similarly, peak angular movements may lead to additional axial strains of up to 25% at the external cortex and shear movements may lead to shear strains of up to 100%. Such strains are great enough to yield and possibly refracture the intra gap fracture tissue that may be composed of a combination of granulation tissue, fibrous cartilage, cartilage and bone. It was also shown that the procedure of releasing the fixator column to telescope (dynamize) has little influence on peak cyclic axial motion and on loading at the fracture, although increases occurred in peak transverse and torsional shear strains of up to 100%. Since permanent inter fragmentary translation also arises from the consequent compaction of the intra gap tissue, it may be permanent displacement rather than any change in the amplitude of motion that is responsible for the beneficial effect on healing claimed for the dynamizing procedure. In unstable fractures that are unable to support tibial load at the fracture, the peak amplitudes of cyclic movement were as great as those reported for fractures stabilized by plaster casts, and were approximately twice the movement of the stable fractures simulating early healing. Therefore, patients with unstable fractures supported by external fixators, may be expected to have similar patterns of healing to plaster-casted patients with similar fractures.

Biomechanical Phenomena↗

PubMed1990

The finite element analysis of brain oedema associated with intracranial meningiomas.

The mathematical model of vasogenic brain oedema, which was presented at the previous meeting in 1987, was applied to the analysis of peritumoural brain oedema associated with meningiomas. Magnetic resonance images of 90 patients with intracranial meningiomas were reviewed to analyze the spatial extension of peritumoural brain oedema. It is assumed that the heterogeneous pattern of distribution of peritumoural oedema reflects the variability of the compact density of the fibers in the white matter. A two dimensional finite element model was constructed with 786 triangular elements from a horizontal section of the human brain. The development of oedema, the change of interstitial pressure, the deformation of the brain and the absorption of oedema fluid could be simulated by the finite element method. The result of computer simulation represented interactive behaviour of the brain tissue, extracellular fluid, and cerebrospinal fluid in the clinical situation. The finite element method (FEM) may provide a new experimental tool to analyze the pathophysiology of vasogenic brain oedema.

Brain↗

PubMed1983

Uniform regional heating of the lower trunk: numerical evaluation of tumor temperature distributions.

The temperature distributions in deep seated tumors resulting from uniform heating of the abdominal and pelvic regions of the trunk are predicted from a one dimensional numerical solution of the bio-heat transfer equation. The effect of tumor size and location are investigated for two tumor perfusion models: uniform perfusion and a concentric annulus perfusion model. Tumor temperature distributions are considered acceptable if the range of temperatures in the tumor lie between 42 degrees C and 60 degrees C. This range of tumor temperatures is defined as Tave +/- 2 sigma where sigma is the population standard deviation of tumor temperatures from the average computed at the nodal points in the finite difference array. To simulate practical clinical restrictions, muscle and fat temperatures are not allowed to exceed 44 degrees C, significant portions of the viscera are not allowed to exceed 42 degrees C, and the total absorbed power required to maintain steady state cannot exceed two kilowatts. Over 100 possible cases are presented in a compact form. From this study it appears that heating systems with power deposition patterns approximately uniform are promising for heating deep-seated tumors. Small, detectable tumors (approximately 2 cm in size) are adequately heated for a wider range of conditions than are larger tumors. Excessively high temperatures in deep-seated, normal tissue could be a significant limitation for this technique.

Abdominal Neoplasms↗

PubMed2002

Cell adhesion and proliferation on biomimetic calcium-phosphate coatings produced by a sodium silicate gel methodology.

The present study describes a methodology to produce bioactive coatings on the surface of starch based biodegradable polymers or other polymeric biomaterials. As an alternative to the more typical bioactive glass percursors, a sodium silicate gel is being employed as a nucleating agent, for inducing the formation of a calcium-phosphate (Ca-P) layer. The method has the advantage of being able to coat efficiently both compact materials and porous 3D architectures aimed at being used on tissue replacement applications and as bone tissue engineering scaffolds. This treatment is also very effective in reducing the incubation periods, being possible to observe the formation of an apatite-like layer, only after 6 h of immersion in a simulated body fluid (SBF). The influence of the SBF concentration on the formation of the apatite coating was also studied. The apatite coatings formed under different conditions were analyzed and compared in terms of morphology, chemical composition and structure. After the first days of SBF immersion, the apatite-like films exhibit the typical cauliflower like morphology. With increasing immersion times, these films exhibited a partially amorphous nature and the Ca/P ratios became very closer to the value attributed to hydroxyapatite (1.67). The obtained results are very promising for pre-calcifying bone tissue engineering scaffolds. Therefore, in order to study cell behavior and response to these apatite coatings, adhesion, morphology, and proliferation of a human osteoblast cell line (SaOS-2) was also analyzed after being cultured in the coatings formed after 15 days of immersion in SBF. Results indicate a good correlation between crystallinity of the apatite like coatings formed in these conditions and respective cell spreading and morphology. In general, higher cell proliferation was observed for higher crystalline Ca-P coatings.

Journal Article↗

PubMed2005

The peptide-chain size dependence of positive dissociation energy effect in metallized and protonated polydentate oligoglycine peptides.

The dependence of the positive dissociation energy (PDE) on the size of both protonated and various metal cationized (M+/2+=Na+, K+, Mg2+, and Ca2+) oligoglycines GnHM (G=glycine; n=1-5, and including 6 for GnHK) in the gas phase has been first determined at the B3LYP level with different basis sets. Results show that these PDEs become negative ones when n>or=5 for GnHNa, n>or=6 for GnHK, n>or=2 for GnHMg, and n>or=3 for GnHCa. Moreover, the PDE effect decreases gradually along the increase of oligoglycine size for all these PDE systems. More charge transfer to the ambient ligand and large electrostatic effect of the two divalent cation (Mg2+ and Ca2+) involved systems make them lose the PDE effect more rapidly, and hold more compact and oblate shapes than the monovalent ones. Differently, polydentate GnHK prefers a spherical to oblate shape along with the increase of oligoglycine size.

Cations↗

PubMed2001

Limits on the cosmological abundance of supermassive compact objects from a millilensing search in gamma-ray burst data.

A new search for the gravitational lens effects of a significant cosmological density of supermassive compact objects (SCOs) on gamma-ray bursts (GRBs) has yielded a null result. We inspected the timing data of 774 BATSE-triggered GRBs for evidence of millilensing: repeated peaks similar in light-curve shape and spectra. Our null detection leads us to conclude that, in all candidate universes simulated, Omega(SCO)<0.1 is favored for SCO masses in the range 10(5)<M(SCO)/M( middle dot in circle)<10(9), while in some universes and mass ranges the density limits are as much as 10 times lower. Therefore, a cosmologically significant population of SCOs near globular cluster mass did not come out of the primordial universe or condense at recombination.

Journal Article↗

PubMed1999

Autonomic modification of the atrioventricular node during atrial fibrillation: role in the slowing of ventricular rate.

BACKGROUND: Postganglionic vagal stimulation (PGVS) by short bursts of subthreshold current evokes release of acetylcholine from myocardial nerve terminals. PGVS applied to the atrioventricular node (AVN) slows nodal conduction. However, little is known about the ability of PGVS to control ventricular rate (VR) during atrial fibrillation (AF). METHODS AND RESULTS: To quantify the effects and establish the mechanism of PGVS on the AVN, AF was simulated by random high right atrial pacing in 11 atrial-AVN rabbit heart preparations. Microelectrode recordings of cellular action potentials (APs) were obtained from different AVN regions. Five intensities and 5 modes of PGVS delivery were evaluated. PGVS resulted in cellular hyperpolarization, along with depressed and highly heterogeneous intranodal conduction. Compact nodal AP exhibited decremental amplitude and dV/dt and multiple-hump components, and at high PGVS intensities, a high degree of concealed conduction resulted in a dramatic slowing of the VR. Progressive increase of PGVS intensity and/or rate of delivery showed a significant logarithmic correlation with a decrease in VR (P<0.001). Strong PGVS reduced the mean VR from 234 to 92 bpm (P<0.001). The PGVS effects on the cellular responses and VR during AF were fully reproduced in a model of direct acetylcholine injection into the compact AVN via micropipette. CONCLUSIONS: These studies confirmed that PGVS applied during AF could produce substantial VR slowing because of acetylcholine-induced depression of conduction in the AVN.

Animals↗

PubMed2005

Structure of bacterial extracellular polymeric substances at different pH values as determined by SAXS.

Extracellular polymeric substances (EPS) play an important role in cell aggregation, cell adhesion, and biofilm formation, and protect cells from a hostile environment. The EPS was isolated by trichloroacetic acid/ethanol extraction from broth culture of a marine bacterium isolate. The EPS was composed of glucose and galactose as determined by HPLC and TLC; the protein content was on average 15 +/- 5% of EPS dry mass. The solution structure of EPS at different values of pH was revealed by small-angle x-ray scattering. Scattering curves of EPS solutions (0.4%, w/v) consistently showed two nearly linear log-log regions with slopes a and b in the q-ranges from 0.06 nm(-1) to 0.26 nm(-1), and from 0.27 nm(-1) to 0.88 nm(-1), respectively. Slope a was sensitive to pH changes whereas slope b was not. The observed sensitivity to pH was not a consequence of ionic strength variation with pH, as checked by salt addition. The pH variation causes major rearrangements of EPS structure mainly at length scales above 24 nm. To get a better understanding of the pH effect on EPS structure, the original model proposed by Geissler was refined into a mathematical model that enabled fitting of the experimental scattering curves in the pH range from 0.7 to 11.0. The model describes EPS structure as a network of randomly coiled polymeric chains with denser domains of polymeric chains. The results obtained from the model indicate that dense domains increase in average size from 19 nm at pH 11.0 to 52 nm at pH 0.7. The average distance between the polysaccharide chains at pH 0.7 was 2.3 nm, which indicates a compact EPS structure. Swelling was found to be at a maximum around pH = 8.8, where the average distance between the chains was 4.8 nm.

Biopolymers↗

PubMed1999

Structural characterization by computer experiments of the lipid-free LDL-receptor-binding domain of apolipoprotein E.

The structure and dynamics of the lipid-free LDL-receptor-binding domain of apolipoprotein E (apoE-RBD) has been investigated by Molecular Dynamics Simulations. ApoE-RBD in its monomeric lipid-free form is a singular four-helix bundle made up of four elongated amphipathic helices. Analysis of one 1.5 ns molecular dynamics trajectory of apoE-RBD performed in water indicates that the lipid-free domain adopts a structure that exhibits characteristics found in native proteins: it has very stable helices and presents a compact structure. Yet its interior exhibits a larger number of transient atomic-size cavities relative to that found in other proteins of similar size and its apolar side chains are more mobile. The latter features distinguish the elongated four-helix bundle as a slightly disordered structure, which shows a structural likeness with some de novo designed four-helix bundle proteins and shares with the latter a leucine-rich residue composition. We anticipate that these unique properties compared with other native helix bundles may be related to the postulated ability of apoE-RBD to undergo an opening of its bundle upon interaction with phospholipids. The distribution of empty cavities computed along the trajectory in the interface regions between the different pairs of helices reveals that the tertiary contacts in one of the interfaces are weaker suggesting that this particular interface could be more easily ruptured upon lipid association.

Algorithms↗

PubMed1988

Computer simulation of neuronal circuit models of rhythmic behavior in the electroencephalogram.

A computer program for modeling some features of the electroencephalogram (EEG) recorded by scalp electrodes in terms of the time- and space-dependent interactions of populations of neurons in different hypothetical brain configurations was developed. The input of the model consists of: (1) geometric and anatomic data characterizing the brain configuration; (2) physiologic features characterizing neurons; and (3) functions describing the time-dependent afferent impulses to the brain configuration under study. The output of the model consists of plots of selected intracellular and extracellular potentials as a function of time. In application of the model to various brain configurations, some configurations were sufficiently compact spatially that propagation times of action potentials between elements were either taken to be constant or were nearly independent of distance within the accuracy of the calculations. Other configurations represented cerebral cortex alone or a combined thalamocortical system in which many elements interacted via global interconnections. The basic requirement for rhythmic behavior is the existence of circuits containing inhibitory neurons. The characteristic frequencies of rhythmic oscillations are primarily determined by the local circuit parameters and are relatively independent of global circuit parameters.

Action Potentials↗