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PubMed2006

Packing hyperspheres in high-dimensional Euclidean spaces.

We present a study of disordered jammed hard-sphere packings in four-, five-, and six-dimensional Euclidean spaces. Using a collision-driven packing generation algorithm, we obtain the first estimates for the packing fractions of the maximally random jammed (MRJ) states for space dimensions d=4, 5, and 6 to be phi(MRJ) approximately 0.46, 0.31, and 0.20, respectively. To a good approximation, the MRJ density obeys the scaling form phi(MRJ)=c1/2(d)+(c2d)/2d, where c1=-2.72 and c2=2.56, which appears to be consistent with the high-dimensional asymptotic limit, albeit with different coefficients. Calculations of the pair correlation function g2(r) and structure factor S(k) for these states show that short-range ordering appreciably decreases with increasing dimension, consistent with a recently proposed "decorrelation principle," which, among other things, states that unconstrained correlations diminish as the dimension increases and vanish entirely in the limit d-->infinity. As in three dimensions (where phi(MRJ) approximately 0.64), the packings show no signs of crystallization, are isostatic, and have a power-law divergence in g2(r) at contact with power-law exponent approximately 0.4. Across dimensions, the cumulative number of neighbors equals the kissing number of the conjectured densest packing close to where g2(r) has its first minimum. Additionally, we obtain estimates for the freezing and melting packing fractions for the equilibrium hard-sphere fluid-solid transition, phi(F) approximately 0.32 and phi(M) approximately 0.39, respectively, for d=4, and phi(F) approximately 0.20 and phi(M) approximately 0.25, respectively, for d=5. Although our results indicate the stable phase at high density is a crystalline solid, nucleation appears to be strongly suppressed with increasing dimension.

Journal Article↗

PubMed2000

The effect of immediate vs. delayed post space preparation on the apical seal of a root canal filling: a study in an increased-sensitivity pressure-driven system.

A 5 mm remaining length of root canal filling, after post space preparation, is commonly assumed to maintain sealing ability similar to that of the intact filling. Post spaces were prepared either immediately using hot pluggers, or later, using drills. The sealing ability of the fillings, 5 mm remaining length, were compared with each other and with an intact root canal filling control, using radioactive tracer in a pressure-driven system. When no pressure was applied, no differences could be detected between either of the groups and the control. When a pressure of 120 mm Hg was applied to the same teeth, the control group clearly maintained a better seal than each of the experimental groups, which did not significantly differ from each other. These results suggest that (a) the pressure-driven system was more sensitive than the passive leakage assay that failed to detect differences even at 14 days; (b) a remaining root canal filling of 5 mm was inferior to the intact root canal filling; and (c) the immediate post space preparation with hot pluggers did not differ from a delayed preparation with drills.

Analysis of Variance↗

PubMed1985

Simulated spontaneous breathing. A new model for testing anaesthetic circuits.

A carbon-dioxide-producing lung model capable of simulating spontaneous breathing is presented. It consists of a piston in a cylinder, a mixing chamber and a dead space volume. The piston is driven by a direct-current motor controlled by a micro-processor and a servo unit. Respiratory waveform and rate, tidal volume, carbon dioxide production and dead space are easily adjustable within a wide range. The model is easy to handle and accurately mimics a given breathing pattern. It seems suitable for investigations of rebreathing and carbon dioxide elimination in different anaesthetic circuits.

Airway Resistance↗

PubMedDate not supplied

Vibrografic signs of autonomous muscle tone studied in long term space missions.

Signs of resting muscle tone, assessed by cardiac driven microvibrations (MV), were studied in two cosmonauts during long term space missions on the Russian MIR station. In the 1 g environment, MV showed the typical 7-13 Hz resonance oscillations triggered by the heart beat. In 0 g, these pulsations were damped and the waveform became similar to an acceleration ballistocardiogram. If resting tone was slightly increased by extending the arm in 0 g, the resonance oscillations reappeared in most cases. By means of a simple vibromechanic analog it is demonstrated that the elastic component of muscle has to be reduced during the fully relaxed state in 0g.

Aerospace Medicine↗

PubMed2001

Stochastic magnetohydrodynamic turbulence in space dimensions d > or =2.

Interplay of kinematic and magnetic forcing in a model of a conducting fluid with randomly driven magnetohydrodynamic equations has been studied in space dimensions d > or =2 by means of the renormalization group. A perturbative expansion scheme, parameters of which are the deviation of the spatial dimension from two and the deviation of the exponent of the powerlike correlation function of random forcing from its critical value, has been used in one-loop approximation. Additional divergences have been taken into account that arise at two dimensions and have been inconsistently treated in earlier investigations of the model. It is shown that in spite of the additional divergences, the kinetic fixed point associated with the Kolmogorov scaling regime remains stable for all space dimensions d > or =2 for rapidly enough falling off correlations of the magnetic forcing. A scaling regime driven by thermal fluctuations of the velocity field has been identified and analyzed. The absence of a scaling regime near two dimensions driven by the fluctuations of the magnetic field has been confirmed. A renormalization scheme has been put forward and numerically investigated to interpolate between the epsilon expansion and the double expansion.

Journal Article↗

PubMed2005

Limits on the excitable behavior of a semiconductor laser with optical feedback.

Recently, it was proposed that semiconductor lasers with optical feedback present a complex behavior that can be described as noise driven excitable. In this work we investigate in which region of parameter space this description is adequate. We conclude that the region of the parameter space in which the system displays noise driven excitable behavior is a subset of the region in which presents low frequency fluctuations.

Journal Article↗

PubMed2002

Annular flow film characteristics in variable gravity.

Annular flow is a frequently occurring flow regime in many industrial applications. The need for a better understanding of this flow regime is driven by the desire to improve the design of many terrestrial and space systems. Annular two-phase flow occurs in the mining and transportation of oil and natural gas, petrochemical processes, and boilers and condensers in heating and refrigeration systems. The flow regime is also anticipated during the refueling of space vehicles, and thermal management systems for space use. Annular flow is mainly inertia driven with little effect of buoyancy. However, the study of this flow regime is still desirable in a microgravity environment. The influence of gravity can create an unstable, chaotic film. The absence of gravity, therefore, allows for a more stable and axisymmetric film. Such conditions allow for the film characteristics to be easily studied at low gas flow rates. Previous studies conducted by the Microgravity Research Group dealt with varying the gas or liquid mass fluxes at a reduced gravitational acceleration.(1,2) The study described here continues this work by examining the effect of changing the gravitational acceleration (hypergravity) on the film characteristics. In particular, the film thickness and the associated pressure drops are examined. The film thickness was measured using a pair of two-wire conductance probes. Experimental data was collected over a range of annular flow set points by changing the liquid and gas mass flow rates, the liquid-to-gas density ratio and the gravitational acceleration. The liquid-to-gas density ratio was varied by collecting data with helium-water and air-water at the same flow rates. The gravitational effect was examined by collecting data during the microgravity and pull-up (hypergravity) portions of the parabolic flights.

Journal Article↗

PubMed2001

Dynamics and instability of electron phase-space tubes.

Two-dimensional simulations of beam-driven turbulence in the auroral ionosphere have shown the formation and instability of phase-space tubes. These tubes are a generalization of electron phase-space holes in a one-dimensional plasma. In a strongly magnetized plasma, such tubes vibrate at frequencies below the bounce frequency of the trapping potential. A theory for these vibrations yields quantitative agreement with kinetic simulations. Furthermore, the theory predicts that the vibrations can become unstable when resonantly coupled to electrostatic whistlers-also in agreement with simulations.

Journal Article↗

PubMed2003

[Effect of aquaporin-1 and sodium channel on pleural fluid transport in mice].

OBJECTIVE: To investigate the effect of sodium channel and aquaporin-1 on pleural fluid transport. METHODS: Mice were briefly anesthetized, and the pleural space was infused with 0.25 ml of hyperosmolar or isosmolar solution, with terbutaline or amiloride in instilled solution. The mice were treated with either intraperitoneal dexamethasone or intravenous HgCl(2). Mice were euthanized at specified times for measurement of pleural fluid osmolality, volume and (125)I-album in concentration. The rate of pleural fluid filtration and clearance was calculated, which was used to indicate the effect of sodium channel regulator (amiloride and terbutaline) and aquaporin regulator (dexamethasone and HgCl(2)) on pleural fluid transport. RESULTS: Amiloride decreased the osmotically driven water transport and isosmolar fluid clearance in pleural space (P < 0.05). Terbutaline increased osmotically driven water transport and isosmolar fluid clearance in pleural space (P < 0.05). HgCl(2) decreased, while dexamethasone increased, the osmotically driven water transport in pleural space (P < 0.05). HgCl(2) and dexamethasone had no effect on pleural isosmolar fluid clearance (P > 0.05). CONCLUSIONS: Sodium channel may play a role in osmotic and isosmolar fluid transport in pleural space. Aquaporin-1 may play a role in osmotic fluid transport in pleural space, while having no effect on isosmolar fluid clearance.

Animals↗

PubMed2005

A second pathway for gas out of the pressure chamber--what is being squeezed?

We report a qualitative description of the flows of gas that occur through a leaf when its balance pressure is measured in the pressure chamber. There are two distinct pathways: (a) a bulk flow of gas through the intercellular air spaces, and (b) a diffusion-driven pathway where gas is dissolved into solution under high pressure and comes out of solution at the liquid/atmosphere surface of the cut end where the pressure is atmospheric. The intercellular space flow is well known. It is argued that this flow shows to a reasonable approximation, that the externally supplied gas is squeezing the non-gaseous part of the leaf, and the outer boundary of the non-gaseous material is the boundary of the system that is being manipulated. The second pathway, the diffusion-driven flow, has not (we believe) been described before, and is analogous to a diver getting the bends. The diffusion-based flow demonstrates that gas spaces can and do form inside the outer boundary of the non-gaseous part of the leaf when a balance pressure is measured. These interior gas spaces alter the value recorded for the balance pressure, and complicate any interpretation of what this measurement tells us about the water status of the plant. A hypothesis is proposed that the diffusion-based flow from the xylem comes from vessels that are embolized, and that percentage embolisms might be measured by the proportion of vessels showing the diffusion-driven flow.

Acacia↗

PubMed2004

No stellar p-mode oscillations in space-based photometry of Procyon.

Pressure-driven (p-mode) oscillations at the surface of the Sun, resulting from sound waves travelling through the solar interior, are a powerful probe of solar structure, just as seismology can reveal details about the interior of the Earth. Astronomers have hoped to exploit p-mode asteroseismology in Sun-like stars to test detailed models of stellar structure and evolution, but the observations are extremely difficult. The bright star Procyon has been considered one of the best candidates for asteroseismology, on the basis of models and previous reports of p-modes detected in ground-based spectroscopy. Here we present a search for p-modes in 32 days of nearly continuous photometric satellite-based observations of Procyon. If there are p-modes in Procyon, they must have lifetimes less than 2-3 days and/or peak amplitudes <15 parts per million, which defy expectations from the Sun's oscillations and previous theoretical predictions. Target selection for future planned asteroseismology space missions may need to be reconsidered, as will the theory of stellar oscillations.

Journal Article↗

PubMed1996

Salt and water transport across alveolar and distal airway epithelia in the adult lung.

Substantial progress has been made in understanding the role of the distal airway and alveolar epithelial barriers in regulating lung fluid balance. Molecular, cellular, and whole animal studies have demonstrated that reabsorption of fluid from the distal air spaces of the lung is driven by active sodium transport. Several different in vivo, in situ, and isolated lung preparations have been used to study the mechanisms that regulate fluid transport in the normal and injured lung. Catecholamine-dependent and -independent regulatory mechanisms have been identified that modulate fluid transport, probably by acting on apical sodium channel uptake or the activity of the Na, K-ATPase pumps. Recently, a family of molecular water channels (aquaporins) has been identified that are small (approximately 30 kDa) integral membrane proteins expressed widely in fluid-transporting epithelia and endothelia. At present, four different water channels have been identified in trachea and lung. Measurements of osmotic water permeability in in situ perfused lung and isolated perfused airways suggest a significant contribution of these molecular water channels to measured water permeability. However, further studies are required to determine the role of these water channels in normal pulmonary physiology and disease. Recent studies have provided new insights into the role of the alveolar epithelial barrier in clinical and experimental acute lung injury. Unlike the lung endothelium, the alveolar epithelium is resistant to several clinically relevant types of injury, including endotoxemia and bacteremia as well as aspiration of hyperosmolar solutions. In addition, even when the alveolar barrier has been injured, its capacity to transport edema fluid from the distal air spaces of the lung recovers rapidly. Future studies need to integrate new insights into the molecular mechanisms of alveolar epithelial sodium and water transport with functional studies in the normal and injured lung.

Adult↗

PubMed2005

Refining the rules of gliadin T cell epitope binding to the disease-associated DQ2 molecule in celiac disease: importance of proline spacing and glutamine deamidation.

Celiac disease is driven by intestinal T cells responsive to proline-rich gluten peptides that often harbor glutamate residues formed by tissue transglutaminase-mediated glutamine conversion. The disease is strongly associated with the HLA variant DQ2.5 (DQA1*05, DQB1*02), and intestinal gluten-reactive T cells from DQ2.5-positive patients are uniquely restricted by this HLA molecule. In this study, we describe the mapping of two novel T cell epitopes of gamma-gliadin and the experimental identification of the DQ2.5 binding register of these and three other gamma-gliadin epitopes. The new data extend the knowledge base for understanding the binding of gluten peptides to DQ2.5. The alignment of the experimentally determined binding registers of nine gluten epitopes reveal positioning of proline residues in positions P1, P3, P6, and P8 but never in positions P2, P4, P7, and P9. Glutamate residues formed by tissue transglutaminase-mediated deamidation are found in position P1, P4, P6, P7, or P9, but only deamidations in positions P4 and P6, and rarely in P7, seem to be crucial for T cell recognition. The majority of these nine epitopes are recognized by celiac lesion T cells when presented by the related but nonassociated DQ2.2 (DQA1*0201, DQB1*02) molecule. Interestingly, the DQ2.2 presentation for most epitopes is less efficient than presentation by the DQ2.5 molecule, and this is particularly prominent for the alpha-gliadin epitopes. Contrary to previous findings, our data do not show selective presentation of DQ2.5 over DQ2.2 for gluten epitopes that carry proline residues at the P3 position.

Amino Acid Sequence↗

PubMed2003

The automatic discovery of structural principles describing protein fold space.

The study of protein structure has been driven largely by the careful inspection of experimental data by human experts. However, the rapid determination of protein structures from structural-genomics projects will make it increasingly difficult to analyse (and determine the principles responsible for) the distribution of proteins in fold space by inspection alone. Here, we demonstrate a machine-learning strategy that automatically determines the structural principles describing 45 folds. The rules learnt were shown to be both statistically significant and meaningful to protein experts. With the increasing emphasis on high-throughput experimental initiatives, machine-learning and other automated methods of analysis will become increasingly important for many biological problems.

Algorithms↗

PubMed1994

Streaming potential measurements at low ionic concentrations reflect bone microstructure.

Streaming potentials (SPs) have been proposed as one transduction pathway for mechanically driven bone remodeling. The fluid spaces in which SPs are generated will determine, in part, the structural information that they can provide to bone cells. Streaming potential measurements across cortical bone strips soaked in a range of saline concentrations were used to estimate the mean radii of fluid spaces that contribute to generation of electrokinetic fields. Using a cylindrical pore model, a pore radius of less than 200 A fit SP magnitude as a function of concentration. This pore size was shown to be consistent with estimates obtained from data reported earlier for SP as a function of concentration using a non-specific model, but was smaller than previously reported estimates for pore radius. A pore size in this range indicates that flow either in bone microporosity, or canaliculi that are substantially occluded by cellular material, must generate streaming potentials. Further, the fact that such small pores generate SPs in bone indicates that SPs could provide information regarding local matrix structure to bone cells.

Animals↗

PubMed2001

Site-specific molecular design and its relevance to pharmacogenomics and chemical biology.

The emergence of the new discipline of pharmacogenomics reflects the growing convergence of chemical and genomic space. The massive information-driven growth in both computational chemistry and structural biology is leading to unprecedented opportunities in both chemical and biological design. In this paper we relate current opinion in structural biology to recent developments in computational drug design. Sequence information now permits protein structure prediction and, together with experimental protein structure determination, a complete database of ligand-binding sites and protein-protein interactions can be assembled. When aligned with site exploration and virtual screening, this information provides a foundation for structure-based pharmacogenomics. In association with chemical genomics, structure-based design will allow major new insights into a compound's biological and pharmaceutical properties.

Binding Sites↗

PubMed1997

Mitochondrial protein import. Tom40 plays a major role in targeting and translocation of preproteins by forming a specific binding site for the presequence.

During preprotein transport across the mitochondrial outer membrane, the N-terminal presequence initially binds to a surface-exposed site, termed cis site, of the protein translocation complex of this membrane (the TOM complex). The presequence then moves into the translocation pore and becomes exposed at the intermembrane space side. Membrane passage is driven by specific interaction of the presequence with the trans site. We have used chemical cross-linking to identify components in the vicinity of the translocating presequence. Preproteins bound to the surface-exposed cis site can be cross-linked via their N-terminal presequence to Tom20 and Tom22, demonstrating their direct association with this part of the preprotein. In addition, the presequence establishes an early contact to Tom40, a membrane-embedded protein of the TOM complex. Upon further entry of the preprotein into the translocation pore, the presequence loses its contact with Tom20/Tom22, but remains in firm association with Tom40. Our study suggests that Tom40 plays an important function in guiding the presequence of a preprotein across the mitochondrial outer membrane. We propose that Tom40 forms a major part of the trans presequence binding site.

Animals↗

PubMed1999

Impulse and Movement Space-Time Variability.

In 3 experiments, the authors examined movement space-time variability as a function of the force-time properties of the initial impulse in a movement timing task. In the range of motion and movement time task conditions, peak force, initial rate of force, and force duration were manipulated either independently or in combination across a range of parameter values. The findings showed that (a) impulse variability is predicted well by the elaboration of the isometric force variability scaling functions of L. G. Carlton, K. H. Kim, Y. T. Liu, and K. M. Newell (1993) to movement, and (b) the movement spatial and temporal outcome variability are complementary and well predicted by an equation treating the variance of force and time in Newton's 2nd law as independent random variables. Collectively, the findings suggest that movement outcome variability is the product of a coherent space-time function that is driven by the nonlinear scaling of the force-time properties of the initial impulse.

Journal Article↗