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PubMed1997

Models of CO2 concentrating mechanisms in microalgae taking into account cell and chloroplast structure.

Detailed mathematical models have been developed for the functioning of CO2 concentration mechanisms in microalgae. The models treat a microalgal cell as several compartments: pyrenoid, chloroplast stroma, cytoplasm and periplasmic space. Cases for both the active bicarbonate transport through the plasmalemma and the passive CO2 diffusion through it with the subsequent concentrating of CO2 inside the chloroplast are analyzed. CO2 evolution from bicarbonate inside the pyrenoid is modeled. The great diffusion resistance for CO2 flux from the pyrenoid is caused by a starch envelope and the concentric thylakoid membranes surrounding it. The role of carbonic anhydrase in the periplasmic space, cytoplasm and inside the chloroplast is evaluated numerically. The models also offer an explanation for the absence of 'short-circuited' inorganic carbon fluxes between the external medium and the cytoplasm under active bicarbonate transport through the plasmalemma and in the presence of carbonic anhydrase in the cytoplasm. If the cytoplasm is driven from the space between a chloroplast envelope and plasmalemma upon the microalgae adaptation to low concentration of the dissolved inorganic carbon, the inorganic carbon leak might be avoided. The models reproduce accurately the majority of known experimental data. The high efficiency of CO2 concentrating mechanisms in microalgae can be explained by a considerable diffusion resistance for CO2 flux from the pyrenoid and by the effective scavenging of CO2 leaking outward from the chloroplast to cytoplasm and from cell to periplasmic space.

Carbon Dioxide↗
PubMed2001

Glassy systems under time-dependent driving forces: application to slow granular rheology.

We study the dynamics of a glassy model with infinite range interactions externally driven by an oscillatory force. We find a well-defined transition in the (temperature-amplitude-frequency) phase diagram between (i) a "glassy" state characterized by the slow relaxation of one-time quantities, aging in two-time quantities and a modification of the equilibrium fluctuation-dissipation relation; and (ii) a "liquid" state with a finite relaxation time. In the glassy phase, the degrees of freedom governing the slow relaxation are thermalized to an effective temperature. Using Monte Carlo simulations, we investigate the effect of trapping regions in phase space on the driven dynamics. We find that it alternates between periods of rapid motion and periods of trapping. These results confirm the strong analogies between the slow granular rheology and the dynamics of glasses. They also provide a theoretical underpinning to earlier attempts to present a thermodynamic description of moderately driven granular materials.

Journal Article↗
PubMed2006

Analysis of functional image analysis contest (FIAC) data with brainvoyager QX: From single-subject to cortically aligned group general linear model analysis and self-organizing group independent component analysis.

The Functional Image Analysis Contest (FIAC) 2005 dataset was analyzed using BrainVoyager QX. First, we performed a standard analysis of the functional and anatomical data that includes preprocessing, spatial normalization into Talairach space, hypothesis-driven statistics (one- and two-factorial, single-subject and group-level random effects, General Linear Model [GLM]) of the block- and event-related paradigms. Strong sentence and weak speaker group-level effects were detected in temporal and frontal regions. Following this standard analysis, we performed single-subject and group-level (Talairach-based) Independent Component Analysis (ICA) that highlights the presence of functionally connected clusters in temporal and frontal regions for sentence processing, besides revealing other networks related to auditory stimulation or to the default state of the brain. Finally, we applied a high-resolution cortical alignment method to improve the spatial correspondence across brains and re-run the random effects group GLM as well as the group-level ICA in this space. Using spatially and temporally unsmoothed data, this cortex-based analysis revealed comparable results but with a set of spatially more confined group clusters and more differential group region of interest time courses.

Algorithms↗
PubMed2005

Mechanisms to explain the reverse perivascular transport of solutes out of the brain.

Experimental studies and observations in the human brain indicate that interstitial fluid and solutes, such as amyloid-beta (Abeta), are eliminated from grey matter of the brain along pericapillary and periarterial pathways. It is unclear, however, what constitutes the motive force for such transport within blood vessel walls, which is in the opposite direction to blood flow. In this paper the potential for global pressure differences to achieve such transport are considered. A mathematical model is constructed in order to test the hypothesis that perivascular drainage of interstitial fluid and solutes out of brain tissue is driven by pulsations of the blood vessel walls. Here it is assumed that drainage occurs through a thin layer between astrocytes and endothelial cells or between smooth muscle cells. The model suggests that, during each pulse cycle, there are periods when fluid and solutes are driven along perivascular spaces in the reverse direction to the flow of blood. It is shown that successful drainage may depend upon some attachment of solutes to the lining of the perivascular space, in order to produce a valve-like effect, although an alternative without this requirement is also postulated. Reduction in pulse amplitude, as in ageing cerebral vessels, would prolong the attachment time, encourage precipitation of Abeta peptides in vessel walls, and impair elimination of Abeta from the brain. These factors may play a role in the pathogenesis of cerebral amyloid angiopathy and in the accumulation of Abeta in the brain in Alzheimer's disease.

Amyloid beta-Peptides↗
PubMed2000

Eigenvector 1: An Optimal Correlation Space for Active Galactic Nuclei.

We identify a correlation space involving optical and UV emission-line parameters as well as the soft X-ray spectral index that provides optimal discrimination between all principal classes of active galactic nuclei (AGNs). Most of the sources in our three high-quality data samples show a strong intercorrelation with narrow-line Seyfert 1 (NLSy1) galaxies and steep-spectrum radio galaxies occupying opposite extrema in the space. NLSy1 sources show a clear continuity with broader line sources, indicating that they are not a disjoint class of AGN as is sometimes suggested. We interpret the principal intercorrelation in the parameter space as being driven by the AGN luminosity-to-black hole mass ratio (L&solm0;M is proportional to the Eddington ratio). Source orientation no doubt also plays an important role, but it is not yet clear whether FWHM Hbeta or C iv lambda1549 line shift is the better indicator. We tentatively identify two radio-quiet populations: an almost pure radio-quiet population A, with FWHM</=4000, and population B, which occupies the same parameter domain as the flat-spectrum radio-loud sources. A possible interpretation sees population A/NLSy1 as lower mass/high accretion rate sources and population B/radio-loud sources as the opposite.

Journal Article↗
PubMed2000

Quantum recurrences: probe to study quantum chaos

We study the phase space of periodically modulated gravitational cavity by means of quantum recurrence phenomena. We report that the quantum recurrences serve as a tool to connect phase space of the driven system with a spectrum in the quantum domain. With the help of quantum recurrences we investigate the quasienergy spectrum of the system for a certain fixed modulation strength. In addition, we study transition of spectrum from discrete to continuum as a function of modulation strength.

Journal Article↗
PubMed1988

Estimate of attenuation coefficient for ultrasonic tissue characterization using time-varying state-space model.

The images generated from ultrasound pulse-echo signals have long been used to aid clinical diagnosis. Recently, there has been a growing interest in quantitatively determining the acoustic parameters of the tissue as a means of classification and diagnosis. For example, the frequency-dependent attenuation is known to be correlated with different diseases in the liver. In this paper we introduce a new technique for estimating the attenuation coefficient. The effect of attenuation on an interrogating signal with a gaussian-shaped spectrum can be obtained by studying the Wigner distribution of reflected rf data based on a one-dimensional signal model. We show that under the condition that the attenuation varies linearly with frequency, the spectral mean of the reflected signal decreases linearly with time. The estimation algorithm models the pulse-echo signal as the output of a second-order time-varying state-space innovations model driven by white noise. The state coupling matrix A and the output coupling vector C vary with time in a known fashion; moreover, they are also functions of an unknown constant parameter theta. The attenuation coefficient, which is one of the elements of theta, can be estimated directly using a recursive system identification algorithm. The algorithm was verified using both computer-generated synthetic data and in-vivo liver data of known diagnosis. The results show correlation between the estimated parameter and the pathological state of the tissue.

Algorithms↗
PubMed1995

The pathophysiology of angiogenesis.

The formation of new capillary blood vessels, a process termed "angiogenesis", is one of the most pervasive and fundamentally essential biological processes encountered in mammalian organizations. Angiogenesis is an important event in a variety of physiological settings, such as embryonic development, chronic inflammation, and wound repair. It is a process that is tightly regulated in both time and space. Angiogenesis is driven by a cocktail of growth factors and pro-angiogenic cytokines and is tempered by an equally diverse group of inhibitors of neovascularization. Angiogenesis is also central to the etiology and pathogenesis of a number of pathological processes that include, among others, solid tumors, diseases of the eye, and chronic inflammatory disorders such as rheumatoid arthritis, psoriasis, and periodontitis. Based on recent work from several laboratories, it is now eminently clear that most if not all angiogenesis and vasoproliferative-dependent disease processes are not only a consequence of the unrestricted production of normal or aberrant forms of pro-angiogenic mediators but also the result of a relative deficiency in angiogenic-inhibitory molecules. In this review, I will describe how these multifunctional mediator systems function to coordinate and regulate the angiogenic response, and how disruption in the molecular controls that regulate the production of pro-angiogenic and angiostatic mediators leads to aberrant angiogenesis and disease. The implications of these findings in the development of novel therapeutic strategies for the treatment of diseases characterized by disregulated angiogenesis will also be discussed.

Animals↗
PubMed2006

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

Recently we have developed a normal-modes-based algorithm that predicts the direction of protein conformational changes given the initial state crystal structure together with a small number of pairwise distance constraints for the end state. Here we significantly extend this method to accurately model both the direction and amplitude of protein conformational changes. The new protocol implements a multisteps search in the conformational space that is driven by iteratively minimizing the error of fitting the given distance constraints and simultaneously enforcing the restraint of low elastic energy. At each step, an incremental structural displacement is computed as a linear combination of the lowest 10 normal modes derived from an elastic network model, whose eigenvectors are reorientated to correct for the distortions caused by the structural displacements in the previous steps. We test this method on a list of 16 pairs of protein structures for which relatively large conformational changes are observed (root mean square deviation >3 angstroms), using up to 10 pairwise distance constraints selected by a fluctuation analysis of the initial state structures. This method has achieved a near-optimal performance in almost all cases, and in many cases the final structural models lie within root mean square deviation of 1 approximately 2 angstroms from the native end state structures.

Computer Simulation↗
PubMed2005

Mean-field glass transition in a model liquid.

We investigate the liquid-glass phase transition in a system of pointlike particles interacting via a finite-range attractive potential in D -dimensional space. The phase transition is driven by an "entropy crisis" where the available phase space volume collapses dramatically at the transition. We describe the general strategy underlying the first-principles replica calculation for this type of transition; its application to our model system then allows for an analytic description of the liquid-glass phase transition within a mean-field approximation, provided the parameters are chosen suitably. We find a transition exhibiting all the features associated with an entropy crisis, including the characteristic finite jump of the order parameter at the transition while the free energy and its first derivative remain continuous.

Journal Article↗
PubMedDate not supplied

Thoracic sonography for pneumothorax: the clinical evaluation of an operational space medicine spin-off.

The recent interest in the use of ultrasound (US) to detect pneumothoraces after acute trauma in North America was initially driven by an operational space medicine concern. Astronauts aboard the International Space Station (ISS) are at risk for pneumothoraces, and US is the only potential medical imaging available. Pneumothoraces are common following trauma, and are a preventable cause of death, as most are treatable with relatively simple interventions. While pneumothoraces are optimally diagnosed clinically, they are more often inapparent even on supine chest radiographs (CXR) with recent series reporting a greater than 50% rate of occult pneumothoraces. In the course of basic scientific investigations in a conventional and parabolic flight laboratory, investigators familiarized themselves with the sonographic features of both pneumothoraces and normal pulmonary ventilation. By examining the visceral-parietal pleural interface (VPPI) with US, investigators became confident in diagnosing pneumothoraces. This knowledge was subsequently translated into practice at an American and a Canadian trauma center. The sonographic examination was found to be more accurate and sensitive than CXR (US 96% and 100% versus US 74% and 36%) in specific circumstances. Initial studies have also suggested that detecting the US features of pleural pulmonary ventilation in the left lung field may offer the ability to exclude serious endotracheal tube malpositions such as right mainstem and esophageal intubations. Applied thoracic US is an example of a clinically useful space medicine spin-off that is improving health care on earth.

Aerospace Medicine↗
PubMed2006

Clustering in randomly driven Hamiltonian systems.

The motion of oscillatorylike nonlinear Hamiltonian systems, driven by a weak noise, is considered. A general method to find regions of stability in the phase space of a randomly driven system, based on a specific Poincaré map, is proposed and justified. Physical manifestations of these regions of stability are coherent clusters. We illustrate the method and demonstrate the appearance of coherent clusters with two models motivated by the problems of waveguide sound propagation and Lagrangian mixing of passive scalars in the ocean. We find bunches of sound rays propagating coherently in an underwater waveguide through a randomly fluctuating ocean at long distances. We find clusters of passive particles to be advected coherently for a comparatively long time by a random two-dimensional flow modeling mixing around a fixed vortex.

Journal Article↗
PubMed1986

The role of the macula densa in renin release: studies by microperfusion.

The role of the macula densa in control of renin release and in mediation of tubulo-glomerular feedback was investigated following orthograde microperfusion in Munich Wistar rats. Tubules of surface glomeruli were perfused, drip-fixed with glutaraldehyde and biopsy cores taken containing perfused and non-perfused glomeruli. Serial sections were examined by light and electron microscopy. In some animals dilated basolateral spaces were observed between cells in control maculae densa but no spaces were found following microperfusion with hypertonic NaCl, isotonic mannitol or hypotonic NaCl containing 1 mg/l frusemide. In other animals no spaces were found in control cores, and perfusion with the above solutions had no effect. However, in such animals, tubules perfused with hypotonic NaCl (71 mmol/kg H2O) had prominent basolateral spaces in their maculae densa. The presence of dilated basolateral intercellular spaces is generally associated with osmotically driven water flow. The extent of dilatation of such spaces in the macula densa is correlated with transepithelial osmotic or ionic gradients and may indicate activity of these cells in the recognition of distal tubular fluid composition.

Animals↗
PubMed2004

The coordination of rotations of the eyes, head and trunk in saccadic turns produced in natural situations.

In real life situations large gaze saccades may involve rotations of the trunk, as well as the eyes and head. When this happens the rotation of the head-in-space is similar whether or not the trunk is also rotating. However, the rotation of the head on the trunk (i.e. the neck movement) is very different in the two circumstances. For similar head-in-space rotations to occur, the neck and trunk movements cannot simply add independently: they must be coordinated. It is argued that this is achieved via a feedback loop in which the semi-circular canals monitor the rotation of the head-in-space, and the neck is driven by an error signal representing the difference between the intended head-in-space trajectory and the actual trajectory. This mechanism, which is essentially the same as the vestibulo-collic reflex, nulls out disturbances to the head-in-space trajectory, whether these are caused by active or passive trunk rotation.

Abdomen↗
PubMed1994

The high-resolution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from nuclear magnetic resonance nuclear Overhauser effect data.

The solution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli has been determined by NMR in combination with distance geometry and restrained molecular dynamics. The structure is based on 1520 experimental restraints identified from both three-dimensional 1H-1H-13C and 1H-1H-15N nuclear Overhauser effect multiple-quantum coherence spectroscopy and two-dimensional 1H-1H nuclear Overhauser effect spectra. Thirty-two four-dimensional coordinate frames were produced by metric matrix distance geometry, subjected to distance bounds driven dynamics, projected into three-dimensional space and again subjected to distance-bounds driven dynamics. These 32 distance geometry structures were refined further by restrained molecular dynamics (40 ps) in the GROMOS in vacuo force field. All 32 structures reached acceptable energy minima while satisfying the imposed restraints. Two of these structures were subjected to a further 200 ps of molecular dynamics simulation in water, using time-dependent distance restraining, followed by a 200 ps free simulation without any distance restraining. The resulting structure is very similar to the X-ray structure of Bacillus subtilis HPr, but differs mainly in the position of the two loops containing the active site histidine residue 15 and residues 53 to 57 relative to the rest of the structure. The unfavorable phi torsion angle that was found for residue 16 in the active center of unphosphorylated Streptococcus faecalis HPr was proposed to play a role in the activity of the protein. Although present at the early stages of the structure calculations, this torsion-angle strain disappeared in the final model obtained from molecular dynamics simulations in water using time-averaged distance restraining and upon releasing the distance restraints. This suggests that the strain may be an artifact of crystallization conditions instead of an essential element in the phosphorylation/dephosphorylation process.

Bacterial Proteins↗
PubMed2000

Study of cosmic rays and light flashes on board Space Station MIR: the SilEye experiment.

The SilEye experiment aims to study the cause and processes related to the anomalous Light Flashes (LF) perceived by astronauts in orbit and their relation with Cosmic Rays. These observations will be also useful in the study of the long duration manned space flight environment. Two PC-driven silicon detector telescopes have been built and placed aboard Space Station MIR. SilEye-1 was launched in 1995 and provided particles track and LF information; the data gathered indicate a linear dependence of FLF(Hz) ( 4 2) 10(3) 5.3 1.7 10(4) Fpart(Hz) if South Atlantic Anomaly fluxes are not included. Even though higher statistic is required, this is an indication that heavy ion interactions with the eye are the main LF cause. To improve quality and quantity of measurements, a second apparatus, SilEye-2, was placed on MIR in 1997, and started work from August 1998. This instrument provides energetic information, which allows nuclear identification in selected energy ranges; we present preliminary measurements of the radiation field inside MIR performed with SilEye-2 detector in June 1998.

Cosmic Radiation↗
PubMed2001

Optimized shielding for space radiation protection.

Future deep space mission and International Space Station exposures will be dominated by the high-charge and -energy (HZE) ions of the Galactic Cosmic Rays (GCR). A few mammalian systems have been extensively tested over a broad range of ion types and energies. For example, C3H10T1/2 cells, V79 cells, and Harderian gland tumors have been described by various track-structure dependent response models. The attenuation of GCR induced biological effects depends strongly on the biological endpoint, response model used, and material composition. Optimization of space shielding is then driven by the nature of the response model and the transmission characteristics of the given material.

Aluminum↗