Minimum depth, mean depth or something in between?

Reliable information about the seafloor and river-bed bathymetry is of high interest for a large number of applications. A Multi-Beam echo sounder (MBES) system is able to produce high-resolution bathymetry data at relatively small cost. These measurements, providing a depth for each beam and every ping, are processed to obtain a more ordered structure, such as a grid. Most approaches for assigning a depth to the centre of a cell (in a grid) use the shallowest or the mean depth in each cell. However, while the grid derived from the mean depth might be too deep compared to the shallowest depth, using the shallowest depth approach can result in an artificially shallow grid, affected by outliers. This paper introduces a number of alternatives to the current methods by combining the mean depth with statistical properties derived from the point cloud of the MBES data. In addition, the possibility of assigning a depth based on the regression coefficients of each cell is considered. The methods introduced have been tested on data acquired in different survey areas. The resulting grids have been compared to their shallowest and mean counterparts to obtain a better understanding of their advantages and limitations.La información fidedigna sobre la batimetría del fondo marino y del fondo fluvial es de gran interés para un gran número de aplicaciones. Un sistema de ecosonda multihaz (MBES) puede producir datos de batimetría de alta resolución a un coste relativamente pequeño. Estas mediciones, que proporcionan una profundidad para cada haz y cada pulso, son procesadas para obtener una estructura más ordenada, como una retícula. La mayoría de los enfoques para atribuir una profundidad al centro de una celda (en una retícula) utilizan la profundidad menos profunda o la profundidad media en cada celda. Sin embargo, mientras que la retícula derivada de la profundidad media podría ser demasiado profunda comparada con la profundidad menor, el uso del enfoque de la profundidad menor puede resultar en una retícula artificialmente poco profunda, afectada por valores anómalos. Este artículo introduce un número de alternativas a los métodos actuales mediante la combinación de la profundidad media con propiedades estadísticas derivadas del punto de la nube de los datos MBES. Además, se considera la posibilidad de atribuir una profundidad basada en los coeficientes de regresión de cada celda. Los métodos introducidos han sido probados en datos adquiridos en diferentes áreas de levantamien-tos. Las retículas resultantes han sido comparadas a sus contrapartidas menos profundas y medias para lograr una mayor comprensión de sus ventajas y limitaciones.Des informations fiables sur la bathymétrie des fonds marins et des lits fluviaux présentent un grand intérêt pour de nombreuses applications. Les systèmes de sondeurs acoustiques multifaisceaux (SMF) sont à même de produire des données bathymétriques à haute résolution à un coût relativement faible. Ces mesurages, qui fournissent une profondeur pour chaque faisceau et pour chaque ping, sont traités afin d’obtenir une structure plus ordonnée, une grille par exemple. La plupart des approches permettant d’attribuer une profondeur au centre d’une cellule (dans une grille) utilisent la profondeur la plus petite ou la profondeur moyenne au sein de chaque cellule. Néanmoins, si la grille dérivée de la profondeur moyenne peut être trop profonde par comparaison à la profondeur minimale, l’utilisation de l’approche de la profondeur la plus petite peut aboutir à une grille artificielle-ment peu profonde, affectée par des valeurs anormales. Cet article présente plusieurs alternatives aux méthodes actuelles en combinant la profondeur moyenne avec des propriétés statistiques dérivées du nuage de points des données issues de SMF. En outre, la possibilité d’attribuer une profondeur basée sur les coefficients de régression de chaque cellule est envisagée. Les méthodes présentées ont été testées sur des données acquises dans différentes zones hydrographiées. Les grilles qui en ont résulté ont été comparées à leurs équivalents en eaux peu profondes et de profondeur moyenne afin de parvenir à une meilleure compréhension de leurs avantages et de leurs limites

Unified regression model of binding equilibria in crowded environments

Molecular crowding is a critical feature distinguishing intracellular environments from idealized solution-based environments and is essential to understanding numerous biochemical reactions, from protein folding to signal transduction. Many biochemical reactions are dramatically altered by crowding, yet it is extremely difficult to predict how crowding will quantitatively affect any particular reaction systems. We previously developed a novel stochastic off-lattice model to efficiently simulate binding reactions across wide parameter ranges in various crowded conditions. We now show that a polynomial regression model can incorporate several interrelated parameters influencing chemistry under crowded conditions. The unified model of binding equilibria accurately reproduces the results of particle simulations over a broad range of variation of six physical parameters that collectively yield a complicated, non-linear crowding effect. The work represents an important step toward the long-term goal of computationally tractable predictive models of reaction chemistry in the cellular environment

Three-Dimensional Stochastic Off-Lattice Model of Binding Chemistry in Crowded Environments

Molecular crowding is one of the characteristic features of the intracellular environment, defined by a dense mixture of varying kinds of proteins and other molecules. Interaction with these molecules significantly alters the rates and equilibria of chemical reactions in the crowded environment. Numerous fundamental activities of a living cell are strongly influenced by the crowding effect, such as protein folding, protein assembly and disassembly, enzyme activity, and signal transduction. Quantitatively predicting how crowding will affect any particular process is, however, a very challenging problem because many physical and chemical parameters act synergistically in ways that defy easy analysis. To build a more realistic model for this problem, we extend a prior stochastic off-lattice model from two-dimensional (2D) to three-dimensional (3D) space and examine how the 3D results compare to those found in 2D. We show that both models exhibit qualitatively similar crowding effects and similar parameter dependence, particularly with respect to a set of parameters previously shown to act linearly on total reaction equilibrium. There are quantitative differences between 2D and 3D models, although with a generally gradual nonlinear interpolation as a system is extended from 2D to 3D. However, the additional freedom of movement allowed to particles as thickness of the simulation box increases can produce significant quantitative change as a system moves from 2D to 3D. Simulation results over broader parameter ranges further show that the impact of molecular crowding is highly dependent on the specific reaction system examined

Human Umbilical Cord Blood Treatment in a Mouse Model of ALS: Optimization of Cell Dose

Amyotrophic Lateral Sclerosis (ALS) is a multicausal disease characterized by motor neuron degeneration in the spinal cord and brain. Cell therapy may be a promising new treatment for this devastating disorder. We recently showed that a single low dose (10(6) cells) of mononuclear human umbilical cord blood (MNC hUCB) cells administered intravenously to G93A mice delayed symptom progression and modestly prolonged lifespan. The aim of this pre-clinical translation study is to optimize the dose of MNC hUCB cells to retard disease progression in G93A mice. Three different doses of MNC hUCB cells, 10x10(6), 25x10(6) and 50x10(6), were administered intravenously into pre-symptomatic G93A mice. Motor function tests and various assays to determine cell effects were performed on these mice.Our results showed that a cell dose of 25x10(6) cells significantly increased lifespan of mice by 20-25% and delayed disease progression by 15%. The most beneficial effect on decreasing pro-inflammatory cytokines in the brain and spinal cord was found in this group of mice. Human Th2 cytokines were found in plasma of mice receiving 25x10(6) cells, although prevalent human Th1 cytokines were indicated in mice with 50x10(6) cells. High response of splenic cells to mitogen (PHA) was indicated in mice receiving 25x10(6) (mainly) and 10x10(6) cells. Significantly increased lymphocytes and decreased neutrophils in the peripheral blood were found only in animals receiving 25x10(6) cells. Stable reduction in microglia density in both cervical and lumbar spinal cords was also noted in mice administered with 25x10(6) cells.These results demonstrate that treatment for ALS with an appropriate dose of MNC hUCB cells may provide a neuroprotective effect for motor neurons through active involvement of these cells in modulating the host immune inflammatory system response

Interactive histogenesis of axonal strata and proliferative zones in the human fetal cerebral wall

Development of the cerebral wall is characterized by partially overlapping histogenetic events. However, little is known with regards to when, where, and how growing axonal pathways interact with progenitor cell lineages in the proliferative zones of the human fetal cerebrum. We analyzed the developmental continuity and spatial distribution of the axonal sagittal strata (SS) and their relationship with proliferative zones in a series of human brains (8-40 post-conceptional weeks; PCW) by comparing histological, histochemical, and immunocytochemical data with magnetic resonance imaging (MRI). Between 8.5 and 11 PCW, thalamocortical fibers from the intermediate zone (IZ) were initially dispersed throughout the subventricular zone (SVZ), while sizeable axonal "invasion" occurred between 12.5 and 15 PCW followed by callosal fibers which "delaminated" the ventricular zone-inner SVZ from the outer SVZ (OSVZ). During midgestation, the SS extensively invaded the OSVZ, separating cell bands, and a new multilaminar axonal-cellular compartment (MACC) was formed. Preterm period reveals increased complexity of the MACC in terms of glial architecture and the thinning of proliferative bands. The addition of associative fibers and the formation of the centrum semiovale separated the SS from the subplate. In vivo MRI of the occipital SS indicates a "triplet" structure of alternating hypointense and hyperintense bands. Our results highlighted the developmental continuity of sagittally oriented "corridors" of projection, commissural and associative fibers, and histogenetic interaction with progenitors, neurons, and glia. Histogenetical changes in the MACC, and consequently, delineation of the SS on MRI, may serve as a relevant indicator of white matter microstructural integrity in the developing brain

Cytoplasmic viscosity near the cell plasma membrane: translational diffusion of a small fluorescent solute measured by total internal reflection-fluorescence photobleaching recovery.

Total internal reflection-fluorescence recovery after photobleaching (TIR-FRAP) was applied to measure solute translational diffusion in the aqueous phase of membrane-adjacent cytoplasm. TIR fluorescence excitation in aqueous solutions and fluorescently labeled cells was produced by laser illumination at a subcritical angle utilizing a quartz prism; microsecond-resolution FRAP was accomplished by acousto-optic modulators and electronic photomultiplier gating. A mathematical model was developed to determine solute diffusion coefficient from the time course of photobleaching recovery, bleach time, bleach intensity, and evanescent field penetration depth; the model included irreversible and reversible photobleaching processes, with triplet state diffusion. The validity and accuracy of TIR-FRAP measurements were first examined in aqueous fluorophore solutions. Diffusion coefficients for fluorescein isothiocyanate-dextrans (10-2000 kDa) determined by TIR-FRAP (recovery t1/2 0.5-2.2 ms) agreed with values measured by conventional spot photobleaching. Model predictions for the dependence of recovery curve shape on solution viscosity, bleach time, and bleach depth were validated experimentally using aqueous fluorescein solutions. To study solute diffusion in cytosol, MDCK epithelial cells were fluorescently labeled with the small solute 2',7'-bis-2-carboxyethyl-5-carboxyfluorescein-acetoxymethyl-ester (BCECF). A reversible photobleaching process (t1/2 approximately 0.5 ms) was identified that involved triplet-state relaxation and could be eliminated by triplet-state quenching with 100% oxygen. TIR-FRAP t1/2 values for irreversible BCECF bleaching, representing BCECF translational diffusion in the evanescent field, were in the range 2.2-4.8 ms (0.2-1 ms bleach times), yielding a BCECF diffusion coefficient 6-10-fold less than that in water. These results establish the theory and the first experimental application of TIR-FRAP to measure aqueous-phase solute diffusion, and indicate slowed translational diffusion of a small solute in membrane-adjacent cytosol

Single photon radioluminescence. II. Signal detection and biological applications.

A quantitative theory for excitation of fluorescent molecules by beta decay electrons is reported in the accompanying manuscript; experimental detection methods and biological applications are reported here. The single photon signals produced by an excited fluorophore (single photon radioluminescence, SPR) provide quantitative information about the distance between radioisotope and fluorophore. Instrumentation was constructed for SPR signal detection. Photons produced in a 0.5-ml sample volume were detected by a cooled photomultiplier and photon counting electronics. To minimize electronic noise and drift for detection of very small SPR signals, a mechanical light chopper was used for gated-signal detection, and a pulse height analyzer for noise rejection. SPR signals of approximately 1 cps were reproducibly measurable. The influence of inner filter effect, sample turbidity, and fluorophore environment (lipid, protein, and carbohydrate) on SPR signals were evaluated experimentally. SPR was then applied to measure lipid exchange kinetics, ligand binding, and membrane transport, and to determine an intermolecular distance in an intact membrane. (a. Lipid exchange kinetics.) Transfer of 12-anthroyloxystearic acid (12-AS) from sonicated lipid vesicles and micelles to vesicles containing 3H-cholesterol was measured from the time course of increasing SPR signal. At 22 degrees C, the half-times for 12-AS transfer from vesicles and micelles were 3.3 and 1.1 min, respectively. (b. Ligand binding.) Binding of 3H-oleic acid to albumin in solution, and 3H-2,2'-dihydro-4,4'-diisothiocyanodisulfonic stilbene (3H-H2DIDS) to band 3 on the erythrocyte membranes were detected by the radioluminescence of the intrinsic tryptophans. The SPR signal from 5 microCi 3H-oleic acid bound to 0.3 mM albumin decreased from 13 +/- 2 cps to 3 +/- 2 cps upon addition of nonradioactive oleic acid, giving 2.7 high affinity oleic acid binding sites per albumin. The SPR signal from 1 microCi 3H-H2DIDS bound selectively to erythrocyte band 3 in erythrocyte ghosts (1.5 mg protein/ml) was 2.2 +/- 0.8 cps. (c. Membrane transport). Dilution of J774 macrophages loaded with 3H-3-O-methylglucose and BCECF gave a decreasing SPR signal with a half-time of 81 s due to methylglucose efflux; the SPR measurement of the efflux rate was in agreement with a conventional tracer efflux rate determination by filtration. 20 microM cytochalasin B inhibited efflux by 97%. (d. Distance determination.) The SPR signal from erythrocyte membranes labeled with 27 microCi 3H-oleic acid and 10 microM of fluorescein-labeled wheat germ agglutinin was 5.7 +/- 0.5 cps, giving an average glycocalyx-to-bilayer distance of 5 nm. The results establish methods for experimental detection of SPR signals and demonstrate the applications of radioluminescence to the measurement of lipid exchange kinetics, ligand binding, membrane transport, and submicroscopic distances in intact membranes in real time

Cytoplasmic viscosity near the cell plasma membrane: measurement by evanescent field frequency-domain microfluorimetry.

The purpose of this study was to determine whether the unique physical milieu just beneath the cell plasma membrane influences the rheology of fluid-phase cytoplasm. Cytoplasmic viscosity was evaluated from the picosecond rotation of the small fluorophore 2',7'-bis-(2-carboxyethyl)-5-carboxyfluorescein (BCECF) by parallel-acquisition Fourier transform microfluorimetry (Fushimi and Verkman, 1991). Information about viscosity within < 200 nm of cell plasma membranes was obtained by selective excitation of fluorophores in an evanescent field created by total internal reflection (TIR) of impulse-modulated s-plane-polarized laser illumination (488 nm) at a glass-aqueous interface. Measurements of fluorescence lifetime and time-resolved anisotropy were carried out in solutions containing fluorescein or BCECF at known viscosities, and monolayers of BCECF-labeled Swiss 3T3 fibroblasts and Madin-Darby canine kidney (MDCK) cells. Specific concerns associated with time-resolved fluorescence measurements in the evanescent field were examined theoretically and/or experimentally, including variations in lifetime due to fluorophore proximity to the interface, and the use of the s and p polarized excitation. In fluorescein solutions excited with s-plane polarized light, there was a 5-10% decrease in fluorescein lifetime with TIR compared to trans (subcritical) illumination, but no change in rotational correlation time (approximately 98 ps/cP). Intracellular BCECF had a single lifetime of 3.7 +/- 0.1 ns near the cell plasma membrane. Apparent fluid-phase viscosity near the cell plasma membrane was 1.1 +/- 0.2 cP (fibroblast) and 1.0 +/- 0.2 cP (MDCK), not significantly different from the viscosity measured in bulk cytoplasm far from the plasma membrane. The results establish the methodology for time-resolved microfluorimetric measurement of polarization in the evanescent field and demonstrate that the cell plasma membrane has little effect on the fluid-phase viscosity of adjacent cytoplasm