Projection structure of frog rhodopsin in two crystal forms.

Rhodopsin is the G protein-coupled receptor that upon light activation triggers the visual transduction cascade. Rod cell outer segment disc membranes were isolated from dark-adapted frog retinas and were extracted with Tween detergents to obtain two-dimensional rhodopsin crystals for electron crystallography. When Tween 80 was used, tubular structures with a p2 lattice (a = 32 A, b = 83 A, gamma = 91 degrees) were formed. The use of a Tween 80/Tween 20 mixture favored the formation of larger p22(1)2(1) lattices (a = 40 A, b = 146 A, gamma = 90 degrees). Micrographs from frozen hydrated frog rhodopsin crystals were processed, and projection structures to 7-A resolution for the p22(1)2(1) form and to 6-A resolution for the p2 form were calculated. The maps of frog rhodopsin in both crystal forms are very similar to the 9-A map obtained previously for bovine rhodopsin and show that the arrangement of the helices is the same. In a tentative topographic model, helices 4, 6, and 7 are nearly perpendicular to the plane of the membrane. In the higher-resolution projection maps of frog rhodopsin, helix 5 looks more tilted than it appeared previously. The quality of the two frog rhodopsin crystals suggests that they would be suitable to obtain a three-dimensional structure in which all helices would be resolved.

Three-dimensional structure of a cysteine-rich repeat from the low-density lipoprotein receptor.

The low-density lipoprotein (LDL) receptor plays a central role in mammalian cholesterol metabolism, clearing lipoproteins which bear apolipoproteins E and B-100 from plasma. Mutations in this molecule are associated with familial hypercholesterolemia, a condition which leads to an elevated plasma cholesterol concentration and accelerated atherosclerosis. The N-terminal segment of the LDL receptor contains a heptad of cysteine-rich repeats that bind the lipoproteins. Similar repeats are present in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. The first repeat of the human LDL receptor has been expressed in Escherichia coli as a glutathione S-transferase fusion protein, and the cleaved and purified receptor module has been shown to fold to a single, fully oxidized form that is recognized by the monoclonal antibody IgG-C7 in the presence of calcium ions. The three-dimensional structure of this module has been determined by two-dimensional NMR spectroscopy and shown to consist of a beta-hairpin structure, followed by a series of beta turns. Many of the side chains of the acidic residues, including the highly conserved Ser-Asp-Glu triad, are clustered on one face of the module. To our knowledge, this structure has not previously been described in any other protein and may represent a structural paradigm both for the other modules in the LDL receptor and for the homologous domains of several other proteins. Calcium ions had only minor effects on the CD spectrum and no effect on the 1H NMR spectrum of the repeat, suggesting that they induce no significant conformational change.

Reproducibility and accuracy of echocardiographic measurements of left ventricular parameters using real-time three-dimensional echocardiography

OBJECTIVES We sought to determine whether assessment of left ventricular (LV) function with real-time (RT) three-dimensional echocardiography (3DE) could reduce the variation of sequential LV measurements and provide greater accuracy than two-dimensional echocardiography (2DE). BACKGROUND Real-time 3DE has become feasible as a standard clinical tool, but its accuracy for LV assessment has not been validated. METHODS Unselected patients (n = 50; 41 men; age, 64 +/- 8 years) presenting for evaluation of LV function were studied with 2DE and RT-3DE. Test-retest variation was performed by a complete restudy by a separate sonographer within 1 h without alteration of hemodynamics or therapy. Magnetic resonance imaging (MRI) images were obtained during a breath-hold, and measurements were made off-line. RESULTS The test-retest variation showed similar measurements for volumes but wider scatter of LV mass measurements with M-mode and 2DE than 3DE. The average MRI end-diastolic volume was 172 +/- 53 ml; LV volumes were underestimated by 2DE (mean difference, -54 +/- 33; p < 0.01) but only slightly by RT-3DE (-4 +/- 29; p = 0.31). Similarly, end-systolic volume by MRI (91 +/- 53 ml) was underestimated by 2DE (mean difference, -28 +/- 28; p < 0.01) and by RT-3DE (mean difference, -3 +/- 18; p = 0.23). Ejection fraction by MRI was similar by 2DE (p = 0.76) and RT-3DE (p = 0.74). Left ventricular mass (183 +/- 50 g) was overestimated by M-mode (mean difference, 68 +/- 86 g; p < 0.01) and 2DE (16 +/- 57; p = 0.04) but not RT-3DE (0 +/- 38 g; p = 0.94). There was good inter- and intra-observer correlation between RT-3DE by two sonographers for volumes, ejection fraction, and mass. CONCLUSIONS Real-time 3DE is a feasible approach to reduce test-retest variation of LV volume, ejection fraction, and mass measurements in follow-up LV assessment in daily practice. (C) 2004 by the American College of Cardiology Foundation.

Numerical evaluation of three dimensional effects in planar flow birefringence

The influence of three dimensional effects on isochromatic birefringence is evaluated for planar flows by means of numerical simulation. Two fluid models are investigated in channel and abrupt contraction geometries. In practice, the flows are confined by viewing windows, which alter the stresses along the optical path. The observed optical properties differ therefore from their counterpart in an ideal two-dimensional flow. To investigate the influence of these effects, the stress optical rule and the differential propagation Mueller matrix are used. The material parameters are selected so that a retardation of multiple orders is achieved, as is typical for highly birefringent melts. Errors due to three dimensional effects are mainly found on the symmetry plane, and increase significantly with the flow rate. Increasing the geometric aspect ratio improve the accuracy provided that the error on the retardation is less than one order. (C) 2004 Elsevier B.V. All rights reserved.

Three-dimensional simulation of the rolling of a saturated fibro-porous media

This paper describes recent advances made in computational modelling of the sugar cane liquid extraction process. The saturated fibro-porous material is rolled between circumferentially grooved rolls, which enhance frictional grip and provide a low-resistance path for liquid flow during the extraction process. Previously reported two-dimensional (2D) computational models, account for the large deformation of the porous material by solving the fully coupled governing fibre stress and fluid-flow equations using finite element techniques. While the 2D simulations provide much insight into the overarching cause-effect relationships, predictions of mechanical quantities such as roll separating force and particularly torque as a function of roll speed and degree of compression are not satisfactory for industrial use. It is considered that the unsatisfactory response in roll torque prediction may be due to the stress levels that exist between the groove tips and roots which have been largely neglected in the geometrically simplified 2D model. This paper gives results for both two- and three-dimensional finite element models and highlights their strengths and weaknesses in predicting key milling parameters. (c) 2005 Elsevier B.V. All rights reserved.

Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information.

A principled approach to interactive hierarchical non-linear visualization of high-dimensional data

Hierarchical visualization systems are desirable because a single two-dimensional visualization plot may not be sufficient to capture all of the interesting aspects of complex high-dimensional data sets. We extend an existing locally linear hierarchical visualization system PhiVis [1] in several directions: bf(1) we allow for em non-linear projection manifolds (the basic building block is the Generative Topographic Mapping -- GTM), bf(2) we introduce a general formulation of hierarchical probabilistic models consisting of local probabilistic models organized in a hierarchical tree, bf(3) we describe folding patterns of low-dimensional projection manifold in high-dimensional data space by computing and visualizing the manifold's local directional curvatures. Quantities such as magnification factors [3] and directional curvatures are helpful for understanding the layout of the nonlinear projection manifold in the data space and for further refinement of the hierarchical visualization plot. Like PhiVis, our system is statistically principled and is built interactively in a top-down fashion using the EM algorithm. We demonstrate the visualization system principle of the approach on a complex 12-dimensional data set and mention possible applications in the pharmaceutical industry.

Three-dimensional magnetic resonance imaging of the phakic crystalline lens during accommodation

To quantify changes in crystalline lens curvature, thickness, equatorial diameter, surface area, and volume during accommodation using a novel two-dimensional magnetic resonance imaging (MRI) paradigm to generate a complete three-dimensional crystalline lens surface model.

Two-axis temperature-insensitive accelerometer based on multicore fiber Bragg gratings

We report a compact two-dimensional accelerometer based upon a simple fiber cantilever constructed from a short length of multicore optical fiber. Two-axis measurement is demonstrated up to 3 kHz. Differential measurement between fiber Bragg gratings written in the multicore fiber provides temperature- insensitive measurements.

Investigation of two-wave mixing in arbitrary oriented sillenite crystals

A generalized systematic description of the Two-Wave Mixing (TWM) process in sillenite crystals allowing for arbitrary orientation of the grating vector is presented. An analytical expression for the TWM gain is obtained for the special case of plane waves in a thin crystal (|g|d«1) with large optical activity (|g|/?«1, g is the coupling constant, ? the rotatory power, d the crystal thickness). Using a two-dimensional formulation the scope of the nonlinear equations describing TWM can be extended to finite beams in arbitrary geometries and to any crystal parameters. Two promising applications of this formulation are proposed. The polarization dependence of the TWM gain is used for the flattening of Gaussian beam profiles without expanding them. The dependence of the TWM gain on the interaction length is used for the determination of the crystal orientation. Experiments carried out on Bi12GeO20 crystals of a non-standard cut are in good agreement with the results of modelling.

Interacting nonequilibrium systems with two temperatures

We investigate a simplified model of two fully connected magnetic systems maintained at different temperatures by virtue of being connected to two independent thermal baths while simultaneously being interconnected with each other. Using generating functional analysis, commonly used in statistical mechanics, we find exactly soluble expressions for their individual magnetization that define a two-dimensional nonlinear map, the equations of which have the same form as those obtained for densely connected equilibrium systems. Steady states correspond to the fixed points of this map, separating the parameter space into a rich set of nonequilibrium phases that we analyze in asymptotically high and low (nonequilibrium) temperature limits. The theoretical formalism is shown to revert to the classical nonequilibrium steady state problem for two interacting systems with a nonzero heat transfer between them that catalyzes a phase transition between ambient nonequilibrium states. © 2013 American Physical Society.

Investigation of two-wave mixing in arbitrary oriented sillenite crystals

A generalized systematic description of the Two-Wave Mixing (TWM) process in sillenite crystals allowing for arbitrary orientation of the grating vector is presented. An analytical expression for the TWM gain is obtained for the special case of plane waves in a thin crystal (|g|d«1) with large optical activity (|g|/?«1, g is the coupling constant, ? the rotatory power, d the crystal thickness). Using a two-dimensional formulation the scope of the nonlinear equations describing TWM can be extended to finite beams in arbitrary geometries and to any crystal parameters. Two promising applications of this formulation are proposed. The polarization dependence of the TWM gain is used for the flattening of Gaussian beam profiles without expanding them. The dependence of the TWM gain on the interaction length is used for the determination of the crystal orientation. Experiments carried out on Bi12GeO20 crystals of a non-standard cut are in good agreement with the results of modelling.

Linear stability of flow past two circular cylinders in a side-by-side arrangement

The linear stability of flow past two circular cylinders in a side-by-side arrangement is investigated theoretically, numerically and experimentally under the assumption of a two-dimensional flow field, in order to explore the origin of in-phase and antiphase oscillatory flows. Steady symmetric flow is realized at a small Reynolds number, but becomes unstable above a critical Reynolds number though the solution corresponding to the flow still satisfies the basic equations irrespective of the magnitude of the Reynolds number. We obtained the solution numerically and investigated its linear stability. We found that there are two kinds of unstable modes, i.e., antisymmetric and symmetric modes, which lead to in-phase and antiphase oscillatory flows, respectively. We determined the critical Reynolds numbers for the two modes and evaluated the critical distance at which the most unstable disturbance changes from the antisymmetric to the symmetric mode, or vice versa. ©2005 The Physical Society of Japan.

Regarding the benefit of zero-dimensional noise

Baker and Meese (2012) (B&M) provided an empirically driven criticism of the use of two-dimensional (2D) pixel noise in equivalent noise (EN) experiments. Their main objection was that in addition to injecting variability into the contrast detecting mechanisms, 2D noise also invokes gain control processes from a widely tuned contrast gain pool (e.g., Foley, 1994). B&M also developed a zero-dimensional (0D) noise paradigm in which all of the variance is concentrated in the mechanisms involved in the detection process. They showed that this form of noise conformed much more closely to expectations than did a 2D variant.