The unsteady flow of a weakly compressible fluid in a thin porous layer III: three-dimensional computations

We describe a novel method for determining the pressure and velocity fields for a weakly compressible fluid flowing in a thin three-dimensional layer composed of an inhomogeneous, anisotropic porous medium, with vertical side walls and variable upper and lower boundaries, in the presence of vertical wells injecting and/or extracting fluid. Our approach uses the method of matched asymptotic expansions to derive expressions for all significant process quantities, the computation of which requires only the solution of linear, elliptic, two-dimensional boundary value and eigenvalue problems. In this article, we provide full implementation details and present numerical results demonstrating the efficiency and accuracy of our scheme.

FACSGen 2.0 animation software: generating three-dimensional FACS-valid facial expressions for emotion research

In this article, we present FACSGen 2.0, new animation software for creating static and dynamic threedimensional facial expressions on the basis of the Facial Action Coding System (FACS). FACSGen permits total control over the action units (AUs), which can be animated at all levels of intensity and applied alone or in combination to an infinite number of faces. In two studies, we tested the validity of the software for the AU appearance defined in the FACS manual and the conveyed emotionality of FACSGen expressions. In Experiment 1, four FACS-certified coders evaluated the complete set of 35 single AUs and 54 AU combinations for AU presence or absence, appearance quality, intensity, and asymmetry. In Experiment 2, lay participants performed a recognition task on emotional expressions created with FACSGen software and rated the similarity of expressions displayed by human and FACSGen faces. Results showed good to excellent classification levels for all AUs by the four FACS coders, suggesting that the AUs are valid exemplars of FACS specifications. Lay participants’ recognition rates for nine emotions were high, and comparisons of human and FACSGen expressions were very similar. The findings demonstrate the effectiveness of the software in producing reliable and emotionally valid expressions, and suggest its application in numerous scientific areas, including perception, emotion, and clinical and euroscience research.

Wave-activity conservation laws for the three-dimensional anelastic and Boussinesq equations with a horizontally homogeneous background flow

Wave-activity conservation laws are key to understanding wave propagation in inhomogeneous environments. Their most general formulation follows from the Hamiltonian structure of geophysical fluid dynamics. For large-scale atmospheric dynamics, the Eliassen–Palm wave activity is a well-known example and is central to theoretical analysis. On the mesoscale, while such conservation laws have been worked out in two dimensions, their application to a horizontally homogeneous background flow in three dimensions fails because of a degeneracy created by the absence of a background potential vorticity gradient. Earlier three-dimensional results based on linear WKB theory considered only Doppler-shifted gravity waves, not waves in a stratified shear flow. Consideration of a background flow depending only on altitude is motivated by the parameterization of subgrid-scales in climate models where there is an imposed separation of horizontal length and time scales, but vertical coupling within each column. Here we show how this degeneracy can be overcome and wave-activity conservation laws derived for three-dimensional disturbances to a horizontally homogeneous background flow. Explicit expressions for pseudoenergy and pseudomomentum in the anelastic and Boussinesq models are derived, and it is shown how the previously derived relations for the two-dimensional problem can be treated as a limiting case of the three-dimensional problem. The results also generalize earlier three-dimensional results in that there is no slowly varying WKB-type requirement on the background flow, and the results are extendable to finite amplitude. The relationship A E =cA P between pseudoenergy A E and pseudomomentum A P, where c is the horizontal phase speed in the direction of symmetry associated with A P, has important applications to gravity-wave parameterization and provides a generalized statement of the first Eliassen–Palm theorem.

A three-dimensional open-framework indium selenide: [C7H10N][In9Se14]

An open-framework indium selenide, [C7H10N][In9Se14], has been prepared under solvothermal conditions in the presence of 3,5-dimethylpyridine, and characterized by single crystal diffraction, thermogravimetry, elemental analysis, FTIR spectroscopy and UV-Vis diffuse reflectance. The crystal structure of [C7H10N][In9Se14] contains an unusual building unit, in which corner-linked and edge-linked InSe45- tetrahedra coexist. The presence of one-dimensional circular channels, of ca. 6 Å diameter, results in approximately 25% of solvent accessible void space.

First results from a 3-dimensional middle atmosphere model

Initial results are presented from a middle atmosphere extension to a version of the European Centre For Medium Range Weather Forecasting tropospheric model. The extended version of the model has been developed as part of the UK Universities Global Atmospheric Modelling Project and extends from the ground to approximately 90 km. A comprehensive solar radiation scheme is included which uses monthly averaged climatological ozone values. A linearised infrared cooling scheme is employed. The basic climatology of the model is described; the parametrization of drag due to orographically forced gravity waves is shown to have a dramatic effect on the simulations of the winter hemisphere.

Humans use predictive kinematic models to calibrate visual cues to three-dimensional surface slant

When the sensory consequences of an action are systematically altered our brain can recalibrate the mappings between sensory cues and properties of our environment. This recalibration can be driven by both cue conflicts and altered sensory statistics, but neither mechanism offers a way for cues to be calibrated so they provide accurate information about the world, as sensory cues carry no information as to their own accuracy. Here, we explored whether sensory predictions based on internal physical models could be used to accurately calibrate visual cues to 3D surface slant. Human observers played a 3D kinematic game in which they adjusted the slant of a surface so that a moving ball would bounce off the surface and through a target hoop. In one group, the ball’s bounce was manipulated so that the surface behaved as if it had a different slant to that signaled by visual cues. With experience of this altered bounce, observers recalibrated their perception of slant so that it was more consistent with the assumed laws of kinematics and physical behavior of the surface. In another group, making the ball spin in a way that could physically explain its altered bounce eliminated this pattern of recalibration. Importantly, both groups adjusted their behavior in the kinematic game in the same way, experienced the same set of slants and were not presented with low-level cue conflicts that could drive the recalibration. We conclude that observers use predictive kinematic models to accurately calibrate visual cues to 3D properties of world.

Bilayer graphene formed by passage of current through graphite: evidence for a three-dimensional structure

The passage of an electric current through graphite or few-layer graphene can result in a striking structural transformation, but there is disagreement about the precise nature of this process. Some workers have interpreted the phenomenon in terms of the sublimation and edge reconstruction of essentially flat graphitic structures. An alternative explanation is that the transformation actually involves a change from a flat to a three-dimensional structure. Here we describe detailed studies of carbon produced by the passage of a current through graphite which provide strong evidence that the transformed carbon is indeed three-dimensional. The evidence comes primarily from images obtained in the scanning transmission electron microscope using the technique of high-angle annular dark-field imaging, and from a detailed analysis of electron energy loss spectra. We discuss the possible mechanism of the transformation, and consider potential applications of “three-dimensional bilayer graphene”.

In silico identification and three-dimensional modelling of the missense mutation in ADAMTS2 in a sheep flock with dermatosparaxis

Background Dermatosparaxis (Ehlers–Danlos syndrome in humans) is characterized by extreme fragility of the skin. It is due to the lack of mature collagen caused by a failure in the enzymatic processing of procollagen I. We investigated the condition in a commercial sheep flock. Hypothesis/Objectives Mutations in the ADAM metallopeptidase with thrombospondin type 1 motif, 2 (ADAMTS2) locus, are involved in the development of dermatosparaxis in humans, cattle and the dorper sheep breed; consequently, this locus was investigated in the flock. Animals A single affected lamb, its dam, the dam of a second affected lamb and the rams in the flock were studied. Methods DNA was purified from blood, PCR primers were used to detect parts of the ADAMS2 gene and nucleotide sequencing was performed using Sanger's procedure. Skin samples were examined using standard histology procedures. Results A missense mutation was identified in the catalytic domain of ADAMTS2. The mutation is predicted to cause the substitution in the mature ADAMTS2 of a valine molecule by a methionine molecule (V15M) affecting the catalytic domain of the enzyme. Both the ‘sorting intolerant from tolerant’ (SIFT) and the PolyPhen-2 methodologies predicted a damaging effect for the mutation. Three-dimensional modelling suggested that this mutation may alter the stability of the protein folding or distort the structure, causing the protein to malfunction. Conclusions and clinical importance Detection of the mutation responsible for the pathology allowed us to remove the heterozygote ram, thus preventing additional cases in the flock.

Na5(Ga4S)(GaS4)3·6H2O: a three-dimensional thiogallate containing a novel octahedral building block

The new thiogallate Na5(Ga4S)(GaS4)3·6H2O has been prepared solvothermally, using 3,5-dimethyl pyridine as a solvent, and characterised by powder and single crystal X-ray diffraction. This material, which exhibits a three-dimensional crystal structure, crystallises in the cubic space group View the MathML sourceF4¯3c (a = 17.557(4) Å). The crystal structure contains octahedral building blocks [Ga4S (GaS4)6]20−, linked into a three-dimensional network with a perovskite-type topology, and sodium hydrate clusters, [Na5(H2O)6]5+, filling the cavities in the [Ga4S(GaS4)6/2]5− framework. UV–Vis diffuse reflectance measurements indicate that this material is a wide band gap semiconductor, with a band gap of ca. 4.4 eV.

Human neural stem cell-derived cultures in three- dimensional substrates form spontaneously functional neuronal networks

Differentiated human neural stem cells were cultured in an inert three-dimensional (3D) scaffold and, unlike two-dimensional (2D) but otherwise comparable monolayer cultures, formed spontaneously active, functional neuronal networks that responded reproducibly and predictably to conventional pharmacological treatments to reveal functional, glutamatergic synapses. Immunocytochemical and electron microscopy analysis revealed a neuronal and glial population, where markers of neuronal maturity were observed in the former. Oligonucleotide microarray analysis revealed substantial differences in gene expression conferred by culturing in a 3D vs a 2D environment. Notable and numerous differences were seen in genes coding for neuronal function, the extracellular matrix and cytoskeleton. In addition to producing functional networks, differentiated human neural stem cells grown in inert scaffolds offer several significant advantages over conventional 2D monolayers. These advantages include cost savings and improved physiological relevance, which make them better suited for use in the pharmacological and toxicological assays required for development of stem cell-based treatments and the reduction of animal use in medical research.

Three dimensional analysis of cardiovascular development in mouse embryos using X-ray microcomputed tomography

Micro-computed tomography (μCT) has been successfully used to study the cardiovascular system of mouse embryos in situ. With the use of barium as a suitable contrast agent, blood vessels have been imaged and analysed quantitatively such as blood volume and vessel sizes on embryos of ages 14.5 to 16.5 days old. The advantage of using this imaging modality is that it has provided three dimensional information whilst leaving samples intact for further study.

Three-dimensional gallium sulphide open framework

The synthesis and crystal structure of four gallium sulphide open frameworks, built from supertetrahedral clusters, are described. The structures of [C4NH12]6[Ga10S18][C4NH12]6[Ga10S18](1) and [C4NH12]12[Ga20S35.5(S3)0.5O](2) contain supertetrahedral T3 clusters, while in the isostructural compounds [C4NH12]16[Ga10S18M4Ga16S33][C4NH12]16[Ga10S18M4Ga16S33] (M=CoM=Co(3), Zn (4)), T3 and T4 clusters alternate. These materials exhibit three-dimensional frameworks, with topologies consisting of two interpenetrating diamond lattices, and contain over 50% of solvent accessible void space. UV–Vis diffuse reflectance measurements indicate that these compounds are semiconducting, with band gaps over the range 3.4–4.1 eV.

Reverse correlation reveals how observers sample visual information when estimating three-dimensional shape

Human observers exhibit large systematic distance-dependent biases when estimating the three-dimensional (3D) shape of objects defined by binocular image disparities. This has led some to question the utility of disparity as a cue to 3D shape and whether accurate estimation of 3D shape is at all possible. Others have argued that accurate perception is possible, but only with large continuous perspective transformations of an object. Using a stimulus that is known to elicit large distance-dependent perceptual bias (random dot stereograms of elliptical cylinders) we show that contrary to these findings the simple adoption of a more naturalistic viewing angle completely eliminates this bias. Using behavioural psychophysics, coupled with a novel surface-based reverse correlation methodology, we show that it is binocular edge and contour information that allows for accurate and precise perception and that observers actively exploit and sample this information when it is available.

Disparity-defined objects moving in depth do not elicit three-dimensional shape constancy

Observers generally fail to recover three-dimensional shape accurately from binocular disparity. Typically, depth is overestimated at near distances and underestimated at far distances [Johnston, E. B. (1991). Systematic distortions of shape from stereopsis. Vision Research, 31, 1351–1360]. A simple prediction from this is that disparity-defined objects should appear to expand in depth when moving towards the observer, and compress in depth when moving away. However, additional information is provided when an object moves from which 3D Euclidean shape can be recovered, be this through the addition of structure from motion information [Richards, W. (1985). Structure from stereo and motion. Journal of the Optical Society of America A, 2, 343–349], or the use of non-generic strategies [Todd, J. T., & Norman, J. F. (2003). The visual perception of 3-D shape from multiple cues: Are observers capable of perceiving metric structure? Perception and Psychophysics, 65, 31–47]. Here, we investigated shape constancy for objects moving in depth. We found that to be perceived as constant in shape, objects needed to contract in depth when moving toward the observer, and expand in depth when moving away, countering the effects of incorrect distance scaling (Johnston, 1991). This is a striking example of the failure of shape con- stancy, but one that is predicted if observers neither accurately estimate object distance in order to recover Euclidean shape, nor are able to base their responses on a simpler processing strategy.

A moving observer in a three-dimensional world

For many tasks, such as retrieving a previously viewed object, an observer must form a representation of the world at one location and use it at another. A world-based 3D reconstruction of the scene built up from visual information would fulfil this requirement, something computer vision now achieves with great speed and accuracy. However, I argue that it is neither easy nor necessary for the brain to do this. I discuss biologically plausible alternatives, including the possibility of avoiding 3D coordinate frames such as ego-centric and world-based representations. For example, the distance, slant and local shape of surfaces dictate the propensity of visual features to move in the image with respect to one another as the observer’s perspective changes (through movement or binocular viewing). Such propensities can be stored without the need for 3D reference frames. The problem of representing a stable scene in the face of continual head and eye movements is an appropriate starting place for understanding the goal of 3D vision, more so, I argue, than the case of a static binocular observer.