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.

Synthesis and structure-activity relationship studies of CD4 down-modulating cyclotriazadisulfonamide (CADA) analogues

HIV attachment via the CD4 receptor is an important target for developing novel approaches to HIV chemotherapy. Cyclotriazadisulfonamide (CADA) inhibits HIV at submicromolar levels by specifically down-modulating cell-surface and intracellular CD4. An effective five-step synthesis of CADA in 30% overall yield is reported. This synthesis has also been modified to produce more than 50 analogues. Many tail-group analogues have been made by removing the benzyl tail of CADA and replacing it with various alkyl, acyl, alkoxycarbonyl and aminocarbonyl substituents. A series of sidearm analogues, including two unsymmetrical compounds, have also been prepared by modifying the CADA synthesis, replacing the toluenesulfonyl sidearms with other sulfonyl groups. Testing 30 of these compounds in MT-4 cells shows a wide range of CD4 down-modulation potency, which correlates with ability to inhibit HIV-1. Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) approaches. The X-ray crystal structures of four compounds, including CADA, show the same major conformation of the central 12-membered ring. The solid-state structure of CADA was energy minimized and used to generate the remaining 29 structures, which were similarly minimized and aligned to produce the 3D-QSAR models. Both models indicate that steric bulk of the tail group, and, to a lesser extent, the sidearms mainly determine CD4 down-modulation potency in this series of compounds.

Structural studies on acridine derivatives binding to telomeric DNA

Acridine derivatives can inhibit a variety of nuclear enzymes by binding or intercalating to DNA. This class of compounds is of great interest in the development of novel anticancer agents. Despite the availability of crystallographic data for some of the compounds complexed with DNA, uncertainties remain about the mechanisms of action, binding preferences and biological targets. To investigate the intercalation of several acridine derivatives, a variety of techniques are being employed. Single-crystal X-ray diffraction is being used to determine the high resolution three-dimensional structure of short sequences of quadruplex telomeric DNA with bound drug. This will be compared to the effect of drug binding to long segments of double-stranded DNA using fibre diffraction, with neutron diffraction studies planned to analyse the hydrogen bonding patterns of the DNA-drug complexes. Small-angle neutron scattering (SANS) will also be applied to study drug binding to both short and long sequences of quadruplex and double-stranded DNA in solution. Initial SANS measurements of the telomeric repeat d(TGGGGT) imply that this hexamer is present as a quadruplex. (c) 2006 Elsevier B.V. All rights reserved.

Synthesis, crystal structure and thermal studies of catena(L-glutamato)-aqua copper(II) monohydrate

The synthesis. crystal structure and thermal study of the blue catena-(L-glutamato)-aqua copper(II) monohydrate have been reported. The compound crystallizes in P2(1)2(1)2(1) space group and consists of a polymeric three-dimensional network of copper(II) which is coordinated with the amino nitrogen and the carboxylate oxygen Of L-glutamate, the side chain carboxylate oxygen of a neighbouring L-glutamate and the oxygen of a water molecule in the equatorial position. Weak coordination of two additional glutamate oxygen atoms to both the axial positions Completes a distorted octahedron. The crystal structure shows that the lattice water is stabilized by the formation of strong H-bonding network with the coordinated water molecule. Removal and reabsorption of the water molecule have been studied by thermal analysis.

Linking energy and maintenance management for sustainability through three American case studies

Purpose – The purpose of this paper is to present the findings and lessons learned from three case studies conducted for facilities located in California, North America. The findings aim to focus on energy and maintenance management practices and the interdependent link between energy and maintenance. Design/methodology/approach – The research is based on a positivist epistemological philosophical approach informed by action research. The research cycle was completed for each case study. A case study report was provided to each facility management team to foster collaboration with the researcher and to document case study process and results. Findings – Composite findings of the case studies include: there is an interdependent link between energy and maintenance management; reactive maintenance and energy management methods are commonly used; and more proactively operated and managed buildings require the interdependent link between energy maintenance management to be better understood. Research limitations/implications – The three case studies were located in California. Although the case study results can be generalized, determination of how to generalize and apply the results to commercial buildings outside of the USA is beyond the scope of this paper. Practical implications – Detailed discussion of the needs of the three facility management teams are discussed by identifying a current challenge, developing a solution and documenting lessons learned using the research cycle. Originality/value – The paper seeks to demonstrate the interdependencies of energy and maintenance management, two topics which are often researched interdependently. Additionally, the paper provides insight about maintenance management, a topic often cited as being under researched.

A self-similar expansion model for use in solar wind transient propogation studies

Since the advent of wide-angle imaging of the inner heliosphere, a plethora of techniques have been developed to investigate the three-dimensional structure and kinematics of solar wind transients, such as coronal mass ejections, from their signatures in single- and multi-spacecraft imaging observations. These techniques, which range from the highly complex and computationally intensive to methods based on simple curve fitting, all have their inherent advantages and limitations. In the analysis of single-spacecraft imaging observations, much use has been made of the fixed φ fitting (FPF) and harmonic mean fitting (HMF) techniques, in which the solar wind transient is considered to be a radially propagating point source (fixed φ, FP, model) and a radially expanding circle anchored at Sun centre (harmonic mean, HM, model), respectively. Initially, we compare the radial speeds and propagation directions derived from application of the FPF and HMF techniques to a large set of STEREO/Heliospheric Imager (HI) observations. As the geometries on which these two techniques are founded constitute extreme descriptions of solar wind transients in terms of their extent along the line of sight, we describe a single-spacecraft fitting technique based on a more generalized model for which the FP and HM geometries form the limiting cases. In addition to providing estimates of a transient’s speed and propagation direction, the self-similar expansion fitting (SSEF) technique provides, in theory, the capability to estimate the transient’s angular extent in the plane orthogonal to the field of view. Using the HI observations, and also by performing a Monte Carlo simulation, we assess the potential of the SSEF technique.

Dynamic simulation studies of structural formation and transition in electro-magneto-rheological fluids

The computer simulation method has been used to study the structural formation and transition of electro-magneto-rheological (EMR) fluids under compatible electric and magnetic fields. When the fields are applied simultaneously and perpendicularly to each other, the particles rapidly arrange into two-dimensional close-packed layer structures parallel to both fields. The layers then combine together to form thicker sheet-like structures, which finally relax into three-dimensional close-packed structures with the help of the thermal fluctuations. On the other hand, if the electric field is applied firstly to induce the body-centered tetragonal (BCT) columns in the system, and then the magnetic field is applied in the perpendicular direction. the BCT to face-centered cubic (FCC) structure transition is observed in very short time. Following that. the structure keeps on evolving due to the demagnetization effect and finally form the three-dimensional close-packed structures.

Formation and circulation of the cold intermediate layer in the Gulf of Saint Lawrence

[ 1] The local heat content and formation rate of the cold intermediate layer (CIL) in the Gulf of Saint Lawrence are examined using a combination of new in situ wintertime observations and a three-dimensional numerical model. The field observations consist of five moorings located throughout the gulf over the period of November 2002 to June 2003. The observations demonstrate a substantially deeper surface mixed layer in the central and northeast gulf than in regions downstream of the buoyant surface outflow from the Saint Lawrence Estuary. The mixed-layer depth in the estuary remains shallow (< 60 m) throughout winter, with the arrival of a layer of near-freezing waters between 40 and 100 m depth in April. An eddy-permitting ice-ocean model with realistic forcing is used to hindcast the period of observation. The model simulates well the seasonal evolution of mixed-layer depth and CIL heat content. Although the greatest heat losses occur in the northeast, the most significant change in CIL heat content over winter occurs in the Anticosti Trough. The observed renewal of CIL in the estuary in spring is captured by the model. The simulation highlights the role of the northwest gulf, and in particular, the separation of the Gaspe Current, in controlling the exchange of CIL between the estuary and the gulf. In order to isolate the effects of inflow through the Strait of Belle Isle on the CIL heat content, we examine a sensitivity experiment in which the strait is closed. This simulation shows that the inflow has a less important effect on the CIL than was suggested by previous studies.

Acoustic scattering by mildly rough unbounded surfaces in three dimensions

For a nonlocally perturbed half- space we consider the scattering of time-harmonic acoustic waves. A second kind boundary integral equation formulation is proposed for the sound-soft case, based on a standard ansatz as a combined single-and double-layer potential but replacing the usual fundamental solution of the Helmholtz equation with an appropriate half- space Green's function. Due to the unboundedness of the surface, the integral operators are noncompact. In contrast to the two-dimensional case, the integral operators are also strongly singular, due to the slow decay at infinity of the fundamental solution of the three-dimensional Helmholtz equation. In the case when the surface is sufficiently smooth ( Lyapunov) we show that the integral operators are nevertheless bounded as operators on L-2(Gamma) and on L-2(Gamma G) boolean AND BC(Gamma) and that the operators depend continuously in norm on the wave number and on G. We further show that for mild roughness, i.e., a surface G which does not differ too much from a plane, the boundary integral equation is uniquely solvable in the space L-2(Gamma) boolean AND BC(Gamma) and the scattering problem has a unique solution which satisfies a limiting absorption principle in the case of real wave number.

The effect of a large freshwater perturbation on the glacial north Atlantic Ocean using a coupled general circulation model

The commonly held view of the conditions in the North Atlantic at the last glacial maximum, based on the interpretation of proxy records, is of large-scale cooling compared to today, limited deep convection, and extensive sea ice, all associated with a southward displaced and weakened overturning thermohaline circulation (THC) in the North Atlantic. Not all studies support that view; in particular, the "strength of the overturning circulation" is contentious and is a quantity that is difficult to determine even for the present day. Quasi-equilibrium simulations with coupled climate models forced by glacial boundary conditions have produced differing results, as have inferences made from proxy records. Most studies suggest the weaker circulation, some suggest little or no change, and a few suggest a stronger circulation. Here results are presented from a three-dimensional climate model, the Hadley Centre Coupled Model version 3 (HadCM3), of the coupled atmosphere - ocean - sea ice system suggesting, in a qualitative sense, that these diverging views could all have occurred at different times during the last glacial period, with different modes existing at different times. One mode might have been characterized by an active THC associated with moderate temperatures in the North Atlantic and a modest expanse of sea ice. The other mode, perhaps forced by large inputs of meltwater from the continental ice sheets into the northern North Atlantic, might have been characterized by a sluggish THC associated with very cold conditions around the North Atlantic and a large areal cover of sea ice. The authors' model simulation of such a mode, forced by a large input of freshwater, bears several of the characteristics of the Climate: Long-range Investigation, Mapping, and Prediction (CLIMAP) Project's reconstruction of glacial sea surface temperature and sea ice extent.

Assimilation of stratospheric ozone from MIPAS into a global general-circulation model: The September 2002 vortex split

Ozone and temperature profiles from the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) have been assimilated, using three-dimensional variational assimilation, into a stratosphere troposphere version of the Met Office numerical weather-prediction system. Analyses are made for the month of September 2002, when there was an unprecedented split in the southern hemisphere polar vortex. The analyses are validated against independent ozone observations from sondes, limb-occultation and total column ozone satellite instruments. Through most of the stratosphere, precision varies from 5 to 15%, and biases are 15% or less of the analysed field. Problems remain in the vortex and below the 60 hPa. level, especially at the tropopause where the analyses have too much ozone and poor agreement with independent data. Analysis problems are largely a result of the model rather than the data, giving confidence in the MIPAS ozone retrievals, though there may be a small high bias in MIPAS ozone in the lower stratosphere. Model issues include an excessive Brewer-Dobson circulation, which results both from known problems with the tracer transport scheme and from the data assimilation of dynamical variables. The extreme conditions of the vortex split reveal large differences between existing linear ozone photochemistry schemes. Despite these issues, the ozone analyses are able to successfully describe the ozone hole split and compare well to other studies of this event. Recommendations are made for the further development of the ozone assimilation system.