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.

Boundary-layer ventilation by baroclinic lifecycles

Ventilation of the boundary layer has an important effect on local and regional air quality and is a prerequisite for long-range pollution transport. Once in the free troposphere, pollutants can alter the chemical composition of the troposphere and impact on the Earth's radiative forcing. Idealised baroclinic life cycles, LC1 and LC2, have been simulated in a three-dimensional dry hemispheric model in the presence of boundary-layer turbulent fluxes. A passive tracer is added to the simulations to represent pollution emitted at, or near, the surface. A simple conveyor-belt diagnostic is developed to objectively identify regions of the boundary layer that can be ventilated by either warm or cold conveyor belts. Transport of pollutants within and above the boundary layer is examined on synoptic scales. Three different physical mechanisms are found to interact with each other to ventilate pollutants out of the boundary layer. These mechanisms are turbulent mixing within the boundary layer, horizontal advection due to Ekman convergence and divergence within the boundary layer, and advection by the warm conveyor belt. The mass of tracer ventilated by the two life cycles is remarkably similar given the differences in frontal structure, suggesting that the large-scale baroclinicity is an effective constraint on ventilation.

On the attribution of stratospheric ozone and temperature changes to changes in ozone-depleting substances and well-mixed greenhouse gases

The vertical profile of global-mean stratospheric temperature changes has traditionally represented an important diagnostic for the attribution of the cooling effects of stratospheric ozone depletion and CO2 increases. However, CO2-induced cooling alters ozone abundance by perturbing ozone chemistry, thereby coupling the stratospheric ozone and temperature responses to changes in CO2 and ozone-depleting substances (ODSs). Here we untangle the ozone-temperature coupling and show that the attribution of global-mean stratospheric temperature changes to CO2 and ODS changes (which are the true anthropogenic forcing agents) can be quite different from the traditional attribution to CO2 and ozone changes. The significance of these effects is quantified empirically using simulations from a three-dimensional chemistry-climate model. The results confirm the essential validity of the traditional approach in attributing changes during the past period of rapid ODS increases, although we find that about 10% of the upper stratospheric ozone decrease from ODS increases over the period 1975–1995 was offset by the increase in CO2, and the CO2-induced cooling in the upper stratosphere has been somewhat overestimated. When considering ozone recovery, however, the ozone-temperature coupling is a first-order effect; fully 2/5 of the upper stratospheric ozone increase projected to occur from 2010–2040 is attributable to CO2 increases. Thus, it has now become necessary to base attribution of global-mean stratospheric temperature changes on CO2 and ODS changes rather than on CO2 and ozone changes.

Planetary-wave-induced transport in the stratosphere

In the stratosphere, chemical tracers are drawn systematically from the equator to the pole. This observed Brewer–Dobson circulation is driven by wave drag, which in the stratosphere arises mainly from the breaking and dissipation of planetary-scale Rossby waves. While the overall sense of the circulation follows from fundamental physical principles, a quantitative theoretical understanding of the connection between wave drag and Lagrangian transport is limited to linear, small-amplitude waves. However, planetary waves in the stratosphere generally grow to a large amplitude and break in a strongly nonlinear fashion. This paper addresses the connection between stratospheric wave drag and Lagrangian transport in the presence of strong nonlinearity, using a mechanistic three-dimensional primitive equations model together with offline particle advection. Attention is deliberately focused on a weak forcing regime, such that sudden warmings do not occur and a quasi-steady state is reached, in order to examine this question in the cleanest possible context. Wave drag is directly linked to the transformed Eulerian mean (TEM) circulation, which is often used as a surrogate for mean Lagrangian motion. The results show that the correspondence between the TEM and mean Lagrangian velocities is quantitatively excellent in regions of linear, nonbreaking waves (i.e., outside the surf zone), where streamlines are not closed. Within the surf zone, where streamlines are closed and meridional particle displacements are large, the agreement between the vertical components of the two velocity fields is still remarkably good, especially wherever particle paths are coherent so that diabatic dispersion is minimized. However, in this region the meridional mean Lagrangian velocity bears little relation to the meridional TEM velocity, and reflects more the kinematics of mixing within and across the edges of the surf zone. The results from the mechanistic model are compared with those from the Canadian Middle Atmosphere Model to test the robustness of the conclusions.

Forecast, measurement, and modeling of an unprecedented polar ozone filament event over Mauna Loa Observatory, Hawaii

In mid-March 2005 the northern lower stratospheric polar vortex experienced a severe stretching episode, bringing a large polar filament far south of Alaska toward Hawaii. This meridional intrusion of rare extent, coinciding with the polar vortex final warming and breakdown, was followed by a zonal stretching in the wake of the easterly propagating subtropical main flow. This caused polar air to remain over Hawaii for several days before diluting into the subtropics. After being successfully forecasted to pass over Hawaii by the high-resolution potential vorticity advection model Modèle Isentrope du transport Méso-échelle de l'Ozone Stratosphérique par Advection (MIMOSA), the filament was observed on isentropic surfaces between 415 K and 455 K (17–20 km) by the Jet Propulsion Laboratory stratospheric ozone lidar measurements at Mauna Loa Observatory, Hawaii, between 16 and 19 March 2005. It was materialized as a thin layer of enhanced ozone peaking at 1.6 ppmv in a region where the climatological values usually average 1.0 ppmv. These values were compared to those obtained by the three-dimensional Chemistry-Transport Model MIMOSA-CHIM. Agreement between lidar and model was excellent, particularly in the similar appearance of the ozone peak near 435 K (18.5 km) on 16 March, and the persistence of this layer at higher isentropic levels for the following three days. Passive ozone, also modeled by MIMOSA-CHIM, was at about 3–4 ppmv inside the filament while above Hawaii. A detailed history of the modeled chemistry inside the filament suggests that the air mass was still polar ozone–depleted when passing over Hawaii. The filament quickly separated from the main vortex after its Hawaiian overpass. It never reconnected and, in less than 10 days, dispersed entirely in the subtropics

The middle-atmosphere Hadley circulation and equatorial inertial adjustment

In the tropical middle atmosphere the climatological radiative equilibrium temperature is inconsistent with gradient-wind balance and the available angular momentum, especially during solstice seasons. Adjustment toward a balanced state results in a type of Hadley circulation that lies outside the “downward control” view of zonally averaged dynamics. This middle-atmosphere Hadley circulation is reexamined here using a zonally symmetric balance model driven through an annual cycle. It is found that the inclusion of a realistic radiation scheme leads to a concentration of the circulation near the stratopause and to its closing off in the mesosphere, with no need for relaxational damping or a rigid lid. The evolving zonal flow is inertially unstable, leading to a rapid process of inertial adjustment, which becomes significant in the mesosphere. This short-circuits the slower process of angular momentum homogenization by the Hadley circulation itself, thereby weakening the latter. The effect of the meridional circulation associated with extratropical wave drag on the Hadley circulation is considered. It is shown that the two circulations are independent for linear (quasigeostrophic) zonal-mean dynamics, and interact primarily through the advection of temperature and angular momentum. There appears to be no significant coupling in the deep Tropics via temperature advection since the wave-driven circulation is unable to alter meridional temperature gradients in this region. However, the wave-driven circulation can affect the Hadley circulation by advecting angular momentum out of the Tropics. The validity of the zonally symmetric balance model with parameterized inertial adjustment is tested by comparison with a three-dimensional primitive equations model. Fields from a middle-atmosphere GCM are also examined for evidence of these processes. While many aspects of the GCM circulation are indicative of the middle-atmosphere Hadley circulation, particularly in the upper stratosphere, it appears that the circulation is obscured in the mesosphere and lower stratosphere by other processes.

A Gaussian-mixture ensemble transform filter

We generalize the popular ensemble Kalman filter to an ensemble transform filter, in which the prior distribution can take the form of a Gaussian mixture or a Gaussian kernel density estimator. The design of the filter is based on a continuous formulation of the Bayesian filter analysis step. We call the new filter algorithm the ensemble Gaussian-mixture filter (EGMF). The EGMF is implemented for three simple test problems (Brownian dynamics in one dimension, Langevin dynamics in two dimensions and the three-dimensional Lorenz-63 model). It is demonstrated that the EGMF is capable of tracking systems with non-Gaussian uni- and multimodal ensemble distributions. Copyright © 2011 Royal Meteorological Society

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.

Predicting magnetospheric dynamics with a coupled sun-to-Earth model: challenges and first results

Results from the first Sun-to-Earth coupled numerical model developed at the Center for Integrated Space Weather Modeling are presented. The model simulates physical processes occurring in space spanning from the corona of the Sun to the Earth's ionosphere, and it represents the first step toward creating a physics-based numerical tool for predicting space weather conditions in the near-Earth environment. Two 6- to 7-d intervals, representing different heliospheric conditions in terms of the three-dimensional configuration of the heliospheric current sheet, are chosen for simulations. These conditions lead to drastically different responses of the simulated magnetosphere-ionosphere system, emphasizing, on the one hand, challenges one encounters in building such forecasting tools, and on the other hand, emphasizing successes that can already be achieved even at this initial stage of Sun-to-Earth modeling.