Sand and nest temperatures and an estimate of hatchling sex ratio from the Heron Island green turtle (Chelonia mydas) rookery, Southern Great Barrier Reef

Sand and nest temperatures were monitored during the 2002-2003 nesting season of the green turtle, Chelonia mydas, at Heron Island, Great Barrier Reef, Australia. Sand temperatures increased from similar to 24 degrees C early in the season to 27-29 degrees C in the middle, before decreasing again. Beach orientation affected sand temperature at nest depth throughout the season; the north facing beach remained 0.7 degrees C warmer than the east, which was 0.9 degrees C warmer than the south, but monitored nest temperatures were similar across all beaches. Sand temperature at 100 cm depth was cooler than at 40 cm early in the season, but this reversed at the end. Nest temperatures increased 2-4 degrees C above sand temperatures during the later half of incubation due to metabolic heating. Hatchling sex ratio inferred from nest temperature profiles indicated a strong female bias.

How lifetimes shape epigenotype within and across generations

Despite our detailed characterization of the human genome at the level of the primary DNA sequence, we are still far from understanding the molecular events underlying phenotypic variation. Epigenetic modifications to the DNA sequence and associated chromatin are known to regulate gene expression and, as such, are a significant contributor to phenotype. Studies of inbred mice and monozygotic twins show that variation in the epigenotype can be seen even between genetically identical individuals and that this, in some cases at least, is associated with phenotypic differences. Moreover, recent evidence suggests that the epigenome can be influenced by the environment and these changes can last a lifetime. However, we also know that epigenetic states in real-time are in continual flux and, as a result, the epigenome exhibits instability both within and across generations. We still do not understand the rules governing the establishment and maintenance of the epigenotype at any particular locus. The underlying DNA sequence itself and the sequence at unlinked loci (modifier loci) are certainly involved. Recent support for the existence of transgenerational epigenetic inheritance in mammals suggests that the epigenetic state of the locus in the previous generation may also play a role. Over the next decade, many of these processes will be better understood, heralding a greater capacity for us to correlate measurable molecular marks with phenotype and providing the opportunity for improved diagnosis and presymptomatic healthcare.

Influence of nanowire density on the shape and optical properties of ternary InGaAs nanowires

We have synthesized ternary InGaAs nanowires on (111)B GaAs surfaces by metal-organic chemical vapor deposition. Au colloidal nanoparticles were employed to catalyze nanowire growth. We observed the strong influence of nanowire density on nanowire height, tapering, and base shape specific to the nanowires with high In composition. This dependency was attributed to the large difference of diffusion length on (111)B surfaces between In and Ga reaction species, with In being the more mobile species. Energy dispersive X-ray spectroscopy analysis together with high-resolution electron microscopy study of individual InGaAs nanowires shows large In/Ga compositional variation along the nanowire supporting the present diffusion model. Photoluminescence spectra exhibit a red shift with decreasing nanowire density due to the higher degree of In incorporation in more sparsely distributed InGaAs nanowires.

3D statistical shape models to embed spatial relationship information

This paper presents the creation of 3D statistical shape models of the knee bones and their use to embed information into a segmentation system for MRIs of the knee. We propose utilising the strong spatial relationship between the cartilages and the bones in the knee by embedding this information into the created models. This information can then be used to automate the initialisation of segmentation algorithms for the cartilages. The approach used to automatically generate the 3D statistical shape models of the bones is based on the point distribution model optimisation framework of Davies. Our implementation of this scheme uses a parameterized surface extraction algorithm, which is used as the basis for the optimisation scheme that automatically creates the 3D statistical shape models. The current approach is illustrated by generating 3D statistical shape models of the patella, tibia and femoral bones from a segmented database of the knee. The use of these models to embed spatial relationship information to aid in the automation of segmentation algorithms for the cartilages is then illustrated.

Automatic segmentation of the knee bones using 3D active shape models

This paper presents an automated segmentation approach for MR images of the knee bones. The bones are the first stage of a segmentation system for the knee, primarily aimed at the automated segmentation of the cartilages. The segmentation is performed using 3D active shape models (ASM), which are initialized using an affine registration to an atlas. The 3D ASMs of the bones are created automatically using a point distribution model optimization scheme. The accuracy and robustness of the segmentation approach was experimentally validated using an MR database of fat suppressed spoiled gradient recall images.

The role of local luminance amplitude in the interpretation of shape-from-shading in textured surfaces

Luminance changes within a scene are ambiguous; they can indicate reflectance changes, shadows, or shading due to surface undulations. How does vision distinguish between these possibilities? When a surface painted with an albedo texture is shaded, the change in local mean luminance (LM) is accompanied by a similar modulation of the local luminance amplitude (AM) of the texture. This relationship does not necessarily hold for reflectance changes or for shading of a relief texture. Here we concentrate on the role of AM in shape-from-shading. Observers were presented with a noise texture onto which sinusoidal LM and AM signals were superimposed, and were asked to indicate which of two marked locations was closer to them. Shape-from-shading was enhanced when LM and AM co-varied (in-phase), and was disrupted when they were out-of-phase. The perceptual differences between cue types (in-phase vs out-of-phase) were enhanced when the two cues were present at different orientations within a single image. Similar results were found with a haptic matching task. We conclude that vision can use AM to disambiguate luminance changes. LM and AM have a positive relationship for rendered, undulating, albedo textures, and we assess the degree to which this relationship holds in natural images. [Supported by EPSRC grants to AJS and MAG].

Local luminance amplitude modulates the interpretation of shape-from-shading in textured surfaces

The pattern of illumination on an undulating surface can be used to infer its 3-D form (shape-from-shading). But the recovery of shape would be invalid if the luminance changes actually arose from changes in reflectance. So how does vision distinguish variation in illumination from variation in reflectance to avoid illusory depth? When a corrugated surface is painted with an albedo texture, the variation in local mean luminance (LM) due to shading is accompanied by a similar modulation in local luminance amplitude (AM). This is not so for reflectance variation, nor for roughly textured surfaces. We used depth mapping and paired comparison methods to show that modulations of local luminance amplitude play a role in the interpretation of shape-from-shading. The shape-from-shading percept was enhanced when LM and AM co-varied (in-phase) and was disrupted when they were out of phase or (to a lesser degree) when AM was absent. The perceptual differences between cue types (in-phase vs out-of-phase) were enhanced when the two cues were present at different orientations within a single image. Our results suggest that when LM and AM co-vary (in-phase) this indicates that the source of variation is illumination (caused by undulations of the surface), rather than surface reflectance. Hence, the congruence of LM and AM is a cue that supports a shape-from-shading interpretation. © 2006 Elsevier Ltd. All rights reserved.

The role of texture amplitude in shape from shading: evidence from a haptic matching task

The pattern of illumination on an undulating surface can be used to infer its 3-D form (shape from shading). But the recovery of shape would be invalid if the shading actually arose from reflectance variation. When a corrugated surface is painted with an albedo texture, the variation in local mean luminance (LM) due to shading is accompanied by a similar modulation in texture amplitude (AM). This is not so for reflectance variation, nor for roughly textured surfaces. We used a haptic matching technique to show that modulations of texture amplitude play a role in the interpretation of shape from shading. Observers were shown plaid stimuli comprising LM and AM combined in-phase (LM+AM) on one oblique and in anti-phase (LM-AM) on the other. Stimuli were presented via a modified ReachIN workstation allowing the co-registration of visual and haptic stimuli. In the first experiment, observers were asked to adjust the phase of a haptic surface, which had the same orientation as the LM+AM combination, until its peak in depth aligned with the visually perceived peak. The resulting alignments were consistent with the use of a lighting-from-above prior. In the second experiment, observers were asked to adjust the amplitude of the haptic surface to match that of the visually perceived surface. Observers chose relatively large amplitude settings when the haptic surface was oriented and phase-aligned with the LM+AM cue. When the haptic surface was aligned with the LM-AM cue, amplitude settings were close to zero. Thus the LM/AM phase relation is a significant visual depth cue, and is used to discriminate between shading and reflectance variations. [Supported by the Engineering and Physical Sciences Research Council, EPSRC].

The role of texture in shape from shading: are humans biased towards seeing relief textures?

When a textured surface is modulated in depth and illuminated, the level of illumination varies across the surface, producing coarse-scale luminance modulations (LM) and amplitude modulation (AM) of the fine-scale texture. If the surface has an albedo texture (reflectance variation) then the LM and AM components are always in-phase, but if the surface has a relief texture the phase relation between LM and AM varies with the direction and nature of the illuminant. We showed observers sinusoidal luminance and amplitude modulations of a binary noise texture, in various phase relationships, in a paired-comparisons design. In the first experiment, the combinations under test were presented in different temporal intervals. Observers indicated which interval contained the more depthy stimulus. LM and AM in-phase were seen as more depthy than LM alone which was in turn more depthy than LM and AM in anti-phase, but the differences were weak. In the second experiment the combinations under test were presented in a single interval on opposite obliques of a plaid pattern. Observers were asked to indicate the more depthy oblique. Observers produced the same depth rankings as before, but now the effects were more robust and significant. Intermediate LM/AM phase relationships were also tested: phase differences less than 90 deg were seen as more depthy than LM-only, while those greater than 90 deg were seen as less depthy. We conjecture that the visual system construes phase offsets between LM and AM as indicating relief texture and thus perceives these combinations as depthy even when their phase relationship is other than zero. However, when different LM/AM pairs are combined in a plaid, the signals on the obliques are unlikely to indicate corrugations of the same texture, and in this case the out-of-phase pairing is seen as flat. [Supported by the Engineering and Physical Sciences Research Council (EPSRC)].

The role of texture amplitude in shape from shading

When a textured surface is modulated in depth and illuminated, parts of the surface receive different levels of illumination; the resulting variations in luminance can be used to infer the shape of the depth modulations-shape from shading. The changes in illumination also produce changes in the amplitude of the texture, although local contrast remains constant. We investigated the role of texture amplitude in supporting shape from shading. If a luminance plaid is added to a binary noise texture (LM), shape from shading produces perception of corrugations in two directions. If the amplitude of the noise is also modulated (AM) such that it is in-phase with one of the luminance sinusoids and out-of-phase with the other, the resulting surface is seen as corrugated in only one directionöthat supported by the in-phase pairing. We confirmed this subjective report experimentally, using a depth-mapping technique. Further, we asked naïve observers to indicate the direction of corrugations in plaids made up of various combinations of LM and AM. LM+AM was seen as having most depth, then LM-only, then LM-AM, and then AM-only. Our results suggest that while LM is required to see depth from shading, its phase relative to any AM component is also important.