Analysis of shape uses local apparent position rather than physical position.
Ontology highlight
ABSTRACT:
SUBMITTER: Dickinson JE
PROVIDER: S-EPMC8419882 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Local solid shape applies to the surface curvature of small surface patches-essentially regions of approximately constant curvatures-of volumetric objects that are smooth volumetric regions in Euclidean 3-space. This should be distinguished from local shape in pictorial space. The difference is categorical. Although local solid shape has naturally been explored in haptics, results in vision are not forthcoming. We describe a simple experiment in which observers judge shape quality and magnitude of cinematographic presentations. Without prior training, observers readily use continuous shape index and Casorati curvature scales with reasonable resolution.
| S-EPMC5016822 | biostudies-other
Project description:Perceiving the positions of objects is a prerequisite for most other visual and visuomotor functions, but human perception of object position varies from one individual to the next. The source of these individual differences in perceived position and their perceptual consequences are unknown. Here, we tested whether idiosyncratic biases in the underlying representation of visual space propagate across different levels of visual processing. In Experiment 1, using a position matching task, we found stable, observer-specific compressions and expansions within local regions throughout the visual field. We then measured Vernier acuity (Experiment 2) and perceived size of objects (Experiment 3) across the visual field and found that individualized spatial distortions were closely associated with variations in both visual acuity and apparent object size. Our results reveal idiosyncratic biases in perceived position and size, originating from a heterogeneous spatial resolution that carries across the visual hierarchy.
| S-EPMC7423464 | biostudies-literature
Project description:BackgroundProtein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation.ResultsUsing a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations.ConclusionThe conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.
| S-EPMC3224362 | biostudies-literature
Project description:The stiffness of the extracellular matrix (ECM) is known to influence cell behavior. The ability to manipulate the stiffness of ECM has important implications in understanding how cells interact mechanically with their microenvironment. This article describes an approach to manipulating the stiffness ECM, whereby magnetic beads are embedded in the ECM through bioconjugation between the streptavidin-coated beads and the collagen fibers and then manipulated by an external magnetic field. It also reports both analytical results (obtained by formal modeling and numerical simulation) and statistically meaningful experimental results (obtained by atomic force microscopy) that demonstrate the effectiveness of this approach. These results clearly suggest the possibility of creating desired stiffness gradients in ECM in vitro to influence cell behavior.
| S-EPMC3907242 | biostudies-literature
Project description:We present an auxiliary learning task for the problem of neuron segmentation in electron microscopy volumes. The auxiliary task consists of the prediction of local shape descriptors (LSDs), which we combine with conventional voxel-wise direct neighbor affinities for neuron boundary detection. The shape descriptors capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction. On a study comparing several existing methods across various specimen, imaging techniques, and resolutions, auxiliary learning of LSDs consistently increases segmentation accuracy of affinity-based methods over a range of metrics. Furthermore, the addition of LSDs promotes affinity-based segmentation methods to be on par with the current state of the art for neuron segmentation (flood-filling networks), while being two orders of magnitudes more efficient-a critical requirement for the processing of future petabyte-sized datasets.
| S-EPMC9911350 | biostudies-literature
Project description:Stimuli for apparent motion can have ambiguity in frame-to-frame correspondences among visual elements. This occurs when visual inputs cause a correspondence problem that allows multiple alternatives of perceptual solutions. Herein we examined the influence of local visual motions on a perceptual solution under such a multistable situation. We repeatedly alternated two frames of stimuli in a circular configuration in which discrete elements in two different colors alternated in space and switched their colors frame by frame. These stimuli were compatible with three perceptual solutions: globally consistent clockwise and counterclockwise rotations and color flickers at the same locations without such global apparent motion. We added a sinusoidal grating continuously drifting within each element to examine whether the perceptual solution for the global apparent motion was affected by the local continuous motions. We found that the local motions suppressed global apparent motion and promoted another perceptual solution that the local elements were only flickering between the two colors and drifting within static windows. It was concluded that local continuous motions as counterevidence against global apparent motion contributed to individuating visual objects and integrating visual features for maintaining object identity at the same location.
| S-EPMC10309164 | biostudies-literature
Project description:Object shape is an important cue to material identity and for the estimation of material properties. Shape features can affect material perception at different levels: at a microscale (surface roughness), mesoscale (textures and local object shape), or megascale (global object shape) level. Examples for local shape features include ripples in drapery, clots in viscous liquids, or spiraling creases in twisted objects. Here, we set out to test the role of such shape features on judgments of material properties softness and weight. For this, we created a large number of novel stimuli with varying surface shape features. We show that those features have distinct effects on softness and weight ratings depending on their type, as well as amplitude and frequency, for example, increasing numbers and pointedness of spikes makes objects appear harder and heavier. By also asking participants to name familiar objects, materials, and transformations they associate with our stimuli, we can show that softness and weight judgments do not merely follow from semantic associations between particular stimuli and real-world object shapes. Rather, softness and weight are estimated from surface shape, presumably based on learned heuristics about the relationship between a particular expression of surface features and material properties. In line with this, we show that correlations between perceived softness or weight and surface curvature vary depending on the type of surface feature. We conclude that local shape features have to be considered when testing the effects of shape on the perception of material properties such as softness and weight.
| S-EPMC7416911 | biostudies-literature
Project description:Entropy drives the phase behavior of colloids ranging from dense suspensions of hard spheres or rods to dilute suspensions of hard spheres and depletants. Entropic ordering of anisotropic shapes into complex crystals, liquid crystals, and even quasicrystals was demonstrated recently in computer simulations and experiments. The ordering of shapes appears to arise from the emergence of directional entropic forces (DEFs) that align neighboring particles, but these forces have been neither rigorously defined nor quantified in generic systems. Here, we show quantitatively that shape drives the phase behavior of systems of anisotropic particles upon crowding through DEFs. We define DEFs in generic systems and compute them for several hard particle systems. We show they are on the order of a few times the thermal energy ([Formula: see text]) at the onset of ordering, placing DEFs on par with traditional depletion, van der Waals, and other intrinsic interactions. In experimental systems with these other interactions, we provide direct quantitative evidence that entropic effects of shape also contribute to self-assembly. We use DEFs to draw a distinction between self-assembly and packing behavior. We show that the mechanism that generates directional entropic forces is the maximization of entropy by optimizing local particle packing. We show that this mechanism occurs in a wide class of systems and we treat, in a unified way, the entropy-driven phase behavior of arbitrary shapes, incorporating the well-known works of Kirkwood, Onsager, and Asakura and Oosawa.
| S-EPMC4234574 | biostudies-literature
Project description:Soil covers most of Earth's continental surface and is fundamental to life-sustaining processes such as agriculture. Given its rich biodiversity, soil is also a major source for natural product drug discovery from soil microorganisms. However, the study of the soil small molecule profile has been challenging due to the complexity and heterogeneity of this matrix. In this study, we implemented high-resolution liquid chromatography-tandem mass spectrometry and large-scale data analysis tools such as molecular networking to characterize the relative contributions of city, state and regional processes on backyard soil metabolite composition, in 188 soil samples collected from 14 USA States, representing five USA climate regions. We observed that region, state and city of collection all influence the overall soil metabolite profile. However, many metabolites were only detected in unique sites, indicating that uniquely local phenomena also influence the backyard soil environment, with both human-derived and naturally-produced (plant-derived, microbially-derived) metabolites identified. Overall, these findings are helping to define the processes that shape the backyard soil metabolite composition, while also highlighting the need for expanded metabolomic studies of this complex environment.
| S-EPMC7143036 | biostudies-literature
Project description:Sex ratio theory provides a powerful source of testable predictions about sex allocation strategies. Although studies of invertebrates generally support predictions derived from the sex ratio theory, evidence for adaptive sex ratio biasing in vertebrates remains contentious. This may be due to the fact that most studies of vertebrates have focused on facultative adjustment in relation to maternal condition, rather than processes that might produce uniform sex biases across individuals. Here, we examine the effects of local resource enhancement (LRE) and local resource competition (LRC) on birth sex ratios (BSRs). We also examine the effects of sex differences in the costs of rearing male and female offspring on BSRs. We present data from 102 primate species and show that BSRs are skewed in favour of the dispersing sex in species that do not breed cooperatively, as predicted by the LRC model. In accordance with the LRE model, BSRs are generally skewed in favour of the more beneficial sex in cooperatively breeding primate species. There is no evidence that BSRs reflect the extent of sexual size dimorphism, an indirect measure of the costs of rearing male and female offspring. These analyses suggest that adaptive processes may play an important role in the evolution of BSRs in vertebrates.
| S-EPMC2587797 | biostudies-other