Local Solid Shape.
Ontology highlight
ABSTRACT:
SUBMITTER: Koenderink J
PROVIDER: S-EPMC5016822 | biostudies-other | 2015 Oct
REPOSITORIES: biostudies-other
Publications
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 ...[more]
Similar Datasets
Project description:Solid-solid phase transitions are the most ubiquitous in nature, and many technologies rely on them. However, studying them in detail is difficult because of the extreme conditions (high pressure/temperature) under which many such transitions occur and the high-resolution equipment needed to capture the intermediate states of the transformations. These difficulties mean that basic questions remain unanswered, such as whether so-called diffusionless solid-solid transitions, which have only local particle rearrangement, require thermal activation. Here, we introduce a family of minimal model systems that exhibits solid-solid phase transitions that are driven by changes in the shape of colloidal particles. By using particle shape as the control variable, we entropically reshape the coordination polyhedra of the particles in the system, a change that occurs indirectly in atomic solid-solid phase transitions via changes in temperature, pressure, or density. We carry out a detailed investigation of the thermodynamics of a series of isochoric, diffusionless solid-solid phase transitions within a single shape family and find both transitions that require thermal activation or are "discontinuous" and transitions that occur without thermal activation or are "continuous." In the discontinuous case, we find that sufficiently large shape changes can drive reconfiguration on timescales comparable with those for self-assembly and without an intermediate fluid phase, and in the continuous case, solid-solid reconfiguration happens on shorter timescales than self-assembly, providing guidance for developing means of generating reconfigurable colloidal materials.
| S-EPMC5441791 | 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:Mass-spring models have been a standard approach in molecular modeling for the last few decades, such as elastic network models (ENMs) that are widely used for normal mode analysis. In this work, we present a vastly different elastic solid model (ESM) of macromolecules that shares the same simplicity and efficiency as ENMs in producing the equilibrium dynamics and moreover, offers some significant new features that may greatly benefit the research community. ESM is different from ENM in that it treats macromolecules as elastic solids. Our particular version of ESM presented in this work, named αESM, captures the shape of a given biomolecule most economically using alpha shape, a well-established technique from the computational geometry community. Consequently, it can produce most economical coarse-grained models while faithfully preserving the shape and thus makes normal mode computations and visualization of extremely large complexes more manageable. Secondly, as a solid model, ESM's close link to finite element analysis renders it ideally suited for studying mechanical responses of macromolecules under external force. Lastly, we show that ESM can be applied also to structures without atomic coordinates such as those from cryo-electron microscopy. The complete MATLAB code of αESM is provided.
| S-EPMC7297265 | 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
Project description:An influential theory of spatial navigation states that the boundary shape of an environment is preferentially encoded over and above other spatial cues, such that it is impervious to interference from alternative sources of information. We explored this claim with 3 intradimensional-extradimensional shift experiments, designed to examine the interaction of landmark and geometric features of the environment in a virtual navigation task. In Experiments 1 and 2, participants were first required to find a hidden goal using information provided by the shape of the arena or landmarks integrated into the arena boundary (Experiment 1) or within the arena itself (Experiment 2). Participants were then transferred to a different-shaped arena that contained novel landmarks and were again required to find a hidden goal. In both experiments, participants who were navigating on the basis of cues that were from the same dimension that was previously relevant (intradimensional shift) learned to find the goal significantly faster than participants who were navigating on the basis of cues that were from a dimension that was previously irrelevant (extradimensional shift). This suggests that shape information does not hold special status when learning about an environment. Experiment 3 replicated Experiment 2 and also assessed participants' recognition of the global shape of the navigated arenas. Recognition was attenuated when landmarks were relevant to navigation throughout the experiment. The results of these experiments are discussed in terms of associative and non-associative theories of spatial learning.
| S-EPMC3933217 | biostudies-literature
Project description:Visualization of medical organs and biological structures is a challenging task because of their complex geometry and the resultant occlusions. Global spherical and planar mapping techniques simplify the complex geometry and resolve the occlusions to aid in visualization. However, while resolving the occlusions these techniques do not preserve the geometric context, making them less suitable for mission-critical biomedical visualization tasks. In this paper, we present a shape-preserving local mapping technique for resolving occlusions locally while preserving the overall geometric context. More specifically, we present a novel visualization algorithm, LMap, for conformally parameterizing and deforming a selected local region-of-interest (ROI) on an arbitrary surface. The resultant shape-preserving local mappings help to visualize complex surfaces while preserving the overall geometric context. The algorithm is based on the robust and efficient extrinsic Ricci flow technique, and uses the dynamic Ricci flow algorithm to guarantee the existence of a local map for a selected ROI on an arbitrary surface. We show the effectiveness and efficacy of our method in three challenging use cases: (1) multimodal brain visualization, (2) optimal coverage of virtual colonoscopy centerline flythrough, and (3) molecular surface visualization.
| S-EPMC6309451 | biostudies-literature
Project description:Several recent advances have emerged in biotherapy and the development of personal drugs. However, studies exploring effective manufacturing methods of personal drugs remain limited. In this study, solid drugs based on poly(ethylene glycol)diacrylate (PEGDA) hydrogel and doxorubicin were fabricated, and their final geometry was varied through UV-light patterning. The results suggested that the final drug concentration was affected by the geometrical volume as well as the UV-light exposure time. The analysis of PEGDA showed no effect on the surrounding cells, indicating its high biocompatibility. However, with the addition of doxorubicin, it showed an excellent therapeutic effect, indicating that drugs inside the PEGDA structure could be successfully released. This approach enables personal drugs to be fabricated in a simple, fast, and uniform manner, with perfectly tuned geometry.
| S-EPMC9269401 | biostudies-literature