Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Three-Dimensional Morphology of Growing Dendrites.

ABSTRACT: The processes controlling the morphology of dendrites have been of great interest to a wide range of communities, since they are examples of an out-of-equilibrium pattern forming system, there is a clear connection with battery failure processes, and their morphology sets the properties of many metallic alloys. We determine the three-dimensional morphology of free growing metallic dendrites using a novel X-ray tomographic technique that improves the temporal resolution by more than an order of magnitude compared to conventional techniques. These measurements show that the growth morphology of metallic dendrites is surprisingly different from that seen in model systems, the morphology is not self-similar with distance back from the tip, and that this morphology can have an unexpectedly strong influence on solute segregation in castings. These experiments also provide benchmark data that can be used to validate simulations of free dendritic growth.

SUBMITTER: Gibbs JW

PROVIDER: S-EPMC4490335 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The Three-Dimensional Morphology of Growing Dendrites.

Gibbs J W JW Mohan K A KA Gulsoy E B EB Shahani A J AJ Xiao X X Bouman C A CA De Graef M M Voorhees P W PW

Scientific reports 20150703

The processes controlling the morphology of dendrites have been of great interest to a wide range of communities, since they are examples of an out-of-equilibrium pattern forming system, there is a clear connection with battery failure processes, and their morphology sets the properties of many metallic alloys. We determine the three-dimensional morphology of free growing metallic dendrites using a novel X-ray tomographic technique that improves the temporal resolution by more than an order of m ...[more]

PMID: 26139473

Similar Datasets

Three-dimensional facial morphology in Cantu syndrome.

Project description:Cantú syndrome (CS) was first described in 1982, and is caused by pathogenic variants in ABCC9 and KCNJ8 encoding regulatory and pore forming subunits of ATP-sensitive potassium (KATP ) channels, respectively. It is characterized by congenital hypertrichosis, osteochondrodysplasia, extensive cardiovascular abnormalities and distinctive facial anomalies including a broad nasal bridge, long philtrum, epicanthal folds, and prominent lips. Many genetic syndromes, such as CS, involve facial anomalies that serve as a significant clue in the initial identification of the respective disorder before clinical or molecular diagnosis are undertaken. However, an overwhelming number of CS patients receive misdiagnoses based on an evaluation of coarse facial features. By analyzing three-dimensional images of CS faces, we quantified facial dysmorphology in a cohort of both male and female CS patients with confirmed ABCC9 variants. Morphometric analysis of different regions of the face revealed gender-specific significant differences in face shape. Moreover, we show that 3D facial photographs can distinguish between CS and other genetic disorders with specific facial dysmorphologies that have been mistaken for CS-associated anomalies in the past, hence assisting in an earlier clinical and molecular diagnosis. This optimizes genetic counseling and reduces stress for patients and parents by avoiding unnecessary misdiagnosis.

| S-EPMC7217184 | biostudies-literature

Discriminating power of localized three-dimensional facial morphology.

Project description:Many genetic syndromes involve a facial gestalt that suggests a preliminary diagnosis to an experienced clinical geneticist even before a clinical examination and genotyping are undertaken. Previously, using visualization and pattern recognition, we showed that dense surface models (DSMs) of full face shape characterize facial dysmorphology in Noonan and in 22q11 deletion syndromes. In this much larger study of 696 individuals, we extend the use of DSMs of the full face to establish accurate discrimination between controls and individuals with Williams, Smith-Magenis, 22q11 deletion, or Noonan syndromes and between individuals with different syndromes in these groups. However, the full power of the DSM approach is demonstrated by the comparable discriminating abilities of localized facial features, such as periorbital, perinasal, and perioral patches, and the correlation of DSM-based predictions and molecular findings. This study demonstrates the potential of face shape models to assist clinical training through visualization, to support clinical diagnosis of affected individuals through pattern recognition, and to enable the objective comparison of individuals sharing other phenotypic or genotypic properties.

| S-EPMC1285182 | biostudies-literature

A three-dimensional statistical shape model of the growing mandible.

Project description:Mandibular growth and morphology are important topics in the field of oral and maxillofacial surgery. For diagnostic and planning purposes, a normative database or statistical shape model of the growing mandible can be of great benefit. A collection of 874 cadaveric children's mandibles with dental age between 1 and 12 years old were digitized using computed tomography scanning and reconstructed to three-dimensional models. Point correspondence was achieved using iterative closest point and coherent point drift algorithms. Principal component analysis (PCA) was applied to find the main modes of variation in the data set. The average mandible was presented, along with the first ten PCA modes. The first mode explained 78% of the total variance; combining the first ten modes accumulated to 95% of the total variance. The first mode was strongly correlated with age and hence, with natural growth. This is the largest study on three-dimensional mandibular shape and development conducted thus far. The main limitation is that the samples lack information such as gender and cause of death. Clinical application of the model first requires validation with contemporary samples.

| S-EPMC8458295 | biostudies-literature

Emergence of three-dimensional order and structure in growing biofilms.

Project description:Surface-attached bacterial biofilms are self-replicating active liquid crystals and the dominant form of bacterial life on earth (1-4). In conventional liquid crystals and solid-state materials, the interaction potentials between the molecules that comprise the system determine the material properties. However, for growth-active biofilms it is unclear whether potential-based descriptions can account for the experimentally observed morphologies, and which potentials would be relevant. Here, we overcame previous limitations of single-cell imaging techniques (5,6) to reconstruct and track all individual cells inside growing three-dimensional (3D) biofilms with up to 10,000 individuals. Based on these data, we identify, constrain, and provide a microscopic basis for an effective cell-cell interaction potential, which captures and predicts the growth dynamics, emergent architecture, and local liquid crystalline order of Vibrio cholerae biofilms. Furthermore, we show how external fluid flows control the microscopic structure and 3D morphology of biofilms. Our analysis implies that local cellular order and global biofilm architecture in these active bacterial communities can arise from mechanical cell-cell interactions, which cells can modulate by regulating the production of particular matrix components. These results establish an experimentally validated foundation for improved continuum theories of active matter and thereby contribute to solving the important problem of controlling biofilm growth.

| S-EPMC6544526 | biostudies-literature

Three-dimensional morphology of the human embryonic brain.

Project description:The morphogenesis of the cerebral vesicles and ventricles was visualized in 3D movies using images derived from human embryo specimens between Carnegie stage 13 and 23 from the Kyoto Collection. These images were acquired with a magnetic resonance microscope equipped with a 2.35-T superconducting magnet. Three-dimensional images using the same scale demonstrated brain development and growth effectively. The non-uniform thickness of the brain tissue, which may indicate brain differentiation, was visualized with thickness-based surface color mapping. A closer view was obtained of the unique and complicated differentiation of the rhombencephalon, especially with regard to the internal view and thickening of the brain tissue. The present data contribute to a better understanding of brain and cerebral ventricle development.

| S-EPMC4510431 | biostudies-other

Computer-Assisted Three-Dimensional Morphology Evaluation of Intracranial Aneurysms.

Project description:ObjectivePrecise morphologic evaluation is important for intracranial aneurysm (IA) management. At present, clinicians manually measure the IA size and neck diameter on 2-dimensional (2D) digital subtraction angiographic (DSA) images and categorize the IA shape as regular or irregular on 3-dimensional (3D)-DSA images, which could result in inconsistency and bias. We investigated whether a computer-assisted 3D analytical approach could improve IA morphology assessment.MethodsFive neurointerventionists evaluated the size, neck diameter, and shape of 39 IAs using current and computer-assisted 3D approaches. In the computer-assisted 3D approach, the size, neck diameter, and undulation index (UI, a shape irregularity metric) were extracted using semiautomated reconstruction of aneurysm geometry using 3D-DSA, followed by IA neck identification and computerized geometry assessment.ResultsThe size and neck diameter measured using the manual 2D approach were smaller than computer-assisted 3D measurements by 2.01 mm (P < 0.001) and 1.85 mm (P < 0.001), respectively. Applying the definitions of small IAs (<7 mm) and narrow-necked IAs (<4 mm) from the reported data, interrater variation in manual 2D measurements resulted in inconsistent classification of the size of 14 IAs and the necks of 19 IAs. Visual inspection resulted in an inconsistent shape classification for 23 IAs among the raters. Greater consistency was achieved using the computer-assisted 3D approach for size (intraclass correlation coefficient [ICC], 1.00), neck measurements (ICC, 0.96), and shape quantification (UI; ICC, 0.94).ConclusionsComputer-assisted 3D morphology analysis can improve accuracy and consistency in measurements compared with manual 2D measurements. It can also more reliably quantify shape irregularity using the UI. Future application of computer-assisted analysis tools could help clinicians standardize morphology evaluations, leading to more consistent IA evaluations.

| S-EPMC6383522 | biostudies-literature

Flipped Well-Plate Hanging-Drop Technique for Growing Three-Dimensional Tumors.

Project description:Three-dimensional (3D) tumor culture techniques are gaining popularity as in vitro models of tumoral tissue analogues. Despite the widespread interest, need, and present-day effort, most of the 3D tumor culturing methodologies have not gone beyond the inventors' laboratories. This, in turn, limits their applicability and standardization. In this study, we introduce a straightforward and user-friendly approach based on standard 96-well plates with basic amenities for growing 3D tumors in a scaffold-free/scaffold-based format. Hanging drop preparation can be easily employed by flipping a universal 96-well plate. The droplets of the medium generated by the well-plate flip (WPF) method can be easily modified to address various mechanisms and processes in cell biology, including cancer. To demonstrate the applicability and practicality of the conceived approach, we utilized human colorectal carcinoma cells (HCT116) to first show the generation of large scaffold-free 3D tumor spheroids over 1.5 mm in diameter in single-well plates. As a proof-of-concept, we also demonstrate matrix-assisted tumor culture techniques in advancing the broader use of 3D culture systems. The conceptualized WPF approach can be adapted for a range of applications in both basic and applied biological/engineering research.

| S-EPMC9289396 | biostudies-literature

Anthropometric Study of Three-Dimensional Facial Morphology in Malay Adults.

Project description:ObjectivesTo establish the three-dimensional (3D) facial soft tissue morphology of adult Malaysian subjects of the Malay ethnic group; and to determine the morphological differences between the genders, using a non-invasive stereo-photogrammetry 3D camera.Material and methodsOne hundred and nine subjects participated in this research, 54 Malay men and 55 Malay women, aged 20-30 years old with healthy BMI and with no adverse skeletal deviation. Twenty-three facial landmarks were identified on 3D facial images captured using a VECTRA M5-360 Head System (Canfield Scientific Inc, USA). Two angular, 3 ratio and 17 linear measurements were identified using Canfield Mirror imaging software. Intra- and inter-examiner reliability tests were carried out using 10 randomly selected images, analyzed using the intra-class correlation coefficient (ICC). Multivariate analysis of variance (MANOVA) was carried out to investigate morphologic differences between genders.ResultsICC scores were generally good for both intra-examiner (range 0.827-0.987) and inter-examiner reliability (range 0.700-0.983) tests. Generally, all facial measurements were larger in men than women, except the facial profile angle which was larger in women. Clinically significant gender dimorphisms existed in biocular width, nose height, nasal bridge length, face height and lower face height values (mean difference > 3mm). Clinical significance was set at 3mm.ConclusionFacial soft tissue morphological values can be gathered efficiently and measured effectively from images captured by a non-invasive stereo-photogrammetry 3D camera. Adult men in Malaysia when compared to women had a wider distance between the eyes, a longer and more prominent nose and a longer face.

| S-EPMC5051712 | biostudies-literature

Growth hormone receptor gene variant and three-dimensional mandibular morphology.

Project description:ObjectiveTo examine the relationship between three-dimensional mandibular morphology and growth hormone receptor (GHR) gene variants in a healthy Japanese population.Materials and methodsThe subjects, who were unrelated Japanese orthodontic patients, consisted of 64 men and 114 women. Using the Taqman genotyping assay, GHR gene rs6184 and rs6180 variants were detected in genomic DNA extracted from saliva. Mandibular volume and length were measured from cone-beam computed tomography images that were analyzed using Analyze image-processing software. The relationship between GHR gene variants and three-dimensional mandibular morphology was statistically examined.ResultsStatistical significance for the relationship between the distance between the left and right coronoid processes and rs6180 was noted (P < .05).ConclusionOur results indicate that the GHR variant rs6180 is associated with the distance between the left and right coronoid process in the Japanese subjects.

| S-EPMC8388580 | biostudies-literature

Application of the Mirror Technique for Three-Dimensional Electron Microscopy of Neurochemically Identified GABA-ergic Dendrites.

Project description:In the nervous system synaptic input arrives chiefly on dendrites and their type and distribution have been assumed pivotal in signal integration. We have developed an immunohistochemistry (IH)-correlated electron microscopy (EM) method - the "mirror" technique - by which synaptic input to entire dendrites of neurochemically identified interneurons (INs) can be mapped due preserving high-fidelity tissue ultrastructure. Hence, this approach allows quantitative assessment of morphometric parameters of synaptic inputs along the whole length of dendrites originating from the parent soma. The method exploits the fact that adjoining sections have truncated or cut cell bodies which appear on the common surfaces in a mirror fashion. In one of the sections the histochemical marker of the GABAergic subtype, calbindin was revealed in cell bodies whereas in the other section the remaining part of the very same cell bodies were subjected to serial section EM to trace and reconstruct the synaptology of entire dendrites. Here, we provide exemplary data on the synaptic coverage of two dendrites belonging to the same calbindin-D28 K immunopositive IN and determine the spatial distribution of asymmetric and symmetric synapses, surface area and volume of the presynaptic boutons, morphometric parameters of synaptic vesicles, and area extent of the active zones.

| S-EPMC8093522 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data