Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Hydration State of Bone Tissue Affects Contrast in Neutron Tomographic Images.

ABSTRACT: Neutron tomography has emerged as a promising imaging technique for specific applications in bone research. Neutrons have a strong interaction with hydrogen, which is abundant in biological tissues, and they can penetrate through dense materials such as metallic implants. However, in addition to long imaging times, two factors have led to challenges in running in situ mechanical characterization experiments on bone tissue using neutron tomography: 1) the high water content in specimens reduces the visibility of internal trabecular structures; 2) the mechanical properties of bone are dependent on the hydration state of the tissue, with drying being reported to cause increased stiffness and brittleness. This study investigates the possibility of improving image quality in terms of neutron transmission and contrast between material phases by drying and rehydrating in heavy water. Rat tibiae and trabecular bovine bone plugs were imaged with neutron tomography at different hydration states and mechanical testing of the bone plugs was carried out to assess effects of drying and rehydration on the mechanical properties of bone. From analysis of image histograms, it was found that drying reduced the contrast between bone and soft tissue, but the contrast was restored with rehydration. Contrast-to-noise ratios and line profiles revealed that the contrast between bone tissue and background was reduced with increasing rehydration duration but remained sufficient for identifying internal structures as long as no free liquid was present inside the specimen. The mechanical analysis indicated that the proposed fluid exchange protocol had no adverse effects on the mechanical properties.

SUBMITTER: Tornquist E

PROVIDER: S-EPMC9247154 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Improving contrast to noise ratio of resonance frequency contrast images (phase images) using balanced steady-state free precession.

Project description:Recent MRI studies have exploited subtle magnetic susceptibility differences between brain tissues to improve anatomical contrast and resolution. These susceptibility differences lead to resonance frequency shifts which can be visualized by reconstructing the signal phase in conventional gradient echo (GRE) acquisition techniques. In this work, a method is proposed to improve the contrast to noise ratio per unit time (CNR efficiency) of anatomical MRI based on resonance frequency contrast. The method, based on the balanced steady-state free precession (bSSFP) MRI acquisition technique, was evaluated in its ability to generate contrast between gray and white matter in human brain at 3T and 7T. The results show substantially improved CNR efficiency of bSSFP phase images (2.85±0.21 times at 3 T and 1.71±0.11 times at 7 T) compared to the GRE data in a limited spatial area. This limited spatial coverage is attributed to the sensitivity of bSSFP to macroscopic B(0) inhomogeneities. With this CNR improvement, high resolution bSSFP phase images (resolution=0.3×0.3×2 mm(3), acquisition time=10min) acquired at 3T had sufficient CNR to allow the visualization of cortical laminar structures in invivo human primary visual cortex. Practical application of the proposed method may require improvement of B(0) homogeneity and stability by additional preparatory scans and/or compensation schemes such as respiration and drift compensation. Without these additions, the CNR benefits of the method may be limited to studies at low field or limited regions of interest.

| S-EPMC3020255 | biostudies-literature

Hydration affects the physical and mechanical properties of baleen tissue.

Project description:Baleen, an anisotropic oral filtering tissue found only in the mouth of mysticete whales and made solely of alpha-keratin, exhibits markedly differing physical and mechanical properties between dried or (as in life) hydrated states. On average baleen is 32.35% water by weight in North Atlantic right whales (Eubalaena glacialis) and 34.37% in bowhead whales (Balaena mysticetus). Baleen's wettability measured by water droplet contact angles shows that dried baleen is hydrophobic whereas hydrated baleen is highly hydrophilic. Three-point flexural bending tests of mechanical strength reveal that baleen is strong yet ductile. Dried baleen is brittle and shatters at about 20-30?N?mm-2 but hydrated baleen is less stiff; it bends with little force and absorbed water is squeezed out when force is applied. Maximum recorded stress was 4× higher in dried (mean 14.29?N?mm-2) versus hydrated (mean 3.69?N?mm-2) baleen, and the flexural stiffness was >10× higher in dried (mean 633N?mm-2) versus hydrated (mean 58?N?mm-2) baleen. In addition to documenting hydration's powerful effects on baleen, this study indicates that baleen is far more pliant and malleable than commonly supposed, with implications for studies of baleen's structure and function as well as its susceptibility to oil or other hydrophobic pollutants.

| S-EPMC5099004 | biostudies-literature

Unsupervised segmentation of low-contrast multichannel images: discrimination of tissue components in microscopic images of unstained specimens.

Project description:Low-contrast images, such as color microscopic images of unstained histological specimens, are composed of objects with highly correlated spectral profiles. Such images are very hard to segment. Here, we present a method that nonlinearly maps low-contrast color image into an image with an increased number of non-physical channels and a decreased correlation between spectral profiles. The method is a proof-of-concept validated on the unsupervised segmentation of color images of unstained specimens, in which case the tissue components appear colorless when viewed under the light microscope. Specimens of human hepatocellular carcinoma, human liver with metastasis from colon and gastric cancer and mouse fatty liver were used for validation. The average correlation between the spectral profiles of the tissue components was greater than 0.9985, and the worst case correlation was greater than 0.9997. The proposed method can potentially be applied to the segmentation of low-contrast multichannel images with high spatial resolution that arise in other imaging modalities.

| S-EPMC4477329 | biostudies-literature

Synchrotron Radiation-Based Refraction-Contrast Tomographic Images Using X-ray Dark-Field Imaging Optics in Human Lung Adenocarcinoma and Histologic Correlations.

Project description:The aim of this study was to evaluate the clinical implication of synchrotron radiation imaging techniques for human lung adenocarcinoma in comparison with pathologic examination. A refraction-based tomographic imaging technique called the X-ray dark-field imaging (XDFI) method was used to obtain computed tomographic images of human lung adenocarcinoma at the beam line at Photon Factory BL 14B at the High Energy Accelerator Research Organization (KEK) in Tsukuba, Japan. Images of normal lung tissue were also obtained using the same methods and reconstructed as 3D images. Both reconstructed images were compared with pathologic examinations from histologic slides which were made with identical samples. Pulmonary alveolar structure including terminal bronchioles, alveolar sacs, and vasculatures could be identified in synchrotron radiation images of normal lung. Hyperplasia of interstitial tissue and dysplasia of alveolar structures were noticed in images of lung adenocarcinoma. Both synchrotron radiation images were considerably correlated with images from histologic slides. Lepidic patterns of cancer tissue were distinguished from the invasive area in synchrotron radiation images of lung adenocarcinoma. Refraction-contrast tomographic techniques using synchrotron radiation could provide high-resolution images of lung adenocarcinoma which are compatible with those from pathologic examinations.

| S-EPMC7999731 | biostudies-literature

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI.

Project description:We proposed a method for segmentation of brain tissues-gray matter, white matter, and cerebrospinal fluid-using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed method was evaluated with respect to the processing time and the similarity of the segmented masks of brain tissues with those obtained using FSL, FreeSurfer, and SPM12. The processing time of the proposed method (28 ± 0 s) was significantly shorter than those of FSL and SPM12 (444 ± 4 s and 159 ± 2 s for FSL and SPM12, respectively). In the similarity assessment, the tissue mask of the brain obtained by the proposed method showed higher consistency with those obtained using FSL than with those obtained using SPM12. The proposed method misclassified the subcortical structures and large vessels since it is based on the intensities of multi-contrast images obtained using MP2RAGE, which uses a similar segmentation approach as FSL but is not based on a template image or a parcellated brain atlas, which are used for FreeSurfer and SPM12, respectively. However, the proposed method showed good segmentation in the cerebellum and white matter in the medial part of the brain in comparison with the other methods. Thus, because the proposed method using different contrast images of MP2RAGE sequence showed the shortest processing time and similar segmentation ability as the other methods, it may be useful for both neuroimaging research and clinical diagnosis.

| S-EPMC6394968 | biostudies-literature

Computer-aided interpretation approach for optical tomographic images.

Project description:A computer-aided interpretation approach is proposed to detect rheumatic arthritis (RA) in human finger joints using optical tomographic images. The image interpretation method employs a classification algorithm that makes use of a so-called self-organizing mapping scheme to classify fingers as either affected or unaffected by RA. Unlike in previous studies, this allows for combining multiple image features, such as minimum and maximum values of the absorption coefficient for identifying affected and not affected joints. Classification performances obtained by the proposed method were evaluated in terms of sensitivity, specificity, Youden index, and mutual information. Different methods (i.e., clinical diagnostics, ultrasound imaging, magnet resonance imaging, and inspection of optical tomographic images), were used to produce ground truth benchmarks to determine the performance of image interpretations. Using data from 100 finger joints, findings suggest that some parameter combinations lead to higher sensitivities, while others to higher specificities when compared to single parameter classifications employed in previous studies. Maximum performances are reached when combining the minimum/maximum ratio of the absorption coefficient and image variance. In this case, sensitivities and specificities over 0.9 can be achieved. These values are much higher than values obtained when only single parameter classifications were used, where sensitivities and specificities remained well below 0.8.

| S-EPMC3017575 | biostudies-other

Protein crowding affects hydration structure and dynamics.

Project description:The effect of protein crowding on the structure and dynamics of water was examined from explicit solvent molecular dynamics simulations of a series of protein G and protein G/villin systems at different protein concentrations. Hydration structure was analyzed in terms of radial distribution functions, three-dimensional hydration sites, and preservation of tetrahedral coordination. Analysis of hydration dynamics focused on self-diffusion rates and dielectric constants as a function of crowding. The results show significant changes in both structure and dynamics of water under highly crowded conditions. The structure of water is altered mostly beyond the first solvation shell. Diffusion rates and dielectric constants are significantly reduced following linear trends as a function of crowding reflecting highly constrained water in crowded environments. The reduced dynamics of diffusion is expected to be strongly related to hydrodynamic properties of crowded cellular environments while the reduced dielectric constant under crowded conditions has implications for the stability of biomolecules in crowded environments. The results from this study suggest a prescription for modeling solvation in simulations of cellular environments.

| S-EPMC3305823 | biostudies-literature

Protein hydration in solution: experimental observation by x-ray and neutron scattering.

Project description:The structure of the protein-solvent interface is the subject of controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal structure (lysozyme, Escherichia coli thioredoxin reductase, and protein R1 of E. coli ribonucleotide reductase) were investigated in parallel by x-ray and neutron scattering in H2O and D2O solutions. The analysis of the protein-solvent interface is based on the significantly different contrasts for the protein and for the hydration shell. The results point to the existence of a first hydration shell with an average density approximately 10% larger than that of the bulk solvent in the conditions studied. Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces.

| S-EPMC19315 | biostudies-literature

High-resolution high-throughput thermal neutron tomographic imaging of fossiliferous cave breccias from Sumatra.

Project description:We employ high-throughput thermal-neutron tomographic imaging to visualise internal diagnostic features of dense fossiliferous breccia from three Pleistocene cave localities in Sumatra, Indonesia. We demonstrate that these seemingly homogeneous breccias are an excellent source of data to aid in determining taphonomic and depositional histories of complex depositional sites such as tropical caves. X-ray Computed Tomographic (CT) imaging is gaining importance amongst palaeontologists as a non-destructive approach to studying fossil remains. Traditional methods of fossil preparation risk damage to the specimen and may destroy contextual evidence in the surrounding matrix. CT imaging can reveal the internal composition and structure of fossils contained within consolidated sediment/rock matrices prior to any destructive mechanical or chemical preparation. Neutron computed tomography (NCT) provides an alternative contrast to X-rays, and in some circumstances, is capable of discerning denser matrices impenetrable to or yielding no contrast with CT imaging. High-throughput neutron imaging reduces neutron fluence during scanning which means there is less residual neutron-induced radioactivation in geological samples; allowing for earlier subsequent analyses. However, this approach remains unutilised in palaeontology, archaeology or geological surveys. Results suggest that the primary agents in the formation of the breccias and concentration of incorporated vertebrate remains are several rapid depositional phases of water and sediment gravity flow. This study highlights the potential for future analyses of breccia deposits in palaeontological studies in caves around the world.

| S-EPMC8497489 | biostudies-literature

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

Project description:Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms.

| S-EPMC3083928 | 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