Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Four-dimensional visualization of rising microbubbles.

ABSTRACT: Four-dimensional imaging, which indicates imaging in three spatial dimensions as a function of time, provides useful evidence to investigate the interactions of rising bubbles. However, this has been largely unexplored for microbubbles, mostly due to problems associated with strong light scattering and shallow depth of field in optical imaging. Here, tracking x-ray microtomography is used to visualize rising microbubbles in four dimensions. Bubbles are tracked by moving the cell to account for their rise velocity. The sizes, shapes, time-dependent positions, and velocities of individual rising microbubbles are clearly identified, despite substantial overlaps between bubbles in the field of view. Our tracking x-ray microtomography affords opportunities for understanding bubble-bubble (or particle) interactions at microscales - important in various fields such as microfluidics, biomechanics, and floatation.

SUBMITTER: Jung JW

PROVIDER: S-EPMC4035580 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Four-dimensional visualization of rising microbubbles.

Jung Ji Won JW Jeon Hyung Min HM Pyo Jaeyeon J Lim Jae-Hong JH Weon Byung Mook BM Kohmura Yoshiki Y Ishikawa Tetsuya T Je Jung Ho JH

Scientific reports 20140528

Four-dimensional imaging, which indicates imaging in three spatial dimensions as a function of time, provides useful evidence to investigate the interactions of rising bubbles. However, this has been largely unexplored for microbubbles, mostly due to problems associated with strong light scattering and shallow depth of field in optical imaging. Here, tracking x-ray microtomography is used to visualize rising microbubbles in four dimensions. Bubbles are tracked by moving the cell to account for t ...[more]

PMID: 24866552

Similar Datasets

Four-dimensional microscope- integrated optical coherence tomography to enhance visualization in glaucoma surgeries.

Project description:We report the first use of swept-source microscope-integrated optical coherence tomography (SS-MIOCT) capable of live four-dimensional (4D) (three-dimensional across time) imaging intraoperatively to directly visualize tube shunt placement and trabeculectomy surgeries in two patients with severe open-angle glaucoma and elevated intraocular pressure (IOP) that was not adequately managed by medical intervention or prior surgery. We performed tube shunt placement and trabeculectomy surgery and used SS-MIOCT to visualize and record surgical steps that benefitted from the enhanced visualization. In the case of tube shunt placement, SS-MIOCT successfully visualized the scleral tunneling, tube shunt positioning in the anterior chamber, and tube shunt suturing. For the trabeculectomy, SS-MIOCT successfully visualized the scleral flap creation, sclerotomy, and iridectomy. Postoperatively, both patients did well, with IOPs decreasing to the target goal. We found the benefit of SS-MIOCT was greatest in surgical steps requiring depth-based assessments. This technology has the potential to improve clinical outcomes.

| S-EPMC5369296 | biostudies-literature

Four-dimensional visualization of the simultaneous activity of alternative adeno-associated virus replication origins.

Project description:The adeno-associated virus (AAV) inverted terminal repeats (ITRs) contain the AAV Rep protein-binding site (RBS) and the terminal resolution site (TRS), which together act as a minimal origin of DNA replication. The AAV p5 promoter also contains an RBS, which is involved in Rep-mediated regulation of promoter activity, as well as a functional TRS, and origin activity of these signals has in fact been demonstrated previously in the presence of adenovirus helper functions. Here, we show that in the presence of herpes simplex virus type 1 (HSV-1) and AAV Rep protein, p5 promoter-bearing plasmids are efficiently amplified to form large head-to-tail concatemers, which are readily packaged in HSV-1 virions if an HSV-1 DNA-packaging/cleavage signal is provided in cis. We also demonstrate simultaneous and independent replication from the two alternative AAV replication origins, p5 and ITR, on the single-cell level using multicolor-fluorescence live imaging, a finding which raises the possibility that both origins may contribute to the AAV life cycle. Furthermore, we assess the differential affinities of Rep for the two different replication origins, p5 and ITR, both in vitro and in live cells and identify this as a potential mechanism to control the replicative and promoter activities of p5.

| S-EPMC1211535 | biostudies-literature

High-frame rate four dimensional optoacoustic tomography enables visualization of cardiovascular dynamics and mouse heart perfusion.

Project description:Functional imaging of mouse models of cardiac health and disease provides a major contribution to our fundamental understanding of the mammalian heart. However, imaging murine hearts presents significant challenges due to their small size and rapid heart rate. Here we demonstrate the feasibility of high-frame-rate, noninvasive optoacoustic imaging of the murine heart. The temporal resolution of 50 three-dimensional frames per second provides functional information at important phases of the cardiac cycle without the use of gating or other motion-reduction methods. Differentiation of the blood oxygenation state in the heart chambers was enabled by exploiting the wavelength dependence of optoacoustic signals. Real-time volumetric tracking of blood perfusion in the cardiac chambers was also evaluated using indocyanine green. Taken together, the newly-discovered capacities offer a unique tool set for in-vivo structural and functional imaging of the whole heart with high spatio-temporal resolution in all three dimensions.

| S-EPMC4486932 | biostudies-other

Four-dimensional visualization of subpleural alveolar dynamics in vivo during uninterrupted mechanical ventilation of living swine.

Project description:Pulmonary alveoli have been studied for many years, yet no unifying hypothesis exists for their dynamic mechanics during respiration due to their miniature size (100-300 μm dimater in humans) and constant motion, which prevent standard imaging techniques from visualizing four-dimensional dynamics of individual alveoli in vivo. Here we report a new platform to image the first layer of air-filled subpleural alveoli through the use of a lightweight optical frequency domain imaging (OFDI) probe that can be placed upon the pleura to move with the lung over the complete range of respiratory motion. This device enables in-vivo acquisition of four-dimensional microscopic images of alveolar airspaces (alveoli and ducts), within the same field of view, during continuous ventilation without restricting the motion or modifying the structure of the alveoli. Results from an exploratory study including three live swine suggest that subpleural alveolar air spaces are best fit with a uniform expansion (r (2) = 0.98) over a recruitment model (r (2) = 0.72). Simultaneously, however, the percentage change in volume shows heterogeneous alveolar expansion within just a 1 mm x 1 mm field of view. These results signify the importance of four-dimensional imaging tools, such as the device presented here. Quantification of the dynamic response of the lung during ventilation may help create more accurate modeling techniques and move toward a more complete understanding of alveolar mechanics.

| S-EPMC3829543 | biostudies-other

Four-dimensional joint visualization of electrode degradation and liquid water distribution inside operating polymer electrolyte fuel cells.

Project description:Understanding of degradation mechanisms present in polymer electrolyte fuel cells (PEFCs) is important to continue the integration of this clean energy technology into everyday life. Further comprehension of the interaction between various components during fuel cell operation is also critical in this context. In this work, a four-dimensional operando X-ray computed tomography method is developed for combined visualization of all PEFC components as well as transient water distribution residing in the cell, which results as a by-product of the electrochemical reaction. Time resolved, identical-location visualization through degradation stages is uniquely enabled by the non-invasive and non-destructive qualities of this method. By applying an accelerated stress test that targets cathode catalyst layer (CCL) corrosion, novel observations resulting from morphological changes of the CCL such as reduction in the water volume in the adjacent gas diffusion layer, CCL crack formation and propagation, membrane swelling, as well as quantification of local carbon loss is achieved. Additionally, insight into features that contribute to reduced fuel cell performance is enabled by the use of this specialized imaging technique, such as increased membrane undulation causing delamination and separation of the CCL from the microporous layer, which greatly affects liquid water pathways and overall device performance.

| S-EPMC6372714 | biostudies-literature

ECG and navigator-free four-dimensional whole-heart coronary MRA for simultaneous visualization of cardiac anatomy and function.

Project description:To develop a cardiac and respiratory self-gated four-dimensional (4D) coronary MRA technique for simultaneous cardiac anatomy and function visualization.A contrast-enhanced, ungated spoiled gradient echo sequence with self-gating (SG) and 3DPR trajectory was used for image acquisition. Data were retrospectively binned into different cardiac and respiratory phases based on information extracted from SG projections using principal component analysis. Each cardiac phase was reconstructed using a respiratory motion-corrected self-calibrating SENSE framework, and those belong to the quiescent period were retrospectively combined for coronary visualization. Healthy volunteer studies were conducted to evaluate the efficacy of the SG method, the accuracy of the left ventricle (LV) function parameters and the quality of coronary artery visualization.SG performed reliably for all subjects including one with poor electrocardiogram (ECG). The LV function parameters showed excellent agreement with those from a conventional cine protocol. For coronary imaging, the proposed method yielded comparable apparent signal to noise ratio and coronary sharpness and lower apparent contrast to noise ratio on three subjects compared with an ECG and navigator-gated Cartesian protocol and an ECG-gated, respiratory motion-corrected 3DPR protocol.A fully self-gated 4D whole-heart imaging technique was developed, potentially allowing cardiac anatomy and function assessment from a single measurement.

| S-EPMC4198505 | biostudies-literature

Four-dimensional micro-building blocks.

Project description:Four-dimensional (4D) printing relies on multimaterial printing, reinforcement patterns, or micro/nanofibrous additives as programmable tools to achieve desired shape reconfigurations. However, existing programming approaches still follow the so-called origami design principle to generate reconfigurable structures by self-folding stacked 2D materials, particularly at small scales. Here, we propose a programmable modular design that directly constructs 3D reconfigurable microstructures capable of sophisticated 3D-to-3D shape transformations by assembling 4D micro-building blocks. 4D direct laser writing is used to print two-photon polymerizable, stimuli-responsive hydrogels to construct building blocks at micrometer scales. Denavit-Hartenberg (DH) parameters, used to define robotic arm kinematics, are introduced as guidelines for how to assemble the micro-building blocks and plan the 3D motion of assembled chain blocks. Last, a 3D-printed microscaled transformer capable of changing its shape from a race car to a humanoid robot is devised and fabricated using the DH parameters to guide the motion of various assembled compartments.

| S-EPMC6968937 | biostudies-literature

Four-Dimensional Chromosome Structure Prediction.

Project description:Chromatin conformation plays an important role in a variety of genomic processes, including genome replication, gene expression, and gene methylation. Hi-C data is frequently used to analyze structural features of chromatin, such as AB compartments, topologically associated domains, and 3D structural models. Recently, the genomics community has displayed growing interest in chromatin dynamics. Here, we present 4DMax, a novel method, which uses time-series Hi-C data to predict dynamic chromosome conformation. Using both synthetic data and real time-series Hi-C data from processes, such as induced pluripotent stem cell reprogramming and cardiomyocyte differentiation, we construct smooth four-dimensional models of individual chromosomes. These predicted 4D models effectively interpolate chromatin position across time, permitting prediction of unknown Hi-C contact maps at intermittent time points. Furthermore, 4DMax correctly recovers higher order features of chromatin, such as AB compartments and topologically associated domains, even at time points where Hi-C data is not made available to the algorithm. Contact map predictions made using 4DMax outperform naïve numerical interpolation in 87.7% of predictions on the induced pluripotent stem cell dataset. A/B compartment profiles derived from 4DMax interpolation showed higher similarity to ground truth than at least one profile generated from a neighboring time point in 100% of induced pluripotent stem cell experiments. Use of 4DMax may alleviate the cost of expensive Hi-C experiments by interpolating intermediary time points while also providing valuable visualization of dynamic chromatin changes.

| S-EPMC8465368 | biostudies-literature

Skittle: a 2-dimensional genome visualization tool.

Project description:BackgroundIt is increasingly evident that there are multiple and overlapping patterns within the genome, and that these patterns contain different types of information--regarding both genome function and genome history. In order to discover additional genomic patterns which may have biological significance, novel strategies are required. To partially address this need, we introduce a new data visualization tool entitled Skittle.ResultsThis program first creates a 2-dimensional nucleotide display by assigning four colors to the four nucleotides, and then text-wraps to a user adjustable width. This nucleotide display is accompanied by a "repeat map" which comprehensively displays all local repeating units, based upon analysis of all possible local alignments. Skittle includes a smooth-zooming interface which allows the user to analyze genomic patterns at any scale.Skittle is especially useful in identifying and analyzing tandem repeats, including repeats not normally detectable by other methods. However, Skittle is also more generally useful for analysis of any genomic data, allowing users to correlate published annotations and observable visual patterns, and allowing for sequence and construct quality control.ConclusionsPreliminary observations using Skittle reveal intriguing genomic patterns not otherwise obvious, including structured variations inside tandem repeats. The striking visual patterns revealed by Skittle appear to be useful for hypothesis development, and have already led the authors to theorize that imperfect tandem repeats could act as information carriers, and may form tertiary structures within the interphase nucleus.

| S-EPMC2817707 | biostudies-literature

Four-dimensional computed tomography: musculoskeletal applications.

Project description:Four-dimensional computed tomography (4DCT), or dynamic CT, is an emerging modality with a wealth of orthopedic applications for both clinical practice and research. This technology creates CT volumes of a moving structure at multiple time points to depict real-time motion. Recent advances in acquisition technology and reduction in radiation dosage have allowed for increased adoption of the modality and have made imaging of joint motion feasible and safe. Musculoskeletal 4DCT has been used primarily to investigate wrist motion; however, the utility of 4DCT has been shown in other areas, including the shoulder, elbow, hip, knee and ankle. Imaging these joints through a full range of motion provides new insight into dynamic phenomena such as instability, impingement and joint kinematics. Although 4DCT has not yet been widely adopted in orthopedic practice and research, future use has the potential to enable a deeper understanding of musculoskeletal conditions and to improve patient care.

| S-EPMC9200445 | 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