Decomposition of two-component ultrasound pulses in cancellous bone using modified least squares prony method--phantom experiment and simulation.
Ontology highlight
ABSTRACT:
SUBMITTER: Wear KA
PROVIDER: S-EPMC9180631 | biostudies-literature | 2010 Feb
REPOSITORIES: biostudies-literature
Publications
Decomposition of two-component ultrasound pulses in cancellous bone using modified least squares prony method--phantom experiment and simulation.
Ultrasound in medicine & biology 20100201 2
Porous media such as cancellous bone often support the simultaneous propagation of two compressional waves. When small bone samples are interrogated in through-transmission with broadband sources, these two waves often overlap in time. The modified least-squares Prony's (MLSP) method was tested for decomposing a 500 kHz-center-frequency signal containing two overlapping components: one passing through a polycarbonate plate (to produce the "fast" wave) and another passing through a cancellous-bon ...[more]
Similar Datasets
Project description:Classical nonparametric spectral analysis uses sliding windows to capture the dynamic nature of most real-world time series. This universally accepted approach fails to exploit the temporal continuity in the data and is not well-suited for signals with highly structured time-frequency representations. For a time series whose time-varying mean is the superposition of a small number of oscillatory components, we formulate nonparametric batch spectral analysis as a Bayesian estimation problem. We introduce prior distributions on the time-frequency plane that yield maximum a posteriori (MAP) spectral estimates that are continuous in time yet sparse in frequency. Our spectral decomposition procedure, termed spectrotemporal pursuit, can be efficiently computed using an iteratively reweighted least-squares algorithm and scales well with typical data lengths. We show that spectrotemporal pursuit works by applying to the time series a set of data-derived filters. Using a link between Gaussian mixture models, l1 minimization, and the expectation-maximization algorithm, we prove that spectrotemporal pursuit converges to the global MAP estimate. We illustrate our technique on simulated and real human EEG data as well as on human neural spiking activity recorded during loss of consciousness induced by the anesthetic propofol. For the EEG data, our technique yields significantly denoised spectral estimates that have significantly higher time and frequency resolution than multitaper spectral estimates. For the neural spiking data, we obtain a new spectral representation of neuronal firing rates. Spectrotemporal pursuit offers a robust spectral decomposition framework that is a principled alternative to existing methods for decomposing time series into a small number of smooth oscillatory components.
| S-EPMC4273341 | biostudies-literature
Project description:The most widely-used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms and analysis algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. All commercial tiling array platforms performed well, although each platform and analysis algorithm had distinct performance and cost characteristics. Simple sequence repeats and genome redundancy tend to result in false positives on oligonucleotide platforms. The spike-in DNA samples and the resulting array data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. Keywords: chip-ChIP simulation For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2007-12-01 | GSE9732 | GEO
Project description:Different tissues have complex anisotropic structures to support biological functions. Mimicking these complex structures in vitro remains a challenge in biomaterials designs in support of tissue regeneration. Here, inspired by different types of silk nanofibers, a composite materials strategy was pursued towards this challenge. A combination of fabrication methods was utilized to achieve separate control of amorphous and beta-sheet rich silk nanofibers in the same solution. Aqueous solutions containing these two structural types of silk nanofibers were then simultaneously treated with an electric field and with ethylene glycol diglycidyl ether (EGDE). Under these conditions, the beta-sheet rich silk nanofibers in the mixture responded to the electric field while the amorphous nanofibers were active in the crosslinking process with the EGDE. As a result, cryogels with anisotropic structures were prepared, including mimics for cortical- and cancellous-like bone biomaterials as a complex osteoinductive niche. In vitro studies revealed that mechanical cues of the cryogels induced osteodifferentiation of stem cells while the anisotropy inside the cryogels influenced immune reactions of macrophages. These bioactive cryogels also stimulated improved bone regeneration in vivo through modulation of inflammation, angiogenesis and osteogenesis responses, suggesting an effective strategy to develop bioactive matrices with complex anisotropic structures beneficial to tissue regeneration.
| S-EPMC10437128 | biostudies-literature
Project description:Organ phantoms are widely used for evaluating medical technologies, training clinical practitioners, as well as surgical planning. In the context of cardiovascular disease, a patient-specific cardiac phantom can play an important role for interventional cardiology procedures. However, phantoms with complicated structures are difficult to fabricate by conventional manufacturing methods. The emergence of three-dimensional (3D) printing with soft materials provides the opportunity to produce phantoms with complex geometries and realistic properties. In this work, the aim was to explore the use of a direct 3D printing technique to produce multimodal imaging cardiac phantoms and to test the physical properties of the new materials used, namely the Poro-Lay series and TangoPlus. The cardiac phantoms were first modeled using real data segmented from a patient chest computer tomography (CT) scan and then printed with the novel materials. They were then tested quantitatively in terms of stiffness and ultrasound (US) acoustic values and qualitatively with US, CT, and magnetic resonance imaging systems. From the stiffness measurements, Lay-fomm 40 had the closest Young's modulus to real myocardium with an error of 29-54%, while TangoPlus had the largest difference. From the US acoustics measurements, Lay-fomm 40 also demonstrated the closest soft tissue-mimicking properties with both the smallest attenuation and impedance differences. Furthermore, the imaging results show that the phantoms are compatible with multiple imaging modalities and thus have potential to be used for interventional procedure simulation and testing of novel interventional devices. In conclusion, direct 3D printing with Poro-Lay and TangoPlus is a promising method for manufacture of multimodal imaging phantoms with complicated structures, especially for soft patient-specific phantoms.
| S-EPMC7774877 | biostudies-literature
Project description:Energy resolving detectors provide more than one spectral measurement in one image acquisition. The purpose of this study is to investigate, with simulation, the ability to decompose four materials using energy discriminating detectors and least squares minimization techniques.Three least squares parameter estimation decomposition techniques were investigated for four-material breast imaging tasks in the image domain. The first technique treats the voxel as if it consisted of fractions of all the materials. The second method assumes that a voxel primarily contains one material and divides the decomposition process into segmentation and quantification tasks. The third is similar to the second method but a calibration was used. The simulated computed tomography (CT) system consisted of an 80 kVp spectrum and a CdZnTe (CZT) detector that could resolve the x-ray spectrum into five energy bins. A postmortem breast specimen was imaged with flat panel CT to provide a model for the digital phantoms. Hydroxyapatite (HA) (50, 150, 250, 350, 450, and 550 mg/ml) and iodine (4, 12, 20, 28, 36, and 44 mg/ml) contrast elements were embedded into the glandular region of the phantoms. Calibration phantoms consisted of a 30/70 glandular-to-adipose tissue ratio with embedded HA (100, 200, 300, 400, and 500 mg/ml) and iodine (5, 15, 25, 35, and 45 mg/ml). The x-ray transport process was simulated where the Beer-Lambert law, Poisson process, and CZT absorption efficiency were applied. Qualitative and quantitative evaluations of the decomposition techniques were performed and compared. The effect of breast size was also investigated.The first technique decomposed iodine adequately but failed for other materials. The second method separated the materials but was unable to quantify the materials. With the addition of a calibration, the third technique provided good separation and quantification of hydroxyapatite, iodine, glandular, and adipose tissues. Quantification with this technique was accurate with errors of 9.83% and 6.61% for HA and iodine, respectively. Calibration at one point (one breast size) showed increased errors as the mismatch in breast diameters between calibration and measurement increased. A four-point calibration successfully decomposed breast diameter spanning the entire range from 8 to 20 cm. For a 14 cm breast, errors were reduced from 5.44% to 1.75% and from 6.17% to 3.27% with the multipoint calibration for HA and iodine, respectively.The results of the simulation study showed that a CT system based on CZT detectors in conjunction with least squares minimization technique can be used to decompose four materials. The calibrated least squares parameter estimation decomposition technique performed the best, separating and accurately quantifying the concentrations of hydroxyapatite and iodine.
| S-EPMC3021557 | biostudies-other
Project description:BackgroundWe previously developed a computational model to aid clinicians in positioning implantable cardioverter-defibrillators (ICDs), especially in the case of abnormal anatomies that commonly arise in pediatric cases. We have validated the model clinically on the body surface; however, validation within the volume of the heart is required to establish complete confidence in the model and improve its use in clinical settings.ObjectiveThe goal of this study was to use an animal model and thoracic phantom to record the ICD potential field within the heart and on the torso to validate our defibrillation simulation system.MethodsWe recorded defibrillator shock potentials from an ICD suspended together with an animal heart in a human-shaped torso tank and compared them with simulated values. We also compared the scaled distribution threshold, an analog to the defibrillation threshold, calculated from the measured and simulated electric fields within the myocardium.ResultsICD potentials recorded on the tank and cardiac surface and within the myocardium agreed well with those predicted by the simulation. A quantitative comparison of the recorded and simulated potentials yielded a mean correlation of 0.94 and a relative error of 19.1%. The simulation can also predict scaled distribution thresholds similar to those calculated from the measured potential fields.ConclusionWe found that our simulation could predict potential fields with high correlation with the measured values within the heart and on the torso surface. These results support the use of this model for the optimization of ICD placements.
| S-EPMC7117986 | biostudies-literature
Project description:The most widely-used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms and analysis algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. All commercial tiling array platforms performed well, although each platform and analysis algorithm had distinct performance and cost characteristics. Simple sequence repeats and genome redundancy tend to result in false positives on oligonucleotide platforms. The spike-in DNA samples and the resulting array data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated. Keywords: chip-ChIP simulation For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each replicate array, we labeled 1µg of spike-in sample and 1µg of control sample. The Bioprime Plus Array CGH labeling Module (Invitrogen Catolog number 18095-014) was used. The spike-in was labeled with the red channel dye (Alexa Fluor-647) and the control was labeled with the green channel dye (Alexa Fluor-555) in two of the replicates. A dye swap was performed for the third replicate. These samples were then competitively hybridized to three replicate 244k arrays from Agilent, (AMADID 25150451). We hybridized the samples to the arrays using the Agilent Array CGH protocol, with some modifications. Briefly, labeled DNA was combined with Cot-1 DNA, blocking reagent, and hybridization buffer. The hybridizations were carried out at 60°C. The arrays were scanned using an Agilent dual laser scanner, and the images were processed using Agilent Feature Extraction Software.
2010-05-22 | E-GEOD-9732 | biostudies-arrayexpress
Project description:Inertial cavitation induced by pulsed high-intensity focused ultrasound (pHIFU) has previously been shown to successfully permeabilize tumor tissue and enhance chemotherapeutic drug uptake. In addition to HIFU frequency, peak rarefactional pressure ( p- ), and pulse duration, the threshold for cavitation-induced bioeffects has recently been correlated with asymmetric distortion caused by nonlinear propagation, diffraction and formation of shocks in the focal waveform, and therefore with the transducer F -number. To connect previously observed bioeffects with bubble dynamics and their attendant physical mechanisms, the dependence of inertial cavitation behavior on shock formation was investigated in transparent agarose gel phantoms using high-speed photography and passive cavitation detection (PCD). Agarose phantoms with concentrations ranging from 1.5% to 5% were exposed to 1-ms pulses using three transducers of the same aperture but different focal distances ( F -numbers of 0.77, 1.02, and 1.52). Pulses had central frequencies of 1, 1.5, or 1.9 MHz and a range of p- at the focus varying within 1-18 MPa. Three distinct categories of bubble behavior were observed as the acoustic power increased: stationary near-spherical oscillation of individual bubbles, proliferation of multiple bubbles along the pHIFU beam axis, and fanned-out proliferation toward the transducer. Proliferating bubbles were only observed under strongly nonlinear or shock-forming conditions regardless of frequency, and only where the bubbles reached a certain threshold size range. In stiffer gels with higher agarose concentrations, the same pattern of cavitation behavior was observed, but the dimensions of proliferating clouds were smaller. These observations suggest mechanisms that may be involved in bubble proliferation: enhanced growth of bubbles under shock-forming conditions, subsequent shock scattering from the gel-bubble interface, causing an increase in the repetitive tension created by the acoustic wave, and the appearance of a new growing bubble in the proximal direction. Different behaviors corresponded to specific spectral characteristics in the PCD signals: broadband noise in all cases, narrow peaks of backscattered harmonics in the case of stationary bubbles, and broadened, shifted harmonic peaks in the case of proliferating bubbles. The shift in harmonic peaks can be interpreted as a Doppler shift from targets moving at speeds of up to 2 m/s, which correspond to the observed bubble proliferation speeds.
| S-EPMC8500614 | biostudies-literature
Project description:The carcinogenesis of urethane (ethyl carbamate), a byproduct of fermentation that is consistently found in various food products, was investigated with a combination of kinetic experiments and quantum chemical calculations. The main objective of the study was to find ΔG(⧧), the activation free energy for the rate-limiting step of the SN2 reaction among the ultimate carcinogen of urethane, vinyl carbamate epoxide (VCE), and different nucleobases of the DNA. In the experimental part, the second-order reaction rate constants for the formation of the main 7-(2-oxoethyl)guanine adduct in aqueous solutions of deoxyguanosine and in DNA were determined. A series of ab initio, density functional theory (DFT), and semiempirical molecular orbital (MO) calculations was then performed to determine the activation barriers for the reaction between VCE and nucleobases methylguanine, methyladenine, and methylcytosine. Effects of hydration were incorporated with the use of the solvent reaction field method of Tomasi and co-workers and the Langevine dipoles model of Florian and Warshel. The computational results for the main adduct were found to be in good agreement with the experiment, thus presenting strong evidence for the validity of the proposed SN2 mechanism. This allowed us to predict the activation barriers of reactions leading to side products for which kinetic experiments have not yet been performed. Our calculations have shown that the main 7-(2-oxoethyl)deoxyguanosine adduct indeed forms preferentially because the emergence of other adducts either proceeds across a significantly higher activation barrier or the geometry of the reaction requires the Watson-Crick pairs of the DNA to be broken. The computational study also considered the questions of stereoselectivity, the ease of the elimination of the leaving group, and the relative contributions of the two possible reaction paths for the formation of the 1,N(2)-ethenodeoxyguanosine adduct.
| S-EPMC4731881 | biostudies-literature
Project description:BackgroundThe aim of this study was to compare anesthesiology residents' acquisition of gripping and needling skills in either single-or double-operator ultrasound-guided nerve block using a hand-made phantom.DesignProspective, randomized controlled study.MethodsAfter a tutorial session, 47 ultrasound-novice residents performed needling with double and single operator (Jedi, Bedforth, On-lock) grip techniques in each of the 3 interventional task sessions.ResultsThe time to perform the correct grip and needling decreased significantly between sessions for each technique (P < .001). While the double operator tasks required a shorter time than the single operator tasks in all 3 sessions (P < .001), there was no significant difference between the single-operator techniques. The number of needling attempts was similar between techniques and sessions. Participants rated the workload higher for the single-operator techniques on the National Aeronautics and Space Administration Task Load Index.ConclusionHands-on training of phantom models may be beneficial for the acquisition of single-operator grip skills.
| S-EPMC9439790 | biostudies-literature