PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Experimental validation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14Linked to original sources
PubMed2005

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome.

Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did not contain an apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-mRNA contamination during library construction, or alternatively represent nonspecific "transcriptional noise." Here we show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts of unknown function whose expression appears to be regulated. The ncRNA transcripts have larger exons and fewer introns than protein-coding transcripts. Analysis of the genomic landscape around these sequences indicates that some cDNA clones were produced not from terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes. A significant proportion of these transcripts exhibit tissue-specific expression patterns, as well as dynamic changes in their expression in macrophages following lipopolysaccharide stimulation. Taken together, the data provide strong support for the conclusion that ncRNAs are an important, regulated component of the mammalian transcriptome.

Animals↗
PubMed2006

Experimental validation of predicted mammalian erythroid cis-regulatory modules.

Multiple alignments of genome sequences are helpful guides to functional analysis, but predicting cis-regulatory modules (CRMs) accurately from such alignments remains an elusive goal. We predict CRMs for mammalian genes expressed in red blood cells by combining two properties gleaned from aligned, noncoding genome sequences: a positive regulatory potential (RP) score, which detects similarity to patterns in alignments distinctive for regulatory regions, and conservation of a binding site motif for the essential erythroid transcription factor GATA-1. Within eight target loci, we tested 75 noncoding segments by reporter gene assays in transiently transfected human K562 cells and/or after site-directed integration into murine erythroleukemia cells. Segments with a high RP score and a conserved exact match to the binding site consensus are validated at a good rate (50%-100%, with rates increasing at higher RP), whereas segments with lower RP scores or nonconsensus binding motifs tend to be inactive. Active DNA segments were shown to be occupied by GATA-1 protein by chromatin immunoprecipitation, whereas sites predicted to be inactive were not occupied. We verify four previously known erythroid CRMs and identify 28 novel ones. Thus, high RP in combination with another feature of a CRM, such as a conserved transcription factor binding site, is a good predictor of functional CRMs. Genome-wide predictions based on RP and a large set of well-defined transcription factor binding sites are available through servers at http://www.bx.psu.edu/.

Amino Acid Motifs↗
PubMed2001

Experimental validation for the diffraction effect in the ultrasonic field of piston transducers and its influence on absorption and dispersion measurements.

The aim of this work was to study the diffraction effects in the ultrasonic field of piston source transducers and their importance for accurate measurements of attenuation and dispersion in viscoelastic materials. In laboratory measurements, the diffraction phenomena are mainly due to the beam spread of the ultrasonic wave propagating in viscoelastic materials. This effect is essentially related to the estimated attenuation and dispersion in the material. In this work, a frequency domain system identification approach, using the maximum likelihood estimator (MLE), was applied to the measured data in order to determine a function for correcting the diffraction losses in both normal and oblique incidences for a large frequency band (300 kHz to 3 MHz). The effective radius of the used transmitter was determined by the inverse problem when ultrasonic beam propagation was investigated in a water medium. Using the estimated radius, the propagation through viscoelastic materials was established, and the acoustic parameters of these materials were estimated. Attention was paid to the determination of the attenuation and dispersion in the materials. These quantities were compared to those obtained without diffraction correction in order to see the influence of introducing the diffraction correction into the propagation model.

Journal Article↗
PubMed2002

Experimental validation of a linear model for data reduction in chirp-pulse microwave CT.

Chirp-pulse microwave computerized tomography (CP-MCT) is an imaging modality developed at the Department of Biocybernetics, University of Niigata (Niigata, Japan), which intends to reduce the microwave-tomography problem to an X-ray-like situation. We have recently shown that data acquisition in CP-MCT can be described in terms of a linear model derived from scattering theory. In this paper, we validate this model by showing that the theoretically computed response function is in good agreement with the one obtained from a regularized multiple deconvolution of three data sets measured with the prototype of CP-MCT. Furthermore, the reliability of the model as far as image restoration in concerned, is tested in the case of space-invariant conditions by considering the reconstruction of simple on-axis cylindrical phantoms.

Computer Simulation↗
PubMed1994

New method for quantitatively determining aortic regurgitant volume using Doppler color flow imaging: experimental validation study.

We have developed a method to provide the two-dimensional distribution of blood flow velocity and the blood flow volume rate in the ascending aorta from the cross-sectional Doppler color flow image. Regional blood flow velocities were determined by converting color intensities of the cross-sectional Doppler color flow image into the corresponding flow velocities with the correction with the spatial ultrasound beam incident angle. The spatial ultrasound beam incident angle was estimated from the geometric characteristics of the color flow image contour. The method was validated in a steady flow model circuit comparing the calculated flow volume rates by the method with those simultaneously measured by an electromagnetic flowmeter. We performed an open chest dog experiment and calculated the blood flow volume rate at the ascending aorta before and after the aortic regurgitation was made. The calculated ejection flow volume rate and regurgitant volume were validated by the comparison with those simultaneously measured by an electromagnetic flowmeter. Based on these data, we can conclude that the current method provides accurate measurements of regurgitant volume as well as ejection flow volume rate in the ascending aorta.

Animals↗
PubMedDate not supplied

Numerical simulation and experimental validation of blood flow in arteries with structured-tree outflow conditions.

Blood flow in the large systemic arteries is modeled using one-dimensional equations derived from the axisymmetric Navier-Stokes equations for flow in compliant and tapering vessels. The arterial tree is truncated after the first few generations of large arteries with the remaining small arteries and arterioles providing outflow boundary conditions for the large arteries. By modeling the small arteries and arterioles as a structured tree, a semi-analytical approach based on a linearized version of the governing equations can be used to derive an expression for the root impedance of the structured tree in the frequency domain. In the time domain, this provides the proper outflow boundary condition. The structured tree is a binary asymmetric tree in which the radii of the daughter vessels are scaled linearly with the radius of the parent vessel. Blood flow and pressure in the large vessels are computed as functions of time and axial distance within each of the arteries. Comparison between the simulations and magnetic resonance measurements in the ascending aorta and nine peripheral locations in one individual shows excellent agreement between the two.

Adult↗
PubMed2006

Stresses and strains in the medial meniscus of an ACL deficient knee under anterior loading: a finite element analysis with image-based experimental validation.

The menisci are believed to play a stabilizing role in the ACL-deficient knee, and are known to be at risk for degradation in the chronically unstable knee. Much of our understanding of this behavior is based on ex vivo experiments or clinical studies in which we must infer the function of the menisci from external measures of knee motion. More recently, studies using magnetic resonance (MR) imaging have provided more clear visualization of the motion and deformation of the menisci within the tibio-femoral articulation. In this study, we used such images to generate a finite element model of the medial compartment of an ACL-deficient knee to reproduce the meniscal position under anterior loads of 45, 76, and 107 N. Comparisons of the model predictions to boundaries digitized from images acquired in the loaded states demonstrated general agreement, with errors localized to the anterior and posterior regions of the meniscus, areas in which large shear stresses were present. Our model results suggest that further attention is needed to characterize material properties of the peripheral and horn attachments. Although overall translation of the meniscus was predicted well, the changes in curvature and distortion of the meniscus in the posterior region were not captured by the model, suggesting the need for refinement of meniscal tissue properties.

Aged↗
PubMed2006

Experimental validation of an inverse heat transfer algorithm for optimizing hyperthermia treatments.

Hyperthermia is a cancer treatment modality in which body tissue is exposed to elevated temperatures to destroy cancerous cells. Hyperthermia treatment planning refers to the use of computational models to optimize the heating protocol with the goal of isolating thermal damage to predetermined treatment areas. This paper presents an algorithm to optimize a hyperthermia treatment protocol using the conjugate gradient method with the adjoint problem. The output of the minimization algorithm is a heating protocol that will cause a desired amount of thermal damage. The transient temperature distribution in a cylindrical region is simulated using the bioheat transfer equation. Temperature and time are integrated to calculate the extent of thermal damage in the region via a first-order rate process based on the Arrhenius equation. Several validation experiments are carried out by applying the results of the minimization algorithm to an albumen tissue phantom. Comparisons of metrics describing the damage region (the height and radius of the volume of thermally ablated phantom) show good agreement between the desired extent of damage and the measured extent of damage. The sensitivity of the bioheat transfer model and the Arrhenius damage model to their constituent parameters is calculated to create a tolerable range of error between the desired and measured extent of damage. The measured height and radius of the ablated region fit well within the tolerable range of error found in the sensitivity analysis.

Algorithms↗
PubMedDate not supplied

Hybrid positron detection and optical coherence tomography system: design, calibration, and experimental validation with rabbit atherosclerotic models.

We evaluate the performance of our novel hybrid optical coherence tomography (OCT) and scintillating probe, demonstrate simultaneous OCT imaging and scintillating detection, and validate the system using an atherosclerotic rabbit model. Preliminary data obtained from the rabbit model suggest that our prototype positron probe detects local uptake of fluorodeoxyglucose (FDG) labeled with 18F positron (beta) radionuclide emitter, and the high-uptake regions correlate with sites of injury and extensive atherosclerosis areas. Preliminary data also suggest that coregistered high-resolution OCT images provide imaging of detailed plaque microstructures, which cannot be resolved by positron detection.

Animals↗
PubMed2002

An approximated 3-d model of the Langevin transducer and its experimental validation.

In this work, an approximated 3-D analytical model of the Langevin transducer is proposed. The model, improving the classical 1-D approach describing the thickness extensional mode, allows us to predict also the radial modes of both the piezoelectric ceramic disk and the loading masses; furthermore, it is able to describe the coupling between radial and thickness extensional modes. In order to validate the model, the computed frequency spectrum is compared with that obtained by measurements carried out on 13 manufactured samples of different thicknesses to diameter ratios. The comparison shows that the model predicts with quite good accuracy the resonance frequencies of the two lowest frequency modes, i.e., those of practical interest, all over the explored range. Finally, the coupling effect between thickness and radial modes on the frontal displacement is measured and discussed.

Journal Article↗
PubMed2004

Experimental validation of a tractable numerical model for focused ultrasound heating in flow-through tissue phantoms.

Heating from high intensity focused ultrasound (HIFU) can be used to control bleeding, both from individual blood vessels as well as from gross damage to the capillary bed. The presence of vascularity can limit one's ability to elevate the temperature owing to convective heat transport. In an effort to better understand the heating process in tissues with vascular structure we have developed a numerical simulation that couples models for ultrasound propagation, acoustic streaming, ultrasound heating and blood cooling in a Newtonian viscous medium. The 3-D simulation allows for the study of complicated biological structures and insonation geometries. We have also undertaken a series of in vitro experiments employing non-uniform flow-through tissue phantoms and designed to provide verification of the model predictions. We show that blood flow of 2 cm/s (6.4 ml/min through a 2.6 mm 'vessel') can reduce peak temperature in a vessel wall by 25%. We also show that HIFU intensities of 6.5 x 10(5) W/m2 can induce acoustic streaming with peak velocities up to 5 cm/s and this can reduce heating near a vessel wall by more than 10%. These results demonstrate that convective cooling is important in HIFU and can be accounted for within simulation models.

Algorithms↗
PubMed2003

Experimental validation of low virulence in field strains of Listeria monocytogenes.

Several reports have described Listeria monocytogenes strains which were nonpathogenic or weakly pathogenic, but little is known about these low-virulence strains. We found that 9 field L. monocytogenes strains were hypovirulent and 17 were avirulent, based on the number of mice contaminated and the colonization of their spleens after subcutaneous inoculation. All these strains possessed the known virulence genes. We have now assessed the low virulence of these strains in other assays before determining how they differ from virulent strains. We have shown that the low-virulence strains exhibited a phenotypic stability and were not a mixture of virulent and avirulent bacteria. They did not recover virulence after many passages in mice and colonized the spleens of mice more poorly than virulent strains after i.v. inoculation. Their lethal capacities, determined by 50% lethal dose (LD(50)), were lower than those of virulent strains. Like Listeria innocua, 14 of 17 avirulent strains had no LD(50) and were eliminated by the lymph nodes after subcutaneous inoculation. The virulent, hypovirulent, and avirulent strains were always significantly different, whatever the tests of virulence used, confirming the importance of these low-virulence field strains in identifying the proteins involved in virulence.

Animals↗