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Quantitative Imaging (quantitative + imaging)
Selected AbstractsQuantitative imaging of cartilage morphology at 3.0 Tesla in the presence of gadopentate dimeglumine (Gd-DTPA)MAGNETIC RESONANCE IN MEDICINE, Issue 2 2007Felix Eckstein Abstract MRI-based cartilage morphometry was previously validated in the absence of gadopentate dimeglumine (Gd-DTPA). However, Gd-DTPA is required for compositional (proteoglycan) imaging using delayed gadolinium-enhanced MRI of cartilage (dGEMRIC). Therefore, the effect of Gd-DTPA on cartilage morphometry was studied. A total of 165 female participants (67 with and 98 without osteoarthritis [OA]) were imaged at 3.0 Tesla before and 2 hr after intravenous Gd-DTPA injection. Flip angles in post-Gd-DTPA scans varied between 12° and 35°. Cartilage volume and thickness of post- vs. pre-Gd-DTPA scans showed intraclass correlation coefficients (ICCs) of 0.85 , r , 0.95, mean differences between ,2.1% and +1.1%, and standard deviations (SDs) of differences between 4.7% and 9.2%. Mixed-effect models found no consistent impact of flip angle and OA status on post- vs. pre-Gd-DTPA differences. Accurate morphological measurements of cartilage can be obtained after Gd-DTPA injection, allowing compositional and morphological imaging to be combined into one session. Magn Reson Med 58:402,406, 2007. © 2007 Wiley-Liss, Inc. [source] Infection of Arabidopsis thaliana leaves with Albugo candida (white blister rust) causes a reprogramming of host metabolismMOLECULAR PLANT PATHOLOGY, Issue 2 2000Hsueh-Mei Chou Albugo candida (Pers.) (O.) Kunze is a biotrophic pathogen which infects the crucifer Arabidopsis thaliana (L.) Heynh forming discrete areas of infection. Eight days after inoculation of leaves, white blisters became visible on the under surface of the leaf although no symptoms were apparent on the upper surface. By day 14, the region of leaf invaded by fungal mycelium had become chlorotic. Recently it has been hypothesized that an accumulation of soluble carbohydrates, following an increase in invertase activity, may trigger sugar signal transduction pathways leading to the repression of photosynthetic gene expression and to the induction of defence proteins. This hypothesis was investigated by quantifying localized changes in carbohydrate and photosynthetic metabolism and the expression of genes encoding photosynthetic and defence proteins. Quantitative imaging of chlorophyll fluorescence revealed that the rate of photosynthesis declined progressively in the invaded regions of the leaf. However, in uninfected regions of the infected leaf the rate of photosynthesis was similar to that measured in the control leaf until late on during the infection cycle when it declined. Images of nonphotochemical fluorescence quenching (NPQ) suggested that the capacity of the Calvin cycle had been reduced in infected regions and that there was a complex metabolic heterogeneity within the infected leaf. A. candida also caused localized changes in the carbohydrate metabolism of the leaf; soluble carbohydrates accumulated in the infected region whereas the amount of starch declined. The reverse was seen in uninfected regions of the infected leaf; carbohydrates did not accumulate until late on during infection and the amount of starch increased as the infection progressed. There was an increase in the activity of invertases which was confined to regions of the leaf invaded by the fungal mycelium. The increase in apoplastic invertase activity was of host origin, as mRNA levels of the AT,FRUCT1 gene (measured by semiquantitative RT-PCR) increased 40-fold in the infected region. The increase in soluble invertase activity resulted from the appearance of a new isoform in the invaded region of the leaf. Current evidence suggests that this was of fungal origin. Northern blot analysis of cab and rbcS showed that photosynthetic gene expression was repressed in the infected leaf from 6 days after inoculation (DAI) when compared to control leaves. In contrast, there was no detectable induction of defence proteins in the infected leaf. These data are discussed in the context of the sugar-sensing hypothesis presented above. [source] Molecular imaging in small animals,roles for micro-CTJOURNAL OF CELLULAR BIOCHEMISTRY, Issue S39 2002Erik L. Ritman Abstract X-ray micro-CT is currently used primarily to generate 3D images of micro-architecture (and the function that can be deduced from it) and the regional distribution of administered radiopaque indicators, within intact rodent organs or biopsies from large animals and humans. Current use of X-ray micro-CT can be extended in three ways to increase the quantitative imaging of molecular transport and accumulation within such specimens. (1) By use of heavy elements, other than the usual iodine, attached to molecules of interest or to surrogates for those molecules. The accumulation of the indicator in the physiological compartments, and the transport to and from such compartments, can be quantitated from the imaged spatial distribution of these contrast agents. (2) The high spatial resolution of conventional X-ray attenuation-based CT images can be used to improve the quantitative nature of radionuclide-based tomographic images (SPECT & PET) by providing correction for attenuation of the emitted gamma rays and the accurate delineation of physiological spaces known to selectively accumulate those indicators. Similarly, other imaging modalities which also localize functions in 2D images (such as histological sections subsequently obtained from the same specimen), can provide a synergistic combination with CT-based 3D microstructure. (3) By increasing the sensitivity and specificity of X-ray CT image contrast by use of methods such as: K-edge subtraction imaging, X-ray fluorescence imaging, imaging of the various types of scattered X-ray and the consequences of the change in the speed of X-rays through different tissues, such as refraction and phase shift. These other methods of X-ray imaging can increase contrast by more than an order of magnitude over that due to conventionally-used attenuation of X-ray. To fully exploit their potentials, much development of radiopaque indicators, scanner hardware and image reconstruction and analysis software will be needed. J. Cell. Biochem. Suppl. 39: 116,124, 2002. © 2002 Wiley-Liss, Inc. [source] Weighting hyperspectral image data for improved multivariate curve resolution resultsJOURNAL OF CHEMOMETRICS, Issue 9 2008Howland D. T. Jones Abstract The combination of hyperspectral confocal fluorescence microscopy and multivariate curve resolution (MCR) provides an ideal system for improved quantitative imaging when multiple fluorophores are present. However, the presence of multiple noise sources limits the ability of MCR to accurately extract pure-component spectra when there is high spectral and/or spatial overlap between multiple fluorophores. Previously, MCR results were improved by weighting the spectral images for Poisson-distributed noise, but additional noise sources are often present. We have identified and quantified all the major noise sources in hyperspectral fluorescence images. Two primary noise sources were found: Poisson-distributed noise and detector-read noise. We present methods to quantify detector-read noise variance and to empirically determine the electron multiplying CCD (EMCCD) gain factor required to compute the Poisson noise variance. We have found that properly weighting spectral image data to account for both noise sources improved MCR accuracy. In this paper, we demonstrate three weighting schemes applied to a real hyperspectral corn leaf image and to simulated data based upon this same image. MCR applied to both real and simulated hyperspectral images weighted to compensate for the two major noise sources greatly improved the extracted pure emission spectra and their concentrations relative to MCR with either unweighted or Poisson-only weighted data. Thus, properly identifying and accounting for the major noise sources in hyperspectral images can serve to improve the MCR results. These methods are very general and can be applied to the multivariate analysis of spectral images whenever CCD or EMCCD detectors are used. Copyright © 2008 John Wiley & Sons, Ltd. [source] Method for quantitative imaging of the macromolecular 1H fraction in tissuesMAGNETIC RESONANCE IN MEDICINE, Issue 5 2003Stefan Ropele Abstract A new method was developed for mapping the relative density of the macromolecular protons involved in magnetization transfer (MT). This method employs a stimulated echo preparation scheme in order to modulate the phase distribution within a spin ensemble. This labeled spin ensemble is then used as an intrinsic indicator, which is diluted due to magnetization exchange with macromolecular protons. A pulse sequence is presented which compensates for longitudinal relaxation, allows observation of the dilution effect only, and provides for calculation of parameter maps using indicator dilution theory. Compared to other quantitative MT techniques, neither additional relaxation time measurements nor knowledge regarding the lineshape of the macromolecular proton pool are required. Moreover, the inherent low specific absorption rate and the low sensitivity for B1 errors make this method favorable in a clinical setting. This sequence was used to measure the macromolecular proton density in cross-linked bovine serum albumin. Using a navigated echo planar readout, the sequence was also employed to visualize the macromolecular content of human brain in vivo. Magn Reson Med 49:864,871, 2003. © 2003 Wiley-Liss, Inc. [source] A toolkit for the characterization of CCD cameras for transmission electron microscopyACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2010M. Vulovic Charge-coupled devices (CCD) are nowadays commonly utilized in transmission electron microscopy (TEM) for applications in life sciences. Direct access to digitized images has revolutionized the use of electron microscopy, sparking developments such as automated collection of tomographic data, focal series, random conical tilt pairs and ultralarge single-particle data sets. Nevertheless, for ultrahigh-resolution work photographic plates are often still preferred. In the ideal case, the quality of the recorded image of a vitrified biological sample would solely be determined by the counting statistics of the limited electron dose the sample can withstand before beam-induced alterations dominate. Unfortunately, the image is degraded by the non-ideal point-spread function of the detector, as a result of a scintillator coupled by fibre optics to a CCD, and the addition of several inherent noise components. Different detector manufacturers provide different types of figures of merit when advertising the quality of their detector. It is hard for most laboratories to verify whether all of the anticipated specifications are met. In this report, a set of algorithms is presented to characterize on-axis slow-scan large-area CCD-based TEM detectors. These tools have been added to a publicly available image-processing toolbox for MATLAB. Three in-house CCD cameras were carefully characterized, yielding, among others, statistics for hot and bad pixels, the modulation transfer function, the conversion factor, the effective gain and the detective quantum efficiency. These statistics will aid data-collection strategy programs and provide prior information for quantitative imaging. The relative performance of the characterized detectors is discussed and a comparison is made with similar detectors that are used in the field of X-ray crystallography. [source] Visualizing and quantifying the differential cleavages of the eukaryotic translation initiation factors eIF4GI and eIF4GII in the enterovirus-infected cellBIOTECHNOLOGY & BIOENGINEERING, Issue 6 2009Yueh-Ying Hsu Abstract Enterovirus (EV) infection has been shown to cause a marked shutoff of host protein synthesis, an event mainly achieved through the cleavages of eukaryotic translation initiation factors eIF4GI and eIF4GII that are mediated by viral 2A protease (2Apro). Using fluorescence resonance energy transfer (FRET), we developed genetically encoded and FRET-based biosensors to visualize and quantify the specific proteolytic process in intact cells. This was accomplished by stable expression of a fusion substrate construct composed of the green fluorescent protein 2 (GFP2) and red fluorescent protein 2 (DsRed2), with a cleavage motif on eIF4GI or eIF4GII connected in between. The FRET biosensor showed a real-time and quantifiable impairment of FRET upon EV infection. Levels of the reduced FRET closely correlated with the cleavage kinetics of the endogenous eIF4Gs isoforms. The FRET impairments were solely attributed to 2Apro catalytic activity, irrespective of other viral-encoded protease, the activated caspases or general inhibition of protein synthesis in the EV-infected cells. The FRET biosensors appeared to be a universal platform for several related EVs. The spatiotemporal and quantitative imaging enabled by FRET can shed light on the protease,substrate behaviors in their normal milieu, permitting investigation into the molecular mechanism underlying virus-induced host translation inhibition. Biotechnol. Bioeng. 2009; 104: 1142,1152. © 2009 Wiley Periodicals, Inc. [source] Quantitative real-time analysis of HIV-1 gene expression dynamics in single living primary cellsBIOTECHNOLOGY JOURNAL, Issue 6 2006Asier Sáez-Cirión Abstract Studies on the regulation of viral transcription upon infection of the target cells have provided important information on the viral and host factors that influence pathogenesis. However, these studies have been limited so far to steady-state analysis of gene expression. Here we report an image based photon-counting method that allows real-time quantitative imaging of viral gene expression in infected single cells. Employing an HIV-1 vector bearing the firefly luciferase reporter gene, we exploited a single cell photon imaging methodology (a customized and highly sensitive imaging microscope) to measure viral gene expression following integration into a host genome in situ. Our approach reveals real-time dynamics of viral gene expression in living HIV natural target cells (primary human CD4 T cells and macrophages), and promises itself as a powerful tool for quantitative studies on a wide variety of virus-host cell interactions. [source] | |||||||||||||