Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “quantification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 793 records · Page 44Linked to original sources
PubMed2002

Discriminative quantification of cytochrome P4502D6 and 2D7/8 pseudogene expression by TaqMan real-time reverse transcriptase polymerase chain reaction.

The human drug oxidizing cytochrome P450, CYP2D6, is expressed at highly variable levels mainly due to a common genetic polymorphism which leads to the poor metabolizer phenotype in carriers of two nonfunctional alleles and to the extensive metabolizer phenotype in carriers of one or more functional alleles. Investigation of the role of CYP2D6 mRNA for expression and the possibility of using mRNA expression as a surrogate marker has been hampered by the presence of two pseudogenes, CYP2D7P and CYP2D8P. We therefore developed highly specific TaqMan real-time reverse transcriptase-PCR assays for the discriminative quantification of CYP2D6 and CYP2D7/8P transcripts. By in vitro transcription of plasmids containing the CYP2D6 cDNA or a hybrid CYP2D6/7 cDNA constructed by in vitro mutagenesis, authentic cRNAs were synthesized to be used for specificity testing and for absolute quantification. The method was used to determine CYP2D transcripts in a large number of human livers samples. CYP2D6 was not normally distributed with a median mRNA content of 3.2 transcripts per picogram of total RNA in all livers (range 0.32-14.8, N = 74). Expression in genetic poor metabolizers (1.81, N = 6) was significantly lower compared to extensive metabolizers (3.33, N = 68, P = 0.022). Similar expression levels were found for CYP2D7/8P (median 3.38 transcripts/pg, range 0.46-14.3), which were correlated to CYP2D6 mRNA (r(S) = 0.46, P < 0.0001) but did not depend on CYP2D6 genotype. These data demonstrate genotype-dependent mRNA expression for CYP2D6 and they emphasize the necessity of differentiating between the functional CYP2D6 and the CYP2D pseudogenes.

Base Sequence↗
PubMed1995

Lesion size quantification in SPECT using an artificial neural network classification approach.

An artificial neural network (ANN) has been developed to determine the size of lesions detected in single photon emission computed tomographic images. The network is the Learning Vector Quantizer and is trained to perform size quantification based on image neighborhoods extracted around the lesions. The ANN is compared to the optimal, Bayesian algorithm developed to perform the same task using the unreconstructed, projection data. The performance of the neural network is evaluated at two different noise levels. The Bayesian algorithm provides the upper bound for size quantification performance against which the ANN is compared. In the ideal case where the Bayesian algorithm has explicit knowledge of the underlying distributions, its performance is superior to that of the neural network. However, in the more realistic case where the distributions need to be estimated from the same learning sample the ANN was trained on, the two algorithms have comparable performances.

Algorithms↗
PubMed1999

Quantification of murine cytokine mRNAs using real time quantitative reverse transcriptase PCR.

Recently, a novel technique for "real time" quantitative Reverse Transcriptase-PCR which measures PCR-product accumulation during the exponential phase of the PCR reaction using a dual-labelled fluorogenic probe, has been developed. This method allows direct detection of PCR-product formation by measuring the increase in fluorescent emission continuously during the PCR reaction. Here we present data validating this PCR-method for the quantification of murine cytokines and other factors playing a role in immune regulation (IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-10, IL-12p40, IL-13, IL-15, IFN-gammaTNF-alphaTGF-beta and iNOS). For each substance of interest, a set of primers and internal probe was designed, which specifically amplify the target cDNA, not co-amplifying contaminating genomic DNA. Furthermore, a corresponding reference plasmid cDNA clone was constructed, allowing direct quantification. Additionally, normalization to the housekeeping genes beta-actin or GAPDH was performed. The assay is very sensitive and accurate. It is a "closed-tube" PCR reaction, avoiding time-consuming and hazardous post-PCR manipulations and decreasing the potential risk of PCR contamination.

Animals↗
PubMed2001

Double quantum filtered (1)H NMR spectroscopy enables quantification of lactate in muscle.

In this study we address the question of quantification of muscle lactate using double quantum filtered (DQF) (1)H NMR spectroscopy where dipolar and scalar coupled spectra are acquired. For this, lactate content in muscle samples was independently determined using a conventional enzymatic assay and DQF, (1)H NMR spectroscopy. NMR quantification of lactate relied on comparison of muscle spectra with similarly acquired spectra of standard lactate solutions. Transverse relaxation, T(2), and dipolar coupling effects were investigated at two different orientations of muscle fibers relative to B(o) and at various lactate concentrations. In all cases, we found a biexponential T(2) decay of the lactate methyl signal with a long T(2) of 142 ms (+/-8 ms, n=24) and a short T(2) of 37 ms (+/-6 ms, n=24). Lactate content of muscle determined by NMR spectroscopy agreed with the results obtained from enzymatic assays of the same samples provided that T(2) effects as well as the presence of both scalar and dipolar coupling interactions of lactate in muscle were taken into account.

Abdominal Muscles↗
PubMed2002

A new time-domain frequency-selective quantification algorithm.

In this paper a new time-domain frequency-selective quantification algorithm is presented. Frequency-selective quantification refers to a method that analyzes spectral components in a selected frequency region, ignoring all the other components outside. The algorithm, referred to as MeFreS (Metropolis Frequency-Selective), is based on rank minimization of an opportune Hankel matrix. The minimization procedure is satisfied by the down-hill simplex method, implemented with the simulated annealing method. MeFreS does not use any preprocessing step or filter to suppress nuisance peaks, but the signal model function is directly fitted. In this manner, neither inherent signal distortions nor estimation biases to be corrected occur. The algorithm was tested with Monte Carlo simulations. A comparison with VARPRO and AMARESw algorithms was carried out. Finally, two samples of known content from NMR data were quantified.

Algorithms↗
PubMed1997

Successful quantification of cytomegalovirus DNA by competitive PCR and detection with capillary electrophoresis.

Human cytomegalovirus (HCMV) is responsible for severe infections in immunocompromised patients. Viral load has recently been identified as one of the major risk factors for subsequent development of HCMV disease. In this context, we developed a protocol allowing rapid, sensitive and precise quantification of HCMV DNA using competitive PCR run to saturation. Long primers were used for amplification, and internal DNA standard was constructed by PCR, with a primer inducing formation of a loop on the target sequence. The obtained fragment differed from the wild one (142 bp) by 6 bp. Quantitative analysis of PCR-amplified HCMV DNA was carried out using an original system combining capillary gel electrophoresis and u.v. detection. This procedure was evaluated on renal transplant recipients, and the results of quantitative PCR were compared with those of viraemia, qualitative DNAemia and HCMV-related symptoms. High levels of HCMV DNA were associated with HCMV-related symptoms, and in all cases a significant decrease of viral load was observed following DHPG treatment. Competitive PCR with capillary electrophoresis detection appears to provide a sensitive quantification method for HCMV DNA in leukocytes and is easily adaptable to routine laboratory use.

Cytomegalovirus↗
PubMed2000

Quantification of Staphylococcus aureus cell surface adhesins using flow cytometry.

The initiation of many infectious diseases involves specific adhesion of bacteria to host tissue proteins and carbohydrates. Staphylococcus aureus is known to bind specifically to several proteins in the extracellular matrix (ECM). We report the quantification of the collagen and fibronectin adhesin densities on the staphylococcal surface using flow cytometry. Our results are in agreement with previous reports on the transcription of the respective genes and demonstrate different patterns of temporal expression for the two adhesins in the strains studied. We demonstrate a convenient technique for quantification of bacterial adhesins that can be used in studies aimed at characterization of bacterial adhesion to ECM components and understanding expression of adhesins during the course of an infection.

Adhesins, Bacterial↗
PubMed1995

A novel, microcarrier-based in vitro assay for rapid and reliable quantification of three-dimensional cell migration and angiogenesis.

Angiogenesis in situ occurs within the interstitial extracellular matrix. The complexity of currently used three-dimensional in vitro angiogenesis systems makes it difficult to quantify cellular growth and neovessel formation. To overcome this problem we were interested to develop an angiogenesis system which allows rapid and reliable quantification of three-dimensional neovessel formation in vitro. Endothelial cells were seeded on gelatine-coated microcarriers (MCs). Cell-coated MCs were suspended in a solution of fibrinogen which was then induced to polymerize by addition of thrombin. By this way, MCs were entrapped in a three-dimensional fibrin matrix. Within a few hours, endothelial cells began to leave their supporting microcarriers and to migrate into the fibrin gel. Without addition of stimulators of angiogenesis, endothelial cells showed incoherent migration into the matrix. In contrast, in response to fibronectin, basic fibroblast growth factor (bFGF), or vascular endothelial growth factor (VEGF), respectively, endothelial cells assembled to form multicellular capillary-like structures occasionally exceeding 1000 microns in length. Each MC gave rise to a limited number of capillaries. A single culture dish contained hundreds of MCs, ensuring that a sufficient number of random samples was present for a reliable statistical evaluation. The angiogenic response could be easily quantified by determination of the average number of capillary-like formations per MC (cap/MC). The capillary count for macrovascular endothelial cells from the bovine pulmonary artery was 0.14 cap/MC when no angiogenic stimulators were contained within the fibrin gel. Addition of 200 micrograms/ml fibronectin increased capillary formation to 0.63 cap/MC (P < 0.0001) at Day 6. Already after 3 days, addition of bFGF (30 ng/ml) yielded a capillary count of 1.05 and addition of VEGF (100 ng/ml) resulted in 0.91 cap/MC. In contrast, addition of hyaluronic acid stimulated migration of dispersed endothelial cells into the fibrin matrix without leading to significant capillary formation (0.09 cap/MC). Hydrocortisone alone or in combination with heparin led to a significant inhibition of bFGF-stimulated angiogenesis. We thus have developed a convenient angiogenesis in vitro system which allows reliable quantification of capillary formation in a three-dimensional environment. Based on this assay we conclude that apart from proliferation and migration of endothelial cells, angiogenesis additionally requires the assembly of cells to form multicellular capillaries. This process is strongly induced by the extracellular matrix protein fibronectin. Hyaluronic acid, on the other hand, promotes migration but not capillary formation (assembly).

Animals↗
PubMed1999

Thermodiffusion for continuous quantification of hepatic microcirculation--validation and potential in liver transplantation.

Hepatic microcirculation is a main determinant of reperfusion injury and graft quality in liver transplantation. Methods available for the quantification of hepatic microcirculation are indirect, are invasive, or preclude postoperative application. The aim of this study was the validation of thermodiffusion in a new modification allowing long-term use in the clinical setting. In six pigs Doppler flowmeters were positioned around the hepatic artery and portal vein for the measurement of total liver blood flow. Liver perfusion was quantified by thermodiffusion and compared to H(2) clearance as an established technique under baseline conditions, during different degrees of portal venous obstruction and during occlusion of the hepatic artery. Thermodiffusion measurements were recorded for five days postoperatively followed by histological evaluation of the hepatic puncture site. Perfusion data obtained by thermodiffusion were significantly correlated to H(2) clearance (r = 0.94, P < 0. 001) and to liver blood flow (r = 0.9, P < 0.05). The agreement between thermodiffusion and H(2) clearance was excellent (mean difference -2.1 ml/100 g/min; limits of agreement -12.5 and 8.3 ml/100 g/min). Occlusion of the portal vein or hepatic artery was immediately detected by thermodiffusion, indicating a decrease of perfusion by 64 +/- 7% or 27 +/- 5% of baseline, respectively. Perfusion values at baseline and during vascular occlusion were reproducible during the entire observation period. Histological changes of the liver tissue adjacent to the thermodiffusion probes were minute and did not influence long-term measurements. In vivo validation proved that enhanced thermodiffusion is a minimally invasive technique for the continuous, real-time quantification of hepatic microcirculation. Changes in liver perfusion can be safely detected over several days postoperatively. The implication for liver transplantation has led to the clinical application of thermodiffusion.

Animals↗
PubMed2000

A novel approach to the quantification of hepatic stellate cells in intravital fluorescence microscopy of the liver using a computerized image analysis system.

Hepatic stellate cells (HSC) are nonparenchymal liver cells which reside in the space of Disse within the hepatic microcirculatory unit. HSC can be distinguished using intravital fluorescent microscopy (IVFM) due to the autofluorescence from their intracellular vitamin A. Herein we report on a novel approach for the quantification of video-recorded rat HSC images acquired by IVFM (excitation 360 nm/emission 420 nm) by the combined use of the "Cell counting macro" and the "Measurement macros" in the NIH image software. The approach involved two major steps using (i) the "Cell counting macro" for automatic detection, threshold-setting, and generation of a binary image of the vitamin A autofluorescence in the HSC images and (ii) the "Compute percent black and white" command in the "Measurement macros" to automatically determine the HSC density (%), which was then expressed as percentage of the total area of vitamin A autofluorescence-associated sites per observation area. Comparing the vitamin A autofluorescence areas in the original and the binary fashion HSC images revealed that the "Cell counting macro" was an optimal option for the analysis of the low-magnification (x10 objective) HSC images, whereas this macro was not suitable for the analysis of the higher magnification (40x objective) HSC images unless modifications were made. Our analysis revealed that HSC represent approximately 4-5% of the total area of the liver surface. In analyzing the higher magnification HSC microfluorographs, the use of the original "Cell counting macro" resulted in a significant underestimation of HSC density (60% reduction, P < 0.01) when compared with those analyzed using our modified macro. This study represents the first report of an automatic and reliable approach to the intravital fluorescent microscopic quantification of HSC using a computer-NIH image analysis system.

Animals↗
PubMed1992

Quantification of Gi alpha-proteins in the failing and nonfailing human myocardium.

Heterotrimeric Gi-proteins play an important role in the regulation of cardiac adenylate cyclase. Besides a downregulation of beta-adrenoceptors with an accompanying reduction of the positive inotropic effects of cAMP-dependent positive inotropic agents, an increase of pertussis toxin substrates (Gi alpha-proteins) has been observed. The increase of Gi alpha has been reported to be associated with a reduced adenylate cyclase activity in dilated cardiomyopathy from hearts with heart failure class NYHA IV. Since the quantification of Gi alpha-proteins with the pertussis toxin labeling method is hampered by a number of biological and technical factors, Gi alpha-proteins were quantified radioimmunologically using the iodinated C-terminus 125I-KENLKDCGLF as tracer, purified retinal transducin alpha as standard, and an antiserum (DS 4) raised against the same peptide. With this technique Gi alpha-proteins were increased by 118% in dilated cardiomyopathy and 48% in ischemic cardiomyopathy, although pertussis toxin substrates were only increased by 40% in dilated cardiomyopathy and no change was observed in ischemic cardiomyopathy. In cardiomyopathic tissue, an inverse relationship was observed between the increase of Gi alpha and the positive inotropic effects of isoprenaline or milrinone. These data provide evidence for a functional role of Gi alpha in the reduced positive inotropic effects of cAMP-dependent positive inotropic agents. In addition, results obtained with pertussis toxin labeling for quantification of Gi alpha-proteins do not necessarily reflect the expression of Gi alpha-proteins in the human myocardium.

Amino Acid Sequence↗
PubMed1994

Choice of reference region in the quantification of single-photon emission tomography in primary degenerative dementia.

This study evaluated the effect of using two different reference regions in the quantification of single-photon emission tomography (SPET). SPET scans of 30 patients with Alzheimer's disease (AD) and 30 patients with frontotemporal dementia were compared with the scans of ten age-matched controls. Regions of interest (ROIs) were defined on transaxial slices by a semi-automatic method. Regional cerebral blood flow indices (rCBFi) in each ROI were determined by normalizing the count densities to both cerebellar and occipital cortex reference regions. Mean rCBFi for each ROI were calculated for the patient and control groups and significant group differences determined. The number and topographical distribution of ROIs with significant group differences varied depending upon the choice of reference region. The magnitude of these differences was greatest when the cerebellum was used as the reference region. The disparity between results obtained with the two reference regions was most apparent in the AD group. The reasons for these differences are discussed and we conclude that the cerebellum is the more appropriate choice of reference region in the quantification of SPET in primary degenerative dementia.

Alzheimer Disease↗
PubMed1984

Multivariate analysis of factors affecting postoperative survival in malignant astrocytoma. Importance of DNA quantification.

Fifty-eight patients with supratentorial malignant astrocytoma were analyzed statistically to evaluate the factors most important for predicting postoperative survival. Clinical information such as age, sex, duration of preoperative symptom, Karnofsky score at admission and at discharge, location of tumor, amount of tumor removal, number of operations, and postoperative survival in months, together with data on radiation and chemotherapy were analyzed by chi square test, t-test, and multivariate analysis. Cytofluorometric DNA quantification using paraffin embedded specimens was also performed in 20 cases and these data were also evaluated. Multiple correlation coefficient, and therefore the total statistical accuracy, increased to 0.824 when data of DNA quantification, percentages of S phase cells and of polyploid cells, were included. Multivariate analysis revealed that 6 items were the major factors for predicting postoperative survival, i.e. the location of tumor, the Karnofsky score at discharge, the percentage of S phase cells, the number of operations, the percentage of polyploid cells, and the amount of tumor removed. Based on this analysis, the estimated survival time could be expressed as a formula.

Adolescent↗
PubMed1996

Employment of bioluminescence for the quantification of adenosine phosphates in the human cornea.

BACKGROUND: Quantification of adenosine phosphates in human corneal extracts has been performed using spectrophotometry. We employed the bioluminescence technique to obtain a more sensitive assay for adenosine phosphates and to reduce the volume of the test sample. METHODS: The bioluminescence assay for ATP, already known from sterility control, was modified and expanded. Standard curves were established using a standard solution with equimolar concentrations of ATP, ADP and AMP. To monitor the method, adenosine phosphates were measured in 35 human corneal extracts using both spectrophometry and bioluminescence. RESULTS: Linear standard curves ranging from 1 to 45 pmol were established. The two methods yielded comparable results despite the use of a basic dilution of 1:100 for the new technique. CONCLUSION: Bioluminescence provides a highly sensitive quantification of adenosine phosphates in the human cornea and facilitates an extremely detailed evaluation of the metabolic status of the cornea.

Adenine Nucleotides↗
PubMed1990

Immunochemical quantification of Cu/Zn superoxide dismutase in prenatal diagnosis of Down's syndrome.

Cu/Zn superoxide dismutase (SOD) was quantified by enzyme immunoassay for prenatal diagnosis of Down's syndrome. Overall, 154 samples of amniotic fluid, 72 samples of amniotic cells and 31 samples of chorionic tissue were investigated. Due to the large biological variance of the SOD concentrations in normal pregnancies (range for amniotic fluid 10.5-154.9, for amniotic cells 40.0-338.8, and for chorionic tissue 132.2-649.5 g SOD/g protein) the cases of Down's syndrome detected by karyotype analysis were not reliably identified by Cu/Zn SOD quantification. As in erythrocytes obtained from patients with Down's syndrome, a trisomy 21 was easily and accurately detected in the erythrocytes from very small quantities (about 50 microliters) of umbilical blood. The SOD concentrations in normal cases (n = 40) varied between 11.4 and 17.3 and in the cases of trisomy 21, as confirmed by karyotyping (n = 4), between 22.5 and 23.2 ng/one million cells. SOD quantification in fetal erythrocyte is a helpful additional method in prenatal Down syndrome diagnosis under certain conditions, which are discussed.

Amniotic Fluid↗
PubMed1985

An improved method for the quantification of the in vivo kinetics of a representative population of 111In-labelled human platelets.

The recommended and commonly used methods for the isolation of platelets from whole blood do not harvest a representative platelet population. There is evidence that these methods may result in the loss of a functionally more active platelet subpopulation. We describe a method whereby a completely representative population of platelets was isolated from the whole blood of 28 normal human volunteers by repeated washing of platelets from the red-cell layer. The harvesting efficiency was 98.3% +/- 2.8%. The platelets were labelled with 111In-oxine in a saline milieu with a labelling efficiency of 86.4% +/- 6.8%. The disappearance of reinjected labelled autologous platelets from the circulation was almost linear, and the mean platelet survival was estimated to be 224 +/- 23 h. At equilibrium, 61% +/- 12% of the labelled platelets were recovered from the circulation. The in vivo distribution at equilibrium and the sites of sequestration of the senescent labelled platelets were determined by geometric-mean whole-body quantification in six of the volunteers. This improved method permits accurate quantification of organ 111In radioactivity. Following reinjection, the labelled platelets pooled in the spleen and the accumulated activity can be presented by a single exponential function. At equilibrium, 31.1% +/- 6.1% and 9.6% +/- 1.2% of the platelets were in the spleen and liver, respectively. Splenic and hepatic radioactivity increased significantly with time, and at the end of the platelet life span, 35.6% +/- 9.7% and 28.7% +/- 8.3% of the labelled platelets were sequestrated in these organs, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1989

A demonstration of the advantages of immunostaining in the quantification of amyloid plaque deposits.

Extracellular amyloid deposits are a feature of both Alzheimer type dementia and the 'normal' aging process. Quantification of amyloid plaque deposits may well be useful in distinguishing between the senescent changes associated with 'normal' aging and the pathological processes underlying dementia. To determine the most reliable and reproducible method for visualisation of the amyloid we have compared conventional silver staining techniques with beta-amyloid immunocytochemistry on a large sample of post-mortem brain tissue from both demented (n = 15, age range 60-87) and non-demented (n = 65, age range 14-99) patients. The degree of amyloid deposition was rated on a four point scale and ratings for the two techniques were significantly correlated (P less than 0.01). However, the immunocytochemical approach has a number of distinct advantages for quantification. The antibody to beta-amyloid is highly specific and does not stain neurofibrillary tangles or background features, it is considerably more sensitive than silver staining in highlighting diffuse amyloid deposits and, perhaps most importantly, it produces high contrast staining which allows easier image digitisation and subsequent computer image analysis.

Adolescent↗
PubMed1985

Elemental analysis of individual rat blood platelets by electron probe X-ray microanalysis using a direct quantification method.

The elemental content of individual rat blood platelets and their dense granules was determined by electron probe X-ray microanalysis using a direct quantification method with microdroplets as standards. The quantification procedure was a modification of the 'direct mass' method involving a correction for differences in electron beam intensity in the analysis of standards and specimens. Whole air-dried platelets had a mean magnesium content of 12 X 10(-8) nmol (SE = 1 X 10(-8) nmol, n = 68) and a mean calcium content of 3.2 X 10(-8) nmol (SE = 0.3 X 10(-8) nmol, n = 68). A good correlation was found between the magnesium content and the phosphorus content of the dense granules of the platelets (r = 0.95). There was also good correlation (r = 0.77) between the number of dense granules per platelet and the magnesium content of the platelets.

Animals↗