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 1,585 records · Page 88Linked to original sources
PubMedDate not supplied

Separation, identification and quantification of riboflavin and its photoproducts in blood products using high-performance liquid chromatography with fluorescence detection: a method to support pathogen reduction technology.

A medical device using riboflavin (RB) and light is being developed for the reduction of pathogens in platelet concentrates (MIRASOL pathogen reduction technology [PRT]). A high-performance liquid chromatography (HPLC) method for the quantification of RB and its main photoproduct, lumichrome (LC) in blood components has been developed and validated. In addition, the same method has been used to identify and quantify the presence of additional photoproducts-catabolites of RB. Levels of these agents before and after treatment as well as endogenous levels present in normal donor blood are reported using this analytical technique. The method allows for quantitative and qualitative analysis of RB and LC in blood components using HPLC-fluorescence detection, a Zorbax SB-CN (stable bond cyano) column and a methanol-water mobile phase. Quantitation and qualitative analysis of additional photoproducts of RB was also performed, but the method has not been validated for these other components. The method described has passed an 8 day validation and has been found to be adequate for its intended use. The range of the method for RB is 0.016-1.500 microM and for LC is 0.060-1.500 microM. The method detection limit for RB is 0.0006 microM and for LC is 0.012 microM. The acceptance criteria for repeatability were met; the relative standard deviation for RB was 0.64% and for LC was 0.76%. The acceptance criteria for bias were met with a 97% average recovery for RB and a 102% recovery for LC. Samples were centrifuged and diluted 1:50 with 0.9% saline before analysis. No protein precipitation or extraction was required. A mass balance of approximately 93.4-94.4% was achieved after exposure of products to UV light in the intended pathogen reduction treatment method. The method permitted the identification of photoproducts in blood that were both naturally occurring and produced after photolysis of blood samples treated with the PRT process. The identity of these photoproducts has been established using HPLC Tandem Mass Spectrometry (MS/MS) and UV spectroscopic methods and has been correlated with known metabolites and catabolites of RB. HPLC with fluorescence detection using a reverse phase cyano-column allows for accurate separation, identification and quantification of both RB and LC in blood products without the need for solvent extraction or protein precipitation. Additional photoproducts could also be identified and quantified using this method. The presence of these agents in normal, untreated blood suggests that their presence in blood is ubiquitous.

Blood Chemical Analysis↗
PubMed2005

Mass spectrometry-based peptide quantification: applications and limitations.

In various areas of research, proteomics and particularly the quantification of proteins and peptides renders a useful addition to biochemical experiments. The range of possible applications varies from supervision of concentration changes of relevant proteins during biogenesis to differential proteomics approaches, distinguishing, for instance, healthy and diseased states. Furthermore, mass spectrometry-based peptide quantification yields the possibility of using highly sensitive bottom-up approaches for determination of protein regulations as well as multiplexing capability. Thereby, changes in protein abundances may be linked to specific cellular states bearing the opportunity to reveal marker proteins for several diseases.

Amino Acids↗
PubMed2003

Quantification of T cell receptor rearrangement excision circles to estimate thymic function: an important new tool for endocrine-immune physiology.

Although the thymus constitutes a target organ for most protein and steroid hormones, it has been quite difficult to determine the precise control exerted in vivo by the endocrine system upon thymic function. The biological role of the thymus is to ensure the generation of a diversified population of peripheral T cells able to respond to non-self-antigens but nevertheless tolerant to self-antigens. For a long time, thymic function could not be monitored, as a consequence of the absence of adequate technology to differentiate recent thymic emigrants from naive T cells. The generation of T cell receptor (TCR) diversity occurs in the thymus through recombination of gene segments encoding the variable parts of the TCR alpha and beta chains. During these processes, by-products of the rearrangements are generated in the form of TCR excision circles (TRECs). As these molecules are lost upon further cell division, their quantification is actually considered as a very valuable tool to estimate thymic function. The most appropriate TREC is deltaRec-Psi(J)alpha TREC or signal joint TREC resulting from deltaRec-Psi(J)alpha rearrangement (TCRD deletion) that occurs late during thymopoiesis, before V(alpha)-J(alpha) rearrangement. Here we describe how TREC quantification is a powerful and reliable method to evaluate the impact of hormones and endocrine disorders upon thymic function.

Aged↗
PubMed2005

Analysis of estrogenic effects by quantification of green fluorescent protein in juvenile fish of a transgenic medaka.

TheChgH-GFP strain of the teleost medaka contains a regulatory region of the estrogen-responsive choriogenin H (chgH) gene fussed to the green fluorescent protein (GFP) gene. The strain was developed for the identification of environmental estrogens by noninvasive analysis of GFP fluorescence. In the present study, a quantification method for GFP by image analysis was establishedand applied to the analysis of time- and concentration-dependent GFP fluorescence in juvenile fish. Concentration-response analyses were performed with fish exposed for 14 d to 17beta-estradiol (0.37-367 pM), genistein (0.37-367 nM), or p-nonylphenol (0.367-1,835 nM). By means of image analysis, it was shown that ChgH-GFP was induced at 183.5 pM or greater 17beta-estradiol. Time-course and recovery experiments indicated a strong accumulation of GFP in the liver. Results of reverse transcriptase-polymerase chain reaction analysis of choriogenin H and vitellogenin demonstrated induction of gene expression for the same rangeof concentrations as that for GFP analysis. Neither expression of these genes nor GFP fluorescence was induced by genistein and p-nonylphenol. Although the ChgH-GFP strain failed to detect these weakly estrogenic compounds, the simplicity of the GFP quantification during early life stages of fish offers promising possibilities for further developments of transgenic strains using different target regulatory sequences.

Animals↗
PubMed2001

Simultaneous quantification of promazine hydrochloride and its sulfoxide in pharmaceutical preparations.

The use of derivative UV-spectrophotometry is proposed for the simultaneous quantification of promazine hydrochloride in the presence of sulfoxide, and vice versa. For this purpose, mathematical parameters were established for generating derivative spectra of analytes. The determination of promazine was made using the first-order derivative (deltalambda = 10 nm, second polynomial degree) at 268 nm. The quantification of sulfoxide was achieved by applying third-derivative spectra (deltalambda = 14 nm, sixth polynomial degree) based on measurements of the amplitude at 342 - 344 nm. An elaborated method was successfully used to determine analytes in commercial promazine pharmaceuticals. The obtained results agreed well with those obtained by the HPLC method.

Antipsychotic Agents↗
PubMed2004

The detection and quantification of adulteration in olive oil by near-infrared spectroscopy and chemometrics.

A new procedure has been developed for the classification and quantification of the adulteration of pure olive oil by soya oil, sun flower oil, corn oil, walnut oil and hazelnut oil. The study was based on a chemometric analysis of the near-infrared (NIR) spectra of olive-oil mixtures containing different adulterants. The adulteration of olive oil was carefully carried out gravimetrically in a 4 mm quartz cuvette, starting with pure olive oil in the cuvette first. NIR spectra of the 525 adulterated mixtures were measured in the region of 12,000-4000 cm(-1). The spectra were subjected batch wise to multiplicative signal correction (MSC) before calculating the principal component (PCA) models. The MSC-corrected data were subjected to Savitzky-Golay smoothing and a mean normalization procedure before developing partial least-squares calibration (PLS) models. The results revealed that the models predicted the adulterants, corn oil, sun flower oil, soya oil, walnut oil and hazelnut oil involved in olive oil with error limits +/-0.57, +/-1.32, +/-0.96, +/-0.56 and +/-0.57% weight/weight, respectively. Furthermore, the PCA developed models were able to classify unknown adulterated olive oil mixtures with almost 100% certainty. Quantification of the adulterants was carried out using their respective PLS models within the same error limits as mentioned above.

Food Contamination↗
PubMed2000

Quantification of enterovirus RNA in sludge samples using single tube real-time RT-PCR.

We have developed a quantitative RT-PCR method that can be used to determine the amount of enterovirus RNA in urban sludge samples. This method combines Taq-Man technology with the ABI Prism 7700 real-time sequence detection system. We optimized a one-step RT-PCR that uses a dual-labeled fluorogenic probe to quantify the 5' noncoding region of enteroviruses. For accurate quantification of the number of copies, a Mahoney type 1 poliovirus RNA standard was designed and produced using genetic engineering. This fragment, quantified using the Ribogreen method, was used in serial dilutions as an external standard. The method had a 7-log dynamic range (5 to 2 x 10(7)). PCR inhibitors were removed by extracting viral RNA (after virus concentration) using the RNeasy mini kit with added polyvinylpyrrolidone (PVP) and running the amplification reaction with a mixture containing PVP and T4 gene 32 protein. This real-time quantification of enterovirus RNA allows large numbers of samples to be screened. Its sensitivity, simplicity and reproducibility render it suitable as a screening method with which to characterize enteroviruses, the presence of infectious particles being subsequently confirmed by cell culture.

Enterovirus↗
PubMed2004

TaqMan-based quantification of invasive cells in the chick embryo metastasis assay.

The chick embryonic metastasis (CEM) assay is a fast in vivo method to investigate the invasive properties of tumor cells. Until now, most quantification methods were semiquantitative and time-consuming. Here we describe a rapid quantification method using TaqMan technology to quantify the invaded tumor cells in the chorioallantoic membrane of fertilized eggs. This method is based on specific detection of human ALU sequences. Moreover, it provides high sensitivity over a wide linearity range.

Alu Elements↗
PubMed2005

Normalization of soil DNA extraction for accurate quantification of target genes by real-time PCR and DGGE.

The analysis of microbial communities in environmental samples requires accurate and reproducible methods for extraction of DNA from sample matrices that have different physical and chemical characteristics. Even with the same sample type, variations in laboratory methods can result in different DNA yields. To circumvent this problem, we have developed an easy and inexpensive way to normalize the quantities of DNA that involves the addition of an internal standard prepared from plasmid DNA. The method was evaluated by comparing DNA yields using different DNA extraction procedures, after which the DNA was used for microbial community analysis by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S ribosomal RNA (rRNA) and for quantification of 16S rRNA gene copy numbers in environmental samples by real-time PCR. Our results show that use of the internal standard allows normalization of the resulting data and more accurate quantification of gene copy numbers in soil samples. These methods should also have broad application for various other types of environmental samples.

DNA Primers↗
PubMed1996

Rapid quantification of gene expression by competitive RT-PCR and ion-pair reversed-phase HPLC.

Competitive reverse-transcription PCR (RT-PCR) techniques for quantification of gene expression employ titrations in which the products of multiple PCRs must be separated, analyzed and quantified to compute gene expression in a single sample. We have employed a novel, ion-pair reversed-phase HPLC (IP-RP-HPLC) system to analyze and quantify RT-PCRs performed with mutant RNA internal standards. PCR products could be separated and quantified in 6 minutes per reaction using the absorbance signal from an on-line UV detector. Crude PCR products can be analyzed without further processing and without the addition of radioactive or fluorescent markers to reactions. Analysis of titration regression and slope values approached mathematical ideals indicating that amplification of native and competitor RNA occurred with equal efficiency. Further, serial dilution of input RNA over three orders of magnitude did not affect the calculated level of gene expression or the slope of the titration. IP-RP-HPLC appears to offer important advantages to quantitative measurements of gene expression. These include rapid sample analysis and column re-equilibration, reduced sample handling and opportunity for introduction of quantification error, avoidance of fluorescent or radioactive tracers, high detector sensitivity and linearity and excellent quantitative reliability.

Angiotensinogen↗
PubMed1996

Quantification of HIV-1 using multiple competitors in a single-tube assay.

Methods for quantification of human immunodeficiency virus type 1 (HIV-1) based on competitive PCR and fragment analysis have been developed. Samples containing HIV-1 DNA and known amounts of three cloned competitors were co-amplified by PCR with semi-nested primers. The competitor DNAs contained the same long terminal repeat primer binding sequences as the wild-type DNA, but they are different in internal sequences and length. One of the inner primers was fluorescent-labeled to allow discrimination between the wild-type DNA and the three competitors by fragment analysis using a standard automated sequencer. A calibration curve using the peak area of the three competitors enabled accurate determination of target amount with minimal variations. The method presented here can be used for quantification of HIV-1 in clinical samples and will be useful for monitoring disease progression and treatment effects.

Base Sequence↗
PubMed1999

Automated purification and quantification of oligonucleotides.

We have developed automated methods for the trityl-on purification and quantification of synthetic oligonucleotides. Oligonucleotide purification is by solid-phase extraction cartridges using Amberchrom CG-50 resin on an XYZ-axis robotic system. Quantification is by OD260nm using an online UV-visible spectrophotometer with sipper. The purification of 20 oligonucleotides requires 5 min of user set-up time, plus 20 min per sample of robot time. For a 15-25-mer at the 40 nmol scale of synthesis, the method gives a yield of 2.8 ODs from a load of 10.1 OD, i.e., a 28% average yield. Oligonucleotides purified by this method have proven to be successful for primers for automated DNA sequencing.

Autoanalysis↗
PubMed1991

Quantification of training in competitive sports. Methods and applications.

The training of competitive athletes can be assessed by retrospective questionnaires, diaries, physiological monitoring and direct observation of training behaviour. Questionnaires represent the most economical, most comprehensive and least accurate method. Diaries are more valid, but their drawbacks for long term quantitative studies are poor compliance and difficulties in processing the data they generate. Physiological monitoring (of oxygen consumption, heart rate or blood lactate concentration) provides objective measures of training intensity, and direct observation gives valid measures of most aspects of training; however, these methods are impractical for continuous, long term use. Coaches and athletes quantify training for purposes of motivation, systematisation of training and training prescription, but there has been little study of the use of training quantification by these practitioners. Motivation and systematisation are probably achieved best with diaries. Direct observation appears to be the best method of ensuring compliance with a training prescription, although heart rate monitoring is also a promising method for prescribing endurance training intensity. Sport scientists quantify training to study its effects on the performance and health status of competitive athletes. Most studies have been descriptive rather than experimental, and unvalidated questionnaires have been the predominant method of assaying training. The main areas of research include performance prediction and enhancement, overtraining, reproductive dysfunction, injury, illness, and nutritional status. Training has substantial effects in all of these areas. There is a need for more experimental studies that utilise validated measures of training to investigate how to reduce sports injuries and enhance competitive sports performance. More attention could also be given to methodological issues of training quantification.

Athletic Injuries↗
PubMed1998

Quantification of quadriceps and hamstring antagonist activity.

The coactivation of hamstrings and quadriceps, and its relation to knee joint stability and cruciate ligament loading, have been extensively examined over the last decades. The purpose of this review is to present findings on the quantification of antagonist activation around the knee. Coactivation of the quadriceps and hamstrings during many activities has been examined using electromyography (EMG). However, there are several factors that affect antagonist EMG activity, such as the type of muscle action, velocity of the movement, level of effort and angular position. Furthermore, the antagonist EMG can be affected by methodological factors which relate to the data recording, analysis and quantification of the signal. Research has demonstrated that the effect of cross-talk on the hamstrings and quadriceps antagonist EMG depends on electrode size and location, fat layer of the muscles and the technique used to reduce it. There is an inconsistency as to the method used to normalise antagonist EMG depending on the type of movement examined. This makes comparisons between studies difficult and, therefore, further research is recommended. The antagonist function is better represented when the antagonist moment exerted is known; however, the direct measurement of antagonist moments or forces is very difficult. Few studies have used mathematical models to determine the moment or force distribution around the knee, including antagonist forces. This can be attributed to the complexity of the anatomy and function of the knee joint. Despite this, in vivo and in vitro experiments have demonstrated that quadriceps contraction near full extension induces significantly higher anterior shear forces when compared with the forces exerted when the hamstrings act as antagonists, thus indicating the important role of antagonist activity in knee joint stability. However, the magnitude of this contribution to the force distribution around the knee in many activities is unclear.

Adipose Tissue↗
PubMed2006

Comparison between direct microscopy and flow cytometry for rRNA-based quantification of Candidatus Accumulibacter phosphatis in activated sludge.

A comparison of the quantification of a specific microbial group in activated sludge by fluorescent in-situ hybridization, coupled with either direct microscopic counting or flow cytometry, was performed using an enhanced-biological-phosphorus-removal, sequencing-batch reactor. The population dynamics of Candidatus Accumulibacter phosphatis (Cand. A. phosphatis) was evaluated during two separate runs of the reactor. With the operational conditions used, Cand. A. phosphatis was enriched until a failure in the pH controller eliminated its ecological advantage. As a result, the comparison of quantification techniques included Cand. A. phosphatis concentrations as low as 11% and as high as 96% of the total cells in the samples. The analysis demonstrated that, regardless of the particular limitations of each technique, both provided similar results when the activated-sludge flocs were easily dispersed. However, when the activated-sludge samples contained flocs that were difficult to disperse, flow cytometry failed to provide quantitative results.

Biodegradation, Environmental↗
PubMed2007

Comparison of standard- and low-radiation-dose CT for quantification of emphysema.

OBJECTIVE: This study was performed to compare standard- and low-radiation-dose techniques in the CT quantification of emphysema. MATERIALS AND METHODS: The study population consisted of 36 men and 20 women who were current or former heavy smokers and underwent standard-dose (effective tube current, 100-250 mAs) chest CT at our institution within 6 months of having undergone low-dose (effective tube current, 30-60 mAs) chest CT. All CT scans were reconstructed at 5-mm slice thickness with a smooth filter. CT-measured lung volume, mean and median lung attenuation, and percentage of lung volume with attenuation lower than multiple thresholds (emphysema index values) were compared by Pearson correlation, two-tailed and paired Student's t tests, and regression analysis. RESULTS: There were no significant differences in mean attenuation (-848 vs -846 H, p > 0.35) for the low dose and the standard dose or in median lung attenuation (-879 vs -878 H, p > 0.66). Low- and standard-dose emphysema indexes were correlated at all attenuation thresholds (r = 0.86-0.97). Mean emphysema indexes were higher on the low-dose scans, but the mean difference at all thresholds was less than 3%. The differences were significant (p < 0.05) only at the lower index thresholds, correlated with differences in lung volume (r < or = 0.86), and increased with greater differences in dose. CONCLUSION: Low-dose technique has minimal effect on CT quantification of emphysema.

Aged↗
PubMed1995

Quantification of the volume of articular cartilage in the metacarpophalangeal joints of the hand: accuracy and precision of three-dimensional MR imaging.

OBJECTIVE: Cartilage loss is central to the development of joint failure in arthritis. However, radiographic assessment of cartilage loss is highly unreliable. This study examined the accuracy and reproducibility of a noninvasive technique for quantifying the volume of articular cartilage in the metacarpophalangeal joints of the hand by use of three-dimensional (3D) MR imaging. SUBJECTS AND METHODS: Eight metacarpophalangeal joints (four normal, one rheumatoid arthritic, and three normal cadaveric) each were imaged three times with a 1.5-T clinical MR imaging scanner with a small partial volume coil and a fat-saturated 3D spoiled gradient-echo sequence optimized for delineating articular cartilage. The volumes of cartilage over the metacarpal and phalangeal surfaces were quantified by summing the voxels within segmented 3D reconstructions of the images. Cartilage volumes in the three cadaver joints also were estimated by scraping cartilage off the articular surfaces and measuring water displacement in graduated cylinders. These values were used as the gold standard for assessing the accuracy of cartilage volume quantification by MR imaging. RESULTS: The fat-saturated sequence discriminated the articular cartilage from adjacent joint structures with high contrast and high spatial resolution. Cartilage volumes determined by MR imaging for the different subjects ranged from 115 microliters to 222 microliters for metacarpal cartilage and from 34 microliters to 86 microliters for proximal phalangeal cartilage. Accuracy errors for quantifying cartilage volume by MR imaging were -1.8% (95% confidence interval, -3.5% to -0.7%) for metacarpal cartilage and 9.1% (4.3% to 14.7%) for proximal phalangeal cartilage. Reproducibility errors were 5.2% (95% confidence interval, 2.9% to 7.6%) and 9.9% (5.4% to 15.1%), respectively. CONCLUSION: Fat-suppressed T1-weighted 3D MR imaging provides sufficient contrast and spatial resolution to allow accurate and reproducible quantification of articular cartilage volume in the metacarpophalangeal joints of the hand. This technique may be useful for monitoring cartilage loss in patients with arthritis.

Adult↗
PubMed2000

Automatic detection and quantification of ground-glass opacities on high-resolution CT using multiple neural networks: comparison with a density mask.

OBJECTIVE: We compared multiple neural networks with a density mask for the automatic detection and quantification of ground-glass opacities on high-resolution CT under clinical conditions. SUBJECTS AND METHODS: Eighty-four patients (54 men and 30 women; age range, 18-82 years; mean age, 49 years) with a total of 99 consecutive high-resolution CT scans were enrolled in the study. The neural network was designed to detect ground-glass opacities with high sensitivity and to omit air-tissue interfaces to increase specificity. The results of the neural network were compared with those of a density mask (thresholds, -750/-300 H), with a radiologist serving as the gold standard. RESULTS: The neural network classified 6% of the total lung area as ground-glass opacities. The density mask failed to detect 1.3%, and this percentage represented the increase in sensitivity that was achieved by the neural network. The density mask identified another 17.3% of the total lung area to be ground-glass opacities that were not detected by the neural network. This area represented the increase in specificity achieved by the neural network. Related to the extent of the ground-glass opacities as classified by the radiologist, the neural network (density mask) reached a sensitivity of 99% (89%), specificity of 83% (55%), positive predictive value of 78% (18%), negative predictive value of 99% (98%), and accuracy of 89% (58%). CONCLUSION: Automatic segmentation and quantification of ground-glass opacities on high-resolution CT by a neural network are sufficiently accurate to be implemented for the preinterpretation of images in a clinical environment; it is superior to a double-threshold density mask.

Absorptiometry, Photon↗