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PubMed2006

Exact quantification of time signals in Padé-based magnetic resonance spectroscopy.

This study reports on the fast Padé transform (FPT) for parametric signal processing of realistically synthesized free induction decay curves whose main spectral features are similar to those encoded clinically from a healthy human brain by means of magnetic resonance spectroscopy (MRS). Here, for the purpose of diagnostics, it is of paramount importance to be able to perform accurate and robust quantification of the investigated time signals. This amounts to solving the challenging harmonic inversion problem as a spectral decomposition of the given time signal by means of reconstruction of the unknown total number of resonances, their complex frequencies and amplitudes yielding the peak positions, widths, heights and phases. On theoretical grounds, the FPT solves exactly this mathematically ill-conditioned inverse problem for any noiseless synthesized time signal comprised of an arbitrarily large (finite or infinite) number of damped complex exponentials with stationary and non-stationary polynomial-type amplitudes leading to Lorentzian (non-degenerate) and non-Lorentzian (degenerate) spectra. Convergent validation for this fact is given via the proof-of-principle which is thoroughly demonstrated by the exact numerical solution of a typical quantification problem from MRS. The presently designed study is a paradigm shift for signal processing in MRS with particular relevance to clinical oncology, due to the unprecedented capability of the fast Padé transform to unequivocally resolve and quantify isolated, tightly overlapped and nearly coincident resonances.

Algorithms↗
PubMed2006

Rapid dual-injection single-scan 13N-ammonia PET for quantification of rest and stress myocardial blood flows.

Quantification of myocardial blood flows at rest and stress using 13N-ammonia PET is an established method; however, current techniques require a waiting period of about 1 h between scans. The objective of this study was to test a rapid dual-injection single-scan approach, where 13N-ammonia injections are administered 10 min apart during rest and adenosine stress. Dynamic PET data were acquired in six human subjects using imaging protocols that provided separate single-injection scans as gold standards. Rest and stress data were combined to emulate rapid dual-injection data so that the underlying activity from each injection was known exactly. Regional blood flow estimates were computed from the dual-injection data using two methods: background subtraction and combined modelling. The rapid dual-injection approach provided blood flow estimates very similar to the conventional single-injection standards. Rest blood flow estimates were affected very little by the dual-injection approach, and stress estimates correlated strongly with separate single-injection values (r=0.998, mean absolute difference=0.06 ml min-1 g-1). An actual rapid dual-injection scan was successfully acquired in one subject and further demonstrates feasibility of the method. This study with a limited dataset demonstrates that blood flow quantification can be obtained in only 20 min by the rapid dual-injection approach with accuracy similar to that of conventional separate rest and stress scans. The rapid dual-injection approach merits further development and additional evaluation for potential clinical use.

Ammonia↗
PubMed2006

Reproducibility of reference tissue quantification of dynamic contrast-enhanced data: comparison with a fixed vascular input function.

Reference tissues are currently used to analyse dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data. The assessment of tumour response to treatment with anti-cancer drugs is a particularly important application of this type of analysis and requires a measure of reproducibility to define a level above which a significant change due to therapy can be inferred. This study compares the reproducibility of such quantification strategies with that found using a published, group-averaged uptake curve. It is shown that reference tissue quantification gives poorer reproducibility for most parameters than that found using a group-averaged plasma curve (a change in K(trans) of greater than 41.8% and 16.4% would be considered significant in the two approaches, respectively), but successfully incorporates some of the variability observed in plasma kinetics between visits and provides vascular input functions that, across the group, are comparable with the group-averaged curve. This study therefore provides an indirect validation of the methodology.

Antineoplastic Agents↗
PubMed2007

Reference tissue quantification of DCE-MRI data without a contrast agent calibration.

The quantification of dynamic contrast-enhanced (DCE) MRI data conventionally requires a conversion from signal intensity to contrast agent concentration by measuring a change in the tissue longitudinal relaxation rate, R(1). In this paper, it is shown that the use of a spoiled gradient-echo acquisition sequence (optimized so that signal intensity scales linearly with contrast agent concentration) in conjunction with a reference tissue-derived vascular input function (VIF), avoids the need for the conversion to Gd-DTPA concentration. This study evaluates how to optimize such sequences and which dynamic time-series parameters are most suitable for this type of analysis. It is shown that signal difference and relative enhancement provide useful alternatives when full contrast agent quantification cannot be achieved, but that pharmacokinetic parameters derived from both contain sources of error (such as those caused by differences between reference tissue and region of interest proton density and native T(1) values). It is shown in a rectal cancer study that these sources of uncertainty are smaller when using signal difference, compared with relative enhancement (15 +/- 4% compared with 33 +/- 4%). Both of these uncertainties are of the order of those associated with the conversion to Gd-DTPA concentration, according to literature estimates.

Biophysical Phenomena↗
PubMed2003

Accuracy of the quantification of organ activity from planar gamma camera images.

The accuracy in determination of organ activity of (99m)Tc was investigated, with activity estimated from gamma camera images of phantoms, using the conjugate view method. The accuracy depends on several parameters such as the choice of background correction method, the accuracy in determination of the effective attenuation coefficient and the thickness of the body and organs and on the determination of the gamma camera sensitivity. The background correction method has a major influence on the quantification of the activity. Methods which take the volume of the source organ into consideration are recommended. The discrepancy in the determined organ activity varied between an underestimation of 26% and an overestimation of 16% in the MIRD phantom, depending on which organ was studied and on the correction method used. To correct for absorption and scattering, an effective attenuation coefficient was used. A theoretical analysis showed that a change in the effective attenuation coefficient of 0.01 cm(-1) resulted in a 15% change in the calculated activity. Also the thickness of the body and the organ of interest influences the calculated activity. A 2 cm deviation in the body thickness causes a deviation of approximately 10% in the calculated activity. The quantification is improved if the attenuation coefficient is determined by transmission measurements.

Gamma Cameras↗
PubMedDate not supplied

Multicentre validation study of instrument applications for %CDT, an immunoassay for quantification of carbohydrate-deficient transferrin in serum.

This multicentre trial assessed the inter-laboratory transferability and agreement of results for five instrument applications (Immage, BN A, BN II, Cobas Mira and Microtiter) of the Axis-Shield %CDT kit, a new version immunoassay for quantification of the alcohol marker carbohydrate-deficient transferrin (CDT) in serum. Two %CDT kit controls and three authentic serum samples were compared by 14 laboratories in six European countries, and each application was evaluated at three study sites. The %CDT results showed an overall good agreement both within and between sites, although it was also demonstrated that the analysis might be biased due to site performance. The data indicate that transferability of the %CDT assay is high, and that the instrument applications may be used interchangeably in routine quantification of %CDT.

Clinical Chemistry Tests↗
PubMed2002

Variance stabilization applied to microarray data calibration and to the quantification of differential expression.

We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In particular, we derive a transformation h for intensity measurements, and a difference statistic Deltah whose variance is approximately constant along the whole intensity range. This forms a basis for statistical inference from microarray data, and provides a rational data pre-processing strategy for multivariate analyses. For the transformation h, the parametric form h(x)=arsinh(a+bx) is derived from a model of the variance-versus-mean dependence for microarray intensity data, using the method of variance stabilizing transformations. For large intensities, h coincides with the logarithmic transformation, and Deltah with the log-ratio. The parameters of h together with those of the calibration between experiments are estimated with a robust variant of maximum-likelihood estimation. We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays.

Algorithms↗
PubMed2025

UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification.

MOTIVATION: One of the key applications of Unique Molecular Identifiers (UMIs) in high-throughput sequencing is to correct for PCR amplification bias and removal of PCR duplicates, thereby improving quantification in DNA-seq and RNA-seq applications. Accurately grouping error-bearing UMIs that originate from the same input molecule through a UMI deduplication method is a critical step in this process. However, many existing UMI deduplication tools rely on simple Hamming distance comparisons or suboptimal clustering algorithms, often resulting in erroneous UMI groupings, particularly in error-prone long-read sequencing or ultra-high-depth short-read sequencing. RESULTS: We introduce UMI-nea, a tool that utilizes Levenshtein distance comparisons and a novel clustering approach to optimize multithreading workflows. Compared against three other indel-aware UMI deduplication tools, UMI-nea achieves more accurate UMI groupings with efficient run time. It demonstrates robust performance across diverse sequencing platforms, depths, and UMI lengths. Additionally, UMI-nea incorporates a data-guided adaptive UMI filter, further enhancing quantification accuracy. AVAILABILITY AND IMPLEMENTATION: UMI-nea is available on github https://github.com/Qiaseq-research/UMI-nea.git or Zenodo https://doi.org/10.5281/zenodo.16745758. Sequencing data are stored at https://qiagenpublic.blob.core.windows.net/umi-nea-datasets/.

High-Throughput Nucleotide Sequencing↗
PubMed2005

Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.

MOTIVATION: Mass spectrometry yields complex functional data for which the features of scientific interest are peaks. A common two-step approach to analyzing these data involves first extracting and quantifying the peaks, then analyzing the resulting matrix of peak quantifications. Feature extraction and quantification involves a number of interrelated steps. It is important to perform these steps well, since subsequent analyses condition on these determinations. Also, it is difficult to compare the performance of competing methods for analyzing mass spectrometry data since the true expression levels of the proteins in the population are generally not known. RESULTS: In this paper, we introduce a new method for feature extraction in mass spectrometry data that uses translation-invariant wavelet transforms and performs peak detection using the mean spectrum. We examine the method's performance through examples and simulation, and demonstrate the advantages of using the mean spectrum to detect peaks. We also describe a new physics-based computer model of mass spectrometry and demonstrate how one may design simulation studies based on this tool to systematically compare competing methods. AVAILABILITY: MATLAB scripts to implement the methods described in this paper and R code for the virtual mass spectrometer are available at http://bioinformatics.mdanderson.org/software.html SUPPLEMENTARY INFORMATION: http://bioinformatics.mdanderson.org/supplements.html.

Algorithms↗
PubMed2006

MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.

UNLABELLED: MetaQuant is a Java-based program for the automatic and accurate quantification of GC/MS-based metabolome data. In contrast to other programs MetaQuant is able to quantify hundreds of substances simultaneously with minimal manual intervention. The integration of a self-acting calibration function allows the parallel and fast calibration for several metabolites simultaneously. Finally, MetaQuant is able to import GC/MS data in the common NetCDF format and to export the results of the quantification into Systems Biology Markup Language (SBML), Comma Separated Values (CSV) or Microsoft Excel (XLS) format. AVAILABILITY: MetaQuant is written in Java and is available under an open source license. Precompiled packages for the installation on Windows or Linux operating systems are freely available for download. The source code as well as the installation packages are available at http://bioinformatics.org/metaquant

Algorithms↗
PubMed1981

Structure and quantification of a physiological model of the distribution of injected agents and inhaled anaesthetics.

Mapleson's (1973) physiological, circulation-time model of the distribution of inhaled anaesthetics has been elaborated to be suitable for modelling agents in which hepatic metabolism and renal excretion are important factors; as well as the obvious improvement of providing separate compartments for liver and kidney, the arterial and portal supplies to the liver are separately represented, as is the portal blood pool. The separate portal pool also leads to a more realistic total circulation time for the majority of the cardiac output. The quantification for a "standard man" is fully documented and makes use of the latest (1975) report of the International Commission on Radiological Protection, Reference Man, and includes data on the water, fat and protein composition of each tissue compartment. Suggestions are included on adapting the quantification to non-standard men and to other species.

Adult↗
PubMed1993

Quantification of specific DNA O-alkylation products in individual cells by monoclonal antibodies and digital imaging of intensified nuclear fluorescence.

We report the establishment of a standardized, monoclonal antibody (Mab)-based immunocytological assay (quantitative ICA) for the visualization and quantification of low levels of specific DNA O-alkylation products in individual cells by electronically intensified, indirect or direct immunofluorescence. In terms of specific binding to alkali-denatured nuclear DNA and low background noise, 10 Mabs from a collection of 154 Mabs specific for O6-methyl-2'-deoxyguanosine (O6-MedGuo), O6-ethyl-2'-deoxyguanosine (O6-EtdGuo), O6-n-butyl-2'-deoxyguanosine (O6-BudGuo) and O4-ethyl-2'-deoxythymidine (O4-EtdThd) with antibody affinity constants ranging between 1.0 x 10(6)-3.0 x 10(10) l/mol, were found to be best suited for ICA. At present, > or = 200 O6-EtdGuo residues (corresponding to an O6-EtdGuo/dGuo molar ratio in DNA of > or = 8.4 x 10(-8)), > or = 400 O6-BudGuo residues (O6-BudGuo/dGuo, > or = 1.7 x 10(-7)), > or = 1800 O4-EtdThd residues (O4-EtdThd/dThd, > or = 7.5 x 10(-7)) and > or = 4800 O6-MedGuo residues (O6-MedGuo/dGuo, > or = 2.0 x 10(-6)), can be quantified per diploid genome. Using a SIT video camera in combination with multiparameter image digital analysis, DNA adduct-specific rhodamine fluorescence signals are measured relative to nuclear DNA content (DAPI fluorescence). Adduct-specific fluorescence recordings in three different rat cell lines (BT3Ca, Fao and NO) were in excellent agreement with the data obtained by competitive radioimmunoassay (RIA) for hydrolysates of DNA isolated from the respective cells exposed in parallel to the same alkylating carcinogens (N-methyl-, N-ethyl- and N-[n-butyl]-N-nitrosourea). Accordingly, the kinetics of O6-EtdGuo repair, as determined by ICA and RIA, respectively, were superimposable. Cell-specific, quantitative ICA can, therefore, be used for the quantification of specific, stable DNA adducts induced by alkylating carcinogens or chemotherapeutic agents and for DNA repair measurements in individual (e.g. human) cells. Work is currently underway to extend the spectrum of carcinogen--DNA adduct-specific Mabs suited for quantitative ICA.

Alkylation↗
PubMed1997

Improved 32P-postlabelling assay for the quantification of the major platinum-DNA adducts.

For the improvement of chemotherapy with platinum (Pt)-containing drugs a sensitive assay to detect the induced Pt-DNA adducts is needed. Therefore, the 32P-postlabelling assay, described by Blommaert and Saris (Nucleic Acids Res., 1995, 23, 1300-1306), to detect the major adducts Pt-GG and Pt-AG has substantially been improved and compared with ELISA and AAS. For the quantification of the adducts, TpT was added as an internal standard immediately after isolation of the Pt-adducts from digested DNA samples. It was found that 32P-labelling of both GpG and ApG, the dinucleotides obtained after deplatination of the adducts, was equally efficient as that of TpT. To isolate the Pt-adducts on basis of a positive charge, the pH of DNA digests was adjusted to approximately 3 prior to separation by strong cation-exchange chromatography. For the subsequent deplatination a volume of only 12 microl of 0.2 M NaCN was used, which did not interfere with the following labelling step. The quantification of the 32P-labelled dinucleotides was performed by phosphorimaging of spots after separation on TLC as well as by 32P-counting of fractions collected after separation by HPLC. The method was used to determine adduct levels in in vitro cisplatin-treated DNA and in DNA isolated from cisplatin-treated cultured cells, tumor xenografts from cisplatin-treated mice, and from white blood cells and (tumor) tissues from cisplatin-treated patients. The results show a significant correlation with the adduct levels as determined with atomic absorption spectroscopy (high levels) or with specific antibodies (low levels). This assay appears to be useful for the determination of low levels of Pt-adducts in small DNA samples as present in clinical specimens such as blood and tumor tissue, but also in buccal mucosal cells and fine needle aspirates.

Animals↗
PubMed2003

Quantification of chemical vapors in chemosensory research.

Studies of olfaction and chemesthesis often rely on nominal, liquid-phase dilutions to quantify the chemicals tested, even though the associated vapor concentrations constitute the actual stimuli. For more than a decade now, our systematic studies of the olfactory and chemesthetic potency of members of homologous chemical series have routinely included quantification of vapors via gas chromatography. This article depicts the relationships between liquid- and vapor-phase concentrations for 60 volatile organic compounds and summarizes the theoretical and technical factors influencing these relationships. The data presented will allow other investigators working with these materials to express them as vapor concentrations even when they lack the resources to perform the analytical measurements. The paper represents a step toward creation of a practical archive for vapor quantification in chemosensory science.

Calibration↗
PubMed2026

Standardization Challenges in Glycated Albumin Measurement: Methodological Heterogeneity and Quantification Discrepancies.

BACKGROUND: Glycated albumin (GA) is a valuable biomarker for monitoring glycemic status. However, measurement standardization is challenged by methodological heterogeneity, where different analytical principles and target measurands cause quantification discrepancies. This study systematically compared prevailing methodologies to identify a robust reference measurement procedure for widespread standardization. METHODS: We compared a targeted bottom-up proteomics method (ID-LC-MS/MS) with an enzymatic assay and the Japan Society of Clinical Chemistry (JSCC) reference method. A cohort of 129 donor serum specimens and certified reference materials (JCCRM-611) were analyzed to assess methodological comparability. Furthermore, GA concentration-dependent glycation kinetics at the Lys-525 site of albumin was examined. RESULTS: The optimized targeted bottom-up proteomics method showed a strong correlation (r = 0.986) with both the enzymatic assay and JSCC reference method. However, a progressively increasing negative systematic bias was observed at higher GA levels, confirming that Lys-525 underestimates GA at higher levels. In addition, with increasing overall GA concentration, the glycation ratio at the Lys-525 site consistently declined compared to the total glycated lysine residues. CONCLUSIONS: The standardization of GA measurements requires a precise, universally accepted definition to address analytical discrepancies. The present results indicate that quantification targeting all glycated lysine residues (as in the JSCC method) aligns more closely with biologically relevant GA values than site-specific measurement at Lys-525, which shows greater bias at higher concentrations. Therefore, further GA standardization would focus on adopting total glycated lysine residues on albumin as the preferred measurand definition, to improve detection accuracy and clinical comparability.

Serum Albumin↗
PubMed1980

Quantification of myocardial infarction by computer-assisted positron emission tomography.

The accuracy of three-dimensional transverse section positron emission imaging for quantification of myocardial infarction size was validated and compared with the accuracy of two dimensional planar positron imaging. After induction of acute anterior myocardial infarction in anaesthetised dogs, gallium-68 albumin microspheres were injected into the left atrium. Planar and transverse section images of the thorax were obtained with a multicrystal positron camera. After staining with tetrazolium tetrachloride injected intravenously, the hearts were excised, sectioned manually, and planar imaging repeated. Each myocardial infarction was clearly delineated by transverse section imaging with high contrast ratios (mean 0.68 +/- 0.02 SEM); planar imaging identified seven of nine infarcts but with lower contrast ratios (0.24 +/- 0.04; P < 0.001). The volume of infarcted myocardium determined from transverse section images correlated well with true infarct volume (r = 0.94); whereas planar images poorly predicted infarct size (r = 0.63). Thus, computer-assisted transverse section positron imaging provides in vivo localisation of microsphere distribution for improved radioisotopic quantification of myocardial infarction.

Animals↗
PubMed1987

Diagnosis and quantification of aortic regurgitation by pulsed Doppler echocardiography in patients with mitral valve disease.

UNLABELLED: To test the ability of pulsed Doppler echocardiography (PDE) to detect and quantify aortic regurgitation (AR), 55 consecutive patients (14-74 years) with aortic and mitral valve disease were examined clinically and by echocardiography before cardiac catheterisation. The severity of AR was determined angiographically (I-IV) and compared to the extent of the regurgitant jet in the left ventricle measured by PDE. In 13 of 55 patients (3 with mitral stenosis, 3 with mitral incompetence, 3 with combined mitral lesions, 3 with aortic stenosis, one with aortic and mitral stenosis) neither angiography nor PDE showed AR (specificity 100%). Apart from 3 patients with poor echo quality PDE correctly detected AR in 39 of 42 patients (sensitivity 93%). Clinical examination (62%), mode M.mode (62%) and both methods combined (81%) were significantly less sensitive than PDE, especially in mild AR (P less than 0.008). The PDE degree of AR closely correlated with angiography (corrected contingency coefficient 0.91). Differentiation between AR III and IV was not possible. Mitral valve disease did not affect quantification of AR (n = 20 patients). CONCLUSIONS: Pulsed Doppler echocardiography is better than auscultation and M-mode echocardiography in the diagnosis of aortic regurgitation, especially in grades I and II. PDE can reliably discriminate between three degrees of aortic regurgitation (I-III). Mitral valve disease does not affect quantification of aortic regurgitation by PDE.

Adolescent↗
PubMed1987

Quantification of mitral regurgitation by Doppler echocardiography.

The present study was undertaken to evaluate a new non-invasive approach to the quantification of mitral regurgitation. Doppler echocardiography and left ventriculography were performed in 20 patients without valvular heart disease (group A), and in 30 patients with pure mitral regurgitation (group B). Volumetric flows through the aortic and mitral valve orifices were determined by Doppler technique. The aortic flow (AF) was calculated as the product of the aortic orifice area by the systolic velocity integral. The mitral flow (MF) was computed as the product of the corrected mitral orifice area by the diastolic velocity integral. The mitral regurgitant fraction (RF) was calculated as: RF = 1 - AF/MF. In group A, there was a close agreement between aortic and mitral flows (r = 0.94, P less than 0.001), and there was no significant difference between the two measurements. In group B, the mitral flow was significantly higher than the aortic flow. The regurgitant fraction assessed by Doppler echocardiography correlated well with the grades of severity of regurgitation obtained at left ventriculography. We conclude that combined measurement of both aortic and mitral flows by Doppler echocardiography provides a new and promising approach to the noninvasive quantification of mitral regurgitation.

Adult↗