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.

SourceResearch connectionFrom yearThrough year

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

At least 37 records · Page 2Linked to original sources

PubMed1979

[A new method of pericardiocentesis and quantification of pericardial effusions by echocardiography (author's transl)].

With a new method for safe and complete evacuation of pericardial effusions it was possible to check the quantification of pericardial fluid is was possible to check the quantification of pericardial fluid by echocardiography. Using a formula based on the assumption that in systole the pericardial fluid is distributed equally around the contracting heart (like a coat enveloping a sphere), it was demonstrated that pericardial effusions ranging from 250 to 600 ml could be fairly accurately measured. Smaller effusions were not so readily determined. Effusions over 600 ml could be only roughly measured, usually being underestimated.

Echocardiography↗

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↗

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↗

PubMed1979

Quantification of the pregnancy-specific beta1-glycoprotein (SP1) by immunoprecipitation techniques: the influence of a cross-reacting high molecular weight alpha2-protein.

Two serum proteins with SP1 determinants were separated by means of size chromatography and preparative zone electrophoresis. One of the proteins had beta1 electrophoretic mobility and an estimated molecular weight of 90,000, and the other had alpha2-mobility and a molecular weight around 400,000. When available antibody preparations to SP1 were used, the high molecular weight protein formed immunoprecipitates only when polyethyleneglycol (PEG) was added to the agarose. It is shown that the high molecular weight protein has a pronounced effect on quantification of SP1 by rocket immunoelectrophoresis, whereas the effect was less pronounced but still considerable when quantification was performed by radial immunodiffusion.

Antigens↗

PubMed1977

Noninvasive detection and quantification of left-to-right shunts in children using oxygen-15 labeled carbon dioxide.

A method for the detection and quantification of left-to-right intracardiac shunts is described which utilizes a single breath inhalation of oxygen-15 labeled carbon dioxide (C15O2). The inhaled gas rapidly crosses the alveolar membrane and the oxygen-15 label is exchanged through the carbonate cycle to form oxygen-15 labeled water within the pulmonary capillary blood. Pulmonary indicator clearance curves are measured by external scintillation probes. A simplified method of shunt flow quantification was developed from indicator dilution principles and used for the analysis of the clearance curves. Inhalation studies were performed with 62 children on the day prior to cardiac catheterization. The presence or absence of left-to-right shunt was confirmed by contrast angiography in all cases. Twenty-six children were found to have no shunts by C15O2 inhalation, oximetry or angiography. Of the 36 with shunts, 34 were detected by C15O2. Two of these were designated as equivocal because they were considered to be less than the threshold of definitive detection by C15O2 (having Qp/Qs less than 1.2); 32 were positive and there were two false negatives with small ventricular septal defects. There were no false positives by C15O2. The correlation coefficient between C15O2 and oximetry values of shunt flow for those patients with proven shunts was 0.82.

Adolescent↗

PubMed2016

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.

We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.

5-Methylcytosine↗

PubMed2025

Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.

BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information. RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live + dead) sequencing. CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.

Humans↗

PubMed1977

[Left ventricular contraction reserve in coronary heart disease. Evaluation, quantification and prognostic value (author's transl)].

Regional and overall left ventricular contraction reserve was studied in 14 patients with coronary heart disease, in 5 healthy subjects and in 4 patients before and after aorto-coronary bypass surgery. Quantification of overall contraction was based on ventricular volumes and ejection fraction. Regional contraction reserve was calculated with the hemiaxis method and a ventricular score. Contraction reserve under nitroglycerin and in postextrasystolic beats was compared. For routine quantification of contraction reserve the ventricular score is recommended. For research purposes the hemiaxis method is to be preferred. Postextrasystolic beats are better suited for analysis of contraction reserve than are angiograms following administration of nitroglycerin. This is due to the minor expense of the procedure, furthermore, postextrasystolic beats allow better differentiation between contracting and non-contracting areas. Left ventricular contraction reserve is larger in patients with coronary heart disease, angina pectoris and ischemic reactions in the exercise ECG than in control patients. These findings are based on overall and on regional volume parameters. A quantitatively greater improvement in contraction could be provoked in the anterior wall than in the posterior wall. Regional contraction improved significantly in most cases either in the anterior wall or in the posterior wall; rarely it improved simultaneously in both left ventricular regions. In a few cases contraction deteriorated in one area with a simultaneous improvement in the opposite area. Overall and regional ventricular function, as assessed preoperatively by contraction reserve determinations could not be completely regained in normal beats after successful bypass surgery. Differences in the regional contraction reserve seemed to be mainly due to varying degrees of ischemia and scarring.

Angina Pectoris↗

PubMed1979

Quantification of tetanus antitoxin in human sera. II. Comparison of counter-immunoelectrophoresis and passive haemagglutination with toxin neutralization in mice.

We described recently an improved counter-immunoelectrophoretic method for quantification of tetanus antitoxin. The toxin neutralization test in mice is considered to correlate well with protection in humans. In the present study, the correlation coefficient between the two methods was 0.89. Sera containing more than 7.0 I.U./ml could be quantified directly by counter-immunoelectrophoresis, while sera containing less tetanus antitoxin had to be concentrated prior to quantification. The passive haemagglutination test was also compared with the toxin neutralization test in mice. The correlation coefficient between the two methods was 0.76.

Antibodies, Bacterial↗

PubMed2026

Accurate quantification of canine mitochondrial DNA copy number from canine blood and brain samples.

Acute brain injury is difficult to evaluate in veterinary medicine and tools to investigate the potential involvement of mitochondrial involvement are limited. The brain is highly enriched in mitochondria and contains thousands of copies of mitochondrial DNA (mtDNA) per cell, but robust methods for quantifying mitochondrial DNA copy number (mtDNA-CN) in canine tissues are lacking. We describe the development of a quantitative real-time PCR assay for absolute measurement of mtDNA-CN which was validated in canine blood and brain tissue. To minimize amplification of nuclear mitochondrial insertion sequences (NumtS) and repetitive regions, species-specific oligonucleotide primers were designed following in silico genomic filtering. The assay was applied to a small pilot cohort comprising blood samples from dogs with and without acute brain injury (n = 4-6 per group) and cerebral cortex samples (n = 1 per group) to assess feasibility and biological plausibility. In non-brain injury dogs, blood mtDNA-CN ranged from 98 to 288 copies per nuclear genome (mean 193 ± 72), while values in brain-injured cases ranged from 163 to 228 copies per genome (mean 200 ± 33). Cerebral cortex samples exhibited higher mtDNA-CN than blood, consistent with known tissue-specific mitochondrial enrichment. In a single brain-injured case with serial sampling, mtDNA-CN increased over five days. This study presents a validated assay and pilot data for mtDNA-CN quantification in canine samples. While not powered for biomarker evaluation, this method may enable future studies of mitochondrial dynamics in canine brain injury and metabolic disease.

Animals↗

PubMed1976

Quantification of combined radiation therapy and chemotherapy effects on critical normal tissues.

In order to determine the modification of radiation effects on critical normal tissues which occurs with combinations of radiation and cancer chemotherapy, a review of laboratory and clinical data has been carried out. Information on 10 different normal tissues is available. It is clear that the antibiotic cancer chemotherapeutic agents are the most likely to enhance radiation injury, with increased levels reported in all tissues except the central nervous system. The second most common type of injury with combination therapy appears to occur with drugs causing injury to the normal tissue on their own, such as adriamycin in the heart and methotrexate in the central nervous system. Quantification of the dose-effect factor is only available on a limited number of tissues, and, primarily, in experimental animals. From these limited data, it is clear that dose-effect factors between 1.1 and 1.8 are seen, indicating that radiation doses must be reduced by 10-80% for the same level of injury when combined with chemotherapy. The augmentation of radiation damage by cancer chemotherapeutic agents is a serious problem in a wide range of tissues, but a problem which can be dealt with by accurate knowledge as to the dose-effect factor and appropriate modification of the radiation treatment.

Antineoplastic Agents↗

PubMed1978

Specific localization and quantification of biotin transport components in yeast by use of a biotin-conjugated, impermeant, electron-dense label.

Two approaches are described for the localization and quantification of biotin transport components in yeast cells. One approach is based on tracing the fate of a radioactive affinity label for the biotin transport system, [14C]biotinyl-p-nitrophenyl ester (pBNP), through various stages of subcellular fractionations. A complementary method involves the use of a biotin-derivatized, impermeant, electron-dense, affinity-cytochemical label (ferritin-biotin conjugates) for subsequent visualization by electron microscopy. Values of approximately 8,000 and 4,000 sites/cell, respectively, were achieved by the two methods. Complicating factors, future perspectives and the relevance of the two methods to the isolation of transport components are discussed.

Affinity Labels↗

PubMed1979

Quantification of nuclear DNA and intracellular glycogen in a single cell by fluorescent double-staining.

It was found that intracellular glycogen is stabilized against acid treatment when it is stored under dry conditions for three months after methanol fixation. This stabilization allowed quantitative double fluorescence staining for nuclear DNA and intracellular glycogen, in a single cell. A Feulgen nucleal reaction, with acriflavine-Schiff's reagent following 5 N HCl hydrolysis at 25 degrees C for 4 min, was followed by a pararosanilin-Schiff PAS reaction for glycogen. This short term hydrolysis was found to be sufficient for the performance of a acriflavine-Schiff's Feulgen nucleal reaction and to provide good preservation of intracellular glycogen. Quantification of nuclear DNA and intracellular glycogen were consecutively carried out with a digital microfluorometer on a single ascites cancer cell of the AH-13 line stained by this method. It was found that there is a positive linear correlation between the amount of DNA and glycogen in this cell line.

Animals↗

PubMed1978

Early quantification of experimental myocardial infarction with technetium-99m glucoheptonate: scintigraphic and anatomic studies.

Recent advances in understanding of the pathophysiology of myocardial necrosis indicate the need for a noninvasive method that will allow detection and quantification of infarcts in the first few hours after the onset of infarction. Myocardial infarct scintigraphy using technetium-99m glucoheptonate is capable of detecting infarction in dogs and man within 4 to 6 hours of onset. Studies were performed in 45 dogs with acute myocardial infarction: 28 with with an anterior infarct, 5 with an inferior infarct, 6 with an anterior infarct studied after infusion of mannitol and 6 with ligation of the left anterior descending coronary coronary artery and reperfusion of the ischemic area. The dogs were given 20 m Ci of technetium-99m glucoheptonate 1 hour after coronary occlusion, subjected to imaging 5 to 9 hours later and then killed. The experiments revealed that (1) scintigraphic infarct size correlated with infarct weight for anterior (r = 0.85) and inferior (r = 0.88) infarcts; (2) technetium-99m glucoheptonate also concentrated in a rim of myocardium around the infarct that probably represented the ischemic zone; and (3) technetium-99m glucoheptonate uptake by infarcted myocardium could be greatly increased with mannitol and reperfusion.

Animals↗

PubMed1976

Automatic recognition and quantification of interictal epileptic activity in the human scalp EEG.

An attempt was made at using a small computer to recognize and quantify interictal epileptic activity (spikes and sharp waves) in the human scalp EEG. To perform the automatic recognition, the EEG of each channel is broken down into half-waves. A half-wave is characterized by its duration and its amplitude relative to the background activity. A wave is characterized by the durations and amplitudes of its two component half-waves, by the second derivative at its apex measured relative to the background activity, and by the duration and amplitude of the following half-wave. Particular combinations of these parameters were found to characterize spikes and sharp waves and are used for their recognition and quantification. Specific methods are used for the rejection of spike-like or sharp wave-like wave forms such as eye blinks, muscle potentials and sharp alpha activity and were found to perform with a high level of reliability. Interchannel relationships are thoroughly examined to determine areas of maximal epileptogenicity. Sixteen channels can be analyzed in real time. Results are presented in a simple picture containing localizing and quantitative information. Specific questions regarding the time relationships of spikes in different channels can be asked interactively by the user. The system is of potential use in clinical electroencephalography.

Alpha Rhythm↗

PubMed1979

Electroencephalographic quantification by time domain analysis in normal 7--15-year-old children.

Automatic EEG analysis was performed on 239 apparently healthy school age children. The children were classed in 3 age groups: (1) average age of 7; (2) average age of 11; (3) average age of 15. A time analysis method, comparable to classical visual analysis, permitted quantification of the records. The mean amplitude, frequency and percentage time for alpha and theta rhythms were determined for each subject for fronto-central and centro-occipital derivations bilaterally. Records were performed during periods of rest with eyes open and eyes closed. During hyperventilation, records were taken with eyes closed. The normal ranges of parameters were determined by calculating their means and standard deviations, for each age group under each recording condition. Delta and beta rhythm values were not calculated, because of their rarity in this apparently normal sample. The precision obtained by automatic analysis could not have been obtained by means of classical visual analysis. The present findings suggest that the statistical analysis of well-defined groups of normal and pathological children could be of significant value.

Adolescent↗

PubMed1979

Microprocessor-based EEG spike detection and quantification.

A microprocessor-based system for the detection and quantification of sharp EEG waveforms is described. The hierarchical approach utilises initial transient detection based on computation of a second-derivative measure of curvature, followed by pattern-recognition and artifact-rejection routines based on consideration of specific waveform parameters. Initials results demonstrate an ability to approximate human-analysis results, while providing precise measures of amplitude, duration, and sharpness. The decreasing cost of microprocessors makes multichannel configurations economically feasible.

Analog-Digital Conversion↗

PubMed2026

Protocol to improve isoform-level quantification of low-abundance transcripts via STALARD pre-amplification.

STALARD (selective target amplification for low-abundance RNA detection) enables isoform-level quantification of low-abundance RNAs using conventional laboratory equipment. Here, we describe steps for RNA isolation, primer design, reverse transcription, selective target amplification, and downstream analysis. The protocol couples selective pre-amplification with a quantitative reverse-transcription PCR (RT-qPCR) readout and optional nanopore sequencing. Using 1 μg input RNA and 12 pre-amplification cycles, STALARD reduces Cq values by approximately 10-12 cycles, bringing the target into a reliably quantifiable range. For complete details on the use and execution of this protocol, please refer to Jeong et al.1.

Gene Expression↗