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PubMed2003

A novel multiplex quantitative DNA array based PCR (MQDA-PCR) for quantification of transgenic maize in food and feed.

We have developed a novel multiplex quantitative DNA array based PCR method (MQDA-PCR). The MQDA-PCR is general and may be used in all areas of biological science where simultaneous quantification of multiple gene targets is desired. We used quantification of transgenic maize in food and feed as a model system to show the applicability of the method. The method is based on a two-step PCR. In the first few cycles bipartite primers containing a universal 5' 'HEAD' region and a 3' region specific to each genetically modified (GM) construct are employed. The unused primers are then degraded with a single-strand DNA-specific exonuclease. The second step of the PCR is run containing only primers consisting of the universal HEAD region. The removal of the primers is essential to create a competitive, and thus quantitative PCR. Oligo nucleotides hybridising to internal segments of the PCR products are then sequence specifically labelled in a cyclic linear signal amplification reaction. This is done both to increase the sensitivity and the specificity of the assay. Hybridisation of the labelled oligonucleotides to their complementary sequences in a DNA array enables multiplex detection. Quantitative information was obtained in the range 0.1-2% for the different GM constructs tested. Seventeen different food and feed samples were screened using a twelve-plex system for simultaneous detection of seven different GM maize events (Bt176, Bt11, Mon810, T25, GA21, CBH351 and DBT418). Ten samples were GM positive containing mainly mixtures of Mon810, Bt11 and Bt176 DNA. One sample contained appreciable amounts of GA21. An eight-plex MQDA-PCR system for detection of Mon810, Bt11 and Bt176 was evaluated by comparison with simplex 5' nuclease PCRs. There were no significant differences in the quantifications using the two approaches. The samples could, by both methods, be quantified as containing >2%, between 1 and 2%, between 0.1 and 1%, or <0.1% in 43 out of 47 determinations. The described method is modular, and thus suited for future needs in GM detection.

Animal Feed↗

PubMed2004

Determination of detection and quantification limits for SNP allele frequency estimation in DNA pools using real time PCR.

The quantification of single nucleotide polymorphism (SNP) allele frequencies in pooled DNA samples using real time PCR is a promising approach for large-scale diagnostics and genotyping. The limits of detection (LOD) and limits of quantification (LOQ) for mutant SNP alleles are of particular importance for determination of the working range, which, in the case of allele-specific real time PCR, can be limited by the variance of calibration data from serially diluted mutant allele samples as well as by the variance of the 100% wild-type allele samples (blank values). In this study, 3sigma and 10sigma criteria were applied for the calculation of LOD and LOQ values. Alternatively, LOQ was derived from a 20% threshold for the relative standard deviation (%RSD) of measurements by fitting a curve for the relationship between %RSD and copy numbers of the mutant alleles. We found that detection and quantification of mutant alleles were exclusively limited by the variance of calibration data since the estimated LOD(calibration) (696 in 30 000 000 copies, 0.0023%), LOQ(20%RSD) (1470, 0.0049%) and LOQ(calibration) (2319, 0.0077) values were significantly higher than the LOD(blank) (130, 0.0004%) and LOQ(blank) (265, 0.0009%) values derived from measurements of wild-type allele samples. No significant matrix effects of the genomic background DNA on the estimation of LOD and LOQ were found. Furthermore, the impact of large genome sizes and the general application of the procedure for the estimation of LOD and LOQ in quantitative real time PCR diagnostics are discussed.

Calibration↗

PubMed1997

Comparison of high-efficiency and standard haemodialysis providing equal urea clearances by partial and total dialysate quantification.

BACKGROUND: Short-duration high-efficiency haemodialysis has been utilized increasingly in recent years to deliver adequate blood urea clearances per dialysis session. However, high-efficiency and standard-duration haemodialysis schedules, which achieve equal patient urea clearances, may not represent equivalent dialytic therapy due to solute differences in intercompartmental dysequilibrium during dialysis and differences in dialysis mechanics. METHODS: To circumvent the effects of intercompartmental dysequilibrium and postdialysis rebound solute clearances were measured by direct dialysis quantification (total and partial dialysate collections) rather than blood clearances. High-efficiency haemodialysis (dialyser blood flow rate = 400 ml/min; dialysis time = 170.67 min) was compared with standard haemodialysis (dialyser blood flow rate = 200 ml/min; dialysis time = 240 min) performed in random order in six anuric patients using Fresenius F8 dialysers and the same haemodialysis machine. Such haemodialysis schedules were prescribed to provide equivalent urea clearances. RESULTS: Patient plasma water urea clearances measured by direct dialysis quantification were equivalent, whereas high efficiency haemodialysis achieved significantly lower phosphate clearances (P = 0.01), less net bicarbonate absorption (P = 0.01), and lower beta 2 microglobulin removal (P < 0.001) than standard haemodialysis. Estimated total dialysate effluent volumes with partial dialysate collection and total dialysate collection correlated closely (r = 0.95) and there were no differences between patient urea, creatinine and phosphate clearances measured by partial and total dialysate quantification. CONCLUSIONS: The data indicate that even if high-efficiency and standard haemodialysis provide equal whole-body urea clearances, delivered dialysis therapy is not equivalent. The partial dialysate collection method is as accurate as the cumbersome total dialysate collection approach and may be applied to assess delivered dialysis dose by minor modification of current haemodialysis machines.

Hemodialysis Solutions↗

PubMed2004

Assessment of phospholipid malabsorption by quantification of fecal phospholipid.

OBJECTIVES: The standard methods for quantifying fat absorption involve extraction of fat from fecal samples with heptane, ether and ethanol. These solvents do not quantitatively recover phospholipids. Malabsorption of dietary and biliary phosphatidylcholine could potentially result in choline deficiency. Therefore, the authors developed a method extracting and quantifying fecal phospholipids. METHODS: Fecal samples were collected for 72 hours from 18 children with cystic fibrosis and 10 control children. Fat was extracted first with hexane/diethyl ether/ethanol and then with chloroform/methanol. Total fat was quantitated gravimetrically. Phospholipids in extracted fat were separated and quantified using high-performance liquid chromatography with evaporative light-scattering detection (HPLC-ELSD). Phospholipid quantification was validated with a phosphomolybdate colorimetric assay. RESULTS: The combination of solvent systems used in this study significantly improved total fat (p < 0.05) and phospholipid (p < 0.001) extraction compared with either hexane/diethyl ether/ethanol or chloroform/methanol alone. Fecal phospholipid measured by HPLC-ELSD was significantly correlated with lipid-soluble phosphorous using the phosphomolybdate assay (r = 0.75, p < 0.001). This method also allows quantification of fecal phosphatidylcholine and lysophosphatidylcholine. CONCLUSIONS: Hexane/diethyl ether/ethanol followed by chloroform/methanol extraction of fecal samples and quantification of phospholipids using HPLC-ELSD is a new method for investigating phospholipid malabsorption.

Case-Control Studies↗

PubMed1996

Assessment of completeness of thyroid ablation by estimation of neck uptake of 131I on whole-body scans: comparison of quantification and visual assessment of thyroid bed uptake.

Thyroid cancer is treated by thyroidectomy followed by radioiodine ablation of the residual active tissue in the thyroid bed. Completeness of ablation can be assessed from neck images of whole-body 131I scans by visual estimation or quantitative analysis By visual assessment, ablation can be considered complete if there is no uptake in the neck or the uptake is empirically considered too small. By quantification, ablation is considered complete if neck uptake is < 1%. Further radioiodine therapy is considered necessary only if neck uptake exceeds 1% of the administered dose. Both visual assessment and quantification of thyroid bed uptake were applied to 46 scans after diagnostic or therapeutic doses of 131I had been administered to 25 patients who were being followed up for follicular or papillary carcinoma of the thyroid. The results were compared to assess the effect of either method on determining the need for a further ablative dose of 131I. Visual assessment overestimated thyroid bed uptake in 10 of 46 (22%) of the scans. Bearing in mind the unpleasantness of radioiodine ablation and the potential for bone marrow toxicity, it is recommended that quantification of neck uptake should be routinely performed as a guide to completeness of ablation and to determine the need for a therapeutic dose of the isotope. This should help to avoid unnecessary radioiodine treatment in patients with thyroid cancer.

Adult↗

PubMed2006

Improved quantification in 123I cardiac SPECT imaging with deconvolution of septal penetration.

OBJECTIVES: (123)I is becoming an important radionuclide for cardiac imaging. Multiple, low-abundance, high-energy photons associated with (123)I imaging can cause septal penetration in the collimators and degrade quantification of the (123)I cardiac uptake. This study presents a method for the deconvolution of septal penetration (DSP) for improving quantification in (123)I cardiac single photon emission computed tomography (SPECT). METHODS: Distance-dependent point spread functions were measured for low-energy high-resolution collimators on a dual-head SPECT system. The measured point spread functions were used in two-dimensional (2-D) and three-dimensional (3-D) models of the collimator response, respectively. 2-D DSP and 3-D DSP were then developed and implemented using iterative reconstruction. A cardiac torso phantom with an internal calibration source was designed with various heart-to-calibration ratios (HCRs) simulating different levels of a patient's uptake. SPECT acquisitions of the phantom were performed using optimized acquisition and processing parameters for (123)I cardiac SPECT. HCRs were calculated using planar projection and tomographic reconstructions. The paired t-test and regression analysis were used to compare the HCRs given by different calculation methods. RESULTS: SPECT produced more accurate HCRs than planar imaging. The slopes of the regression lines for SPECT using filtered back-projection were statistically significantly higher than those for planar imaging (0.2118 +/- 0.0297 vs. 0.0819 +/- 0.0070, P = 0.0001). 2-D DSP and 3-D DSP yielded similar HCRs that were close to the true HCR. The slopes of the regression lines for 2-D DSP and 3-D DSP were 0.9203 +/- 0.0523 and 0.9101 +/- 0.0304, respectively. The DSP HCRs were significantly more accurate than those calculated without DSP (P < 0.0001). CONCLUSION: DSP significantly improves quantification in (123)I cardiac SPECT imaging. 2-D DSP with its less computational burden shows promise for implementation in clinical practice so as to allow the use of the widely available low-energy, high-resolution collimators for quantitative I cardiac SPECT imaging.

Algorithms↗

PubMed2002

Comparative analysis of HIV-1 viral load assays on subtype quantification: Bayer Versant HIV-1 RNA 3.0 versus Roche Amplicor HIV-1 Monitor version 1.5.

Quantification of HIV-1 subtypes is essential for appropriate clinical management. Whereas viral load assays were initially developed to accurately quantify subtype B, the recent worldwide spread of non-B subtypes and the introduction of treatment programs in regions with non-B subtypes have prompted adaptations of these assays. The Bayer Versant HIV-1 RNA 3.0 Assay (branched DNA [bDNA] 3.0) and the Roche Amplicor HIV-1 Monitor version 1.5 (Amplicor 1.5) assays are reported to quantify all subtypes in group M; however, evaluation of performance characteristics remains limited. In this study, we evaluated the accuracy and reliability of bDNA 3.0 and Amplicor 1.5 on multiple serially diluted viral isolates from HIV-1 group M, subtypes A through F. Testing was conducted on both assay systems in two independent laboratories. Comparative pansubtype quantification from regression analysis showed that quantification by bDNA 3.0 was approximately 0.3 log-fold lower than that by Amplicor 1.5. Comparative pansubtype accuracy analysis showed data points more closely distributed about their respective regression lines and thus showing greater reliability by bDNA 3.0 than by Amplicor 1.5.

Branched DNA Signal Amplification Assay↗

PubMed2003

Plasma RNA quantification and HIV-1 divergent strains.

The diversity of HIV complicates viral load measurement for patient management and treatment monitoring. Numerous studies have shown that non-B group M variants can be underestimated and that group O strains are not detected by commercial tests. More recent versions of the kits used for previous studies have improved the quantification of non-B variants but are still unable to detect or correctly quantify group O strains. In this study, the authors evaluated the new Abbott LCx HIV RNA Quantitative viral load kit with a large collection of samples from Europe and central Africa. One hundred thirty-three group M samples, including 69 from patients infected with non-B variants, and 70 group O samples were tested. The LCx system was compared with the Cobas Amplicor HIV-1 Monitor v1.5 test and with a quantitative real-time polymerase chain reaction method based on LightCycler technology. The LCx and Cobas tests had similar quantification ranges for group M samples and a high degree of linearity (r2 = 0.9582). The LCx method quantified group O variants (31 of the 48 patients were quantifiable) and gave values within the range of those obtained with the LightCycler assay. The two assays were sensitive but showed only moderate linearity (r2 = 0.6195), probably because of higher diversity of group O strains and the use of primers and probes in different regions. In conclusion, the authors showed that the LCx kit allowed quantification of the large group M diversity and group O variants.

Cameroon↗

PubMed2005

Validation of a practical liquid chomatography with ultraviolet detection method for quantification of whole-blood everolimus in a clinical TDM laboratory.

Until now, only LC/MS methods for quantification of everolimus have been published. The authors validated an LC/UV method for quantification of everolimus from whole blood. The authors sought to improve on the protocol for sirolimus determination previously reported by French et al. Everolimus and the internal standard 32-desmethoxy-rapamycin were extracted from whole blood with n-butyl chloride after precipitation of proteins and then reconstituted in mobile phase and washed with hexane to remove lipids. Everolimus was quantified by reverse-phase chromatography of the extraction product at 60 degrees C, using an isocratic 60% acetonitrile/water mobile phase at a flow rate of 1.0 mL/min. Everolimus eluted at approximately 9.6 minutes, and internal standard at approximately 11.6 minutes. A series of 32 calibration curves were linear over the concentration range of 2-100 ng/mL using 0.5 mL of whole blood per sample with r > 0.990 and slope displaying an 8.8 interassay %CV. At the lower limit of quantification, 2 ng/mL, the percentage bias and %CV were -5.0% and 14.7%, respectively. Intraassay precision at weighed-in levels of 6, 12, and 32 ng/mL were 2.4% to 6.4%, and biases were -10.7% to -8.5%. These same quality control materials yielded -6.3% to -0.8% biases from the expected values and 2.4% to 10.9% interday precision, respectively. This method for everolimus determination, validated according to FDA guidelines, provides longer column life and better sensitivity than that of French et al for sirolimus determination. This protocol also provides acceptable accuracy and precision over the expected therapeutic range and allows 1 technologist using 1 LC/UV system to run up to 5000 samples per year with confidence.

Chromatography, Liquid↗

PubMed2005

On-line solid-phase extraction coupled with high-performance liquid chromatography and tandem mass spectrometry (SPE-HPLC-MS-MS) for quantification of bromazepam in human plasma: an automated method for bioequivalence studies.

A validated method for on-line solid-phase extraction coupled with high-performance liquid chromatography tandem mass spectrometry (SPE-HPLC-MS-MS) is described for the quantification of bromazepam in human plasma. The method involves a dilution of 300 muL of plasma with 100 muL of carbamazepine (2.5 ng/mL), used as internal standard, vortex-mixing, centrifugation, and injection of 100 muL of the supernate. The analytes were ionized using positive electrospray mass spectrometry then detected by multiple reaction monitoring (MRM). The m/z transitions 316-->182 (bromazepam) and 237-->194 (carbamazepine) were used for quantification. The calibration curve was linear from 1 ng/mL (limit of quantification) to 200 ng/mL. The retention times of bromazepam and carbamazepine were 2.6 and 3.2 minutes, respectively. The intraday and interday precisions were 3.43%-15.45% and 5.2%-17%, respectively. The intraday and interday accuracy was 94.00%-103.94%. This new automated method has been successfully applied in a bioequivalence study of 2 tablet formulations of 6 mg bromazepam: Lexotan(R) from Produtos Roche Químicos e Farmacêuticos SA, Rio de Janeiro, Brazil (reference) and test formulation from Laboratórios Biosintética Ltda, São Paulo, Brazil. Because the 90% CI of geometric mean ratios between reference and test were completely included in the 80%-125% interval, the 2 formulations were considered bioequivalent. The comparison of different experimental conditions for establishing a dissolution profile in vitro along with our bioavailability data further allowed us to propose rationally based experimental conditions for a dissolution test of bromazepam tablets, actually lacking a pharmacopeial monograph.

Adult↗

PubMed2006

A micromethod for the quantification of atenolol in plasma using high-performance liquid chromatography with fluorescence detection: therapeutic drug monitoring of two patients with severe coronary insufficiency before cardiac surgery.

A simple, rapid, selective, and sensitive analytical method was developed for the quantification of atenolol in small volumes of plasma, by high-performance liquid chromatography with fluorescence detection. Only 200 microL of plasma was used for chromatographic analysis. Separation was performed on a C18 reverse-phase column (4 microm) using a binary mobile phase consisting of 0.05 M of phosphate buffer, pH 5.5, and methanol (80:20, vol/vol) at a flow rate of 0.7 mL/minute. The retention times of atenolol and of the internal standard (sotalol) were 12.7 and 10.4 minutes, respectively. Validation of this analytical method showed a good linear correlation (8-2000 ng/mL), high sensitivity (quantification limit: 8 ng/ml and detection limit: 4 ng/mL), accuracy of 99.3%, and intraday and interday precision of 5.3% and 6.9%, respectively. Absolute recovery was 93.7%. The method was found to be robust, with acceptable stability. The analytical method was validated by the quantification of atenolol in plasma obtained from 2 patients with unstable angina, scheduled for myocardium revascularization surgery, who were chronically treated with 50 mg of atenolol administered per os once a day. The method developed was found to be adequate for use in pharmacokinetic studies and in adjusted dose pharmacotherapy.

Administration, Oral↗

PubMed2002

Combined noninvasive imaging and luminometric quantification of luciferase-labeled human prostate tumors and metastases.

Noninvasive imaging should facilitate the analysis of changes in experimental tumors and metastases-expressing photoproteins and result in improved data consistency and experimental animal welfare. We analyzed quantitative aspects of noninvasive imaging of luciferase-labeled tumors by comparing the efficiency of noninvasive light detection with in vitro quantification of luciferase activity. An intensified charge coupled device video camera was used to noninvasively image luciferase-expressing human prostate tumors and metastases in nude mice, after ip inoculation of luciferin. Repeated imaging of anesthetized animals after intervening growth periods allowed monitoring of tumor and metastases development. Comparison of photon events recorded in tumor images with the number of relative light units from luminometric quantification of homogenates from the same tumors, revealed that the efficiency with which light escapes tumors is inversely related to tumor size and that intensified charge coupled device images alone are not sufficient for quantitative evaluation of tumor growth. However, a combined videometric and luminometric approach did allow quantification and was used to show the cytostatic effects of paclitaxel in three different human prostate tumors growing in nude mice.

Animals↗

PubMed2004

Quantification of aortic valve calcification with electron beam tomography: a histomorphometric validation study.

RATIONALE AND OBJECTIVES: The exact quantification of the amount of calcification in aortic valves may be useful for the identification of risk factors for the progression of aortic valve calcification and to evaluate new therapeutic approaches for aortic valve disease. Electron beam tomography (EBT) allows the in vivo detection of calcifications in coronary vessels and in the aortic valve. The aim of this study was to validate the quantification of aortic valve calcification by EBT with in vivo and in vitro investigations. METHODS: In 15 patients (aortic stenosis in 13, aortic regurgitation in 2 cases), EBT was performed before aortic valve replacement (40 cross sections, 3-mm slice thickness, matrix 512 x 512, field of view 28 cm, ECG trigger at 40% of the cardiac cycle). EBT was repeated on the explanted aortic valve using the same protocol. In both data sets, the amount of aortic valve calcification was determined using a volumetric score. In serial cuts of the explanted valve (distance 1 mm), the calcified volume was determined by an independent investigator using histomorphometric analysis. RESULTS: The mean calcified volume of the aortic valves as quantified by EBT was 1650.0 +/- 1401.0 mmł in vivo (EBT1) and 1544.4 +/- 1266.5 mmł in vitro (EBT2). Histomorphometric analysis showed a mean calcified volume of 1555.7 +/- 1272.5 mmł. The mean difference between EBT1 and EBT2 was 4.2 +/- 14.7%, between EBT1 and histomorphometry 3.6 +/- 12.1%, and between EBT2 and histomorphometry -0.5 +/- 5.9%. CONCLUSION: EBT allows accurate in vivo quantification of aortic valve calcifications.

Aged↗

PubMed2004

Quantification of pulmonary blood flow and volume in healthy volunteers by dynamic contrast-enhanced magnetic resonance imaging using a parallel imaging technique.

RATIONALE AND OBJECTIVES: We sought to optimize the dosage of a paramagnetic contrast medium (CM) for the quantification of pulmonary blood flow and volume by contrast-enhanced dynamic magnetic resonance imaging (MRI) using a parallel imaging technique and to prove the feasibility of the approach in healthy volunteers. METHODS: In a phantom study, the dependency of signal increase on different concentrations of the CM gadodiamide was evaluated by means of an ultra-fast MRI sequence with a generalized autocalibrating partially parallel acquisition technique (acceleration factor = 2). Using the same sequence, measurements were performed in a healthy volunteer after administration of different CM dosages for contrast dosage optimization in vivo. Finally, perfusion measurements were performed in 16 healthy volunteers after the administration of the optimal CM dose. Signal-time curves were evaluated from the pulmonary artery and from predefined regions of the lung. Pulmonary regional blood volume (RBV) and flow (RBF) were estimated using an open 1-compartment model. RESULTS: Phantom studies yielded a linear signal increase up to a concentration of 5.0 mmol/L gadodiamide. Results of contrast dosage optimization in vivo showed that the maximum CM dose providing a linear relationship between signal increase and CM concentration in the pulmonary artery of a healthy volunteer was approximately 0.05 mmol/kg-bw. Quantification of pulmonary blood volume and flow was reproducible in healthy volunteers, yielding mean values for the upper lung zones of 7.1 +/- 2.3 mL/100 mL for RBV and 197 +/- 97 mL/min/100 mL for RBF and for lower lung zones, 12.5 +/- 3.9 mL/100 mL for RBV and 382 +/- 111 mL/min/100 mL for RBF. CONCLUSIONS: If an adequate amount of gadodiamide and fast MR sequences are used, quantification of pulmonary blood flow and volume is feasible.

Adult↗

PubMed2007

Coronary artery stenosis quantification using multislice computed tomography.

RATIONALE AND OBJECTIVES: Reliable noninvasive detection of stenoses with multislice computed tomography (MSCT) is feasible. This study's aim was to analyze the agreement, correlation, and reliability of MSCT with conventional coronary angiography as the reference standard for quantification of coronary artery stenoses. MATERIALS AND METHODS: A total of 118 significant (at least 50%) coronary artery stenoses with a reference vessel diameter of at least 1.5 mm in 62 patients were analyzed by MSCT using 16 detector rows (Aquilion, Toshiba, Otawara, Japan), multisegment reconstruction, and voxel sizes of 0.35x0.35x0.5 mm. The degree of stenosis on MSCT and quantitative coronary angiography (QCA) was measured by correlating the difference between the reference vessel diameter (average of 2 measurements directly proximal and distal to the stenosis) and the stenotic vessel diameter to the reference vessel diameter. RESULTS: Correlation between the percent diameter stenosis determined by MSCT (78.2+/-13.6%) and QCA (76.0+/-14.8%) was significant (P<0.001) but only moderately so (R=0.51). Bland-Altman analysis revealed no systematic under- or overestimation with MSCT but large limits of agreements (+/-27.6%). Also the limits of agreement for interobserver agreement (reliability) of MSCT data were considerably large (+/-24.8%). Among the 27 coronary artery stenoses with a reference diameter of at least 3.5 mm, there was improved correlation (R=0.80) and the limits of agreement between MSCT and QCA were significantly smaller (+/-17.3%, P<0.008). The agreement between MSCT and QCA was not significantly different for stenoses with no calcification or only calcium spots (+/-28.2%) as compared with those with moderate-or-severe calcifications (+/-27.3%; P=0.8). MSCT allowed correct classification of coronary stenoses into low-grade (below 75%) and high-grade stenoses (at least 75%), in 62% (73 of 118). CONCLUSIONS: The accuracy and reliability of coronary artery stenosis quantification with MSCT using isotropic voxel sizes and multisegment reconstruction is still too low to recommend routine clinical application because of rather low agreement, correlation, and reliability. Despite these limitations, the current results demonstrate the potential of MSCT for reliable and accurate quantification of coronary artery stenoses in the near future provided that further improvements in spatial and temporal resolution will be achieved.

Anatomy, Cross-Sectional↗

PubMed2006

Quantification of electromyographic activity during sleep: a phasic electromyographic metric.

Recording of electromyographic (EMG) activity is considered essential for defining rapid eye movement (REM) sleep and for quantifying certain types of movements in sleep, such as periodic leg movements in sleep (PLMS). However, routine analyses of EMG activity beyond such purposes is performed rarely and quantified seldom, and normative data are lacking. In this study, the authors examined systematic application of a visual scoring system for short-duration (approximately 100-millisecond) phasic EMG activity recorded from five different muscle groups (submentalis, left/right anterior tibialis, left/right brachioradialis) recorded from two different age groups of normal subjects and a group of patients with Parkinson's disease. Quantification of this activity was labeled as a phasic electromyographic metric (PEM). PEM data were compiled separately by REM and non-REM sleep. Results indicated that PEM is a normal part of REM sleep in all muscle groups, more specifically constituting about 5% (SD = 3.1%) of 2.5-second intervals of REM sleep in the mentalis in healthy young adults. It occurs at higher rates in patients with Parkinson's disease, and its quantification in the legs may be influenced to some degree by the presence of PLMS. PEM may be a useful metric amenable to quantification with digital techniques. It may have particular relevance for the identification of neurodegenerative conditions in which disinhibition of midbrain dopaminergic pathways results in excessive motor discharge during sleep.

Adolescent↗

PubMed2025

kSanity: A k-mer based application for precision bacterial strain detection and quantification.

MOTIVATION: Accurate detection and quantification of bacterial strains in clinical samples is necessary to measure their colonization and persistence. Past methods to achieve this relied either on strain-specific qPCR assays, or shotgun metagenomic read mapping approaches. The resident microbial community is a major source of interference in both assays because it can contain conspecific strains bearing similarity to the focal strain(s). RESULTS: We present kSanity, a k-mer based application for the detection and quantification of targeted bacterial strains in shotgun metagenomic data. Because kSanity uses exact string matches between the reads and reference, it is less sensitive to interference by conspecific strains. We test the performance of kSanity using a combination of in silico spike-in experiments, and in vivo observational data. Our results demonstrate that kSanity provides precise and accurate quantification of targeted bacterial strains, even when they are present at low sequence coverage in the metagenome. AVAILABILITY AND IMPLEMENTATION: kSanity is available at: https://github.com/ravel-lab/kSanity.

bacterial strain detection↗

PubMed1994

Quantification of noisy MRS signals with the Pseudo-Wigner Distribution.

This paper investigates the estimation errors induced by noise in the quantification of damped sinusoids with the Pseudo-Wigner Distribution (PWD). A constant amplitude single frequency noise is first considered. This simple model shows how underestimation or overestimation errors depend on the relative phase between signal and noise for a fixed signal-to-noise ratio (SNR). In a second step, cross-terms and noise amplitude fluctuations are identified as the main sources of discrepancy between the theoretical model and a practical situation where wideband noise is linearly added to a synthetic free induction decay (FID) signal. Cross-terms can be attenuated by band-pass filtering noise or by using a weighting (or smoothing) window in the PWD. An original procedure is then derived to make an on-line and noise-specific estimation of the statistical error in the quantification step. This property of the Wigner distribution is a unique feature in quantitative MRS. Confidence intervals are evaluated for a single damped sinusoid corrupted by eight random noise sequences with three different SNR's, 20, 10 and 5 dB, respectively. They are shown to match the statistical ranges of quantification results obtained with linear regression, until the SNR drops below 10 dB. Estimation accuracy of amplitude and damping constant is finally evaluated from the comparison of the Cramér-Rao (CR) lower bounds with the variance of estimation errors. CR-bounds are shown to be nearly achieved at each SNR.

Confidence Intervals↗