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At least 271 records · Page 15Linked to original sources
PubMed2004

A new method to locate saddle points for reactions in solution by using the free-energy gradient method and the mean field approximation.

A new method for calculating saddle points of reactions in solution is presented. The main characteristics of the method are: (1) the solute-solvent system is described by the averaged solvent electrostatic potential/molecular dynamics method (ASEP/MD). This is a quantum mechanics/molecular mechanics method (QM/MM) that makes use of the mean field approximation (MFA) and that permits one to simultaneously optimize the electronic structure and geometry of the solute molecule and the solvent structure around it. (2) The transition state is located by the joint use of the free-energy gradient method and the mean field approximation. An application to the study of the Menshutkin reaction between NH(3) and CH(3)Cl in aqueous solution is discussed. The accuracy and usefulness of the proposed method is checked through comparison with other methods.

Journal Article↗
PubMed2003

Novel ROC-type method for testing the efficiency of multivariate statistical methods in fMRI.

The receiver operating characteristic (ROC) method is a useful and popular tool for testing the efficiency of various diagnostic tests applicable to functional MRI (fMRI) data. Typically, the diagnostic tests are applied on simulated and pseudo-human fMRI data, and the area under the ROC curve is used as a measure of the efficiency of the diagnostic test. The effectiveness of such a method depends on how well the simulated data approximate the real data. For multivariate statistical methods, however, this technique is usually inadequate, as the spatial dependence among voxels is ignored for simulated data. In this work a modified ROC method using real fMRI data with a broader scope is proposed. This method can be applied to most fMRI postprocessing techniques, including multivariate analyses such as canonical correlation analysis (CCA). Also, the relationship of the modified ROC method with the conventional ROC method is discussed in detail.

Algorithms↗
PubMed2004

Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods.

To improve the detection of related proteins, it is often useful to include evolutionary information for both the query and target proteins. One method to include this information is by the use of profile-profile alignments, where a profile from the query protein is compared with the profiles from the target proteins. Profile-profile alignments can be implemented in several fundamentally different ways. The similarity between two positions can be calculated using a dot-product, a probabilistic model, or an information theoretical measure. Here, we present a large-scale comparison of different profile-profile alignment methods. We show that the profile-profile methods perform at least 30% better than standard sequence-profile methods both in their ability to recognize superfamily-related proteins and in the quality of the obtained alignments. Although the performance of all methods is quite similar, profile-profile methods that use a probabilistic scoring function have an advantage as they can create good alignments and show a good fold recognition capacity using the same gap-penalties, while the other methods need to use different parameters to obtain comparable performances.

Models, Chemical↗
PubMed1983

Measurement of functional residual capacity during mechanical ventilation. Comparison of a computerized open nitrogen washout method with a closed helium dilution method.

The functional residual capacity of patients treated with mechanical ventilation was measured with two methods: the closed helium dilution method and the open nitrogen washout method with a computerized system. Measurements of FRC were made with and without PEEP. The results obtained did not show significant differences between the methods. Additionally we checked the accuracy of the open nitrogen washout method to measure FRC of patients and healthy subjects breathing high concentrations of oxygen which was the same as breathing air. Both methods were equally reliable and safe when measuring the FRC of patients on mechanical ventilation but the nitrogen method was easier and quicker.

Computers↗
PubMed2003

Perfusion-Perls and -Turnbull methods supplemented by DAB intensification for nonheme iron histochemistry: demonstration of the superior sensitivity of the methods in the liver, spleen, and stomach of the rat.

Perfusion-Perls and -Turnbull methods supplemented by the intensification with 3,3'-diaminobenzidine (+ DAB) enabled stronger and more extensive staining of nonheme iron than the Perls + and Turnbull + DAB methods carried out on tissue sections fixed with 10% formalin in 0.9% saline or PBS. The section- and perfusion-Perls + DAB methods are not specific for the demonstration of nonheme ferric iron but also stain nonheme ferrous iron. However, owing to its high sensitivity, the perfusion-Perls + DAB method would provide useful information about nonheme iron deposition regardless of oxidation states in normal and pathological conditions. The perfusion-Turnbull + DAB method is specifically demonstrable of nonheme ferrous iron and the results from this method showed significant stores of nonheme ferrous iron in the hepatocytes, Kupffer cells, splenic macrophages, and gastric parietal cells of the rat. Since nonheme ferrous iron is considered to be critically involved in free radical generation, the perfusion-Turnbull + DAB method would visualize such populations of cells that are at risk from free radical damage.

3,3'-Diaminobenzidine↗
PubMed1996

Rational experimental design for bioanalytical methods validation. Illustration using an assay method for total captopril in plasma.

Generally, bioanalytical chromographic methods are validated according to a predefined programme and distinguish a pre-validation phase, a main validation phase and a follow-up validation phase. In this paper, a rational, total performance evaluation programme for chromatographic methods is presented. The design was developed in particular for the pre-validation and main validation phases. The entire experimental design can be performed within six analytical runs. The first run (pre-validation phase) is used to assess the validity of the expected concentration-response relationship (lack of fit, goodness of fit), to assess specificity of the method and to assess the stability of processed samples in the autosampler for 30 h (benchtop stability). The latter experiment is performed to justify overnight analyses. Following approval of the method after the pre-validation phase, the next five runs (main validation phase) are performed to evaluate method precision and accuracy, recovery, freezing and thawing stability and over-curve control/dilution. The design is nested, i.e., many experimental results are used for the evaluation of several performance characteristics. Analysis of variance (ANOVA) is used for the evaluation of lack of fit and goodness of fit, precision and accuracy, freezing and thawing stability and over-curve control/dilution. Regression analysis is used to evaluate benchtop stability. For over-curve control/dilution, additional to ANOVA, also a paired comparison is applied. As a consequence, the recommended design combines the performance of as few independent validation experiments as possible with modern statistical methods, resulting in optimum use of information. A demonstration of the entire validation programme is given for an HPLC method for the determination of total captopril in human plasma.

Calibration↗
PubMed1990

Methods for estimating release rates during high frequency quantal secretion and for testing such methods.

The rate of spontaneous quantal release must be estimated in some investigations of synaptic transmission, even when frequencies are so high that individual quanta cannot be distinguished. An obvious method is to measure the time integrals of the summed MEPPs and then dividing this value by the integral of an average MEPP. The method was tested by recording miniature end-plate potentials (MEPPs) at frog neuromuscular junctions, counting the number of MEPPS, and then adding together records from the same junction to simulate high frequencies. The estimates from the integral method agreed well with the actual counts. The method can readily be used with a microcomputer and does not require stationary data. Methods based on fluctuation analysis were also used to estimate quantal frequencies, but they did not always give good estimates. This was not a thorough test of the fluctuation method, but an example of testing with MEPP data. The integral method might be reasonably reliable, but there are further potential complications, like changes in MEPP size and short-circuiting of the end-plate membrane, which may make it difficult to obtain reliable measurements of high frequency quantal secretion without voltage clamping and protocols that permit measurements of individual MEPCs during the course of the frequency measurements.

Animals↗
PubMed1996

Water turnover evaluated by the tritiated water method and by the nutritional method in European hedgehog (Erinaceus europaeus L.).

The total body water (TBW), the fractional water turnover rate (WTR), and the water flux rates (WFR) were studied for the first time by the tritiated-water method in 10 hedgehogs under laboratory conditions during the year. To validate this method, we compared the result to the nutritional method. The TBW varied inversely with body mass (BM) during both the active and the hibernation periods. The WTR varied from 16% to 21% during the hibernation period and after the reproduction. The higher values (from 22% to 26%) were recorded during the reproduction period and during the preparation for hibernation. The same variations in WFR were recorded during the active and hibernation period. The net gain or loss of water followed the gain and loss of BM. The tritiated water (THO) method has been validated by the fact that the same variations in WFR during each month have been measured by the THO method and the nutritional method. Moreover, the THO method can be used to estimate the changes in energy metabolism of hedgehogs in relation with the seasons.

Analysis of Variance↗
PubMed1996

Comparative study of bone mineral density estimated by various methods of single- and dual-energy quantitative computed tomography: the capability of the four-equation four-unknown method.

A dual-energy (DE) quantitative computed tomography (QCT) method, the four-equation four-unknown method (DEQCT 4E-4U), was assessed and compared to single-energy (SE) QCT and standard DEQCT (two-line method). The results of this study indicate that bone mineral density (BMD) was more accurately estimated by the present method than by the SEQCT or standard DEQCT techniques on the basis of a phantom study when a large fat content was present. The results of both the phantom study and a human study also showed that the present method corrected for fat in estimating BMD in the presence of high-fat content. These findings suggest that use of this method for estimating BMD can provide useful information in studies assessing the metabolic state of bone. We propose that CT numbers estimated from excised vertebral bone marrow can serve as a soft-tissue correction for the present method.

Adult↗
PubMed2026

An enhanced multisegment RT-PCR method for influenza A virus sequencing: Improved performance and reduced preparation time over traditional methods.

Influenza A viruses (IAVs) remain a major global health threat, affecting both human and animal populations. Whole-genome sequencing is essential for monitoring viral evolution, zoonotic transmission, and emerging variants. However, conventional RT-PCR methods often result in incomplete gene coverage, amplification biases, and reduced sequencing accuracy, particularly in clinical samples. We developed a robust In-house method for IAV full-genome sequencing using the Oxford Nanopore Technologies (ONT) long-read sequencing platform. This method integrates an in-house multisegment Reverse Transcription PCR (RT-PCR) method with a streamlined 2-pool primer design targeting all eight IAV gene segments. RNA extracted from clinical and stock virus samples was reverse-transcribed and amplified using Superscript IV-based chemistry, followed by magnetic bead purification to ensure high-quality amplicons. Sequencing libraries were prepared with the Native Barcoding Kit 24 (SQK-NBD114.24) and sequenced on R10.4.1 flow cells on the MinION MK1C device. Data analysis using the Iterative Refinement Meta-Assembler (IRMA) confirmed improved read depth, uniform coverage, and complete genome recovery. Compared to conventional methods, our In-House Multisegment 2-Pool (IH-MS2P) RT-PCR method generated higher numbers of matched read counts, minimized chimeric artifacts, and delivered superior genome coverage across human, swine, and avian isolates. This optimized RT-PCR method provides a high-performance, time-efficient, and portable solution for influenza genomics, demonstrating robust applicability even with clinical samples of low RNA yield.

Influenza A virus↗
PubMed2005

A PCR method for detection of bifidobacteria in raw milk and raw milk cheese: comparison with culture-based methods.

Bifidobacteria are well known for their beneficial effects on health and are used as probiotics in food and pharmaceutical products. As they form one of the most important groups in both human and animal feces, their use as fecal indicator organisms in raw milk products has recently been proposed. Bifidobacteria species isolated in humans are different from those isolated in animals. It should therefore be possible to determine contamination origin (human or animal). A method of detecting the Bifidobacterium genus was developed by PCR targeting the hsp60 gene. The genus Bifidobacterium was identified by PCR amplification of a 217-bp hsp60 gene fragment. The degenerated primer pair specific to the Bifidobacterium genus used was tested for it specificity on 127 strains. Sensitivity was measured on artificially contaminated samples. Food can however be a difficult matrix for PCR testing since it contains PCR inhibitors. So an internal PCR control was used. An artificially created DNA fragment of 315 bp was constructed. The PCR detection method was tested on raw milk and cheese samples and compared with three culture-based methods, which comprised enrichment and isolation steps. The enrichment step used Brain Heart Infusion medium with propionic acid, iron citrate, yeast extract, supplemented with mupirocin (BHMup) or not (BH) and the isolation step used Columbia blood agar medium, supplemented with mupirocin (CMup) or not (C). The method using mupirocin at both enrichment and isolation steps and the PCR method performed from the culture in BHMup enrichment medium were shown to be the most efficient. No significant difference was observed in raw milk samples between PCR from BHMup and the culture-based method BHMup/CMup, while a significant difference was noticed between the same methods in raw milk cheese samples, which would favor using PCR. The results suggested that PCR on the hsp60 gene was convenient for a rapid detection of bifidobacteria in raw milk and raw milk cheese samples and that bifidobacteria always present throughout raw milk cheese production could be efficiently used as fecal indicators.

Animals↗
PubMed2003

Comparison of eigenvector methods with classical and model-based methods in analysis of internal carotid arterial Doppler signals.

Doppler ultrasound is known as a reliable technique, which demonstrates the flow characteristics and resistance of arteries in various vascular disease. In this study, internal carotid arterial Doppler signals recorded from 105 subjects were processed by PC-computer using classical, model-based, and eigenvector methods. The classical method (fast Fourier transform), two model-based methods (Burg autoregressive, least-squares modified Yule-Walker autoregressive moving average methods), and three eigenvector methods (Pisarenko, multiple signal classification, and Minimum-Norm methods) were selected for processing internal carotid arterial Doppler signals. Doppler power spectra of internal carotid arterial Doppler signals were obtained using these spectrum analysis techniques. The variations in the shape of the Doppler power spectra were examined in order to obtain medical information. These power spectra were then used to compare the applied methods in terms of their frequency resolution and the effects in determination of stenosis and occlusion in internal carotid arteries.

Arterial Occlusive Diseases↗
PubMed2002

US Environmental Protection Agency Method 326.0, a new method for monitoring inorganic oxyhalides and optimization of the postcolumn derivatization for the selective determination of trace levels of bromate.

The development of US Environmental Protection Agency (EPA) Method 317.0 provided a more sensitive, acceptable alternative to EPA Method 300.1 to be proposed as one of the recommended compliance monitoring methods for Stage II of the Disinfectants/Disinfection By-Products (DBP) Rule. This work was initiated to evaluate other postcolumn reagents (PCRs) that might be utilized to provide an additional, alternative method in order to augment compliance monitoring flexibility for inorganic oxyhalide DBP anions. Modifications of the method reported by Salhi and von Gunten, which included adjustment and optimization of flow-rates, reaction temperature, and delivery of the PCR, improved the method performance. Method 326.0 incorporates an acidic solution of potassium iodide containing catalytic amounts of molybdenum(VI) as the PCR and provides acceptable precision and accuracy for all analytes and a postcolumn bromate detection limit in reagent water of 0.17 microg/l.

Bromates↗
PubMed1985

Light microscopical localization of enzymes by means of cerium-based methods. I. Detection of acid phosphatase by a new cerium-lead-technique (Ce-Pb-method).

Cerium-III-ions are more and more used as capturing reagent and opaque marker for the electron microscopic localization of a number of H2O2-generating enzymes as well as phosphohydrolases. Contrary to its advantages over common lead methods in the histochemical detection of enzyme activities at the electron microscopic level, cerium-based methods proved to be a failure for light microscopic investigations. Therefore, our cerium-based method for the ultrahistochemical detection of acid phosphatase was developed for further observations at the light microscopic level. The principle of that new Ce-Pb-method is the conversion of light microscopic not visible cerium phosphate into lead phosphate by the secondary capture reagent alkaline lead citrate. Finally, the lead phosphate can be visualized as lead sulfide in the section. The Ce-Pb-method in its finally proposed manner was compared with a common lead method and showed a range of advantages. Because of that fact, the new Ce-Pb-method is recommended for a broader use in histochemistry, e.g. for the light microscopic enzyme investigation parallel to ultrahistochemical preparations.

Acid Phosphatase↗
PubMed1986

The "Ring" method: a semi-empirical method to calculate dose distributions of irregularly shaped photon beams.

The "Ring" method provides a fast dose calculation and isodose presentation for photon beams with blocks. The method takes into account the change in scatter due to the blocks at each calculation point. Firstly, the dose in a point is calculated assuming that no blocks are present. Secondly, the scatter reduction caused by the blocks is calculated and subtracted. To determine the scatter reduction the irradiated surface is divided in concentric rings around a point at the surface at the intersection with a ray line between focus and calculation point. The scatter reduction caused by blocks for each ring is calculated. The effect of scatter for rings with an outer radius greater than 15 cm where the scatter contribution is less than 1.0% is neglected. Results of the method for 4 MV photons using eight rings are presented. Comparison of dose measurements with calculations in an arrow-shaped photon field showed maximum deviations of 4.0%, using the IRREG program of Cunningham, 6.5% using the BLKINP program of Schlegel, which is based on Clarkson's method, 5.0% using the method of Wrede and 2.2% using the "Ring" method. Contrary to the first two calculation programs, the programs using the last two calculation methods provide isodose lines dose values at points.

Radiation Dosage↗
PubMed2003

Error analysis of a Galerkin method to solve the forward problem in MEG using the boundary element method.

Sources of brain activity, e.g. epileptic foci, can be localized with Magnetoencephalography (MEG) measurements by recording the magnetic field outside the head. For a successful surgery a very high localization accuracy is needed. The most often used conductor model in the source localization is an analytic sphere, which is not always adequate, and thus a realistically shaped conductor model is needed. In this paper we examine a Galerkin method with linear basis functions to solve the forward problem in MEG using the boundary element method. Its accuracy is compared to the collocation method with constant and linear basis functions. The accuracies are determined for a unit sphere for which analytic solutions are available. The Galerkin method gives a clear improvement in the accuracy of the forward problem especially for the tangential component of the magnetic field. At realistic MEG measurement distances from the brain the Galerkin method reaches a given accuracy with lower computational costs than the collocation methods starting from a few hundreds of unknowns. With larger meshes the difference for the Galerkin method increases significantly.

Humans↗
PubMed2004

Determination of airborne carbonyls: comparison of a thermal desorption/GC method with the standard DNPH/HPLC method.

The standard method for the determination of gaseous carbonyls is to collect carbonyls onto 2,4-dinitrophenyl hydrazine (DNPH) coated solid sorbent followed by solvent extraction of the solid sorbent and analysis of the derivatives using high-pressure liquid chromatography (HPLC). This paper describes a newly developed approach that involves collection of the carbonyls onto pentafluorophenyl hydrazine (PFPH) coated solid sorbents followed by thermal desorption and gas chromatographic (GC) analysis of the PFPH derivatives with mass spectrometric (MS) detection. Sampling tubes loaded with 510 nmol of PFPH on Tenax sorbent effectively collect gaseous carbonyls, including formaldehyde, acetaldehyde, propanal, butanal, heptanal, octanal, acrolein, 2-furfural, benzaldehyde, p-tolualdehyde, glyoxal, and methylglyoxal, at a flow rate of at least up to 100 mL/min. All of the tested carbonyls are shown to have method detection limits (MDLs) of subnanomoles per sampling tube, corresponding to air concentrations of <0.3 ppbv for a sampled volume of 24 L. These limits are 2-12 times lower than those that can be obtained using the DNPH/HPLC method. The improvement of MDLs is especially pronounced for carbonyls larger than formaldehyde and acetaldehyde. The PFPH/GC method also offers better peak separation and more sensitive and specific detection through the use of MS detection. Comparison studies on ambient samples and kitchen exhaust samples have demonstrated that the two methods do not yield systematic differences in concentrations of the carbonyls that are above their respective MDLs in both methods, including formaldehyde, acetaldehyde, acrolein, and butanal. The lower MDLs afforded by the PFPH/ GC method also enable the determination of a few more carbonyls in both applications.

Adsorption↗
PubMed2002

Improved method for quantifying the avicide 3-chloro-p-toluidine hydrochloride in bird tissues using a deuterated surrogate/GC/MS method.

A method using a deuterated surrogate of the avicide 3-chloro-p-toluidine hydrochloride (CPTH) was developed to quantify the CPTH residues in the gastrointestinal (GI) tract and breast muscle tissues in birds collected in CPTH-baited sunflower and rice fields. This method increased the range of a previous surrogate/gas chromatography/mass spectroscopy method from 0-2 to 0-20 microg/g in tissue samples and greatly simplified the extraction procedure. The modified method also sought to increase recoveries over a range of matrix effects introduced by analyzing tissues from birds collected in the field, where the GI tract contents would be affected by varying diet. The new method was used to determine the CPTH concentration in GI tract samples fortified with CPTH-treated rice bait to simulate the consumption of varying amounts of treated bait by two nontargeted bird species, pigeon (Columbia livia) and house sparrow (Passer domesticus). The new method was then used to examine the CPTH concentrations in the gizzard contents of the targeted bird species, red-winged black bird (Agelaius phoeniceus) and brown-headed cowbird (Molothrus ater), that were collected after feeding at a treated bait site. The method proved sufficiently sensitive to quantify CPTH in the breast muscle tissues and the gizzard contents of red-winged blackbirds and brown-headed cowbirds during an operational baiting program. The levels of CPTH determined for these birds in both tissue samples were determined to be highly correlated. The appearance of CPTH in the breast muscle tissue immediately after feeding was not anticipated. The potential secondary hazard posed by the targeted birds to potential scavengers and predators was also evaluated.

Animals↗