An accurate method of extracting fat droplets in liver images for quantitative evaluation
NASA Astrophysics Data System (ADS)
Ishikawa, Masahiro; Kobayashi, Naoki; Komagata, Hideki; Shinoda, Kazuma; Yamaguchi, Masahiro; Abe, Tokiya; Hashiguchi, Akinori; Sakamoto, Michiie
2015-03-01
The steatosis in liver pathological tissue images is a promising indicator of nonalcoholic fatty liver disease (NAFLD) and the possible risk of hepatocellular carcinoma (HCC). The resulting values are also important for ensuring the automatic and accurate classification of HCC images, because the existence of many fat droplets is likely to create errors in quantifying the morphological features used in the process. In this study we propose a method that can automatically detect, and exclude regions with many fat droplets by using the feature values of colors, shapes and the arrangement of cell nuclei. We implement the method and confirm that it can accurately detect fat droplets and quantify the fat droplet ratio of actual images. This investigation also clarifies the effective characteristics that contribute to accurate detection.
Reese, Matthew O; Dameron, Arrelaine A; Kempe, Michael D
2011-08-01
The development of flexible organic light emitting diode displays and flexible thin film photovoltaic devices is dependent on the use of flexible, low-cost, optically transparent and durable barriers to moisture and/or oxygen. It is estimated that this will require high moisture barriers with water vapor transmission rates (WVTR) between 10(-4) and 10(-6) g/m(2)/day. Thus there is a need to develop a relatively fast, low-cost, and quantitative method to evaluate such low permeation rates. Here, we demonstrate a method where the resistance changes of patterned Ca films, upon reaction with moisture, enable one to calculate a WVTR between 10 and 10(-6) g/m(2)/day or better. Samples are configured with variable aperture size such that the sensitivity and/or measurement time of the experiment can be controlled. The samples are connected to a data acquisition system by means of individual signal cables permitting samples to be tested under a variety of conditions in multiple environmental chambers. An edge card connector is used to connect samples to the measurement wires enabling easy switching of samples in and out of test. This measurement method can be conducted with as little as 1 h of labor time per sample. Furthermore, multiple samples can be measured in parallel, making this an inexpensive and high volume method for measuring high moisture barriers. PMID:21895269
PLIF: A rapid, accurate method to detect and quantitatively assess protein-lipid interactions.
Ceccato, Laurie; Chicanne, Gaëtan; Nahoum, Virginie; Pons, Véronique; Payrastre, Bernard; Gaits-Iacovoni, Frédérique; Viaud, Julien
2016-01-01
Phosphoinositides are a type of cellular phospholipid that regulate signaling in a wide range of cellular and physiological processes through the interaction between their phosphorylated inositol head group and specific domains in various cytosolic proteins. These lipids also influence the activity of transmembrane proteins. Aberrant phosphoinositide signaling is associated with numerous diseases, including cancer, obesity, and diabetes. Thus, identifying phosphoinositide-binding partners and the aspects that define their specificity can direct drug development. However, current methods are costly, time-consuming, or technically challenging and inaccessible to many laboratories. We developed a method called PLIF (for "protein-lipid interaction by fluorescence") that uses fluorescently labeled liposomes and tethered, tagged proteins or peptides to enable fast and reliable determination of protein domain specificity for given phosphoinositides in a membrane environment. We validated PLIF against previously known phosphoinositide-binding partners for various proteins and obtained relative affinity profiles. Moreover, PLIF analysis of the sorting nexin (SNX) family revealed not only that SNXs bound most strongly to phosphatidylinositol 3-phosphate (PtdIns3P or PI3P), which is known from analysis with other methods, but also that they interacted with other phosphoinositides, which had not previously been detected using other techniques. Different phosphoinositide partners, even those with relatively weak binding affinity, could account for the diverse functions of SNXs in vesicular trafficking and protein sorting. Because PLIF is sensitive, semiquantitative, and performed in a high-throughput manner, it may be used to screen for highly specific protein-lipid interaction inhibitors. PMID:27025878
Sobsey, Constance A; Han, Jun; Lin, Karen; Swardfager, Walter; Levitt, Anthony; Borchers, Christoph H
2016-09-01
Malondialdhyde (MDA) is a commonly used marker of lipid peroxidation in oxidative stress. To provide a sensitive analytical method that is compatible with high throughput, we developed a multiple reaction monitoring-mass spectrometry (MRM-MS) approach using 3-nitrophenylhydrazine chemical derivatization, isotope-labeling, and liquid chromatography (LC) with electrospray ionization (ESI)-tandem mass spectrometry assay to accurately quantify MDA in human plasma. A stable isotope-labeled internal standard was used to compensate for ESI matrix effects. The assay is linear (R(2)=0.9999) over a 20,000-fold concentration range with a lower limit of quantitation of 30fmol (on-column). Intra- and inter-run coefficients of variation (CVs) were <2% and ∼10% respectively. The derivative was stable for >36h at 5°C. Standards spiked into plasma had recoveries of 92-98%. When compared to a common LC-UV method, the LC-MS method found near-identical MDA concentrations. A pilot project to quantify MDA in patient plasma samples (n=26) in a study of major depressive disorder with winter-type seasonal pattern (MDD-s) confirmed known associations between MDA concentrations and obesity (p<0.02). The LC-MS method provides high sensitivity and high reproducibility for quantifying MDA in human plasma. The simple sample preparation and rapid analysis time (5x faster than LC-UV) offers high throughput for large-scale clinical applications. PMID:27437618
NASA Astrophysics Data System (ADS)
Bravo, Jaime; Davis, Scott C.; Roberts, David W.; Paulsen, Keith D.; Kanick, Stephen C.
2015-03-01
Quantification of targeted fluorescence markers during neurosurgery has the potential to improve and standardize surgical distinction between normal and cancerous tissues. However, quantitative analysis of marker fluorescence is complicated by tissue background absorption and scattering properties. Correction algorithms that transform raw fluorescence intensity into quantitative units, independent of absorption and scattering, require a paired measurement of localized white light reflectance to provide estimates of the optical properties. This study focuses on the unique problem of developing a spectral analysis algorithm to extract tissue absorption and scattering properties from white light spectra that contain contributions from both elastically scattered photons and fluorescence emission from a strong fluorophore (i.e. fluorescein). A fiber-optic reflectance device was used to perform measurements in a small set of optical phantoms, constructed with Intralipid (1% lipid), whole blood (1% volume fraction) and fluorescein (0.16-10 μg/mL). Results show that the novel spectral analysis algorithm yields accurate estimates of tissue parameters independent of fluorescein concentration, with relative errors of blood volume fraction, blood oxygenation fraction (BOF), and the reduced scattering coefficient (at 521 nm) of <7%, <1%, and <22%, respectively. These data represent a first step towards quantification of fluorescein in tissue in vivo.
Toward Accurate and Quantitative Comparative Metagenomics.
Nayfach, Stephen; Pollard, Katherine S
2016-08-25
Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341
Accurate, meshless methods for magnetohydrodynamics
NASA Astrophysics Data System (ADS)
Hopkins, Philip F.; Raives, Matthias J.
2016-01-01
Recently, we explored new meshless finite-volume Lagrangian methods for hydrodynamics: the `meshless finite mass' (MFM) and `meshless finite volume' (MFV) methods; these capture advantages of both smoothed particle hydrodynamics (SPH) and adaptive mesh refinement (AMR) schemes. We extend these to include ideal magnetohydrodynamics (MHD). The MHD equations are second-order consistent and conservative. We augment these with a divergence-cleaning scheme, which maintains nabla \\cdot B≈ 0. We implement these in the code GIZMO, together with state-of-the-art SPH MHD. We consider a large test suite, and show that on all problems the new methods are competitive with AMR using constrained transport (CT) to ensure nabla \\cdot B=0. They correctly capture the growth/structure of the magnetorotational instability, MHD turbulence, and launching of magnetic jets, in some cases converging more rapidly than state-of-the-art AMR. Compared to SPH, the MFM/MFV methods exhibit convergence at fixed neighbour number, sharp shock-capturing, and dramatically reduced noise, divergence errors, and diffusion. Still, `modern' SPH can handle most test problems, at the cost of larger kernels and `by hand' adjustment of artificial diffusion. Compared to non-moving meshes, the new methods exhibit enhanced `grid noise' but reduced advection errors and diffusion, easily include self-gravity, and feature velocity-independent errors and superior angular momentum conservation. They converge more slowly on some problems (smooth, slow-moving flows), but more rapidly on others (involving advection/rotation). In all cases, we show divergence control beyond the Powell 8-wave approach is necessary, or all methods can converge to unphysical answers even at high resolution.
Groundtruth approach to accurate quantitation of fluorescence microarrays
Mascio-Kegelmeyer, L; Tomascik-Cheeseman, L; Burnett, M S; van Hummelen, P; Wyrobek, A J
2000-12-01
To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results significantly closer to the known ground-truth for these samples.
Cheong, Kit-Leong; Wu, Ding-Tao; Zhao, Jing; Li, Shao-Ping
2015-06-26
In this study, a rapid and accurate method for quantitative analysis of natural polysaccharides and their different fractions was developed. Firstly, high performance size exclusion chromatography (HPSEC) was utilized to separate natural polysaccharides. And then the molecular masses of their fractions were determined by multi-angle laser light scattering (MALLS). Finally, quantification of polysaccharides or their fractions was performed based on their response to refractive index detector (RID) and their universal refractive index increment (dn/dc). Accuracy of the developed method for the quantification of individual and mixed polysaccharide standards, including konjac glucomannan, CM-arabinan, xyloglucan, larch arabinogalactan, oat β-glucan, dextran (410, 270, and 25 kDa), mixed xyloglucan and CM-arabinan, and mixed dextran 270 K and CM-arabinan was determined, and their average recoveries were between 90.6% and 98.3%. The limits of detection (LOD) and quantification (LOQ) were ranging from 10.68 to 20.25 μg/mL, and 42.70 to 68.85 μg/mL, respectively. Comparing to the conventional phenol sulfuric acid assay and HPSEC coupled with evaporative light scattering detection (HPSEC-ELSD) analysis, the developed HPSEC-MALLS-RID method based on universal dn/dc for the quantification of polysaccharides and their fractions is much more simple, rapid, and accurate with no need of individual polysaccharide standard, as well as free of calibration curve. The developed method was also successfully utilized for quantitative analysis of polysaccharides and their different fractions from three medicinal plants of Panax genus, Panax ginseng, Panax notoginseng and Panax quinquefolius. The results suggested that the HPSEC-MALLS-RID method based on universal dn/dc could be used as a routine technique for the quantification of polysaccharides and their fractions in natural resources. PMID:25990349
Two highly accurate methods for pitch calibration
NASA Astrophysics Data System (ADS)
Kniel, K.; Härtig, F.; Osawa, S.; Sato, O.
2009-11-01
Among profiles, helix and tooth thickness pitch is one of the most important parameters of an involute gear measurement evaluation. In principle, coordinate measuring machines (CMM) and CNC-controlled gear measuring machines as a variant of a CMM are suited for these kinds of gear measurements. Now the Japan National Institute of Advanced Industrial Science and Technology (NMIJ/AIST) and the German national metrology institute the Physikalisch-Technische Bundesanstalt (PTB) have each developed independently highly accurate pitch calibration methods applicable to CMM or gear measuring machines. Both calibration methods are based on the so-called closure technique which allows the separation of the systematic errors of the measurement device and the errors of the gear. For the verification of both calibration methods, NMIJ/AIST and PTB performed measurements on a specially designed pitch artifact. The comparison of the results shows that both methods can be used for highly accurate calibrations of pitch standards.
Fast and Accurate Detection of Multiple Quantitative Trait Loci
Nettelblad, Carl; Holmgren, Sverker
2013-01-01
Abstract We present a new computational scheme that enables efficient and reliable quantitative trait loci (QTL) scans for experimental populations. Using a standard brute-force exhaustive search effectively prohibits accurate QTL scans involving more than two loci to be performed in practice, at least if permutation testing is used to determine significance. Some more elaborate global optimization approaches, for example, DIRECT have been adopted earlier to QTL search problems. Dramatic speedups have been reported for high-dimensional scans. However, since a heuristic termination criterion must be used in these types of algorithms, the accuracy of the optimization process cannot be guaranteed. Indeed, earlier results show that a small bias in the significance thresholds is sometimes introduced. Our new optimization scheme, PruneDIRECT, is based on an analysis leading to a computable (Lipschitz) bound on the slope of a transformed objective function. The bound is derived for both infinite- and finite-size populations. Introducing a Lipschitz bound in DIRECT leads to an algorithm related to classical Lipschitz optimization. Regions in the search space can be permanently excluded (pruned) during the optimization process. Heuristic termination criteria can thus be avoided. Hence, PruneDIRECT has a well-defined error bound and can in practice be guaranteed to be equivalent to a corresponding exhaustive search. We present simulation results that show that for simultaneous mapping of three QTLS using permutation testing, PruneDIRECT is typically more than 50 times faster than exhaustive search. The speedup is higher for stronger QTL. This could be used to quickly detect strong candidate eQTL networks. PMID:23919387
Accurate upwind methods for the Euler equations
NASA Technical Reports Server (NTRS)
Huynh, Hung T.
1993-01-01
A new class of piecewise linear methods for the numerical solution of the one-dimensional Euler equations of gas dynamics is presented. These methods are uniformly second-order accurate, and can be considered as extensions of Godunov's scheme. With an appropriate definition of monotonicity preservation for the case of linear convection, it can be shown that they preserve monotonicity. Similar to Van Leer's MUSCL scheme, they consist of two key steps: a reconstruction step followed by an upwind step. For the reconstruction step, a monotonicity constraint that preserves uniform second-order accuracy is introduced. Computational efficiency is enhanced by devising a criterion that detects the 'smooth' part of the data where the constraint is redundant. The concept and coding of the constraint are simplified by the use of the median function. A slope steepening technique, which has no effect at smooth regions and can resolve a contact discontinuity in four cells, is described. As for the upwind step, existing and new methods are applied in a manner slightly different from those in the literature. These methods are derived by approximating the Euler equations via linearization and diagonalization. At a 'smooth' interface, Harten, Lax, and Van Leer's one intermediate state model is employed. A modification for this model that can resolve contact discontinuities is presented. Near a discontinuity, either this modified model or a more accurate one, namely, Roe's flux-difference splitting. is used. The current presentation of Roe's method, via the conceptually simple flux-vector splitting, not only establishes a connection between the two splittings, but also leads to an admissibility correction with no conditional statement, and an efficient approximation to Osher's approximate Riemann solver. These reconstruction and upwind steps result in schemes that are uniformly second-order accurate and economical at smooth regions, and yield high resolution at discontinuities.
NASA Astrophysics Data System (ADS)
Contera, S.
2016-04-01
Multifrequency excitation/monitoring of cantilevers has made it possible both to achieve fast, relatively simple, nanometre-resolution quantitative mapping of mechanical of biological systems in solution using atomic force microscopy (AFM), and single molecule resolution detection by nanomechanical biosensors. A recent paper by Penedo et al [2015 Nanotechnology 26 485706] has made a significant contribution by developing simple methods to improve the signal to noise ratio in liquid environments, by selectively enhancing cantilever modes, which will lead to even more accurate quantitative measurements.
Practical aspects of spatially high accurate methods
NASA Technical Reports Server (NTRS)
Godfrey, Andrew G.; Mitchell, Curtis R.; Walters, Robert W.
1992-01-01
The computational qualities of high order spatially accurate methods for the finite volume solution of the Euler equations are presented. Two dimensional essentially non-oscillatory (ENO), k-exact, and 'dimension by dimension' ENO reconstruction operators are discussed and compared in terms of reconstruction and solution accuracy, computational cost and oscillatory behavior in supersonic flows with shocks. Inherent steady state convergence difficulties are demonstrated for adaptive stencil algorithms. An exact solution to the heat equation is used to determine reconstruction error, and the computational intensity is reflected in operation counts. Standard MUSCL differencing is included for comparison. Numerical experiments presented include the Ringleb flow for numerical accuracy and a shock reflection problem. A vortex-shock interaction demonstrates the ability of the ENO scheme to excel in simulating unsteady high-frequency flow physics.
Accurate paleointensities - the multi-method approach
NASA Astrophysics Data System (ADS)
de Groot, Lennart
2016-04-01
The accuracy of models describing rapid changes in the geomagnetic field over the past millennia critically depends on the availability of reliable paleointensity estimates. Over the past decade methods to derive paleointensities from lavas (the only recorder of the geomagnetic field that is available all over the globe and through geologic times) have seen significant improvements and various alternative techniques were proposed. The 'classical' Thellier-style approach was optimized and selection criteria were defined in the 'Standard Paleointensity Definitions' (Paterson et al, 2014). The Multispecimen approach was validated and the importance of additional tests and criteria to assess Multispecimen results must be emphasized. Recently, a non-heating, relative paleointensity technique was proposed -the pseudo-Thellier protocol- which shows great potential in both accuracy and efficiency, but currently lacks a solid theoretical underpinning. Here I present work using all three of the aforementioned paleointensity methods on suites of young lavas taken from the volcanic islands of Hawaii, La Palma, Gran Canaria, Tenerife, and Terceira. Many of the sampled cooling units are <100 years old, the actual field strength at the time of cooling is therefore reasonably well known. Rather intuitively, flows that produce coherent results from two or more different paleointensity methods yield the most accurate estimates of the paleofield. Furthermore, the results for some flows pass the selection criteria for one method, but fail in other techniques. Scrutinizing and combing all acceptable results yielded reliable paleointensity estimates for 60-70% of all sampled cooling units - an exceptionally high success rate. This 'multi-method paleointensity approach' therefore has high potential to provide the much-needed paleointensities to improve geomagnetic field models for the Holocene.
Accurate and molecular-size-tolerant NMR quantitation of diverse components in solution
Okamura, Hideyasu; Nishimura, Hiroshi; Nagata, Takashi; Kigawa, Takanori; Watanabe, Takashi; Katahira, Masato
2016-01-01
Determining the amount of each component of interest in a mixture is a fundamental first step in characterizing the nature of the solution and to develop possible means of utilization of its components. Similarly, determining the composition of units in complex polymers, or polymer mixtures, is crucial. Although NMR is recognized as one of the most powerful methods to achieve this and is widely used in many fields, variation in the molecular sizes or the relative mobilities of components skews quantitation due to the size-dependent decay of magnetization. Here, a method to accurately determine the amount of each component by NMR was developed. This method was validated using a solution that contains biomass-related components in which the molecular sizes greatly differ. The method is also tolerant of other factors that skew quantitation such as variation in the one-bond C–H coupling constant. The developed method is the first and only way to reliably overcome the skewed quantitation caused by several different factors to provide basic information on the correct amount of each component in a solution. PMID:26883279
Quantitation and accurate mass analysis of pesticides in vegetables by LC/TOF-MS.
Ferrer, Imma; Thurman, E Michael; Fernández-Alba, Amadeo R
2005-05-01
A quantitative method consisting of solvent extraction followed by liquid chromatography/time-of-flight mass spectrometry (LC/TOF-MS) analysis was developed for the identification and quantitation of three chloronicotinyl pesticides (imidacloprid, acetamiprid, thiacloprid) commonly used on salad vegetables. Accurate mass measurements within 3 ppm error were obtained for all the pesticides studied in various vegetable matrixes (cucumber, tomato, lettuce, pepper), which allowed an unequivocal identification of the target pesticides. Calibration curves covering 2 orders of magnitude were linear over the concentration range studied, thus showing the quantitative ability of TOF-MS as a monitoring tool for pesticides in vegetables. Matrix effects were also evaluated using matrix-matched standards showing no significant interferences between matrixes and clean extracts. Intraday reproducibility was 2-3% relative standard deviation (RSD) and interday values were 5% RSD. The precision (standard deviation) of the mass measurements was evaluated and it was less than 0.23 mDa between days. Detection limits of the chloronicotinyl insecticides in salad vegetables ranged from 0.002 to 0.01 mg/kg. These concentrations are equal to or better than the EU directives for controlled pesticides in vegetables showing that LC/TOF-MS analysis is a powerful tool for identification of pesticides in vegetables. Robustness and applicability of the method was validated for the analysis of market vegetable samples. Concentrations found in these samples were in the range of 0.02-0.17 mg/kg of vegetable. PMID:15859598
NASA Astrophysics Data System (ADS)
Kasaragod, Deepa; Sugiyama, Satoshi; Ikuno, Yasushi; Alonso-Caneiro, David; Yamanari, Masahiro; Fukuda, Shinichi; Oshika, Tetsuro; Hong, Young-Joo; Li, En; Makita, Shuichi; Miura, Masahiro; Yasuno, Yoshiaki
2016-03-01
Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that contrasts the polarization properties of tissues. It has been applied to ophthalmology, cardiology, etc. Proper quantitative imaging is required for a widespread clinical utility. However, the conventional method of averaging to improve the signal to noise ratio (SNR) and the contrast of the phase retardation (or birefringence) images introduce a noise bias offset from the true value. This bias reduces the effectiveness of birefringence contrast for a quantitative study. Although coherent averaging of Jones matrix tomography has been widely utilized and has improved the image quality, the fundamental limitation of nonlinear dependency of phase retardation and birefringence to the SNR was not overcome. So the birefringence obtained by PS-OCT was still not accurate for a quantitative imaging. The nonlinear effect of SNR to phase retardation and birefringence measurement was previously formulated in detail for a Jones matrix OCT (JM-OCT) [1]. Based on this, we had developed a maximum a-posteriori (MAP) estimator and quantitative birefringence imaging was demonstrated [2]. However, this first version of estimator had a theoretical shortcoming. It did not take into account the stochastic nature of SNR of OCT signal. In this paper, we present an improved version of the MAP estimator which takes into account the stochastic property of SNR. This estimator uses a probability distribution function (PDF) of true local retardation, which is proportional to birefringence, under a specific set of measurements of the birefringence and SNR. The PDF was pre-computed by a Monte-Carlo (MC) simulation based on the mathematical model of JM-OCT before the measurement. A comparison between this new MAP estimator, our previous MAP estimator [2], and the standard mean estimator is presented. The comparisons are performed both by numerical simulation and in vivo measurements of anterior and
NASA Astrophysics Data System (ADS)
Jenkins, Micah; Gaylord, Thomas K.
2015-03-01
Most quantitative phase microscopy methods require the use of custom-built or modified microscopic configurations which are not typically available to most bio/pathologists. There are, however, phase retrieval algorithms which utilize defocused bright-field images as input data and are therefore implementable in existing laboratory environments. Among these, deterministic methods such as those based on inverting the transport-of-intensity equation (TIE) or a phase contrast transfer function (PCTF) are particularly attractive due to their compatibility with Köhler illuminated systems and numerical simplicity. Recently, a new method has been proposed, called multi-filter phase imaging with partially coherent light (MFPI-PC), which alleviates the inherent noise/resolution trade-off in solving the TIE by utilizing a large number of defocused bright-field images spaced equally about the focal plane. Despite greatly improving the state-ofthe- art, the method has many shortcomings including the impracticality of high-speed acquisition, inefficient sampling, and attenuated response at high frequencies due to aperture effects. In this report, we present a new method, called bright-field quantitative phase microscopy (BFQPM), which efficiently utilizes a small number of defocused bright-field images and recovers frequencies out to the partially coherent diffraction limit. The method is based on a noiseminimized inversion of a PCTF derived for each finite defocus distance. We present simulation results which indicate nanoscale optical path length sensitivity and improved performance over MFPI-PC. We also provide experimental results imaging live bovine mesenchymal stem cells at sub-second temporal resolution. In all, BFQPM enables fast and accurate phase imaging with unprecedented spatial resolution using widely available bright-field microscopy hardware.
Sample normalization methods in quantitative metabolomics.
Wu, Yiman; Li, Liang
2016-01-22
To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. PMID:26763302
Sholder, Gabriel; Loechler, Edward L
2015-01-01
Quantitating relative (32)P-band intensity in gels is desired, e.g., to study primer-extension kinetics of DNA polymerases (DNAPs). Following imaging, multiple (32)P-bands are often present in lanes. Though individual bands appear by eye to be simple and well-resolved, scanning reveals they are actually skewed-Gaussian in shape and neighboring bands are overlapping, which complicates quantitation, because slower migrating bands often have considerable contributions from the trailing edges of faster migrating bands. A method is described to accurately quantitate adjacent (32)P-bands, which relies on having a standard: a simple skewed-Gaussian curve from an analogous pure, single-component band (e.g., primer alone). This single-component scan/curve is superimposed on its corresponding band in an experimentally determined scan/curve containing multiple bands (e.g., generated in a primer-extension reaction); intensity exceeding the single-component scan/curve is attributed to other components (e.g., insertion products). Relative areas/intensities are determined via pixel analysis, from which relative molarity of components is computed. Common software is used. Commonly used alternative methods (e.g., drawing boxes around bands) are shown to be less accurate. Our method was used to study kinetics of dNTP primer-extension opposite a benzo[a]pyrene-N(2)-dG-adduct with four DNAPs, including Sulfolobus solfataricus Dpo4 and Sulfolobus acidocaldarius Dbh. Vmax/Km is similar for correct dCTP insertion with Dpo4 and Dbh. Compared to Dpo4, Dbh misinsertion is slower for dATP (∼20-fold), dGTP (∼110-fold) and dTTP (∼6-fold), due to decreases in Vmax. These findings provide support that Dbh is in the same Y-Family DNAP class as eukaryotic DNAP κ and bacterial DNAP IV, which accurately bypass N(2)-dG adducts, as well as establish the scan-method described herein as an accurate method to quantitate relative intensity of overlapping bands in a single lane, whether generated
Foucault test: a quantitative evaluation method.
Rodríguez, Gustavo; Villa, Jesús; Ivanov, Rumen; González, Efrén; Martínez, Geminiano
2016-08-01
Reliable and accurate testing methods are essential to guiding the polishing process during the figuring of optical telescope mirrors. With the natural advancement of technology, the procedures and instruments used to carry out this delicate task have consistently increased in sensitivity, but also in complexity and cost. Fortunately, throughout history, the Foucault knife-edge test has shown the potential to measure transverse aberrations in the order of the wavelength, mainly when described in terms of physical theory, which allows a quantitative interpretation of its characteristic shadowmaps. Our previous publication on this topic derived a closed mathematical formulation that directly relates the knife-edge position with the observed irradiance pattern. The present work addresses the quite unexplored problem of the wavefront's gradient estimation from experimental captures of the test, which is achieved by means of an optimization algorithm featuring a proposed ad hoc cost function. The partial derivatives thereby calculated are then integrated by means of a Fourier-based algorithm to retrieve the mirror's actual surface profile. To date and to the best of our knowledge, this is the very first time that a complete mathematical-grounded treatment of this optical phenomenon is presented, complemented by an image-processing algorithm which allows a quantitative calculation of the corresponding slope at any given point of the mirror's surface, so that it becomes possible to accurately estimate the aberrations present in the analyzed concave device just through its associated foucaultgrams. PMID:27505659
Nicolotti, Orazio; Gillet, Valerie J; Fleming, Peter J; Green, Darren V S
2002-11-01
Deriving quantitative structure-activity relationship (QSAR) models that are accurate, reliable, and easily interpretable is a difficult task. In this study, two new methods have been developed that aim to find useful QSAR models that represent an appropriate balance between model accuracy and complexity. Both methods are based on genetic programming (GP). The first method, referred to as genetic QSAR (or GPQSAR), uses a penalty function to control model complexity. GPQSAR is designed to derive a single linear model that represents an appropriate balance between the variance and the number of descriptors selected for the model. The second method, referred to as multiobjective genetic QSAR (MoQSAR), is based on multiobjective GP and represents a new way of thinking of QSAR. Specifically, QSAR is considered as a multiobjective optimization problem that comprises a number of competitive objectives. Typical objectives include model fitting, the total number of terms, and the occurrence of nonlinear terms. MoQSAR results in a family of equivalent QSAR models where each QSAR represents a different tradeoff in the objectives. A practical consideration often overlooked in QSAR studies is the need for the model to promote an understanding of the biochemical response under investigation. To accomplish this, chemically intuitive descriptors are needed but do not always give rise to statistically robust models. This problem is addressed by the addition of a further objective, called chemical desirability, that aims to reward models that consist of descriptors that are easily interpretable by chemists. GPQSAR and MoQSAR have been tested on various data sets including the Selwood data set and two different solubility data sets. The study demonstrates that the MoQSAR method is able to find models that are at least as good as models derived using standard statistical approaches and also yields models that allow a medicinal chemist to trade statistical robustness for chemical
Accurate wavelength calibration method for flat-field grating spectrometers.
Du, Xuewei; Li, Chaoyang; Xu, Zhe; Wang, Qiuping
2011-09-01
A portable spectrometer prototype is built to study wavelength calibration for flat-field grating spectrometers. An accurate calibration method called parameter fitting is presented. Both optical and structural parameters of the spectrometer are included in the wavelength calibration model, which accurately describes the relationship between wavelength and pixel position. Along with higher calibration accuracy, the proposed calibration method can provide information about errors in the installation of the optical components, which will be helpful for spectrometer alignment. PMID:21929865
Differential equation based method for accurate approximations in optimization
NASA Technical Reports Server (NTRS)
Pritchard, Jocelyn I.; Adelman, Howard M.
1990-01-01
A method to efficiently and accurately approximate the effect of design changes on structural response is described. The key to this method is to interpret sensitivity equations as differential equations that may be solved explicitly for closed form approximations, hence, the method is denoted the Differential Equation Based (DEB) method. Approximations were developed for vibration frequencies, mode shapes and static displacements. The DEB approximation method was applied to a cantilever beam and results compared with the commonly-used linear Taylor series approximations and exact solutions. The test calculations involved perturbing the height, width, cross-sectional area, tip mass, and bending inertia of the beam. The DEB method proved to be very accurate, and in most cases, was more accurate than the linear Taylor series approximation. The method is applicable to simultaneous perturbation of several design variables. Also, the approximations may be used to calculate other system response quantities. For example, the approximations for displacements are used to approximate bending stresses.
Geng, Hua; Todd, Naomi M; Devlin-Mullin, Aine; Poologasundarampillai, Gowsihan; Kim, Taek Bo; Madi, Kamel; Cartmell, Sarah; Mitchell, Christopher A; Jones, Julian R; Lee, Peter D
2016-06-01
A correlative imaging methodology was developed to accurately quantify bone formation in the complex lattice structure of additive manufactured implants. Micro computed tomography (μCT) and histomorphometry were combined, integrating the best features from both, while demonstrating the limitations of each imaging modality. This semi-automatic methodology registered each modality using a coarse graining technique to speed the registration of 2D histology sections to high resolution 3D μCT datasets. Once registered, histomorphometric qualitative and quantitative bone descriptors were directly correlated to 3D quantitative bone descriptors, such as bone ingrowth and bone contact. The correlative imaging allowed the significant volumetric shrinkage of histology sections to be quantified for the first time (~15 %). This technique demonstrated the importance of location of the histological section, demonstrating that up to a 30 % offset can be introduced. The results were used to quantitatively demonstrate the effectiveness of 3D printed titanium lattice implants. PMID:27153828
Quantifying Methane Fluxes Simply and Accurately: The Tracer Dilution Method
NASA Astrophysics Data System (ADS)
Rella, Christopher; Crosson, Eric; Green, Roger; Hater, Gary; Dayton, Dave; Lafleur, Rick; Merrill, Ray; Tan, Sze; Thoma, Eben
2010-05-01
Methane is an important atmospheric constituent with a wide variety of sources, both natural and anthropogenic, including wetlands and other water bodies, permafrost, farms, landfills, and areas with significant petrochemical exploration, drilling, transport, or processing, or refining occurs. Despite its importance to the carbon cycle, its significant impact as a greenhouse gas, and its ubiquity in modern life as a source of energy, its sources and sinks in marine and terrestrial ecosystems are only poorly understood. This is largely because high quality, quantitative measurements of methane fluxes in these different environments have not been available, due both to the lack of robust field-deployable instrumentation as well as to the fact that most significant sources of methane extend over large areas (from 10's to 1,000,000's of square meters) and are heterogeneous emitters - i.e., the methane is not emitted evenly over the area in question. Quantifying the total methane emissions from such sources becomes a tremendous challenge, compounded by the fact that atmospheric transport from emission point to detection point can be highly variable. In this presentation we describe a robust, accurate, and easy-to-deploy technique called the tracer dilution method, in which a known gas (such as acetylene, nitrous oxide, or sulfur hexafluoride) is released in the same vicinity of the methane emissions. Measurements of methane and the tracer gas are then made downwind of the release point, in the so-called far-field, where the area of methane emissions cannot be distinguished from a point source (i.e., the two gas plumes are well-mixed). In this regime, the methane emissions are given by the ratio of the two measured concentrations, multiplied by the known tracer emission rate. The challenges associated with atmospheric variability and heterogeneous methane emissions are handled automatically by the transport and dispersion of the tracer. We present detailed methane flux
A Simple and Accurate Method for Measuring Enzyme Activity.
ERIC Educational Resources Information Center
Yip, Din-Yan
1997-01-01
Presents methods commonly used for investigating enzyme activity using catalase and presents a new method for measuring catalase activity that is more reliable and accurate. Provides results that are readily reproduced and quantified. Can also be used for investigations of enzyme properties such as the effects of temperature, pH, inhibitors,…
Quantifying Accurate Calorie Estimation Using the "Think Aloud" Method
ERIC Educational Resources Information Center
Holmstrup, Michael E.; Stearns-Bruening, Kay; Rozelle, Jeffrey
2013-01-01
Objective: Clients often have limited time in a nutrition education setting. An improved understanding of the strategies used to accurately estimate calories may help to identify areas of focused instruction to improve nutrition knowledge. Methods: A "Think Aloud" exercise was recorded during the estimation of calories in a standard dinner meal…
Differential equation based method for accurate approximations in optimization
NASA Technical Reports Server (NTRS)
Pritchard, Jocelyn I.; Adelman, Howard M.
1990-01-01
This paper describes a method to efficiently and accurately approximate the effect of design changes on structural response. The key to this new method is to interpret sensitivity equations as differential equations that may be solved explicitly for closed form approximations, hence, the method is denoted the Differential Equation Based (DEB) method. Approximations were developed for vibration frequencies, mode shapes and static displacements. The DEB approximation method was applied to a cantilever beam and results compared with the commonly-used linear Taylor series approximations and exact solutions. The test calculations involved perturbing the height, width, cross-sectional area, tip mass, and bending inertia of the beam. The DEB method proved to be very accurate, and in msot cases, was more accurate than the linear Taylor series approximation. The method is applicable to simultaneous perturbation of several design variables. Also, the approximations may be used to calculate other system response quantities. For example, the approximations for displacement are used to approximate bending stresses.
Accurate upwind-monotone (nonoscillatory) methods for conservation laws
NASA Technical Reports Server (NTRS)
Huynh, Hung T.
1992-01-01
The well known MUSCL scheme of Van Leer is constructed using a piecewise linear approximation. The MUSCL scheme is second order accurate at the smooth part of the solution except at extrema where the accuracy degenerates to first order due to the monotonicity constraint. To construct accurate schemes which are free from oscillations, the author introduces the concept of upwind monotonicity. Several classes of schemes, which are upwind monotone and of uniform second or third order accuracy are then presented. Results for advection with constant speed are shown. It is also shown that the new scheme compares favorably with state of the art methods.
Accurate Method for Determining Adhesion of Cantilever Beams
Michalske, T.A.; de Boer, M.P.
1999-01-08
Using surface micromachined samples, we demonstrate the accurate measurement of cantilever beam adhesion by using test structures which are adhered over long attachment lengths. We show that this configuration has a deep energy well, such that a fracture equilibrium is easily reached. When compared to the commonly used method of determining the shortest attached beam, the present method is much less sensitive to variations in surface topography or to details of capillary drying.
Accurate method for determining adhesion of cantilever beams
de Boer, M.P.; Michalske, T.A.
1999-07-01
Using surface micromachined samples, we demonstrate the accurate measurement of cantilever beam adhesion by using test structures which are adhered over long attachment lengths. We show that this configuration has a deep energy well, such that a fracture equilibrium is easily reached. When compared to the commonly used method of determining the shortest attached beam, the present method is much less sensitive to variations in surface topography or to details of capillary drying. {copyright} {ital 1999 American Institute of Physics.}
Mass Spectrometry Provides Accurate and Sensitive Quantitation of A2E
Gutierrez, Danielle B.; Blakeley, Lorie; Goletz, Patrice W.; Schey, Kevin L.; Hanneken, Anne; Koutalos, Yiannis; Crouch, Rosalie K.; Ablonczy, Zsolt
2010-01-01
Summary Orange autofluorescence from lipofuscin in the lysosomes of the retinal pigment epithelium (RPE) is a hallmark of aging in the eye. One of the major components of lipofuscin is A2E, the levels of which increase with age and in pathologic conditions, such as Stargardt disease or age-related macular degeneration. In vitro studies have suggested that A2E is highly phototoxic and, more specifically, that A2E and its oxidized derivatives contribute to RPE damage and subsequent photoreceptor cell death. To date, absorption spectroscopy has been the primary method to identify and quantitate A2E. Here, a new mass spectrometric method was developed for the specific detection of low levels of A2E and compared to a traditional method of analysis. The new mass spectrometry method allows the detection and quantitation of approximately 10,000-fold less A2E than absorption spectroscopy and the detection and quantitation of low levels of oxidized A2E, with localization of the oxidation sites. This study suggests that identification and quantitation of A2E from tissue extracts by chromatographic absorption spectroscopyoverestimates the amount of A2E. This mass spectrometry approach makes it possible to detect low levels of A2E and its oxidized metabolites with greater accuracy than traditional methods, thereby facilitating a more exact analysis of bis-retinoids in animal models of inherited retinal degeneration as well as in normal and diseased human eyes. PMID:20931136
Method for Accurately Calibrating a Spectrometer Using Broadband Light
NASA Technical Reports Server (NTRS)
Simmons, Stephen; Youngquist, Robert
2011-01-01
A novel method has been developed for performing very fine calibration of a spectrometer. This process is particularly useful for modern miniature charge-coupled device (CCD) spectrometers where a typical factory wavelength calibration has been performed and a finer, more accurate calibration is desired. Typically, the factory calibration is done with a spectral line source that generates light at known wavelengths, allowing specific pixels in the CCD array to be assigned wavelength values. This method is good to about 1 nm across the spectrometer s wavelength range. This new method appears to be accurate to about 0.1 nm, a factor of ten improvement. White light is passed through an unbalanced Michelson interferometer, producing an optical signal with significant spectral variation. A simple theory can be developed to describe this spectral pattern, so by comparing the actual spectrometer output against this predicted pattern, errors in the wavelength assignment made by the spectrometer can be determined.
Exploring accurate Poisson–Boltzmann methods for biomolecular simulations
Wang, Changhao; Wang, Jun; Cai, Qin; Li, Zhilin; Zhao, Hong-Kai; Luo, Ray
2013-01-01
Accurate and efficient treatment of electrostatics is a crucial step in computational analyses of biomolecular structures and dynamics. In this study, we have explored a second-order finite-difference numerical method to solve the widely used Poisson–Boltzmann equation for electrostatic analyses of realistic bio-molecules. The so-called immersed interface method was first validated and found to be consistent with the classical weighted harmonic averaging method for a diversified set of test biomolecules. The numerical accuracy and convergence behaviors of the new method were next analyzed in its computation of numerical reaction field grid potentials, energies, and atomic solvation forces. Overall similar convergence behaviors were observed as those by the classical method. Interestingly, the new method was found to deliver more accurate and better-converged grid potentials than the classical method on or nearby the molecular surface, though the numerical advantage of the new method is reduced when grid potentials are extrapolated to the molecular surface. Our exploratory study indicates the need for further improving interpolation/extrapolation schemes in addition to the developments of higher-order numerical methods that have attracted most attention in the field. PMID:24443709
Quantitative rotating frame relaxometry methods in MRI.
Gilani, Irtiza Ali; Sepponen, Raimo
2016-06-01
Macromolecular degeneration and biochemical changes in tissue can be quantified using rotating frame relaxometry in MRI. It has been shown in several studies that the rotating frame longitudinal relaxation rate constant (R1ρ ) and the rotating frame transverse relaxation rate constant (R2ρ ) are sensitive biomarkers of phenomena at the cellular level. In this comprehensive review, existing MRI methods for probing the biophysical mechanisms that affect the rotating frame relaxation rates of the tissue (i.e. R1ρ and R2ρ ) are presented. Long acquisition times and high radiofrequency (RF) energy deposition into tissue during the process of spin-locking in rotating frame relaxometry are the major barriers to the establishment of these relaxation contrasts at high magnetic fields. Therefore, clinical applications of R1ρ and R2ρ MRI using on- or off-resonance RF excitation methods remain challenging. Accordingly, this review describes the theoretical and experimental approaches to the design of hard RF pulse cluster- and adiabatic RF pulse-based excitation schemes for accurate and precise measurements of R1ρ and R2ρ . The merits and drawbacks of different MRI acquisition strategies for quantitative relaxation rate measurement in the rotating frame regime are reviewed. In addition, this review summarizes current clinical applications of rotating frame MRI sequences. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27100142
Striegel, André M
2013-11-01
There is a variety of small-molecule species (e.g., tackifiers, plasticizers, oligosaccharides) the size-based characterization of which is of considerable scientific and industrial importance. Likewise, quantitation of the amount of oligomers in a polymer sample is crucial for the import and export of substances into the USA and European Union (EU). While the characterization of ultra-high molar mass macromolecules by size-based separation techniques is generally considered a challenge, it is this author's contention that a greater challenge is encountered when trying to perform, for quantitation purposes, separations in and of the oligomeric region. The latter thesis is expounded herein, by detailing the various obstacles encountered en route to accurate, quantitative oligomeric separations by entropically dominated techniques such as size-exclusion chromatography, hydrodynamic chromatography, and asymmetric flow field-flow fractionation, as well as by methods which are, principally, enthalpically driven such as liquid adsorption and temperature gradient interaction chromatography. These obstacles include, among others, the diminished sensitivity of static light scattering (SLS) detection at low molar masses, the non-constancy of the response of SLS and of commonly employed concentration-sensitive detectors across the oligomeric region, and the loss of oligomers through the accumulation wall membrane in asymmetric flow field-flow fractionation. The battle is not lost, however, because, with some care and given a sufficient supply of sample, the quantitation of both individual oligomeric species and of the total oligomeric region is often possible. PMID:23887277
Accurate projector calibration method by using an optical coaxial camera.
Huang, Shujun; Xie, Lili; Wang, Zhangying; Zhang, Zonghua; Gao, Feng; Jiang, Xiangqian
2015-02-01
Digital light processing (DLP) projectors have been widely utilized to project digital structured-light patterns in 3D imaging systems. In order to obtain accurate 3D shape data, it is important to calibrate DLP projectors to obtain the internal parameters. The existing projector calibration methods have complicated procedures or low accuracy of the obtained parameters. This paper presents a novel method to accurately calibrate a DLP projector by using an optical coaxial camera. The optical coaxial geometry is realized by a plate beam splitter, so the DLP projector can be treated as a true inverse camera. A plate having discrete markers on the surface is used to calibrate the projector. The corresponding projector pixel coordinate of each marker on the plate is determined by projecting vertical and horizontal sinusoidal fringe patterns on the plate surface and calculating the absolute phase. The internal parameters of the DLP projector are obtained by the corresponding point pair between the projector pixel coordinate and the world coordinate of discrete markers. Experimental results show that the proposed method can accurately calibrate the internal parameters of a DLP projector. PMID:25967789
Reverse radiance: a fast accurate method for determining luminance
NASA Astrophysics Data System (ADS)
Moore, Kenneth E.; Rykowski, Ronald F.; Gangadhara, Sanjay
2012-10-01
Reverse ray tracing from a region of interest backward to the source has long been proposed as an efficient method of determining luminous flux. The idea is to trace rays only from where the final flux needs to be known back to the source, rather than tracing in the forward direction from the source outward to see where the light goes. Once the reverse ray reaches the source, the radiance the equivalent forward ray would have represented is determined and the resulting flux computed. Although reverse ray tracing is conceptually simple, the method critically depends upon an accurate source model in both the near and far field. An overly simplified source model, such as an ideal Lambertian surface substantially detracts from the accuracy and thus benefit of the method. This paper will introduce an improved method of reverse ray tracing that we call Reverse Radiance that avoids assumptions about the source properties. The new method uses measured data from a Source Imaging Goniometer (SIG) that simultaneously measures near and far field luminous data. Incorporating this data into a fast reverse ray tracing integration method yields fast, accurate data for a wide variety of illumination problems.
Accurate method of modeling cluster scaling relations in modified gravity
NASA Astrophysics Data System (ADS)
He, Jian-hua; Li, Baojiu
2016-06-01
We propose a new method to model cluster scaling relations in modified gravity. Using a suite of nonradiative hydrodynamical simulations, we show that the scaling relations of accumulated gas quantities, such as the Sunyaev-Zel'dovich effect (Compton-y parameter) and the x-ray Compton-y parameter, can be accurately predicted using the known results in the Λ CDM model with a precision of ˜3 % . This method provides a reliable way to analyze the gas physics in modified gravity using the less demanding and much more efficient pure cold dark matter simulations. Our results therefore have important theoretical and practical implications in constraining gravity using cluster surveys.
Quantitative Hydrocarbon Energies from the PMO Method.
ERIC Educational Resources Information Center
Cooper, Charles F.
1979-01-01
Details a procedure for accurately calculating the quantum mechanical energies of hydrocarbons using the perturbational molecular orbital (PMO) method, which does not require the use of a computer. (BT)
Accurate optical CD profiler based on specialized finite element method
NASA Astrophysics Data System (ADS)
Carrero, Jesus; Perçin, Gökhan
2012-03-01
As the semiconductor industry is moving to very low-k1 patterning solutions, the metrology problems facing process engineers are becoming much more complex. Choosing the right optical critical dimension (OCD) metrology technique is essential for bridging the metrology gap and achieving the required manufacturing volume throughput. The critical dimension scanning electron microscope (CD-SEM) measurement is usually distorted by the high aspect ratio of the photoresist and hard mask layers. CD-SEM measurements cease to correlate with complex three-dimensional profiles, such as the cases for double patterning and FinFETs, thus necessitating sophisticated, accurate and fast computational methods to bridge the gap. In this work, a suite of computational methods that complement advanced OCD equipment, and enabling them to operate at higher accuracies, are developed. In this article, a novel method for accurately modeling OCD profiles is presented. A finite element formulation in primal form is used to discretize the equations. The implementation uses specialized finite element spaces to solve Maxwell equations in two dimensions.
Novel dispersion tolerant interferometry method for accurate measurements of displacement
NASA Astrophysics Data System (ADS)
Bradu, Adrian; Maria, Michael; Leick, Lasse; Podoleanu, Adrian G.
2015-05-01
We demonstrate that the recently proposed master-slave interferometry method is able to provide true dispersion free depth profiles in a spectrometer-based set-up that can be used for accurate displacement measurements in sensing and optical coherence tomography. The proposed technique is based on correlating the channelled spectra produced by the linear camera in the spectrometer with previously recorded masks. As such technique is not based on Fourier transformations (FT), it does not require any resampling of data and is immune to any amounts of dispersion left unbalanced in the system. In order to prove the tolerance of technique to dispersion, different lengths of optical fiber are used in the interferometer to introduce dispersion and it is demonstrated that neither the sensitivity profile versus optical path difference (OPD) nor the depth resolution are affected. In opposition, it is shown that the classical FT based methods using calibrated data provide less accurate optical path length measurements and exhibit a quicker decays of sensitivity with OPD.
Accurate camera calibration method specialized for virtual studios
NASA Astrophysics Data System (ADS)
Okubo, Hidehiko; Yamanouchi, Yuko; Mitsumine, Hideki; Fukaya, Takashi; Inoue, Seiki
2008-02-01
Virtual studio is a popular technology for TV programs, that makes possible to synchronize computer graphics (CG) to realshot image in camera motion. Normally, the geometrical matching accuracy between CG and realshot image is not expected so much on real-time system, we sometimes compromise on directions, not to come out the problem. So we developed the hybrid camera calibration method and CG generating system to achieve the accurate geometrical matching of CG and realshot on virtual studio. Our calibration method is intended for the camera system on platform and tripod with rotary encoder, that can measure pan/tilt angles. To solve the camera model and initial pose, we enhanced the bundle adjustment algorithm to fit the camera model, using pan/tilt data as known parameters, and optimizing all other parameters invariant against pan/tilt value. This initialization yields high accurate camera position and orientation consistent with any pan/tilt values. Also we created CG generator implemented the lens distortion function with GPU programming. By applying the lens distortion parameters obtained by camera calibration process, we could get fair compositing results.
Hilbert, David W; Smith, William L; Chadwick, Sean G; Toner, Geoffrey; Mordechai, Eli; Adelson, Martin E; Aguin, Tina J; Sobel, Jack D; Gygax, Scott E
2016-04-01
Bacterial vaginosis (BV) is the most common gynecological infection in the United States. Diagnosis based on Amsel's criteria can be challenging and can be aided by laboratory-based testing. A standard method for diagnosis in research studies is enumeration of bacterial morphotypes of a Gram-stained vaginal smear (i.e., Nugent scoring). However, this technique is subjective, requires specialized training, and is not widely available. Therefore, a highly accurate molecular assay for the diagnosis of BV would be of great utility. We analyzed 385 vaginal specimens collected prospectively from subjects who were evaluated for BV by clinical signs and Nugent scoring. We analyzed quantitative real-time PCR (qPCR) assays on DNA extracted from these specimens to quantify nine organisms associated with vaginal health or disease:Gardnerella vaginalis,Atopobium vaginae, BV-associated bacteria 2 (BVAB2, an uncultured member of the orderClostridiales),Megasphaeraphylotype 1 or 2,Lactobacillus iners,Lactobacillus crispatus,Lactobacillus gasseri, andLactobacillus jensenii We generated a logistic regression model that identifiedG. vaginalis,A. vaginae, andMegasphaeraphylotypes 1 and 2 as the organisms for which quantification provided the most accurate diagnosis of symptomatic BV, as defined by Amsel's criteria and Nugent scoring, with 92% sensitivity, 95% specificity, 94% positive predictive value, and 94% negative predictive value. The inclusion ofLactobacillusspp. did not contribute sufficiently to the quantitative model for symptomatic BV detection. This molecular assay is a highly accurate laboratory tool to assist in the diagnosis of symptomatic BV. PMID:26818677
Danshita, Ippei; Polkovnikov, Anatoli
2010-09-01
We study the quantum dynamics of supercurrents of one-dimensional Bose gases in a ring optical lattice to verify instanton methods applied to coherent macroscopic quantum tunneling (MQT). We directly simulate the real-time quantum dynamics of supercurrents, where a coherent oscillation between two macroscopically distinct current states occurs due to MQT. The tunneling rate extracted from the coherent oscillation is compared with that given by the instanton method. We find that the instanton method is quantitatively accurate when the effective Planck's constant is sufficiently small. We also find phase slips associated with the oscillations.
Accurate finite difference methods for time-harmonic wave propagation
NASA Technical Reports Server (NTRS)
Harari, Isaac; Turkel, Eli
1994-01-01
Finite difference methods for solving problems of time-harmonic acoustics are developed and analyzed. Multidimensional inhomogeneous problems with variable, possibly discontinuous, coefficients are considered, accounting for the effects of employing nonuniform grids. A weighted-average representation is less sensitive to transition in wave resolution (due to variable wave numbers or nonuniform grids) than the standard pointwise representation. Further enhancement in method performance is obtained by basing the stencils on generalizations of Pade approximation, or generalized definitions of the derivative, reducing spurious dispersion, anisotropy and reflection, and by improving the representation of source terms. The resulting schemes have fourth-order accurate local truncation error on uniform grids and third order in the nonuniform case. Guidelines for discretization pertaining to grid orientation and resolution are presented.
An Accurate Projector Calibration Method Based on Polynomial Distortion Representation
Liu, Miao; Sun, Changku; Huang, Shujun; Zhang, Zonghua
2015-01-01
In structure light measurement systems or 3D printing systems, the errors caused by optical distortion of a digital projector always affect the precision performance and cannot be ignored. Existing methods to calibrate the projection distortion rely on calibration plate and photogrammetry, so the calibration performance is largely affected by the quality of the plate and the imaging system. This paper proposes a new projector calibration approach that makes use of photodiodes to directly detect the light emitted from a digital projector. By analyzing the output sequence of the photoelectric module, the pixel coordinates can be accurately obtained by the curve fitting method. A polynomial distortion representation is employed to reduce the residuals of the traditional distortion representation model. Experimental results and performance evaluation show that the proposed calibration method is able to avoid most of the disadvantages in traditional methods and achieves a higher accuracy. This proposed method is also practically applicable to evaluate the geometric optical performance of other optical projection system. PMID:26492247
Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency
NASA Astrophysics Data System (ADS)
Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao
2008-05-01
Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.
Quantitative Methods in Psychology: Inevitable and Useless
Toomela, Aaro
2010-01-01
Science begins with the question, what do I want to know? Science becomes science, however, only when this question is justified and the appropriate methodology is chosen for answering the research question. Research question should precede the other questions; methods should be chosen according to the research question and not vice versa. Modern quantitative psychology has accepted method as primary; research questions are adjusted to the methods. For understanding thinking in modern quantitative psychology, two epistemologies should be distinguished: structural-systemic that is based on Aristotelian thinking, and associative-quantitative that is based on Cartesian–Humean thinking. The first aims at understanding the structure that underlies the studied processes; the second looks for identification of cause–effect relationships between the events with no possible access to the understanding of the structures that underlie the processes. Quantitative methodology in particular as well as mathematical psychology in general, is useless for answering questions about structures and processes that underlie observed behaviors. Nevertheless, quantitative science is almost inevitable in a situation where the systemic-structural basis of behavior is not well understood; all sorts of applied decisions can be made on the basis of quantitative studies. In order to proceed, psychology should study structures; methodologically, constructive experiments should be added to observations and analytic experiments. PMID:21833199
An Integrative Method for Accurate Comparative Genome Mapping
Swidan, Firas; Rocha, Eduardo P. C; Shmoish, Michael; Pinter, Ron Y
2006-01-01
We present MAGIC, an integrative and accurate method for comparative genome mapping. Our method consists of two phases: preprocessing for identifying “maximal similar segments,” and mapping for clustering and classifying these segments. MAGIC's main novelty lies in its biologically intuitive clustering approach, which aims towards both calculating reorder-free segments and identifying orthologous segments. In the process, MAGIC efficiently handles ambiguities resulting from duplications that occurred before the speciation of the considered organisms from their most recent common ancestor. We demonstrate both MAGIC's robustness and scalability: the former is asserted with respect to its initial input and with respect to its parameters' values. The latter is asserted by applying MAGIC to distantly related organisms and to large genomes. We compare MAGIC to other comparative mapping methods and provide detailed analysis of the differences between them. Our improvements allow a comprehensive study of the diversity of genetic repertoires resulting from large-scale mutations, such as indels and duplications, including explicitly transposable and phagic elements. The strength of our method is demonstrated by detailed statistics computed for each type of these large-scale mutations. MAGIC enabled us to conduct a comprehensive analysis of the different forces shaping prokaryotic genomes from different clades, and to quantify the importance of novel gene content introduced by horizontal gene transfer relative to gene duplication in bacterial genome evolution. We use these results to investigate the breakpoint distribution in several prokaryotic genomes. PMID:16933978
IRIS: Towards an Accurate and Fast Stage Weight Prediction Method
NASA Astrophysics Data System (ADS)
Taponier, V.; Balu, A.
2002-01-01
The knowledge of the structural mass fraction (or the mass ratio) of a given stage, which affects the performance of a rocket, is essential for the analysis of new or upgraded launchers or stages, whose need is increased by the quick evolution of the space programs and by the necessity of their adaptation to the market needs. The availability of this highly scattered variable, ranging between 0.05 and 0.15, is of primary importance at the early steps of the preliminary design studies. At the start of the staging and performance studies, the lack of frozen weight data (to be obtained later on from propulsion, trajectory and sizing studies) leads to rely on rough estimates, generally derived from printed sources and adapted. When needed, a consolidation can be acquired trough a specific analysis activity involving several techniques and implying additional effort and time. The present empirical approach allows thus to get approximated values (i.e. not necessarily accurate or consistent), inducing some result inaccuracy as well as, consequently, difficulties of performance ranking for a multiple option analysis, and an increase of the processing duration. This forms a classical harsh fact of the preliminary design system studies, insufficiently discussed to date. It appears therefore highly desirable to have, for all the evaluation activities, a reliable, fast and easy-to-use weight or mass fraction prediction method. Additionally, the latter should allow for a pre selection of the alternative preliminary configurations, making possible a global system approach. For that purpose, an attempt at modeling has been undertaken, whose objective was the determination of a parametric formulation of the mass fraction, to be expressed from a limited number of parameters available at the early steps of the project. It is based on the innovative use of a statistical method applicable to a variable as a function of several independent parameters. A specific polynomial generator
NMR method for accurate quantification of polysorbate 80 copolymer composition.
Zhang, Qi; Wang, Aifa; Meng, Yang; Ning, Tingting; Yang, Huaxin; Ding, Lixia; Xiao, Xinyue; Li, Xiaodong
2015-10-01
(13)C NMR spectroscopic integration employing short relaxation delays and a 30° pulse width was evaluated as a quantitative tool for analyzing the components of polysorbate 80. (13)C NMR analysis revealed that commercial polysorbate 80 formulations are a complex oligomeric mixture of sorbitan polyethoxylate esters and other intermediates, such as isosorbide polyethoxylate esters and poly(ethylene glycol) (PEG) esters. This novel approach facilitates the quantification of the component ratios. In this study, the ratios of the three major oligomers in polysorbate 80 were measured and the PEG series was found to be the major component of commercial polysorbate 80. The degree of polymerization of -CH2CH2O- groups and the ratio of free to bonded -CH2CH2O- end groups, which correlate with the hydrophilic/hydrophobic nature of the polymer, were analyzed, and were suggested to be key factors for assessing the likelihood of adverse biological reactions to polysorbate 80. The (13)C NMR data suggest that the feed ratio of raw materials and reaction conditions in the production of polysorbate 80 are not well controlled. Our results demonstrate that (13)C NMR is a universal, powerful tool for polysorbate analysis. Such analysis is crucial for the synthesis of a high-quality product, and is difficult to obtain by other methods. PMID:26356097
Electric Field Quantitative Measurement System and Method
NASA Technical Reports Server (NTRS)
Generazio, Edward R. (Inventor)
2016-01-01
A method and system are provided for making a quantitative measurement of an electric field. A plurality of antennas separated from one another by known distances are arrayed in a region that extends in at least one dimension. A voltage difference between at least one selected pair of antennas is measured. Each voltage difference is divided by the known distance associated with the selected pair of antennas corresponding thereto to generate a resulting quantity. The plurality of resulting quantities defined over the region quantitatively describe an electric field therein.
Method and apparatus for chromatographic quantitative analysis
Fritz, James S.; Gjerde, Douglas T.; Schmuckler, Gabriella
1981-06-09
An improved apparatus and method for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single eluent and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.
Allele-Specific Quantitative PCR for Accurate, Rapid, and Cost-Effective Genotyping.
Lee, Han B; Schwab, Tanya L; Koleilat, Alaa; Ata, Hirotaka; Daby, Camden L; Cervera, Roberto Lopez; McNulty, Melissa S; Bostwick, Hannah S; Clark, Karl J
2016-06-01
Customizable endonucleases such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) enable rapid generation of mutant strains at genomic loci of interest in animal models and cell lines. With the accelerated pace of generating mutant alleles, genotyping has become a rate-limiting step to understanding the effects of genetic perturbation. Unless mutated alleles result in distinct morphological phenotypes, mutant strains need to be genotyped using standard methods in molecular biology. Classic restriction fragment length polymorphism (RFLP) or sequencing is labor-intensive and expensive. Although simpler than RFLP, current versions of allele-specific PCR may still require post-polymerase chain reaction (PCR) handling such as sequencing, or they are more expensive if allele-specific fluorescent probes are used. Commercial genotyping solutions can take weeks from assay design to result, and are often more expensive than assembling reactions in-house. Key components of commercial assay systems are often proprietary, which limits further customization. Therefore, we developed a one-step open-source genotyping method based on quantitative PCR. The allele-specific qPCR (ASQ) does not require post-PCR processing and can genotype germline mutants through either threshold cycle (Ct) or end-point fluorescence reading. ASQ utilizes allele-specific primers, a locus-specific reverse primer, universal fluorescent probes and quenchers, and hot start DNA polymerase. Individual laboratories can further optimize this open-source system as we completely disclose the sequences, reagents, and thermal cycling protocol. We have tested the ASQ protocol to genotype alleles in five different genes. ASQ showed a 98-100% concordance in genotype scoring with RFLP or Sanger sequencing outcomes. ASQ is time-saving because a single qPCR without post-PCR handling suffices to score
Allele-Specific Quantitative PCR for Accurate, Rapid, and Cost-Effective Genotyping
Lee, Han B.; Schwab, Tanya L.; Koleilat, Alaa; Ata, Hirotaka; Daby, Camden L.; Cervera, Roberto Lopez; McNulty, Melissa S.; Bostwick, Hannah S.; Clark, Karl J.
2016-01-01
Customizable endonucleases such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) enable rapid generation of mutant strains at genomic loci of interest in animal models and cell lines. With the accelerated pace of generating mutant alleles, genotyping has become a rate-limiting step to understanding the effects of genetic perturbation. Unless mutated alleles result in distinct morphological phenotypes, mutant strains need to be genotyped using standard methods in molecular biology. Classic restriction fragment length polymorphism (RFLP) or sequencing is labor-intensive and expensive. Although simpler than RFLP, current versions of allele-specific PCR may still require post-polymerase chain reaction (PCR) handling such as sequencing, or they are more expensive if allele-specific fluorescent probes are used. Commercial genotyping solutions can take weeks from assay design to result, and are often more expensive than assembling reactions in-house. Key components of commercial assay systems are often proprietary, which limits further customization. Therefore, we developed a one-step open-source genotyping method based on quantitative PCR. The allele-specific qPCR (ASQ) does not require post-PCR processing and can genotype germline mutants through either threshold cycle (Ct) or end-point fluorescence reading. ASQ utilizes allele-specific primers, a locus-specific reverse primer, universal fluorescent probes and quenchers, and hot start DNA polymerase. Individual laboratories can further optimize this open-source system as we completely disclose the sequences, reagents, and thermal cycling protocol. We have tested the ASQ protocol to genotype alleles in five different genes. ASQ showed a 98–100% concordance in genotype scoring with RFLP or Sanger sequencing outcomes. ASQ is time-saving because a single qPCR without post-PCR handling suffices to score
Goldoni, Luca; Beringhelli, Tiziana; Rocchia, Walter; Realini, Natalia; Piomelli, Daniele
2016-05-15
Absolute analyte quantification by nuclear magnetic resonance (NMR) spectroscopy is rarely pursued in metabolomics, even though this would allow researchers to compare results obtained using different techniques. Here we report on a new protocol that permits, after pH-controlled serum protein removal, the sensitive quantification (limit of detection [LOD] = 5-25 μM) of hydrophilic nutrients and metabolites in the extracellular medium of cells in cultures. The method does not require the use of databases and uses PULCON (pulse length-based concentration determination) quantitative NMR to obtain results that are significantly more accurate and reproducible than those obtained by CPMG (Carr-Purcell-Meiboom-Gill) sequence or post-processing filtering approaches. Three practical applications of the method highlight its flexibility under different cell culture conditions. We identified and quantified (i) metabolic differences between genetically engineered human cell lines, (ii) alterations in cellular metabolism induced by differentiation of mouse myoblasts into myotubes, and (iii) metabolic changes caused by activation of neurotransmitter receptors in mouse myoblasts. Thus, the new protocol offers an easily implementable, efficient, and versatile tool for the investigation of cellular metabolism and signal transduction. PMID:26898303
Quantitative Method of Measuring Metastatic Activity
NASA Technical Reports Server (NTRS)
Morrison, Dennis R. (Inventor)
1999-01-01
The metastatic potential of tumors can be evaluated by the quantitative detection of urokinase and DNA. The cell sample selected for examination is analyzed for the presence of high levels of urokinase and abnormal DNA using analytical flow cytometry and digital image analysis. Other factors such as membrane associated uroldnase, increased DNA synthesis rates and certain receptors can be used in the method for detection of potentially invasive tumors.
Zapata, Julián; Mateo-Vivaracho, Laura; Lopez, Ricardo; Ferreira, Vicente
2012-03-23
An automatic headspace in-tube extraction (ITEX) method for the accurate determination of acetaldehyde, ethyl acetate, diacetyl and other volatile compounds from wine and beer has been developed and validated. Method accuracy is based on the nearly quantitative transference of volatile compounds from the sample to the ITEX trap. For achieving that goal most methodological aspects and parameters have been carefully examined. The vial and sample sizes and the trapping materials were found to be critical due to the pernicious saturation effects of ethanol. Small 2 mL vials containing very small amounts of sample (20 μL of 1:10 diluted sample) and a trap filled with 22 mg of Bond Elut ENV resins could guarantee a complete trapping of sample vapors. The complete extraction requires 100 × 0.5 mL pumping strokes at 60 °C and takes 24 min. Analytes are further desorbed at 240 °C into the GC injector under a 1:5 split ratio. The proportion of analytes finally transferred to the trap ranged from 85 to 99%. The validation of the method showed satisfactory figures of merit. Determination coefficients were better than 0.995 in all cases and good repeatability was also obtained (better than 7% in all cases). Reproducibility was better than 8.3% except for acetaldehyde (13.1%). Detection limits were below the odor detection thresholds of these target compounds in wine and beer and well below the normal ranges of occurrence. Recoveries were not significantly different to 100%, except in the case of acetaldehyde. In such a case it could be determined that the method is not able to break some of the adducts that this compound forms with sulfites. However, such problem was avoided after incubating the sample with glyoxal. The method can constitute a general and reliable alternative for the analysis of very volatile compounds in other difficult matrixes. PMID:22340891
A method for producing large, accurate, economical female molds
Guenter, A.; Guenter, B.
1996-11-01
A process in which lightweight, highly accurate, economical molds can be produced for prototype and low production runs of large parts for use in composites molding has been developed. This has been achieved by developing existing milling technology, using new materials and innovative material applications to CNC mill large female molds directly. Any step that can be eliminated in the mold building process translates into savings in tooling costs through reduced labor and material requirements.
Method and apparatus for accurately manipulating an object during microelectrophoresis
Parvin, Bahram A.; Maestre, Marcos F.; Fish, Richard H.; Johnston, William E.
1997-01-01
An apparatus using electrophoresis provides accurate manipulation of an object on a microscope stage for further manipulations add reactions. The present invention also provides an inexpensive and easily accessible means to move an object without damage to the object. A plurality of electrodes are coupled to the stage in an array whereby the electrode array allows for distinct manipulations of the electric field for accurate manipulations of the object. There is an electrode array control coupled to the plurality of electrodes for manipulating the electric field. In an alternative embodiment, a chamber is provided on the stage to hold the object. The plurality of electrodes are positioned in the chamber, and the chamber is filled with fluid. The system can be automated using visual servoing, which manipulates the control parameters, i.e., x, y stage, applying the field, etc., after extracting the significant features directly from image data. Visual servoing includes an imaging device and computer system to determine the location of the object. A second stage having a plurality of tubes positioned on top of the second stage, can be accurately positioned by visual servoing so that one end of one of the plurality of tubes surrounds at least part of the object on the first stage.
Method and apparatus for accurately manipulating an object during microelectrophoresis
Parvin, B.A.; Maestre, M.F.; Fish, R.H.; Johnston, W.E.
1997-09-23
An apparatus using electrophoresis provides accurate manipulation of an object on a microscope stage for further manipulations and reactions. The present invention also provides an inexpensive and easily accessible means to move an object without damage to the object. A plurality of electrodes are coupled to the stage in an array whereby the electrode array allows for distinct manipulations of the electric field for accurate manipulations of the object. There is an electrode array control coupled to the plurality of electrodes for manipulating the electric field. In an alternative embodiment, a chamber is provided on the stage to hold the object. The plurality of electrodes are positioned in the chamber, and the chamber is filled with fluid. The system can be automated using visual servoing, which manipulates the control parameters, i.e., x, y stage, applying the field, etc., after extracting the significant features directly from image data. Visual servoing includes an imaging device and computer system to determine the location of the object. A second stage having a plurality of tubes positioned on top of the second stage, can be accurately positioned by visual servoing so that one end of one of the plurality of tubes surrounds at least part of the object on the first stage. 11 figs.
Accurate, Fast and Cost-Effective Diagnostic Test for Monosomy 1p36 Using Real-Time Quantitative PCR
Cunha, Pricila da Silva; Pena, Heloisa B.; D'Angelo, Carla Sustek; Koiffmann, Celia P.; Rosenfeld, Jill A.; Shaffer, Lisa G.; Stofanko, Martin; Gonçalves-Dornelas, Higgor; Pena, Sérgio Danilo Junho
2014-01-01
Monosomy 1p36 is considered the most common subtelomeric deletion syndrome in humans and it accounts for 0.5–0.7% of all the cases of idiopathic intellectual disability. The molecular diagnosis is often made by microarray-based comparative genomic hybridization (aCGH), which has the drawback of being a high-cost technique. However, patients with classic monosomy 1p36 share some typical clinical characteristics that, together with its common prevalence, justify the development of a less expensive, targeted diagnostic method. In this study, we developed a simple, rapid, and inexpensive real-time quantitative PCR (qPCR) assay for targeted diagnosis of monosomy 1p36, easily accessible for low-budget laboratories in developing countries. For this, we have chosen two target genes which are deleted in the majority of patients with monosomy 1p36: PRKCZ and SKI. In total, 39 patients previously diagnosed with monosomy 1p36 by aCGH, fluorescent in situ hybridization (FISH), and/or multiplex ligation-dependent probe amplification (MLPA) all tested positive on our qPCR assay. By simultaneously using these two genes we have been able to detect 1p36 deletions with 100% sensitivity and 100% specificity. We conclude that qPCR of PRKCZ and SKI is a fast and accurate diagnostic test for monosomy 1p36, costing less than 10 US dollars in reagent costs. PMID:24839341
RAId_DbS: Method for Peptide ID using Database Search with Accurate Statistics
NASA Astrophysics Data System (ADS)
Alves, Gelio; Ogurtsov, Aleksey; Yu, Yi-Kuo
2007-03-01
The key to proteomics studies, essential in systems biology, is peptide identification. Under tandem mass spectrometry, each spectrum generated consists of a list of mass/charge peaks along with their intensities. Software analysis is then required to identify from the spectrum peptide candidates that best interpret the spectrum. The library search, which compares the spectral peaks against theoretical peaks generated by each peptide in a library, is among the most popular methods. This method, although robust, lacks good quantitative statistical underpinning. As we show, many library search algorithms suffer from statistical instability. The need for a better statistical basis prompted us to develop RAId_DbS. Taking into account the skewness in the peak intensity distribution while scoring peptides, RAId_DbS provides an accurate statistical significance assignment to each peptide candidate. RAId_DbS will be a valuable tool especially when one intends to identify proteins through peptide identifications.
A more accurate method for measurement of tuberculocidal activity of disinfectants.
Ascenzi, J M; Ezzell, R J; Wendt, T M
1987-01-01
The current Association of Official Analytical Chemists method for testing tuberculocidal activity of disinfectants has been shown to be inaccurate and to have a high degree of variability. An alternate test method is proposed which is more accurate, more precise, and quantitative. A suspension of Mycobacterium bovis BCG was exposed to a variety of disinfectant chemicals and a kill curve was constructed from quantitative data. Data are presented that show the discrepancy between current claims, determined by the Association of Official Analytical Chemists method, of selected commercially available products and claims generated by the proposed method. The effects of different recovery media were examined. The data indicated that Mycobacteria 7H11 and Middlebrook 7H10 agars were equal in recovery of the different chemically treated cells, with Lowenstein-Jensen agar having approximately the same recovery rate but requiring incubation for up to 3 weeks longer for countability. The kill curves generated for several different chemicals were reproducible, as indicated by the standard deviations of the slopes and intercepts of the linear regression curves. PMID:3314707
The development of accurate and efficient methods of numerical quadrature
NASA Technical Reports Server (NTRS)
Feagin, T.
1973-01-01
Some new methods for performing numerical quadrature of an integrable function over a finite interval are described. Each method provides a sequence of approximations of increasing order to the value of the integral. Each approximation makes use of all previously computed values of the integrand. The points at which new values of the integrand are computed are selected in such a way that the order of the approximation is maximized. The methods are compared with the quadrature methods of Clenshaw and Curtis, Gauss, Patterson, and Romberg using several examples.
Method accurately measures mean particle diameters of monodisperse polystyrene latexes
NASA Technical Reports Server (NTRS)
Kubitschek, H. E.
1967-01-01
Photomicrographic method determines mean particle diameters of monodisperse polystyrene latexes. Many diameters are measured simultaneously by measuring row lengths of particles in a triangular array at a glass-oil interface. The method provides size standards for electronic particle counters and prevents distortions, softening, and flattening.
Construction of higher order accurate vortex and particle methods
NASA Technical Reports Server (NTRS)
Nicolaides, R. A.
1986-01-01
The standard point vortex method has recently been shown to be of high order of accuracy for problems on the whole plane, when using a uniform initial subdivision for assigning the vorticity to the points. If obstacles are present in the flow, this high order deteriorates to first or second order. New vortex methods are introduced which are of arbitrary accuracy (under regularity assumptions) regardless of the presence of bodies and the uniformity of the initial subdivision.
Quantitative statistical methods for image quality assessment.
Dutta, Joyita; Ahn, Sangtae; Li, Quanzheng
2013-01-01
Quantitative measures of image quality and reliability are critical for both qualitative interpretation and quantitative analysis of medical images. While, in theory, it is possible to analyze reconstructed images by means of Monte Carlo simulations using a large number of noise realizations, the associated computational burden makes this approach impractical. Additionally, this approach is less meaningful in clinical scenarios, where multiple noise realizations are generally unavailable. The practical alternative is to compute closed-form analytical expressions for image quality measures. The objective of this paper is to review statistical analysis techniques that enable us to compute two key metrics: resolution (determined from the local impulse response) and covariance. The underlying methods include fixed-point approaches, which compute these metrics at a fixed point (the unique and stable solution) independent of the iterative algorithm employed, and iteration-based approaches, which yield results that are dependent on the algorithm, initialization, and number of iterations. We also explore extensions of some of these methods to a range of special contexts, including dynamic and motion-compensated image reconstruction. While most of the discussed techniques were developed for emission tomography, the general methods are extensible to other imaging modalities as well. In addition to enabling image characterization, these analysis techniques allow us to control and enhance imaging system performance. We review practical applications where performance improvement is achieved by applying these ideas to the contexts of both hardware (optimizing scanner design) and image reconstruction (designing regularization functions that produce uniform resolution or maximize task-specific figures of merit). PMID:24312148
Quantitative Statistical Methods for Image Quality Assessment
Dutta, Joyita; Ahn, Sangtae; Li, Quanzheng
2013-01-01
Quantitative measures of image quality and reliability are critical for both qualitative interpretation and quantitative analysis of medical images. While, in theory, it is possible to analyze reconstructed images by means of Monte Carlo simulations using a large number of noise realizations, the associated computational burden makes this approach impractical. Additionally, this approach is less meaningful in clinical scenarios, where multiple noise realizations are generally unavailable. The practical alternative is to compute closed-form analytical expressions for image quality measures. The objective of this paper is to review statistical analysis techniques that enable us to compute two key metrics: resolution (determined from the local impulse response) and covariance. The underlying methods include fixed-point approaches, which compute these metrics at a fixed point (the unique and stable solution) independent of the iterative algorithm employed, and iteration-based approaches, which yield results that are dependent on the algorithm, initialization, and number of iterations. We also explore extensions of some of these methods to a range of special contexts, including dynamic and motion-compensated image reconstruction. While most of the discussed techniques were developed for emission tomography, the general methods are extensible to other imaging modalities as well. In addition to enabling image characterization, these analysis techniques allow us to control and enhance imaging system performance. We review practical applications where performance improvement is achieved by applying these ideas to the contexts of both hardware (optimizing scanner design) and image reconstruction (designing regularization functions that produce uniform resolution or maximize task-specific figures of merit). PMID:24312148
Analytical methods for quantitation of prenylated flavonoids from hops
Nikolić, Dejan; van Breemen, Richard B.
2013-01-01
The female flowers of hops (Humulus lupulus L.) are used as a flavoring agent in the brewing industry. There is growing interest in possible health benefits of hops, particularly as estrogenic and chemopreventive agents. Among the possible active constituents, most of the attention has focused on prenylated flavonoids, which can chemically be classified as prenylated chalcones and prenylated flavanones. Among chalcones, xanthohumol (XN) and desmethylxanthohumol (DMX) have been the most studied, while among flavanones, 8-prenylnaringenin (8-PN) and 6-prenylnaringenin (6-PN) have received the most attention. Because of the interest in medicinal properties of prenylated flavonoids, there is demand for accurate, reproducible and sensitive analytical methods to quantify these compounds in various matrices. Such methods are needed, for example, for quality control and standardization of hop extracts, measurement of the content of prenylated flavonoids in beer, and to determine pharmacokinetic properties of prenylated flavonoids in animals and humans. This review summarizes currently available analytical methods for quantitative analysis of the major prenylated flavonoids, with an emphasis on the LC-MS and LC-MS-MS methods and their recent applications to biomedical research on hops. This review covers all methods in which prenylated flavonoids have been measured, either as the primary analytes or as a part of a larger group of analytes. The review also discusses methodological issues relating to the quantitative analysis of these compounds regardless of the chosen analytical approach. PMID:24077106
Analytical methods for quantitation of prenylated flavonoids from hops.
Nikolić, Dejan; van Breemen, Richard B
2013-01-01
The female flowers of hops (Humulus lupulus L.) are used as a flavoring agent in the brewing industry. There is growing interest in possible health benefits of hops, particularly as estrogenic and chemopreventive agents. Among the possible active constituents, most of the attention has focused on prenylated flavonoids, which can chemically be classified as prenylated chalcones and prenylated flavanones. Among chalcones, xanthohumol (XN) and desmethylxanthohumol (DMX) have been the most studied, while among flavanones, 8-prenylnaringenin (8-PN) and 6-prenylnaringenin (6-PN) have received the most attention. Because of the interest in medicinal properties of prenylated flavonoids, there is demand for accurate, reproducible and sensitive analytical methods to quantify these compounds in various matrices. Such methods are needed, for example, for quality control and standardization of hop extracts, measurement of the content of prenylated flavonoids in beer, and to determine pharmacokinetic properties of prenylated flavonoids in animals and humans. This review summarizes currently available analytical methods for quantitative analysis of the major prenylated flavonoids, with an emphasis on the LC-MS and LC-MS-MS methods and their recent applications to biomedical research on hops. This review covers all methods in which prenylated flavonoids have been measured, either as the primary analytes or as a part of a larger group of analytes. The review also discusses methodological issues relating to the quantitative analysis of these compounds regardless of the chosen analytical approach. PMID:24077106
NASA Astrophysics Data System (ADS)
Przybilla, Norbert; Schaffenroth, Veronika; Nieva, Maria-Fernanda
2015-08-01
OB-type stars present hotbeds for non-LTE physics because of their strong radiation fields that drive the atmospheric plasma out of local thermodynamic equilibrium. We report on recent breakthroughs in the quantitative analysis of the optical and UV-spectra of OB-type stars that were facilitated by application of accurate and precise atomic data on a large scale. An astophysicist's dream has come true, by bringing observed and model spectra into close match over wide parts of the observed wavelength ranges. This facilitates tight observational constraints to be derived from OB-type stars for wide applications in astrophysics. However, despite the progress made, many details of the modelling may be improved further. We discuss atomic data needs in terms of laboratory measurements and also ab-initio calculations. Particular emphasis is given to quantitative spectroscopy in the near-IR, which will be in focus in the era of the upcoming extremely large telescopes.
2010-01-01
High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin. PMID:20403197
Li, Chunyan; Wu, Pei-ming; Wu, Zhizhen; Limnuson, Kanokwan; Mehan, Neal; Mozayan, Cameron; Golanov, Eugene V; Ahn, Chong H; Hartings, Jed A; Narayan, Raj K
2015-10-01
Cerebral blood flow (CBF) plays a critical role in the exchange of nutrients and metabolites at the capillary level and is tightly regulated to meet the metabolic demands of the brain. After major brain injuries, CBF normally decreases and supporting the injured brain with adequate CBF is a mainstay of therapy after traumatic brain injury. Quantitative and localized measurement of CBF is therefore critically important for evaluation of treatment efficacy and also for understanding of cerebral pathophysiology. We present here an improved thermal flow microsensor and its operation which provides higher accuracy compared to existing devices. The flow microsensor consists of three components, two stacked-up thin film resistive elements serving as composite heater/temperature sensor and one remote resistive element for environmental temperature compensation. It operates in constant-temperature mode (~2 °C above the medium temperature) providing 20 ms temporal resolution. Compared to previous thermal flow microsensor based on self-heating and self-sensing design, the sensor presented provides at least two-fold improvement in accuracy in the range from 0 to 200 ml/100 g/min. This is mainly achieved by using the stacked-up structure, where the heating and sensing are separated to improve the temperature measurement accuracy by minimization of errors introduced by self-heating. PMID:26256480
How Accurately Do Spectral Methods Estimate Effective Elastic Thickness?
NASA Astrophysics Data System (ADS)
Perez-Gussinye, M.; Lowry, A. R.; Watts, A. B.; Velicogna, I.
2002-12-01
The effective elastic thickness, Te, is an important parameter that has the potential to provide information on the long-term thermal and mechanical properties of the the lithosphere. Previous studies have estimated Te using both forward and inverse (spectral) methods. While there is generally good agreement between the results obtained using these methods, spectral methods are limited because they depend on the spectral estimator and the window size chosen for analysis. In order to address this problem, we have used a multitaper technique which yields optimal estimates of the bias and variance of the Bouguer coherence function relating topography and gravity anomaly data. The technique has been tested using realistic synthetic topography and gravity. Synthetic data were generated assuming surface and sub-surface (buried) loading of an elastic plate with fractal statistics consistent with real data sets. The cases of uniform and spatially varying Te are examined. The topography and gravity anomaly data consist of 2000x2000 km grids sampled at 8 km interval. The bias in the Te estimate is assessed from the difference between the true Te value and the mean from analyzing 100 overlapping windows within the 2000x2000 km data grids. For the case in which Te is uniform, the bias and variance decrease with window size and increase with increasing true Te value. In the case of a spatially varying Te, however, there is a trade-off between spatial resolution and variance. With increasing window size the variance of the Te estimate decreases, but the spatial changes in Te are smeared out. We find that for a Te distribution consisting of a strong central circular region of Te=50 km (radius 600 km) and progressively smaller Te towards its edges, the 800x800 and 1000x1000 km window gave the best compromise between spatial resolution and variance. Our studies demonstrate that assumed stationarity of the relationship between gravity and topography data yields good results even in
Quantitative Methods for Assessing Drug Synergism
2011-01-01
Two or more drugs that individually produce overtly similar effects will sometimes display greatly enhanced effects when given in combination. When the combined effect is greater than that predicted by their individual potencies, the combination is said to be synergistic. A synergistic interaction allows the use of lower doses of the combination constituents, a situation that may reduce adverse reactions. Drug combinations are quite common in the treatment of cancers, infections, pain, and many other diseases and situations. The determination of synergism is a quantitative pursuit that involves a rigorous demonstration that the combination effect is greater than that which is expected from the individual drug’s potencies. The basis of that demonstration is the concept of dose equivalence, which is discussed here and applied to an experimental design and data analysis known as isobolographic analysis. That method, and a related method of analysis that also uses dose equivalence, are presented in this brief review, which provides the mathematical basis for assessing synergy and an optimization strategy for determining the dose combination. PMID:22737266
A comparison of ancestral state reconstruction methods for quantitative characters.
Royer-Carenzi, Manuela; Didier, Gilles
2016-09-01
Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of seven of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares under Brownian, Brownian-with-trend and Ornstein-Uhlenbeck models, phylogenetic independent contrasts and squared parsimony methods. A review of the relations between these methods shows that the maximum likelihood, the restricted maximum likelihood and the generalized least squares under Brownian model infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide. The respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) directional or stabilizing selection. We give the general form of ancestral state distributions conditioned on leaf states under the simulation models. Ancestral distributions are used first, to give a theoretical lower bound of the expected reconstruction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states. Our simulations show that: (i) the distributions of the reconstruction uncertainty provided by the methods generally make sense (some more than others); (ii) it is essential to detect the presence of an evolutionary trend and to choose a reconstruction method accordingly; (iii) all the methods show good performances on characters under stabilizing selection; (iv) without trend or stabilizing selection, the maximum likelihood method is generally the most accurate. PMID:27234644
Sparse methods for Quantitative Susceptibility Mapping
NASA Astrophysics Data System (ADS)
Bilgic, Berkin; Chatnuntawech, Itthi; Langkammer, Christian; Setsompop, Kawin
2015-09-01
Quantitative Susceptibility Mapping (QSM) aims to estimate the tissue susceptibility distribution that gives rise to subtle changes in the main magnetic field, which are captured by the image phase in a gradient echo (GRE) experiment. The underlying susceptibility distribution is related to the acquired tissue phase through an ill-posed linear system. To facilitate its inversion, spatial regularization that imposes sparsity or smoothness assumptions can be employed. This paper focuses on efficient algorithms for regularized QSM reconstruction. Fast solvers that enforce sparsity under Total Variation (TV) and Total Generalized Variation (TGV) constraints are developed using Alternating Direction Method of Multipliers (ADMM). Through variable splitting that permits closed-form iterations, the computation efficiency of these solvers are dramatically improved. An alternative approach to improve the conditioning of the ill-posed inversion is to acquire multiple GRE volumes at different head orientations relative to the main magnetic field. The phase information from such multi-orientation acquisition can be combined to yield exquisite susceptibility maps and obviate the need for regularized reconstruction, albeit at the cost of increased data acquisition time.
An Inexpensive, Accurate, and Precise Wet-Mount Method for Enumerating Aquatic Viruses
Cunningham, Brady R.; Brum, Jennifer R.; Schwenck, Sarah M.; Sullivan, Matthew B.
2015-01-01
Viruses affect biogeochemical cycling, microbial mortality, gene flow, and metabolic functions in diverse environments through infection and lysis of microorganisms. Fundamental to quantitatively investigating these roles is the determination of viral abundance in both field and laboratory samples. One current, widely used method to accomplish this with aquatic samples is the “filter mount” method, in which samples are filtered onto costly 0.02-μm-pore-size ceramic filters for enumeration of viruses by epifluorescence microscopy. Here we describe a cost-effective (ca. 500-fold-lower materials cost) alternative virus enumeration method in which fluorescently stained samples are wet mounted directly onto slides, after optional chemical flocculation of viruses in samples with viral concentrations of <5 × 107 viruses ml−1. The concentration of viruses in the sample is then determined from the ratio of viruses to a known concentration of added microsphere beads via epifluorescence microscopy. Virus concentrations obtained by using this wet-mount method, with and without chemical flocculation, were significantly correlated with, and had precision equivalent to, those obtained by the filter mount method across concentrations ranging from 2.17 × 106 to 1.37 × 108 viruses ml−1 when tested by using cultivated viral isolates and natural samples from marine and freshwater environments. In summary, the wet-mount method is significantly less expensive than the filter mount method and is appropriate for rapid, precise, and accurate enumeration of aquatic viruses over a wide range of viral concentrations (≥1 × 106 viruses ml−1) encountered in field and laboratory samples. PMID:25710369
Stark, Peter C.; Kuske, Cheryl R.; Mullen, Kenneth I.
2002-01-01
A method for quantitating dsDNA in an aqueous sample solution containing an unknown amount of dsDNA. A first aqueous test solution containing a known amount of a fluorescent dye-dsDNA complex and at least one fluorescence-attenutating contaminant is prepared. The fluorescence intensity of the test solution is measured. The first test solution is diluted by a known amount to provide a second test solution having a known concentration of dsDNA. The fluorescence intensity of the second test solution is measured. Additional diluted test solutions are similarly prepared until a sufficiently dilute test solution having a known amount of dsDNA is prepared that has a fluorescence intensity that is not attenuated upon further dilution. The value of the maximum absorbance of this solution between 200-900 nanometers (nm), referred to herein as the threshold absorbance, is measured. A sample solution having an unknown amount of dsDNA and an absorbance identical to that of the sufficiently dilute test solution at the same chosen wavelength is prepared. Dye is then added to the sample solution to form the fluorescent dye-dsDNA-complex, after which the fluorescence intensity of the sample solution is measured and the quantity of dsDNA in the sample solution is determined. Once the threshold absorbance of a sample solution obtained from a particular environment has been determined, any similarly prepared sample solution taken from a similar environment and having the same value for the threshold absorbance can be quantified for dsDNA by adding a large excess of dye to the sample solution and measuring its fluorescence intensity.
Mackie, David M.; Jahnke, Justin P.; Benyamin, Marcus S.; Sumner, James J.
2016-01-01
The standard methodologies for quantitative analysis (QA) of mixtures using Fourier transform infrared (FTIR) instruments have evolved until they are now more complicated than necessary for many users’ purposes. We present a simpler methodology, suitable for widespread adoption of FTIR QA as a standard laboratory technique across disciplines by occasional users.•Algorithm is straightforward and intuitive, yet it is also fast, accurate, and robust.•Relies on component spectra, minimization of errors, and local adaptive mesh refinement.•Tested successfully on real mixtures of up to nine components. We show that our methodology is robust to challenging experimental conditions such as similar substances, component percentages differing by three orders of magnitude, and imperfect (noisy) spectra. As examples, we analyze biological, chemical, and physical aspects of bio-hybrid fuel cells. PMID:26977411
Kan, Yelena; Lensu, Lasse; Hehl, Gregor; Volkmer, Andreas; Vartiainen, Erik M
2016-05-30
We propose an approach, based on wavelet prism decomposition analysis, for correcting experimental artefacts in a coherent anti-Stokes Raman scattering (CARS) spectrum. This method allows estimating and eliminating a slowly varying modulation error function in the measured normalized CARS spectrum and yields a corrected CARS line-shape. The main advantage of the approach is that the spectral phase and amplitude corrections are avoided in the retrieved Raman line-shape spectrum, thus significantly simplifying the quantitative reconstruction of the sample's Raman response from a normalized CARS spectrum in the presence of experimental artefacts. Moreover, the approach obviates the need for assumptions about the modulation error distribution and the chemical composition of the specimens under study. The method is quantitatively validated on normalized CARS spectra recorded for equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose. PMID:27410113
Meaning in Method: The Rhetoric of Quantitative and Qualitative Research.
ERIC Educational Resources Information Center
Firestone, William A.
The current debate about quantitative and qualitative research methods focuses on whether there is a necessary connection between method-type and research paradigm that makes the different approaches incompatible. This paper argues that the connection is not so much logical as rhetorical. Quantitative methods express the assumptions of a…
Accurate reliability analysis method for quantum-dot cellular automata circuits
NASA Astrophysics Data System (ADS)
Cui, Huanqing; Cai, Li; Wang, Sen; Liu, Xiaoqiang; Yang, Xiaokuo
2015-10-01
Probabilistic transfer matrix (PTM) is a widely used model in the reliability research of circuits. However, PTM model cannot reflect the impact of input signals on reliability, so it does not completely conform to the mechanism of the novel field-coupled nanoelectronic device which is called quantum-dot cellular automata (QCA). It is difficult to get accurate results when PTM model is used to analyze the reliability of QCA circuits. To solve this problem, we present the fault tree models of QCA fundamental devices according to different input signals. After that, the binary decision diagram (BDD) is used to quantitatively investigate the reliability of two QCA XOR gates depending on the presented models. By employing the fault tree models, the impact of input signals on reliability can be identified clearly and the crucial components of a circuit can be found out precisely based on the importance values (IVs) of components. So this method is contributive to the construction of reliable QCA circuits.
Robust and Accurate Shock Capturing Method for High-Order Discontinuous Galerkin Methods
NASA Technical Reports Server (NTRS)
Atkins, Harold L.; Pampell, Alyssa
2011-01-01
A simple yet robust and accurate approach for capturing shock waves using a high-order discontinuous Galerkin (DG) method is presented. The method uses the physical viscous terms of the Navier-Stokes equations as suggested by others; however, the proposed formulation of the numerical viscosity is continuous and compact by construction, and does not require the solution of an auxiliary diffusion equation. This work also presents two analyses that guided the formulation of the numerical viscosity and certain aspects of the DG implementation. A local eigenvalue analysis of the DG discretization applied to a shock containing element is used to evaluate the robustness of several Riemann flux functions, and to evaluate algorithm choices that exist within the underlying DG discretization. A second analysis examines exact solutions to the DG discretization in a shock containing element, and identifies a "model" instability that will inevitably arise when solving the Euler equations using the DG method. This analysis identifies the minimum viscosity required for stability. The shock capturing method is demonstrated for high-speed flow over an inviscid cylinder and for an unsteady disturbance in a hypersonic boundary layer. Numerical tests are presented that evaluate several aspects of the shock detection terms. The sensitivity of the results to model parameters is examined with grid and order refinement studies.
Comparison of methods for quantitative evaluation of endoscopic distortion
NASA Astrophysics Data System (ADS)
Wang, Quanzeng; Castro, Kurt; Desai, Viraj N.; Cheng, Wei-Chung; Pfefer, Joshua
2015-03-01
Endoscopy is a well-established paradigm in medical imaging, and emerging endoscopic technologies such as high resolution, capsule and disposable endoscopes promise significant improvements in effectiveness, as well as patient safety and acceptance of endoscopy. However, the field lacks practical standardized test methods to evaluate key optical performance characteristics (OPCs), in particular the geometric distortion caused by fisheye lens effects in clinical endoscopic systems. As a result, it has been difficult to evaluate an endoscope's image quality or assess its changes over time. The goal of this work was to identify optimal techniques for objective, quantitative characterization of distortion that are effective and not burdensome. Specifically, distortion measurements from a commercially available distortion evaluation/correction software package were compared with a custom algorithm based on a local magnification (ML) approach. Measurements were performed using a clinical gastroscope to image square grid targets. Recorded images were analyzed with the ML approach and the commercial software where the results were used to obtain corrected images. Corrected images based on the ML approach and the software were compared. The study showed that the ML method could assess distortion patterns more accurately than the commercial software. Overall, the development of standardized test methods for characterizing distortion and other OPCs will facilitate development, clinical translation, manufacturing quality and assurance of performance during clinical use of endoscopic technologies.
Blending Qualitative & Quantitative Research Methods in Theses and Dissertations.
ERIC Educational Resources Information Center
Thomas, R. Murray
This guide discusses combining qualitative and quantitative research methods in theses and dissertations. It covers a wide array of methods, the strengths and limitations of each, and how they can be effectively interwoven into various research designs. The first chapter is "The Qualitative and the Quantitative." Part 1, "A Catalogue of…
Accurate compressed look up table method for CGH in 3D holographic display.
Gao, Chuan; Liu, Juan; Li, Xin; Xue, Gaolei; Jia, Jia; Wang, Yongtian
2015-12-28
Computer generated hologram (CGH) should be obtained with high accuracy and high speed in 3D holographic display, and most researches focus on the high speed. In this paper, a simple and effective computation method for CGH is proposed based on Fresnel diffraction theory and look up table. Numerical simulations and optical experiments are performed to demonstrate its feasibility. The proposed method can obtain more accurate reconstructed images with lower memory usage compared with split look up table method and compressed look up table method without sacrificing the computational speed in holograms generation, so it is called accurate compressed look up table method (AC-LUT). It is believed that AC-LUT method is an effective method to calculate the CGH of 3D objects for real-time 3D holographic display where the huge information data is required, and it could provide fast and accurate digital transmission in various dynamic optical fields in the future. PMID:26831987
Turabelidze, Anna; Guo, Shujuan; DiPietro, Luisa A
2010-01-01
Studies in the field of wound healing have utilized a variety of different housekeeping genes for reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis. However, nearly all of these studies assume that the selected normalization gene is stably expressed throughout the course of the repair process. The purpose of our current investigation was to identify the most stable housekeeping genes for studying gene expression in mouse wound healing using RT-qPCR. To identify which housekeeping genes are optimal for studying gene expression in wound healing, we examined all articles published in Wound Repair and Regeneration that cited RT-qPCR during the period of January/February 2008 until July/August 2009. We determined that ACTβ, GAPDH, 18S, and β2M were the most frequently used housekeeping genes in human, mouse, and pig studies. We also investigated nine commonly used housekeeping genes that are not generally used in wound healing models: GUS, TBP, RPLP2, ATP5B, SDHA, UBC, CANX, CYC1, and YWHAZ. We observed that wounded and unwounded tissues have contrasting housekeeping gene expression stability. The results demonstrate that commonly used housekeeping genes must be validated as accurate normalizing genes for each individual experimental condition. PMID:20731795
Quantitative methods for ecological network analysis.
Ulanowicz, Robert E
2004-12-01
The analysis of networks of ecological trophic transfers is a useful complement to simulation modeling in the quest for understanding whole-ecosystem dynamics. Trophic networks can be studied in quantitative and systematic fashion at several levels. Indirect relationships between any two individual taxa in an ecosystem, which often differ in either nature or magnitude from their direct influences, can be assayed using techniques from linear algebra. The same mathematics can also be employed to ascertain where along the trophic continuum any individual taxon is operating, or to map the web of connections into a virtual linear chain that summarizes trophodynamic performance by the system. Backtracking algorithms with pruning have been written which identify pathways for the recycle of materials and energy within the system. The pattern of such cycling often reveals modes of control or types of functions exhibited by various groups of taxa. The performance of the system as a whole at processing material and energy can be quantified using information theory. In particular, the complexity of process interactions can be parsed into separate terms that distinguish organized, efficient performance from the capacity for further development and recovery from disturbance. Finally, the sensitivities of the information-theoretic system indices appear to identify the dynamical bottlenecks in ecosystem functioning. PMID:15556474
NASA Astrophysics Data System (ADS)
Moiseev, N. Ya.
2011-04-01
An approach to the construction of high-order accurate monotone difference schemes for solving gasdynamic problems by Godunov's method with antidiffusion is proposed. Godunov's theorem on monotone schemes is used to construct a new antidiffusion flux limiter in high-order accurate difference schemes as applied to linear advection equations with constant coefficients. The efficiency of the approach is demonstrated by solving linear advection equations with constant coefficients and one-dimensional gasdynamic equations.
Saager, Rolf B.; Truong, Alex; Cuccia, David J.; Durkin, Anthony J.
2011-01-01
We have demonstrated that spatially modulated quantitative spectroscopy (SMoQS) is capable of extracting absolute optical properties from homogeneous tissue simulating phantoms that span both the visible and near-infrared wavelength regimes. However, biological tissue, such as skin, is highly structured, presenting challenges to quantitative spectroscopic techniques based on homogeneous models. In order to more accurately address the challenges associated with skin, we present a method for depth-resolved optical property quantitation based on a two layer model. Layered Monte Carlo simulations and layered tissue simulating phantoms are used to determine the efficacy and accuracy of SMoQS to quantify layer specific optical properties of layered media. Initial results from both the simulation and experiment show that this empirical method is capable of determining top layer thickness within tens of microns across a physiological range for skin. Layer specific chromophore concentration can be determined to <±10% the actual values, on average, whereas bulk quantitation in either visible or near infrared spectroscopic regimes significantly underestimates the layer specific chromophore concentration and can be confounded by top layer thickness. PMID:21806282
Research radiometric calibration quantitative transfer methods between internal and external
NASA Astrophysics Data System (ADS)
Guo, Ju Guang; Ma, Yong hui; Zhang, Guang; Yang, Zhi hui
2015-10-01
This paper puts forward a method by realizing the internal and external radiation calibration transfer for infrared radiation characteristics quantitative measuring system. Through technological innovation and innovation application to establish a theoretical model of the corresponding radiated transfer method. This method can be well in engineering application for technology conversion process of radiometric calibration that with relatively simple and effective calibration in the half light path radiation instead of complex difficult whole optical path radiometric calibration. At the same time, it also will provide the basis of effective support to further carry out the target radiated characteristics quantitative measurement and application for ground type infrared radiated quantitative measuring system.
Method for accurate growth of vertical-cavity surface-emitting lasers
Chalmers, S.A.; Killeen, K.P.; Lear, K.L.
1995-03-14
The authors report a method for accurate growth of vertical-cavity surface-emitting lasers (VCSELs). The method uses a single reflectivity spectrum measurement to determine the structure of the partially completed VCSEL at a critical point of growth. This information, along with the extracted growth rates, allows imprecisions in growth parameters to be compensated for during growth of the remaining structure, which can then be completed with very accurate critical dimensions. Using this method, they can now routinely grow lasing VCSELs with Fabry-Perot cavity resonance wavelengths controlled to within 0.5%. 4 figs.
Method for accurate growth of vertical-cavity surface-emitting lasers
Chalmers, Scott A.; Killeen, Kevin P.; Lear, Kevin L.
1995-01-01
We report a method for accurate growth of vertical-cavity surface-emitting lasers (VCSELs). The method uses a single reflectivity spectrum measurement to determine the structure of the partially completed VCSEL at a critical point of growth. This information, along with the extracted growth rates, allows imprecisions in growth parameters to be compensated for during growth of the remaining structure, which can then be completed with very accurate critical dimensions. Using this method, we can now routinely grow lasing VCSELs with Fabry-Perot cavity resonance wavelengths controlled to within 0.5%.
Liu, Ying; Shi, Xiao-Wei; Liu, E-Hu; Sheng, Long-Sheng; Qi, Lian-Wen; Li, Ping
2012-09-01
Various analytical technologies have been developed for quantitative determination of marker compounds in herbal medicines (HMs). One important issue is matrix effects that must be addressed in method validation for different detections. Unlike biological fluids, blank matrix samples for calibration are usually unavailable for HMs. In this work, practical approaches for minimizing matrix effects in HMs analysis were proposed. The matrix effects in quantitative analysis of five saponins from Panax notoginseng were assessed using high-performance liquid chromatography (HPLC). Matrix components were found to interfere with the ionization of target analytes when mass spectrometry (MS) detection were employed. To compensate the matrix signal suppression/enhancement, two matrix-matched methods, standard addition method with the target-knockout extract and standard superposition method with a HM extract were developed and tested in this work. The results showed that the standard superposition method is simple and practical for overcoming matrix effects for quantitative analysis of HMs. Moreover, the interference components were observed to interfere with light scattering of target analytes when evaporative light scattering detection (ELSD) was utilized for quantitative analysis of HMs but was not indicated when Ultraviolet detection (UV) were employed. Thus, the issue of interference effects should be addressed and minimized for quantitative HPLC-ELSD and HPLC-MS methodologies for quality control of HMs. PMID:22835696
Review of Quantitative Software Reliability Methods
Chu, T.L.; Yue, M.; Martinez-Guridi, M.; Lehner, J.
2010-09-17
The current U.S. Nuclear Regulatory Commission (NRC) licensing process for digital systems rests on deterministic engineering criteria. In its 1995 probabilistic risk assessment (PRA) policy statement, the Commission encouraged the use of PRA technology in all regulatory matters to the extent supported by the state-of-the-art in PRA methods and data. Although many activities have been completed in the area of risk-informed regulation, the risk-informed analysis process for digital systems has not yet been satisfactorily developed. Since digital instrumentation and control (I&C) systems are expected to play an increasingly important role in nuclear power plant (NPP) safety, the NRC established a digital system research plan that defines a coherent set of research programs to support its regulatory needs. One of the research programs included in the NRC's digital system research plan addresses risk assessment methods and data for digital systems. Digital I&C systems have some unique characteristics, such as using software, and may have different failure causes and/or modes than analog I&C systems; hence, their incorporation into NPP PRAs entails special challenges. The objective of the NRC's digital system risk research is to identify and develop methods, analytical tools, and regulatory guidance for (1) including models of digital systems into NPP PRAs, and (2) using information on the risks of digital systems to support the NRC's risk-informed licensing and oversight activities. For several years, Brookhaven National Laboratory (BNL) has worked on NRC projects to investigate methods and tools for the probabilistic modeling of digital systems, as documented mainly in NUREG/CR-6962 and NUREG/CR-6997. However, the scope of this research principally focused on hardware failures, with limited reviews of software failure experience and software reliability methods. NRC also sponsored research at the Ohio State University investigating the modeling of digital systems
Mudunkotuwa, Imali A; Anthony, T Renée; Grassian, Vicki H; Peters, Thomas M
2016-01-01
Titanium dioxide (TiO(2)) particles, including nanoparticles with diameters smaller than 100 nm, are used extensively in consumer products. In a 2011 current intelligence bulletin, the National Institute of Occupational Safety and Health (NIOSH) recommended methods to assess worker exposures to fine and ultrafine TiO(2) particles and associated occupational exposure limits for these particles. However, there are several challenges and problems encountered with these recommended exposure assessment methods involving the accurate quantitation of titanium dioxide collected on air filters using acid digestion followed by inductively coupled plasma optical emission spectroscopy (ICP-OES). Specifically, recommended digestion methods include the use of chemicals, such as perchloric acid, which are typically unavailable in most accredited industrial hygiene laboratories due to highly corrosive and oxidizing properties. Other alternative methods that are used typically involve the use of nitric acid or combination of nitric acid and sulfuric acid, which yield very poor recoveries for titanium dioxide. Therefore, given the current state of the science, it is clear that a new method is needed for exposure assessment. In this current study, a microwave-assisted acid digestion method has been specifically designed to improve the recovery of titanium in TiO(2) nanoparticles for quantitative analysis using ICP-OES. The optimum digestion conditions were determined by changing several variables including the acids used, digestion time, and temperature. Consequently, the optimized digestion temperature of 210°C with concentrated sulfuric and nitric acid (2:1 v/v) resulted in a recovery of >90% for TiO(2). The method is expected to provide for a more accurate quantification of airborne TiO(2) particles in the workplace environment. PMID:26181824
Semi-quantitative method to estimate levels of Campylobacter
Technology Transfer Automated Retrieval System (TEKTRAN)
Introduction: Research projects utilizing live animals and/or systems often require reliable, accurate quantification of Campylobacter following treatments. Even with marker strains, conventional methods designed to quantify are labor and material intensive requiring either serial dilutions or MPN ...
Fluorometric method of quantitative cell mutagenesis
Dolbeare, F.A.
1980-12-12
A method for assaying a cell culture for mutagenesis is described. A cell culture is stained first with a histochemical stain, and then a fluorescent stain. Normal cells in the culture are stained by both the histochemical and fluorescent stains, while abnormal cells are stained only by the fluorescent stain. The two stains are chosen so that the histochemical stain absorbs the wavelengths that the fluorescent stain emits. After the counterstained culture is subjected to exciting light, the fluorescence from the abnormal cells is detected.
Fluorometric method of quantitative cell mutagenesis
Dolbeare, Frank A.
1982-01-01
A method for assaying a cell culture for mutagenesis is described. A cell culture is stained first with a histochemical stain, and then a fluorescent stain. Normal cells in the culture are stained by both the histochemical and fluorescent stains, while abnormal cells are stained only by the fluorescent stain. The two stains are chosen so that the histochemical stain absorbs the wavelengths that the fluorescent stain emits. After the counterstained culture is subjected to exciting light, the fluorescence from the abnormal cells is detected.
Fast Monte Carlo Electron-Photon Transport Method and Application in Accurate Radiotherapy
NASA Astrophysics Data System (ADS)
Hao, Lijuan; Sun, Guangyao; Zheng, Huaqing; Song, Jing; Chen, Zhenping; Li, Gui
2014-06-01
Monte Carlo (MC) method is the most accurate computational method for dose calculation, but its wide application on clinical accurate radiotherapy is hindered due to its poor speed of converging and long computation time. In the MC dose calculation research, the main task is to speed up computation while high precision is maintained. The purpose of this paper is to enhance the calculation speed of MC method for electron-photon transport with high precision and ultimately to reduce the accurate radiotherapy dose calculation time based on normal computer to the level of several hours, which meets the requirement of clinical dose verification. Based on the existing Super Monte Carlo Simulation Program (SuperMC), developed by FDS Team, a fast MC method for electron-photon coupled transport was presented with focus on two aspects: firstly, through simplifying and optimizing the physical model of the electron-photon transport, the calculation speed was increased with slightly reduction of calculation accuracy; secondly, using a variety of MC calculation acceleration methods, for example, taking use of obtained information in previous calculations to avoid repeat simulation of particles with identical history; applying proper variance reduction techniques to accelerate MC method convergence rate, etc. The fast MC method was tested by a lot of simple physical models and clinical cases included nasopharyngeal carcinoma, peripheral lung tumor, cervical carcinoma, etc. The result shows that the fast MC method for electron-photon transport was fast enough to meet the requirement of clinical accurate radiotherapy dose verification. Later, the method will be applied to the Accurate/Advanced Radiation Therapy System ARTS as a MC dose verification module.
System and methods for wide-field quantitative fluorescence imaging during neurosurgery.
Valdes, Pablo A; Jacobs, Valerie L; Wilson, Brian C; Leblond, Frederic; Roberts, David W; Paulsen, Keith D
2013-08-01
We report an accurate, precise and sensitive method and system for quantitative fluorescence image-guided neurosurgery. With a low-noise, high-dynamic-range CMOS array, we perform rapid (integration times as low as 50 ms per wavelength) hyperspectral fluorescence and diffuse reflectance detection and apply a correction algorithm to compensate for the distorting effects of tissue absorption and scattering. Using this approach, we generated quantitative wide-field images of fluorescence in tissue-simulating phantoms for the fluorophore PpIX, having concentrations and optical absorption and scattering variations over clinically relevant ranges. The imaging system was tested in a rodent model of glioma, detecting quantitative levels down to 20 ng/ml. The resulting performance is a significant advance on existing wide-field quantitative imaging techniques, and provides performance comparable to a point-spectroscopy probe that has previously demonstrated significant potential for improved detection of malignant brain tumors during surgical resection. PMID:23903142
Liquid propellant rocket engine combustion simulation with a time-accurate CFD method
NASA Technical Reports Server (NTRS)
Chen, Y. S.; Shang, H. M.; Liaw, Paul; Hutt, J.
1993-01-01
Time-accurate computational fluid dynamics (CFD) algorithms are among the basic requirements as an engineering or research tool for realistic simulations of transient combustion phenomena, such as combustion instability, transient start-up, etc., inside the rocket engine combustion chamber. A time-accurate pressure based method is employed in the FDNS code for combustion model development. This is in connection with other program development activities such as spray combustion model development and efficient finite-rate chemistry solution method implementation. In the present study, a second-order time-accurate time-marching scheme is employed. For better spatial resolutions near discontinuities (e.g., shocks, contact discontinuities), a 3rd-order accurate TVD scheme for modeling the convection terms is implemented in the FDNS code. Necessary modification to the predictor/multi-corrector solution algorithm in order to maintain time-accurate wave propagation is also investigated. Benchmark 1-D and multidimensional test cases, which include the classical shock tube wave propagation problems, resonant pipe test case, unsteady flow development of a blast tube test case, and H2/O2 rocket engine chamber combustion start-up transient simulation, etc., are investigated to validate and demonstrate the accuracy and robustness of the present numerical scheme and solution algorithm.
Fast and accurate determination of the Wigner rotation matrices in the fast multipole method.
Dachsel, Holger
2006-04-14
In the rotation based fast multipole method the accurate determination of the Wigner rotation matrices is essential. The combination of two recurrence relations and the control of the error accumulations allow a very precise determination of the Wigner rotation matrices. The recurrence formulas are simple, efficient, and numerically stable. The advantages over other recursions are documented. PMID:16626188
The U.S. Department of Agriculture Automated Multiple-Pass Method accurately assesses sodium intakes
Technology Transfer Automated Retrieval System (TEKTRAN)
Accurate and practical methods to monitor sodium intake of the U.S. population are critical given current sodium reduction strategies. While the gold standard for estimating sodium intake is the 24 hour urine collection, few studies have used this biomarker to evaluate the accuracy of a dietary ins...
Uncertainty of quantitative microbiological methods of pharmaceutical analysis.
Gunar, O V; Sakhno, N G
2015-12-30
The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods. PMID:26456251
Malik, Afshan N.; Shahni, Rojeen; Rodriguez-de-Ledesma, Ana; Laftah, Abas; Cunningham, Phil
2011-08-19
Highlights: {yields} Mitochondrial dysfunction is central to many diseases of oxidative stress. {yields} 95% of the mitochondrial genome is duplicated in the nuclear genome. {yields} Dilution of untreated genomic DNA leads to dilution bias. {yields} Unique primers and template pretreatment are needed to accurately measure mitochondrial DNA content. -- Abstract: Circulating mitochondrial DNA (MtDNA) is a potential non-invasive biomarker of cellular mitochondrial dysfunction, the latter known to be central to a wide range of human diseases. Changes in MtDNA are usually determined by quantification of MtDNA relative to nuclear DNA (Mt/N) using real time quantitative PCR. We propose that the methodology for measuring Mt/N needs to be improved and we have identified that current methods have at least one of the following three problems: (1) As much of the mitochondrial genome is duplicated in the nuclear genome, many commonly used MtDNA primers co-amplify homologous pseudogenes found in the nuclear genome; (2) use of regions from genes such as {beta}-actin and 18S rRNA which are repetitive and/or highly variable for qPCR of the nuclear genome leads to errors; and (3) the size difference of mitochondrial and nuclear genomes cause a 'dilution bias' when template DNA is diluted. We describe a PCR-based method using unique regions in the human mitochondrial genome not duplicated in the nuclear genome; unique single copy region in the nuclear genome and template treatment to remove dilution bias, to accurately quantify MtDNA from human samples.
Motomura, Kaori; Inoue, Kimiko; Ogura, Atsuo
2016-06-17
Mouse trophoblast stem cells (TSCs) form colonies of different sizes and morphologies, which might reflect their degrees of differentiation. Therefore, each colony type can have a characteristic gene expression profile; however, the expression levels of internal reference genes may also change, causing fluctuations in their estimated gene expression levels. In this study, we validated seven housekeeping genes by using a geometric averaging method and identified Gapdh as the most stable gene across different colony types. Indeed, when Gapdh was used as the reference, expression levels of Elf5, a TSC marker gene, stringently classified TSC colonies into two groups: a high expression groups consisting of type 1 and 2 colonies, and a lower expression group consisting of type 3 and 4 colonies. This clustering was consistent with our putative classification of undifferentiated/differentiated colonies based on their time-dependent colony transitions. By contrast, use of an unstable reference gene (Rn18s) allowed no such clear classification. Cdx2, another TSC marker, did not show any significant colony type-specific expression pattern irrespective of the reference gene. Selection of stable reference genes for quantitative gene expression analysis might be critical, especially when cell lines consisting of heterogeneous cell populations are used. PMID:26853688
MOTOMURA, Kaori; INOUE, Kimiko; OGURA, Atsuo
2016-01-01
Mouse trophoblast stem cells (TSCs) form colonies of different sizes and morphologies, which might reflect their degrees of differentiation. Therefore, each colony type can have a characteristic gene expression profile; however, the expression levels of internal reference genes may also change, causing fluctuations in their estimated gene expression levels. In this study, we validated seven housekeeping genes by using a geometric averaging method and identified Gapdh as the most stable gene across different colony types. Indeed, when Gapdh was used as the reference, expression levels of Elf5, a TSC marker gene, stringently classified TSC colonies into two groups: a high expression groups consisting of type 1 and 2 colonies, and a lower expression group consisting of type 3 and 4 colonies. This clustering was consistent with our putative classification of undifferentiated/differentiated colonies based on their time-dependent colony transitions. By contrast, use of an unstable reference gene (Rn18s) allowed no such clear classification. Cdx2, another TSC marker, did not show any significant colony type-specific expression pattern irrespective of the reference gene. Selection of stable reference genes for quantitative gene expression analysis might be critical, especially when cell lines consisting of heterogeneous cell populations are used. PMID:26853688
Second-order accurate finite volume method for well-driven flows
NASA Astrophysics Data System (ADS)
Dotlić, M.; Vidović, D.; Pokorni, B.; Pušić, M.; Dimkić, M.
2016-02-01
We consider a finite volume method for a well-driven fluid flow in a porous medium. Due to the singularity of the well, modeling in the near-well region with standard numerical schemes results in a completely wrong total well flux and an inaccurate hydraulic head. Local grid refinement can help, but it comes at computational cost. In this article we propose two methods to address the well singularity. In the first method the flux through well faces is corrected using a logarithmic function, in a way related to the Peaceman model. Coupling this correction with a non-linear second-order accurate two-point scheme gives a greatly improved total well flux, but the resulting scheme is still inconsistent. In the second method fluxes in the near-well region are corrected by representing the hydraulic head as a sum of a logarithmic and a linear function. This scheme is second-order accurate.
Accurate determination of specific heat at high temperatures using the flash diffusivity method
NASA Technical Reports Server (NTRS)
Vandersande, J. W.; Zoltan, A.; Wood, C.
1989-01-01
The flash diffusivity method of Parker et al. (1961) was used to measure accurately the specific heat of test samples simultaneously with thermal diffusivity, thus obtaining the thermal conductivity of these materials directly. The accuracy of data obtained on two types of materials (n-type silicon-germanium alloys and niobium), was + or - 3 percent. It is shown that the method is applicable up to at least 1300 K.
An Effective Method to Accurately Calculate the Phase Space Factors for β - β - Decay
Neacsu, Andrei; Horoi, Mihai
2016-01-01
Accurate calculations of the electron phase space factors are necessary for reliable predictions of double-beta decay rates and for the analysis of the associated electron angular and energy distributions. We present an effective method to calculate these phase space factors that takes into account the distorted Coulomb field of the daughter nucleus, yet it allows one to easily calculate the phase space factors with good accuracy relative to the most exact methods available in the recent literature.
Integrating Qualitative and Quantitative Evaluation Methods in Substance Abuse Research.
ERIC Educational Resources Information Center
Dennis, Michael L.; And Others
1994-01-01
Some specific opportunities and techniques are described for combining and integrating qualitative and quantitative methods from the design stage of a substance abuse program evaluation through implementation and reporting. The multiple problems and requirements of such an evaluation make integrated methods essential. (SLD)
Applying Quantitative Genetic Methods to Primate Social Behavior
Brent, Lauren J. N.
2013-01-01
Increasingly, behavioral ecologists have applied quantitative genetic methods to investigate the evolution of behaviors in wild animal populations. The promise of quantitative genetics in unmanaged populations opens the door for simultaneous analysis of inheritance, phenotypic plasticity, and patterns of selection on behavioral phenotypes all within the same study. In this article, we describe how quantitative genetic techniques provide studies of the evolution of behavior with information that is unique and valuable. We outline technical obstacles for applying quantitative genetic techniques that are of particular relevance to studies of behavior in primates, especially those living in noncaptive populations, e.g., the need for pedigree information, non-Gaussian phenotypes, and demonstrate how many of these barriers are now surmountable. We illustrate this by applying recent quantitative genetic methods to spatial proximity data, a simple and widely collected primate social behavior, from adult rhesus macaques on Cayo Santiago. Our analysis shows that proximity measures are consistent across repeated measurements on individuals (repeatable) and that kin have similar mean measurements (heritable). Quantitative genetics may hold lessons of considerable importance for studies of primate behavior, even those without a specific genetic focus. PMID:24659839
NASA Astrophysics Data System (ADS)
Jackson, Phil; Fisher, Keith J.; Attalla, Moetaz Ibrahim
2011-08-01
The reaction between CO2 and aqueous amines to produce a charged carbamate product plays a crucial role in post-combustion capture chemistry when primary and secondary amines are used. In this paper, we report the low energy negative-ion CID results for several anionic carbamates derived from primary and secondary amines commonly used as post-combustion capture solvents. The study was performed using the modern equivalent of a triple quadrupole instrument equipped with a T-wave collision cell. Deuterium labeling of 2-aminoethanol (1,1,2,2,-d4-2-aminoethanol) and computations at the M06-2X/6-311++G(d,p) level were used to confirm the identity of the fragmentation products for 2-hydroxyethylcarbamate (derived from 2-aminoethanol), in particular the ions CN-, NCO- and facile neutral losses of CO2 and water; there is precedent for the latter in condensed phase isocyanate chemistry. The fragmentations of 2-hydroxyethylcarbamate were generalized for carbamate anions derived from other capture amines, including ethylenediamine, diethanolamine, and piperazine. We also report unequivocal evidence for the existence of carbamate anions derived from sterically hindered amines ( Tris(2-hydroxymethyl)aminomethane and 2-methyl-2-aminopropanol). For the suite of carbamates investigated, diagnostic losses include the decarboxylation product (-CO2, 44 mass units), loss of 46 mass units and the fragments NCO- ( m/z 42) and CN- ( m/z 26). We also report low energy CID results for the dicarbamate dianion (-O2CNHC2H4NHCO{2/-}) commonly encountered in CO2 capture solution utilizing ethylenediamine. Finally, we demonstrate a promising ion chromatography-MS based procedure for the separation and quantitation of aqueous anionic carbamates, which is based on the reported CID findings. The availability of accurate quantitation methods for ionic CO2 capture products could lead to dynamic operational tuning of CO2 capture-plants and, thus, cost-savings via real-time manipulation of solvent
Xu, Wentao; Cheng, Nan; Huang, Kunlun; Lin, Yuehe; Wang, Chenguang; Xu, Yuancong; Zhu, Longjiao; Du, Dan; Luo, Yunbo
2016-06-15
Many types of diagnostic technologies have been reported for DNA methylation, but they require a standard curve for quantification or only show moderate accuracy. Moreover, most technologies have difficulty providing information on the level of methylation at specific contiguous multi-sites, not to mention easy-to-use detection to eliminate labor-intensive procedures. We have addressed these limitations and report here a cascade strategy that combines proportion competitive quantitative PCR (PCQ-PCR) and lateral flow nucleic acid biosensor (LFNAB), resulting in accurate and easy-to-use assessment. The P16 gene with specific multi-methylated sites, a well-studied tumor suppressor gene, was used as the target DNA sequence model. First, PCQ-PCR provided amplification products with an accurate proportion of multi-methylated sites following the principle of proportionality, and double-labeled duplex DNA was synthesized. Then, a LFNAB strategy was further employed for amplified signal detection via immune affinity recognition, and the exact level of site-specific methylation could be determined by the relative intensity of the test line and internal reference line. This combination resulted in all recoveries being greater than 94%, which are pretty satisfactory recoveries in DNA methylation assessment. Moreover, the developed cascades show significantly high usability as a simple, sensitive, and low-cost tool. Therefore, as a universal platform for sensing systems for the detection of contiguous multi-sites of DNA methylation without external standards and expensive instrumentation, this PCQ-PCR-LFNAB cascade method shows great promise for the point-of-care diagnosis of cancer risk and therapeutics. PMID:26914373
A Novel Method for the Accurate Evaluation of Poisson's Ratio of Soft Polymer Materials
Lee, Jae-Hoon; Lee, Sang-Soo; Chang, Jun-Dong; Thompson, Mark S.; Kang, Dong-Joong; Park, Sungchan
2013-01-01
A new method with a simple algorithm was developed to accurately measure Poisson's ratio of soft materials such as polyvinyl alcohol hydrogel (PVA-H) with a custom experimental apparatus consisting of a tension device, a micro X-Y stage, an optical microscope, and a charge-coupled device camera. In the proposed method, the initial positions of the four vertices of an arbitrarily selected quadrilateral from the sample surface were first measured to generate a 2D 1st-order 4-node quadrilateral element for finite element numerical analysis. Next, minimum and maximum principal strains were calculated from differences between the initial and deformed shapes of the quadrilateral under tension. Finally, Poisson's ratio of PVA-H was determined by the ratio of minimum principal strain to maximum principal strain. This novel method has an advantage in the accurate evaluation of Poisson's ratio despite misalignment between specimens and experimental devices. In this study, Poisson's ratio of PVA-H was 0.44 ± 0.025 (n = 6) for 2.6–47.0% elongations with a tendency to decrease with increasing elongation. The current evaluation method of Poisson's ratio with a simple measurement system can be employed to a real-time automated vision-tracking system which is used to accurately evaluate the material properties of various soft materials. PMID:23737733
A calibration-independent method for accurate complex permittivity determination of liquid materials
Hasar, U. C.
2008-08-15
This note presents a calibration-independent method for accurate complex permittivity determination of liquid materials. There are two main advantages of the proposed method over those in the literature, which require measurements of two cells with different lengths loaded by the same liquid material. First, it eliminates any inhomogeneity or impurity present in the second sample and decreases the uncertainty in sample thickness. Second, it removes the undesired impacts of measurement plane deterioration on measurements of liquid materials. For validation of the proposed method, we measure the complex permittivity of distilled water and compare its extracted permittivity with the theoretical datum obtained from the Debye equation.
Formation of accurate 1-nm gaps using the electromigration method during metal deposition
NASA Astrophysics Data System (ADS)
Naitoh, Yasuhisa; Wei, Qingshuo; Mukaida, Masakazu; Ishida, Takao
2016-03-01
We investigate the origin of fabricated nanogap width variations using the electromigration method during metal deposition. This method also facilitates improved control over the nanogap width. A large suppression in the variation is achieved by sample annealing at 373 K during the application of bias voltages for electromigration, which indicates that the variation is caused by structural changes. This electromigration method during metal deposition for the fabrication of an accurate 1-nm gap electrode is useful for single-molecule-sized electronics. Furthermore, it opens the door for future research on integrated sub-1-nm-sized nanogap devices.
A fast and accurate method to predict 2D and 3D aerodynamic boundary layer flows
NASA Astrophysics Data System (ADS)
Bijleveld, H. A.; Veldman, A. E. P.
2014-12-01
A quasi-simultaneous interaction method is applied to predict 2D and 3D aerodynamic flows. This method is suitable for offshore wind turbine design software as it is a very accurate and computationally reasonably cheap method. This study shows the results for a NACA 0012 airfoil. The two applied solvers converge to the experimental values when the grid is refined. We also show that in separation the eigenvalues remain positive thus avoiding the Goldstein singularity at separation. In 3D we show a flow over a dent in which separation occurs. A rotating flat plat is used to show the applicability of the method for rotating flows. The shown capabilities of the method indicate that the quasi-simultaneous interaction method is suitable for design methods for offshore wind turbine blades.
Introducing GAMER: A fast and accurate method for ray-tracing galaxies using procedural noise
Groeneboom, N. E.; Dahle, H.
2014-03-10
We developed a novel approach for fast and accurate ray-tracing of galaxies using procedural noise fields. Our method allows for efficient and realistic rendering of synthetic galaxy morphologies, where individual components such as the bulge, disk, stars, and dust can be synthesized in different wavelengths. These components follow empirically motivated overall intensity profiles but contain an additional procedural noise component that gives rise to complex natural patterns that mimic interstellar dust and star-forming regions. These patterns produce more realistic-looking galaxy images than using analytical expressions alone. The method is fully parallelized and creates accurate high- and low- resolution images that can be used, for example, in codes simulating strong and weak gravitational lensing. In addition to having a user-friendly graphical user interface, the C++ software package GAMER is easy to implement into an existing code.
Osher, Lawrence; Blazer, Marie Mantini; Buck, Stacie; Biernacki, Tomasz
2014-01-01
Several published studies have explained in detail how to measure relative metatarsal protrusion on the plain film anteroposterior pedal radiograph. These studies have demonstrated the utility of relative metatarsal protrusion measurement in that it correlates with distal forefoot deformity or pathologic features. The method currently preferred by practitioners in podiatric medicine and surgery often presents one with the daunting challenge of obtaining an accurate measurement when the intermetatarsal 1-2 angle is small. The present study illustrates a novel mathematical solution to this problem that is simple to master, relatively quick to perform, and yields accurate results. Our method was tested and proven by 4 trained observers with varying degrees of clinical skill who independently measured the same 10 radiographs. PMID:24933656
An accurate and practical method for inference of weak gravitational lensing from galaxy images
NASA Astrophysics Data System (ADS)
Bernstein, Gary M.; Armstrong, Robert; Krawiec, Christina; March, Marisa C.
2016-07-01
We demonstrate highly accurate recovery of weak gravitational lensing shear using an implementation of the Bayesian Fourier Domain (BFD) method proposed by Bernstein & Armstrong, extended to correct for selection biases. The BFD formalism is rigorously correct for Nyquist-sampled, background-limited, uncrowded images of background galaxies. BFD does not assign shapes to galaxies, instead compressing the pixel data D into a vector of moments M, such that we have an analytic expression for the probability P(M|g) of obtaining the observations with gravitational lensing distortion g along the line of sight. We implement an algorithm for conducting BFD's integrations over the population of unlensed source galaxies which measures ≈10 galaxies s-1 core-1 with good scaling properties. Initial tests of this code on ≈109 simulated lensed galaxy images recover the simulated shear to a fractional accuracy of m = (2.1 ± 0.4) × 10-3, substantially more accurate than has been demonstrated previously for any generally applicable method. Deep sky exposures generate a sufficiently accurate approximation to the noiseless, unlensed galaxy population distribution assumed as input to BFD. Potential extensions of the method include simultaneous measurement of magnification and shear; multiple-exposure, multiband observations; and joint inference of photometric redshifts and lensing tomography.
An accurate and practical method for inference of weak gravitational lensing from galaxy images
NASA Astrophysics Data System (ADS)
Bernstein, Gary M.; Armstrong, Robert; Krawiec, Christina; March, Marisa C.
2016-04-01
We demonstrate highly accurate recovery of weak gravitational lensing shear using an implementation of the Bayesian Fourier Domain (BFD) method proposed by Bernstein & Armstrong (2014, BA14), extended to correct for selection biases. The BFD formalism is rigorously correct for Nyquist-sampled, background-limited, uncrowded image of background galaxies. BFD does not assign shapes to galaxies, instead compressing the pixel data D into a vector of moments M, such that we have an analytic expression for the probability P(M|g) of obtaining the observations with gravitational lensing distortion g along the line of sight. We implement an algorithm for conducting BFD's integrations over the population of unlensed source galaxies which measures ≈10 galaxies/second/core with good scaling properties. Initial tests of this code on ≈109 simulated lensed galaxy images recover the simulated shear to a fractional accuracy of m = (2.1 ± 0.4) × 10-3, substantially more accurate than has been demonstrated previously for any generally applicable method. Deep sky exposures generate a sufficiently accurate approximation to the noiseless, unlensed galaxy population distribution assumed as input to BFD. Potential extensions of the method include simultaneous measurement of magnification and shear; multiple-exposure, multi-band observations; and joint inference of photometric redshifts and lensing tomography.
Accurate, efficient, and (iso)geometrically flexible collocation methods for phase-field models
NASA Astrophysics Data System (ADS)
Gomez, Hector; Reali, Alessandro; Sangalli, Giancarlo
2014-04-01
We propose new collocation methods for phase-field models. Our algorithms are based on isogeometric analysis, a new technology that makes use of functions from computational geometry, such as, for example, Non-Uniform Rational B-Splines (NURBS). NURBS exhibit excellent approximability and controllable global smoothness, and can represent exactly most geometries encapsulated in Computer Aided Design (CAD) models. These attributes permitted us to derive accurate, efficient, and geometrically flexible collocation methods for phase-field models. The performance of our method is demonstrated by several numerical examples of phase separation modeled by the Cahn-Hilliard equation. We feel that our method successfully combines the geometrical flexibility of finite elements with the accuracy and simplicity of pseudo-spectral collocation methods, and is a viable alternative to classical collocation methods.
Qian, Wei-Jun; Monroe, Matthew E.; Liu, Tao; Jacobs, Jon M.; Anderson, Gordon A.; Shen, Yufeng; Moore, Ronald J.; Anderson, David J.; Zhang, Rui; Calvano, Steve E.; Lowry, Stephen F.; Xiao, Wenzhong; Moldawer, Lyle L.; Davis, Ronald W.; Tompkins, Ronald G.; Camp, David G.; Smith, Richard D.
2007-01-01
SUMMARY Identification of novel diagnostic or therapeutic biomarkers from human blood plasma would benefit significantly from quantitative measurements of the proteome constituents over a range of physiological conditions. Herein we describe an initial demonstration of proteome-wide quantitative analysis of human plasma. The approach utilizes post-digestion trypsin-catalyzed 16O/18O peptide labeling, two-dimensional liquid chromatography (LC)-Fourier transform ion cyclotron resonance ((FTICR) mass spectrometry, and the accurate mass and time (AMT) tag strategy to identify and quantify peptides/proteins from complex samples. A peptide accurate mass and LC-elution time AMT tag database was initially generated using tandem mass spectrometry (MS/MS) following extensive multidimensional LC separations to provide the basis for subsequent peptide identifications. The AMT tag database contains >8,000 putative identified peptides, providing 938 confident plasma protein identifications. The quantitative approach was applied without depletion for high abundant proteins for comparative analyses of plasma samples from an individual prior to and 9 h after lipopolysaccharide (LPS) administration. Accurate quantification of changes in protein abundance was demonstrated by both 1:1 labeling of control plasma and the comparison between the plasma samples following LPS administration. A total of 429 distinct plasma proteins were quantified from the comparative analyses and the protein abundances for 25 proteins, including several known inflammatory response mediators, were observed to change significantly following LPS administration. PMID:15753121
Ricci, Davide; Mennander, Ari A; Pham, Linh D; Rao, Vinay P; Miyagi, Naoto; Byrne, Guerard W; Russell, Stephen J; McGregor, Christopher GA
2008-01-01
Objectives We studied the concordance of transgene expression in the transplanted heart using bicistronic adenoviral vector coding for a transgene of interest (human carcinoembryonic antigen: hCEA - beta human chorionic gonadotropin: βhCG) and for a marker imaging transgene (human sodium iodide symporter: hNIS). Methods Inbred Lewis rats were used for syngeneic heterotopic cardiac transplantation. Donor rat hearts were perfused ex vivo for 30 minutes prior to transplantation with University of Wisconsin (UW) solution (n=3), with 109 pfu/ml of adenovirus expressing hNIS (Ad-NIS; n=6), hNIS-hCEA (Ad-NIS-CEA; n=6) and hNIS-βhCG (Ad-NIS-CG; n=6). On post-operative day (POD) 5, 10, 15 all animals underwent micro-SPECT/CT imaging of the donor hearts after tail vein injection of 1000 μCi 123I and blood sample collection for hCEA and βhCG quantification. Results Significantly higher image intensity was noted in the hearts perfused with Ad-NIS (1.1±0.2; 0.9±0.07), Ad-NIS-CEA (1.2±0.3; 0.9±0.1) and Ad-NIS-CG (1.1±0.1; 0.9±0.1) compared to UW group (0.44±0.03; 0.47±0.06) on POD 5 and 10 (p<0.05). Serum levels of hCEA and βhCG increased in animals showing high cardiac 123I uptake, but not in those with lower uptake. Above this threshold, image intensities correlated well with serum levels of hCEA and βhCG (R2=0.99 and R2=0.96 respectively). Conclusions These data demonstrate that hNIS is an excellent reporter gene for the transplanted heart. The expression level of hNIS can be accurately and non-invasively monitored by serial radioisotopic single photon emission computed tomography (SPECT) imaging. High concordance has been demonstrated between imaging and soluble marker peptides at the maximum transgene expression on POD 5. PMID:17980613
Employing quantitative and qualitative methods in one study.
Mason, S A
There is an apparent lack of epistemological rigour when quantitative and qualitative methods are combined in the same study, because they reflect opposing positivist and interpretive perspectives. When and how to use methodological pluralism is discussed in this article. PMID:8400784
Comparison of methods for accurate end-point detection of potentiometric titrations
NASA Astrophysics Data System (ADS)
Villela, R. L. A.; Borges, P. P.; Vyskočil, L.
2015-01-01
Detection of the end point in potentiometric titrations has wide application on experiments that demand very low measurement uncertainties mainly for certifying reference materials. Simulations of experimental coulometric titration data and consequential error analysis of the end-point values were conducted using a programming code. These simulations revealed that the Levenberg-Marquardt method is in general more accurate than the traditional second derivative technique used currently as end-point detection for potentiometric titrations. Performance of the methods will be compared and presented in this paper.
Hwang, Beomsoo; Jeon, Doyoung
2015-01-01
In exoskeletal robots, the quantification of the user's muscular effort is important to recognize the user's motion intentions and evaluate motor abilities. In this paper, we attempt to estimate users' muscular efforts accurately using joint torque sensor which contains the measurements of dynamic effect of human body such as the inertial, Coriolis, and gravitational torques as well as torque by active muscular effort. It is important to extract the dynamic effects of the user's limb accurately from the measured torque. The user's limb dynamics are formulated and a convenient method of identifying user-specific parameters is suggested for estimating the user's muscular torque in robotic exoskeletons. Experiments were carried out on a wheelchair-integrated lower limb exoskeleton, EXOwheel, which was equipped with torque sensors in the hip and knee joints. The proposed methods were evaluated by 10 healthy participants during body weight-supported gait training. The experimental results show that the torque sensors are to estimate the muscular torque accurately in cases of relaxed and activated muscle conditions. PMID:25860074
Stewart, Michael; Baker, Cindy F; Cooney, Terry
2011-11-01
The methodology of using fish pheromones, or chemical signatures, as a tool to monitor or manage species of fish is rapidly gaining popularity. Unequivocal detection and accurate quantitation of extremely low concentrations of these chemicals in natural waters is paramount to using this technique as a management tool. Various species of lamprey are known to produce a mixture of three important migratory pheromones; petromyzonol sulfate (PS), petromyzonamine disulfate (PADS), and petromyzosterol disulfate (PSDS), but presently there are no established robust methods for quantitation of all three pheromones. In this study, we report a new, highly sensitive and selective method for the rapid identification and quantitation of these pheromones in river water samples. The procedure is based on pre-concentration, followed by liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis. The method is fast, with unambiguous pheromone determination. Practical quantitation limits of 0.25 ng/l were achieved for PS and PADS and 2.5 ng/l for PSDS in river water, using a 200-fold pre-concentration, However, lower quantitation limits can be achieved with greater pre-concentration. The methodology can be modified easily to include other chemicals of interest. Furthermore, the pre-concentration step can be applied easily in the field, circumventing potential stability issues of these chemicals. PMID:22076684
A second order accurate embedded boundary method for the wave equation with Dirichlet data
Kreiss, H O; Petersson, N A
2004-03-02
The accuracy of Cartesian embedded boundary methods for the second order wave equation in general two-dimensional domains subject to Dirichlet boundary conditions is analyzed. Based on the analysis, we develop a numerical method where both the solution and its gradient are second order accurate. We avoid the small-cell stiffness problem without sacrificing the second order accuracy by adding a small artificial term to the Dirichlet boundary condition. Long-time stability of the method is obtained by adding a small fourth order dissipative term. Several numerical examples are provided to demonstrate the accuracy and stability of the method. The method is also used to solve the two-dimensional TM{sub z} problem for Maxwell's equations posed as a second order wave equation for the electric field coupled to ordinary differential equations for the magnetic field.
Accurate near-field calculation in the rigorous coupled-wave analysis method
NASA Astrophysics Data System (ADS)
Weismann, Martin; Gallagher, Dominic F. G.; Panoiu, Nicolae C.
2015-12-01
The rigorous coupled-wave analysis (RCWA) is one of the most successful and widely used methods for modeling periodic optical structures. It yields fast convergence of the electromagnetic far-field and has been adapted to model various optical devices and wave configurations. In this article, we investigate the accuracy with which the electromagnetic near-field can be calculated by using RCWA and explain the observed slow convergence and numerical artifacts from which it suffers, namely unphysical oscillations at material boundaries due to the Gibbs phenomenon. In order to alleviate these shortcomings, we also introduce a mathematical formulation for accurate near-field calculation in RCWA, for one- and two-dimensional straight and slanted diffraction gratings. This accurate near-field computational approach is tested and evaluated for several representative test-structures and configurations in order to illustrate the advantages provided by the proposed modified formulation of the RCWA.
Improved method and apparatus for chromatographic quantitative analysis
Fritz, J.S.; Gjerde, D.T.; Schmuckler, G.
An improved apparatus and method are described for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single element and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.
NASA Astrophysics Data System (ADS)
Yoshidome, Takashi; Ekimoto, Toru; Matubayasi, Nobuyuki; Harano, Yuichi; Kinoshita, Masahiro; Ikeguchi, Mitsunori
2015-05-01
The hydration free energy (HFE) is a crucially important physical quantity to discuss various chemical processes in aqueous solutions. Although an explicit-solvent computation with molecular dynamics (MD) simulations is a preferable treatment of the HFE, huge computational load has been inevitable for large, complex solutes like proteins. In the present paper, we propose an efficient computation method for the HFE. In our method, the HFE is computed as a sum of
A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes
Price, Morgan N.; Huang, Katherine H.; Alm, Eric J.; Arkin, Adam P.
2004-12-01
We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from sixphylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.
Accurate Time/Frequency Transfer Method Using Bi-Directional WDM Transmission
NASA Technical Reports Server (NTRS)
Imaoka, Atsushi; Kihara, Masami
1996-01-01
An accurate time transfer method is proposed using b-directional wavelength division multiplexing (WDM) signal transmission along a single optical fiber. This method will be used in digital telecommunication networks and yield a time synchronization accuracy of better than 1 ns for long transmission lines over several tens of kilometers. The method can accurately measure the difference in delay between two wavelength signals caused by the chromatic dispersion of the fiber in conventional simple bi-directional dual-wavelength frequency transfer methods. We describe the characteristics of this difference in delay and then show that the accuracy of the delay measurements can be obtained below 0.1 ns by transmitting 156 Mb/s times reference signals of 1.31 micrometer and 1.55 micrometers along a 50 km fiber using the proposed method. The sub-nanosecond delay measurement using the simple bi-directional dual-wavelength transmission along a 100 km fiber with a wavelength spacing of 1 nm in the 1.55 micrometer range is also shown.
A quantitative method for evaluating alternatives. [aid to decision making
NASA Technical Reports Server (NTRS)
Forthofer, M. J.
1981-01-01
When faced with choosing between alternatives, people tend to use a number of criteria (often subjective, rather than objective) to decide which is the best alternative for them given their unique situation. The subjectivity inherent in the decision-making process can be reduced by the definition and use of a quantitative method for evaluating alternatives. This type of method can help decision makers achieve degree of uniformity and completeness in the evaluation process, as well as an increased sensitivity to the factors involved. Additional side-effects are better documentation and visibility of the rationale behind the resulting decisions. General guidelines for defining a quantitative method are presented and a particular method (called 'hierarchical weighted average') is defined and applied to the evaluation of design alternatives for a hypothetical computer system capability.
Reconstruction-classification method for quantitative photoacoustic tomography
NASA Astrophysics Data System (ADS)
Malone, Emma; Powell, Samuel; Cox, Ben T.; Arridge, Simon
2015-12-01
We propose a combined reconstruction-classification method for simultaneously recovering absorption and scattering in turbid media from images of absorbed optical energy. This method exploits knowledge that optical parameters are determined by a limited number of classes to iteratively improve their estimate. Numerical experiments show that the proposed approach allows for accurate recovery of absorption and scattering in two and three dimensions, and delivers superior image quality with respect to traditional reconstruction-only approaches.
Quantitative methods for analyzing cell-cell adhesion in development.
Kashef, Jubin; Franz, Clemens M
2015-05-01
During development cell-cell adhesion is not only crucial to maintain tissue morphogenesis and homeostasis, it also activates signalling pathways important for the regulation of different cellular processes including cell survival, gene expression, collective cell migration and differentiation. Importantly, gene mutations of adhesion receptors can cause developmental disorders and different diseases. Quantitative methods to measure cell adhesion are therefore necessary to understand how cells regulate cell-cell adhesion during development and how aberrations in cell-cell adhesion contribute to disease. Different in vitro adhesion assays have been developed in the past, but not all of them are suitable to study developmentally-related cell-cell adhesion processes, which usually requires working with low numbers of primary cells. In this review, we provide an overview of different in vitro techniques to study cell-cell adhesion during development, including a semi-quantitative cell flipping assay, and quantitative single-cell methods based on atomic force microscopy (AFM)-based single-cell force spectroscopy (SCFS) or dual micropipette aspiration (DPA). Furthermore, we review applications of Förster resonance energy transfer (FRET)-based molecular tension sensors to visualize intracellular mechanical forces acting on cell adhesion sites. Finally, we describe a recently introduced method to quantitate cell-generated forces directly in living tissues based on the deformation of oil microdroplets functionalized with adhesion receptor ligands. Together, these techniques provide a comprehensive toolbox to characterize different cell-cell adhesion phenomena during development. PMID:25448695
Accurate Wind Characterization in Complex Terrain Using the Immersed Boundary Method
Lundquist, K A; Chow, F K; Lundquist, J K; Kosovic, B
2009-09-30
This paper describes an immersed boundary method (IBM) that facilitates the explicit resolution of complex terrain within the Weather Research and Forecasting (WRF) model. Two different interpolation methods, trilinear and inverse distance weighting, are used at the core of the IBM algorithm. Functional aspects of the algorithm's implementation and the accuracy of results are considered. Simulations of flow over a three-dimensional hill with shallow terrain slopes are preformed with both WRF's native terrain-following coordinate and with both IB methods. Comparisons of flow fields from the three simulations show excellent agreement, indicating that both IB methods produce accurate results. However, when ease of implementation is considered, inverse distance weighting is superior. Furthermore, inverse distance weighting is shown to be more adept at handling highly complex urban terrain, where the trilinear interpolation algorithm breaks down. This capability is demonstrated by using the inverse distance weighting core of the IBM to model atmospheric flow in downtown Oklahoma City.
Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.
Nyman, Jonas; Pundyke, Orla Sheehan; Day, Graeme M
2016-06-21
We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy. PMID:27230942
2013-01-01
Background Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the gastrointestinal tract microbiota toward that of healthy individuals. Identifying differences in microbiota composition through the use of 16S rRNA gene hypervariable tag sequencing has profound health implications. Current computational methods for comparing microbial communities are usually based on multiple alignments and phylogenetic inference, making them time consuming and requiring exceptional expertise and computational resources. As sequencing data rapidly grows in size, simpler analysis methods are needed to meet the growing computational burdens of microbiota comparisons. Thus, we have developed a simple, rapid, and accurate method, independent of multiple alignments and phylogenetic inference, to support microbiota comparisons. Results We create a metric, called compression-based distance (CBD) for quantifying the degree of similarity between microbial communities. CBD uses the repetitive nature of hypervariable tag datasets and well-established compression algorithms to approximate the total information shared between two datasets. Three published microbiota datasets were used as test cases for CBD as an applicable tool. Our study revealed that CBD recaptured 100% of the statistically significant conclusions reported in the previous studies, while achieving a decrease in computational time required when compared to similar tools without expert user intervention. Conclusion CBD provides a simple, rapid, and accurate method for assessing distances between gastrointestinal tract microbiota 16S hypervariable tag datasets. PMID:23617892
Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method
Burger, Lukas; van Nimwegen, Erik
2008-01-01
Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381
Jha, Abhinav K; Caffo, Brian; Frey, Eric C
2016-04-01
The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest
NASA Astrophysics Data System (ADS)
Jha, Abhinav K.; Caffo, Brian; Frey, Eric C.
2016-04-01
The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest
A new class of accurate, mesh-free hydrodynamic simulation methods
NASA Astrophysics Data System (ADS)
Hopkins, Philip F.
2015-06-01
We present two new Lagrangian methods for hydrodynamics, in a systematic comparison with moving-mesh, smoothed particle hydrodynamics (SPH), and stationary (non-moving) grid methods. The new methods are designed to simultaneously capture advantages of both SPH and grid-based/adaptive mesh refinement (AMR) schemes. They are based on a kernel discretization of the volume coupled to a high-order matrix gradient estimator and a Riemann solver acting over the volume `overlap'. We implement and test a parallel, second-order version of the method with self-gravity and cosmological integration, in the code GIZMO:1 this maintains exact mass, energy and momentum conservation; exhibits superior angular momentum conservation compared to all other methods we study; does not require `artificial diffusion' terms; and allows the fluid elements to move with the flow, so resolution is automatically adaptive. We consider a large suite of test problems, and find that on all problems the new methods appear competitive with moving-mesh schemes, with some advantages (particularly in angular momentum conservation), at the cost of enhanced noise. The new methods have many advantages versus SPH: proper convergence, good capturing of fluid-mixing instabilities, dramatically reduced `particle noise' and numerical viscosity, more accurate sub-sonic flow evolution, and sharp shock-capturing. Advantages versus non-moving meshes include: automatic adaptivity, dramatically reduced advection errors and numerical overmixing, velocity-independent errors, accurate coupling to gravity, good angular momentum conservation and elimination of `grid alignment' effects. We can, for example, follow hundreds of orbits of gaseous discs, while AMR and SPH methods break down in a few orbits. However, fixed meshes minimize `grid noise'. These differences are important for a range of astrophysical problems.
Disordered Speech Assessment Using Automatic Methods Based on Quantitative Measures
NASA Astrophysics Data System (ADS)
Gu, Lingyun; Harris, John G.; Shrivastav, Rahul; Sapienza, Christine
2005-12-01
Speech quality assessment methods are necessary for evaluating and documenting treatment outcomes of patients suffering from degraded speech due to Parkinson's disease, stroke, or other disease processes. Subjective methods of speech quality assessment are more accurate and more robust than objective methods but are time-consuming and costly. We propose a novel objective measure of speech quality assessment that builds on traditional speech processing techniques such as dynamic time warping (DTW) and the Itakura-Saito (IS) distortion measure. Initial results show that our objective measure correlates well with the more expensive subjective methods.
A Simple yet Accurate Method for the Estimation of the Biovolume of Planktonic Microorganisms.
Saccà, Alessandro
2016-01-01
Determining the biomass of microbial plankton is central to the study of fluxes of energy and materials in aquatic ecosystems. This is typically accomplished by applying proper volume-to-carbon conversion factors to group-specific abundances and biovolumes. A critical step in this approach is the accurate estimation of biovolume from two-dimensional (2D) data such as those available through conventional microscopy techniques or flow-through imaging systems. This paper describes a simple yet accurate method for the assessment of the biovolume of planktonic microorganisms, which works with any image analysis system allowing for the measurement of linear distances and the estimation of the cross sectional area of an object from a 2D digital image. The proposed method is based on Archimedes' principle about the relationship between the volume of a sphere and that of a cylinder in which the sphere is inscribed, plus a coefficient of 'unellipticity' introduced here. Validation and careful evaluation of the method are provided using a variety of approaches. The new method proved to be highly precise with all convex shapes characterised by approximate rotational symmetry, and combining it with an existing method specific for highly concave or branched shapes allows covering the great majority of cases with good reliability. Thanks to its accuracy, consistency, and low resources demand, the new method can conveniently be used in substitution of any extant method designed for convex shapes, and can readily be coupled with automated cell imaging technologies, including state-of-the-art flow-through imaging devices. PMID:27195667
A Simple yet Accurate Method for the Estimation of the Biovolume of Planktonic Microorganisms
2016-01-01
Determining the biomass of microbial plankton is central to the study of fluxes of energy and materials in aquatic ecosystems. This is typically accomplished by applying proper volume-to-carbon conversion factors to group-specific abundances and biovolumes. A critical step in this approach is the accurate estimation of biovolume from two-dimensional (2D) data such as those available through conventional microscopy techniques or flow-through imaging systems. This paper describes a simple yet accurate method for the assessment of the biovolume of planktonic microorganisms, which works with any image analysis system allowing for the measurement of linear distances and the estimation of the cross sectional area of an object from a 2D digital image. The proposed method is based on Archimedes’ principle about the relationship between the volume of a sphere and that of a cylinder in which the sphere is inscribed, plus a coefficient of ‘unellipticity’ introduced here. Validation and careful evaluation of the method are provided using a variety of approaches. The new method proved to be highly precise with all convex shapes characterised by approximate rotational symmetry, and combining it with an existing method specific for highly concave or branched shapes allows covering the great majority of cases with good reliability. Thanks to its accuracy, consistency, and low resources demand, the new method can conveniently be used in substitution of any extant method designed for convex shapes, and can readily be coupled with automated cell imaging technologies, including state-of-the-art flow-through imaging devices. PMID:27195667
A simple and accurate resist parameter extraction method for sub-80-nm DRAM patterns
NASA Astrophysics Data System (ADS)
Lee, Sook; Hwang, Chan; Park, Dong-Woon; Kim, In-Sung; Kim, Ho-Chul; Woo, Sang-Gyun; Cho, Han-Ku; Moon, Joo-Tae
2004-05-01
Due to the polarization effect of high NA lithography, the consideration of resist effect in lithography simulation becomes increasingly important. In spite of the importance of resist simulation, many process engineers are reluctant to consider resist effect in lithography simulation due to time-consuming procedure to extract required resist parameters and the uncertainty of measurement of some parameters. Weiss suggested simplified development model, and this model does not require the complex kinetic parameters. For the device fabrication engineers, there is a simple and accurate parameter extraction and optimizing method using Weiss model. This method needs refractive index, Dill"s parameters and development rate monitoring (DRM) data in parameter extraction. The parameters extracted using referred sequence is not accurate, so that we have to optimize the parameters to fit the critical dimension scanning electron microscopy (CD SEM) data of line and space patterns. Hence, the FiRM of Sigma-C is utilized as a resist parameter-optimizing program. According to our study, the illumination shape, the aberration and the pupil mesh point have a large effect on the accuracy of resist parameter in optimization. To obtain the optimum parameters, we need to find the saturated mesh points in terms of normalized intensity log slope (NILS) prior to an optimization. The simulation results using the optimized parameters by this method shows good agreement with experiments for iso-dense bias, Focus-Exposure Matrix data and sub 80nm device pattern simulation.
NASA Astrophysics Data System (ADS)
Li, Yafeng; Zhang, Ning; Zhou, Yueming; Wang, Jianing; Zhang, Yiming; Wang, Jiyun; Xiong, Caiqiao; Chen, Suming; Nie, Zongxiu
2013-09-01
Accurate mass information is of great importance in the determination of unknown compounds. An effective and easy-to-control internal mass calibration method will dramatically benefit accurate mass measurement. Here we reported a simple induced dual-nanospray internal calibration device which has the following three advantages: (1) the two sprayers are in the same alternating current field; thus both reference ions and sample ions can be simultaneously generated and recorded. (2) It is very simple and can be easily assembled. Just two metal tubes, two nanosprayers, and an alternating current power supply are included. (3) With the low-flow-rate character and the versatility of nanoESI, this calibration method is capable of calibrating various samples, even untreated complex samples such as urine and other biological samples with small sample volumes. The calibration errors are around 1 ppm in positive ion mode and 3 ppm in negative ion mode with good repeatability. This new internal calibration method opens up new possibilities in the determination of unknown compounds, and it has great potential for the broad applications in biological and chemical analysis.
A fast GNU method to draw accurate scientific illustrations for taxonomy.
Montesanto, Giuseppe
2015-01-01
Nowadays only digital figures are accepted by the most important journals of taxonomy. These may be produced by scanning conventional drawings, made with high precision technical ink-pens, which normally use capillary cartridge and various line widths. Digital drawing techniques that use vector graphics, have already been described in literature to support scientists in drawing figures and plates for scientific illustrations; these techniques use many different software and hardware devices. The present work gives step-by-step instructions on how to make accurate line drawings with a new procedure that uses bitmap graphics with the GNU Image Manipulation Program (GIMP). This method is noteworthy: it is very accurate, producing detailed lines at the highest resolution; the raster lines appear as realistic ink-made drawings; it is faster than the traditional way of making illustrations; everyone can use this simple technique; this method is completely free as it does not use expensive and licensed software and it can be used with different operating systems. The method has been developed drawing figures of terrestrial isopods and some examples are here given. PMID:26261449
NASA Technical Reports Server (NTRS)
Kim, Hyoungin; Liou, Meng-Sing
2011-01-01
In this paper, we demonstrate improved accuracy of the level set method for resolving deforming interfaces by proposing two key elements: (1) accurate level set solutions on adapted Cartesian grids by judiciously choosing interpolation polynomials in regions of different grid levels and (2) enhanced reinitialization by an interface sharpening procedure. The level set equation is solved using a fifth order WENO scheme or a second order central differencing scheme depending on availability of uniform stencils at each grid point. Grid adaptation criteria are determined so that the Hamiltonian functions at nodes adjacent to interfaces are always calculated by the fifth order WENO scheme. This selective usage between the fifth order WENO and second order central differencing schemes is confirmed to give more accurate results compared to those in literature for standard test problems. In order to further improve accuracy especially near thin filaments, we suggest an artificial sharpening method, which is in a similar form with the conventional re-initialization method but utilizes sign of curvature instead of sign of the level set function. Consequently, volume loss due to numerical dissipation on thin filaments is remarkably reduced for the test problems
A fast GNU method to draw accurate scientific illustrations for taxonomy
Montesanto, Giuseppe
2015-01-01
Abstract Nowadays only digital figures are accepted by the most important journals of taxonomy. These may be produced by scanning conventional drawings, made with high precision technical ink-pens, which normally use capillary cartridge and various line widths. Digital drawing techniques that use vector graphics, have already been described in literature to support scientists in drawing figures and plates for scientific illustrations; these techniques use many different software and hardware devices. The present work gives step-by-step instructions on how to make accurate line drawings with a new procedure that uses bitmap graphics with the GNU Image Manipulation Program (GIMP). This method is noteworthy: it is very accurate, producing detailed lines at the highest resolution; the raster lines appear as realistic ink-made drawings; it is faster than the traditional way of making illustrations; everyone can use this simple technique; this method is completely free as it does not use expensive and licensed software and it can be used with different operating systems. The method has been developed drawing figures of terrestrial isopods and some examples are here given. PMID:26261449
Joint iris boundary detection and fit: a real-time method for accurate pupil tracking.
Barbosa, Marconi; James, Andrew C
2014-08-01
A range of applications in visual science rely on accurate tracking of the human pupil's movement and contraction in response to light. While the literature for independent contour detection and fitting of the iris-pupil boundary is vast, a joint approach, in which it is assumed that the pupil has a given geometric shape has been largely overlooked. We present here a global method for simultaneously finding and fitting of an elliptic or circular contour against a dark interior, which produces consistently accurate results even under non-ideal recording conditions, such as reflections near and over the boundary, droopy eye lids, or the sudden formation of tears. The specific form of the proposed optimization problem allows us to write down closed analytic formulae for the gradient and the Hessian of the objective function. Moreover, both the objective function and its derivatives can be cast into vectorized form, making the proposed algorithm significantly faster than its closest relative in the literature. We compare methods in multiple ways, both analytically and numerically, using real iris images as well as idealizations of the iris for which the ground truth boundary is precisely known. The method proposed here is illustrated under challenging recording conditions and it is shown to be robust. PMID:25136477
A new cation-exchange method for accurate field speciation of hexavalent chromium
Ball, J.W.; McCleskey, R.B.
2003-01-01
A new method for field speciation of Cr(VI) has been developed to meet present stringent regulatory standards and to overcome the limitations of existing methods. The method consists of passing a water sample through strong acid cation-exchange resin at the field site, where Cr(III) is retained while Cr(VI) passes into the effluent and is preserved for later determination. The method is simple, rapid, portable, and accurate, and makes use of readily available, inexpensive materials. Cr(VI) concentrations are determined later in the laboratory using any elemental analysis instrument sufficiently sensitive to measure the Cr(VI) concentrations of interest. The new method allows measurement of Cr(VI) concentrations as low as 0.05 ??g 1-1, storage of samples for at least several weeks prior to analysis, and use of readily available analytical instrumentation. Cr(VI) can be separated from Cr(III) between pH 2 and 11 at Cr(III)/Cr(VI) concentration ratios as high as 1000. The new method has demonstrated excellent comparability with two commonly used methods, the Hach Company direct colorimetric method and USEPA method 218.6. The new method is superior to the Hach direct colorimetric method owing to its relative sensitivity and simplicity. The new method is superior to USEPA method 218.6 in the presence of Fe(II) concentrations up to 1 mg 1-1 and Fe(III) concentrations up to 10 mg 1-1. Time stability of preserved samples is a significant advantage over the 24-h time constraint specified for USEPA method 218.6.
Nebulizer calibration using lithium chloride: an accurate, reproducible and user-friendly method.
Ward, R J; Reid, D W; Leonard, R F; Johns, D P; Walters, E H
1998-04-01
Conventional gravimetric (weight loss) calibration of jet nebulizers overestimates their aerosol output by up to 80% due to unaccounted evaporative loss. We examined two methods of measuring true aerosol output from jet nebulizers. A new adaptation of a widely available clinical assay for lithium (determined by flame photometry, LiCl method) was compared to an existing electrochemical method based on fluoride detection (NaF method). The agreement between the two methods and the repeatability of each method were examined. Ten Mefar jet nebulizers were studied using a Mefar MK3 inhalation dosimeter. There was no significant difference between the two methods (p=0.76) with mean aerosol output of the 10 nebulizers being 7.40 mg x s(-1) (SD 1.06; range 5.86-9.36 mg x s(-1)) for the NaF method and 7.27 mg x s(-1) (SD 0.82; range 5.52-8.26 mg x s(-1)) for the LiCl method. The LiCl method had a coefficient of repeatability of 13 mg x s(-1) compared with 3.7 mg x s(-1) for the NaF method. The LiCl method accurately measured true aerosol output and was considerably easier to use. It was also more repeatable, and hence more precise, than the NaF method. Because the LiCl method uses an assay that is routinely available from hospital biochemistry laboratories, it is easy to use and, thus, can readily be adopted by busy respiratory function departments. PMID:9623700
Jha, Abhinav K.; Song, Na; Caffo, Brian; Frey, Eric C.
2015-01-01
Quantitative single-photon emission computed tomography (SPECT) imaging is emerging as an important tool in clinical studies and biomedical research. There is thus a need for optimization and evaluation of systems and algorithms that are being developed for quantitative SPECT imaging. An appropriate objective method to evaluate these systems is by comparing their performance in the end task that is required in quantitative SPECT imaging, such as estimating the mean activity concentration in a volume of interest (VOI) in a patient image. This objective evaluation can be performed if the true value of the estimated parameter is known, i.e. we have a gold standard. However, very rarely is this gold standard known in human studies. Thus, no-gold-standard techniques to optimize and evaluate systems and algorithms in the absence of gold standard are required. In this work, we developed a no-gold-standard technique to objectively evaluate reconstruction methods used in quantitative SPECT when the parameter to be estimated is the mean activity concentration in a VOI. We studied the performance of the technique with realistic simulated image data generated from an object database consisting of five phantom anatomies with all possible combinations of five sets of organ uptakes, where each anatomy consisted of eight different organ VOIs. Results indicate that the method provided accurate ranking of the reconstruction methods. We also demonstrated the application of consistency checks to test the no-gold-standard output. PMID:26430292
NASA Astrophysics Data System (ADS)
Jha, Abhinav K.; Song, Na; Caffo, Brian; Frey, Eric C.
2015-03-01
Quantitative single-photon emission computed tomography (SPECT) imaging is emerging as an important tool in clinical studies and biomedical research. There is thus a need for optimization and evaluation of systems and algorithms that are being developed for quantitative SPECT imaging. An appropriate objective method to evaluate these systems is by comparing their performance in the end task that is required in quantitative SPECT imaging, such as estimating the mean activity concentration in a volume of interest (VOI) in a patient image. This objective evaluation can be performed if the true value of the estimated parameter is known, i.e. we have a gold standard. However, very rarely is this gold standard known in human studies. Thus, no-gold-standard techniques to optimize and evaluate systems and algorithms in the absence of gold standard are required. In this work, we developed a no-gold-standard technique to objectively evaluate reconstruction methods used in quantitative SPECT when the parameter to be estimated is the mean activity concentration in a VOI. We studied the performance of the technique with realistic simulated image data generated from an object database consisting of five phantom anatomies with all possible combinations of five sets of organ uptakes, where each anatomy consisted of eight different organ VOIs. Results indicate that the method pro- vided accurate ranking of the reconstruction methods. We also demonstrated the application of consistency checks to test the no-gold-standard output.
An improved method for accurate and rapid measurement of flight performance in Drosophila.
Babcock, Daniel T; Ganetzky, Barry
2014-01-01
Drosophila has proven to be a useful model system for analysis of behavior, including flight. The initial flight tester involved dropping flies into an oil-coated graduated cylinder; landing height provided a measure of flight performance by assessing how far flies will fall before producing enough thrust to make contact with the wall of the cylinder. Here we describe an updated version of the flight tester with four major improvements. First, we added a "drop tube" to ensure that all flies enter the flight cylinder at a similar velocity between trials, eliminating variability between users. Second, we replaced the oil coating with removable plastic sheets coated in Tangle-Trap, an adhesive designed to capture live insects. Third, we use a longer cylinder to enable more accurate discrimination of flight ability. Fourth we use a digital camera and imaging software to automate the scoring of flight performance. These improvements allow for the rapid, quantitative assessment of flight behavior, useful for large datasets and large-scale genetic screens. PMID:24561810
Consisitent and Accurate Finite Volume Methods for Coupled Flow and Geomechanics
NASA Astrophysics Data System (ADS)
Nordbotten, J. M.
2014-12-01
We introduce a new class of cell-centered finite volume methods for elasticity and poro-elasticity. As compared to lowest-order finite element discretizations, the new discretization has no additional degrees of freedom, and yet gives more accurate stress and flow fields. This finite volume discretization methods has furthermore the advantage that the mechanical discretization is fully compatible (in terms of grid and variables) with the standard cell-centered finite volume discretizations that are prevailing for commercial simulation of multi-phase flows in porous media. Theoretical analysis proves the convergence of the method. We give results showing that so-called numerical locking is avoided for a large class of structured and unstructured grids. The results are valid in both two and three spatial dimensions. The talk concludes with applications to problems with coupled multi-phase flow, transport and deformation, together with fractured porous media.
NASA Astrophysics Data System (ADS)
Chang, Liyun; Ho, Sheng-Yow; Du, Yi-Chun; Lin, Chih-Ming; Chen, Tainsong
2007-06-01
The calibration of the gantry angle indicator is an important and basic quality assurance (QA) item for the radiotherapy linear accelerator. In this study, we propose a new and practical method, which uses only the digital level, V-film, and general solid phantoms. By taking the star shot only, we can accurately calculate the true gantry angle according to the geometry of the film setup. The results on our machine showed that the gantry angle was shifted by -0.11° compared with the digital indicator, and the standard deviation was within 0.05°. This method can also be used for the simulator. In conclusion, this proposed method could be adopted as an annual QA item for mechanical QA of the accelerator.
Accurate calculation of computer-generated holograms using angular-spectrum layer-oriented method.
Zhao, Yan; Cao, Liangcai; Zhang, Hao; Kong, Dezhao; Jin, Guofan
2015-10-01
Fast calculation and correct depth cue are crucial issues in the calculation of computer-generated hologram (CGH) for high quality three-dimensional (3-D) display. An angular-spectrum based algorithm for layer-oriented CGH is proposed. Angular spectra from each layer are synthesized as a layer-corresponded sub-hologram based on the fast Fourier transform without paraxial approximation. The proposed method can avoid the huge computational cost of the point-oriented method and yield accurate predictions of the whole diffracted field compared with other layer-oriented methods. CGHs of versatile formats of 3-D digital scenes, including computed tomography and 3-D digital models, are demonstrated with precise depth performance and advanced image quality. PMID:26480062
Quick and accurate estimation of the elastic constants using the minimum image method
NASA Astrophysics Data System (ADS)
Tretiakov, Konstantin V.; Wojciechowski, Krzysztof W.
2015-04-01
A method for determining the elastic properties using the minimum image method (MIM) is proposed and tested on a model system of particles interacting by the Lennard-Jones (LJ) potential. The elastic constants of the LJ system are determined in the thermodynamic limit, N → ∞, using the Monte Carlo (MC) method in the NVT and NPT ensembles. The simulation results show that when determining the elastic constants, the contribution of long-range interactions cannot be ignored, because that would lead to erroneous results. In addition, the simulations have revealed that the inclusion of further interactions of each particle with all its minimum image neighbors even in case of small systems leads to results which are very close to the values of elastic constants in the thermodynamic limit. This enables one for a quick and accurate estimation of the elastic constants using very small samples.
Qian, Weijun; Monroe, Matthew E.; Liu, Tao; Jacobs, Jon M.; Anderson, Gordon A.; Shen, Yufeng; Moore, Ronald J.; Anderson, David J.; Zhang, Rui; Calvano, Steven E.; Lowry, Stephen F.; Xiao, Wenzhong; Moldawer, Lyle L.; Davis, Ronald W.; Tompkins, Ronald G.; Camp, David G.; Smith, Richard D.
2005-05-01
Identification of novel diagnostic or therapeutic biomarkers from human blood plasma would benefit significantly from quantitative measurements of the proteome constituents over a range of physiological conditions. We describe here an initial demonstration of proteome-wide quantitative analysis of human plasma. The approach utilizes post-digestion trypsin-catalyzed 16O/18O labeling, two-dimensional liquid chromatography (LC)-Fourier transform ion cyclotron resonance ((FTICR) mass spectrometry, and the accurate mass and time (AMT) tag strategy for identification and quantification of peptides/proteins from complex samples. A peptide mass and time tag database was initially generated using tandem mass spectrometry (MS/MS) following extensive multidimensional LC separations and the database serves as a ‘look-up’ table for peptide identification. The mass and time tag database contains >8,000 putative identified peptides, which yielded 938 confident plasma protein identifications. The quantitative approach was applied to the comparative analyses of plasma samples from an individual prior to and 9 hours after lipopolysaccharide (LPS) administration without depletion of high abundant proteins. Accurate quantification of changes in protein abundance was demonstrated with both 1:1 labeling of control plasma and the comparison between the plasma samples following LPS administration. A total of 429 distinct plasma proteins were quantified from the comparative analyses and the protein abundances for 28 proteins were observed to be significantly changed following LPS administration, including several known inflammatory response mediators.
Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua
2015-01-13
We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207
Pérez-Ortega, Patricia; Lara-Ortega, Felipe J; García-Reyes, Juan F; Gilbert-López, Bienvenida; Trojanowicz, Marek; Molina-Díaz, Antonio
2016-11-01
The feasibility of accurate-mass multi-residue screening methods using liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) using time-of-flight mass spectrometry has been evaluated, including over 625 multiclass food contaminants as case study. Aspects such as the selectivity and confirmation capability provided by HRMS with different acquisition modes (full-scan or full-scan combined with collision induced dissociation (CID) with no precursor ion isolation), and chromatographic separation along with main limitations such as sensitivity or automated data processing have been examined. Compound identification was accomplished with retention time matching and accurate mass measurements of the targeted ions for each analyte (mainly (de)protonated molecules). Compounds with the same nominal mass (isobaric species) were very frequent due to the large number of compounds included. Although 76% of database compounds were involved in isobaric groups, they were resolved in most cases (99% of these isobaric species were distinguished by retention time, resolving power, isotopic profile or fragment ions). Only three pairs could not be resolved with these tools. In-source CID fragmentation was evaluated in depth, although the results obtained in terms of information provided were not as thorough as those obtained using fragmentation experiments without precursor ion isolation (all ion mode). The latter acquisition mode was found to be the best suited for this type of large-scale screening method instead of classic product ion scan, as provided excellent fragmentation information for confirmatory purposes for an unlimited number of compounds. Leaving aside the sample treatment limitations, the main weaknesses noticed are basically the relatively low sensitivity for compounds which does not map well against electrospray ionization and also quantitation issues such as those produced by signal suppression due to either matrix effects from coeluting matrix or from
Some selected quantitative methods of thermal image analysis in Matlab.
Koprowski, Robert
2016-05-01
The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image. PMID:26556680
Informatics Methods to Enable Sharing of Quantitative Imaging Research Data
Levy, Mia A.; Freymann, John B.; Kirby, Justin S.; Fedorov, Andriy; Fennessy, Fiona M.; Eschrich, Steven A.; Berglund, Anders E.; Fenstermacher, David A.; Tan, Yongqiang; Guo, Xiaotao; Casavant, Thomas L.; Brown, Bartley J.; Braun, Terry A.; Dekker, Andre; Roelofs, Erik; Mountz, James M.; Boada, Fernando; Laymon, Charles; Oborski, Matt; Rubin, Daniel L
2012-01-01
Introduction The National Cancer Institute (NCI) Quantitative Research Network (QIN) is a collaborative research network whose goal is to share data, algorithms and research tools to accelerate quantitative imaging research. A challenge is the variability in tools and analysis platforms used in quantitative imaging. Our goal was to understand the extent of this variation and to develop an approach to enable sharing data and to promote reuse of quantitative imaging data in the community. Methods We performed a survey of the current tools in use by the QIN member sites for representation and storage of their QIN research data including images, image meta-data and clinical data. We identified existing systems and standards for data sharing and their gaps for the QIN use case. We then proposed a system architecture to enable data sharing and collaborative experimentation within the QIN. Results There area variety of tools currently used by each QIN institution. We developed a general information system architecture to support the QIN goals. We also describe the remaining architecture gaps we are developing to enable members to share research images and image meta-data across the network. Conclusions As a research network, the QIN will stimulate quantitative imaging research by pooling data, algorithms and research tools. However, there are gaps in current functional requirements that will need to be met by future informatics development. Special attention must be given to the technical requirements needed to translate these methods into the clinical research workflow to enable validation and qualification of these novel imaging biomarkers. PMID:22770688
Pabst, Martin; Fagerer, Stephan R; Köhling, Rudolf; Küster, Simon K; Steinhoff, Robert; Badertscher, Martin; Wahl, Fabian; Dittrich, Petra S; Jefimovs, Konstantins; Zenobi, Renato
2013-10-15
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a fast analysis tool employed for the detection of a broad range of analytes. However, MALDI-MS has a reputation of not being suitable for quantitative analysis. Inhomogeneous analyte/matrix co-crystallization, spot-to-spot inhomogeneity, as well as a typically low number of replicates are the main contributing factors. Here, we present a novel MALDI sample target for quantitative MALDI-MS applications, which addresses the limitations mentioned above. The platform is based on the recently developed microarray for mass spectrometry (MAMS) technology and contains parallel lanes of hydrophilic reservoirs. Samples are not pipetted manually but deposited by dragging one or several sample droplets with a metal sliding device along these lanes. Sample is rapidly and automatically aliquoted into the sample spots due to the interplay of hydrophilic/hydrophobic interactions. With a few microliters of sample, it is possible to aliquot up to 40 replicates within seconds, each aliquot containing just 10 nL. The analyte droplet dries immediately and homogeneously, and consumption of the whole spot during MALDI-MS analysis is typically accomplished within few seconds. We evaluated these sample targets with respect to their suitability for use with different samples and matrices. Furthermore, we tested their application for generating calibration curves of standard peptides with α-cyano-4-hdydroxycinnamic acid as a matrix. For angiotensin II and [Glu(1)]-fibrinopeptide B we achieved coefficients of determination (r(2)) greater than 0.99 without the use of internal standards. PMID:24003910
Quantitative method of measuring cancer cell urokinase and metastatic potential
NASA Technical Reports Server (NTRS)
Morrison, Dennis R. (Inventor)
1993-01-01
The metastatic potential of tumors can be evaluated by the quantitative detection of urokinase and DNA. The cell sample selected for examination is analyzed for the presence of high levels of urokinase and abnormal DNA using analytical flow cytometry and digital image analysis. Other factors such as membrane associated urokinase, increased DNA synthesis rates and certain receptors can be used in the method for detection of potentially invasive tumors.
Parente2: a fast and accurate method for detecting identity by descent
Rodriguez, Jesse M.; Bercovici, Sivan; Huang, Lin; Frostig, Roy; Batzoglou, Serafim
2015-01-01
Identity-by-descent (IBD) inference is the problem of establishing a genetic connection between two individuals through a genomic segment that is inherited by both individuals from a recent common ancestor. IBD inference is an important preceding step in a variety of population genomic studies, ranging from demographic studies to linking genomic variation with phenotype and disease. The problem of accurate IBD detection has become increasingly challenging with the availability of large collections of human genotypes and genomes: Given a cohort’s size, a quadratic number of pairwise genome comparisons must be performed. Therefore, computation time and the false discovery rate can also scale quadratically. To enable accurate and efficient large-scale IBD detection, we present Parente2, a novel method for detecting IBD segments. Parente2 is based on an embedded log-likelihood ratio and uses a model that accounts for linkage disequilibrium by explicitly modeling haplotype frequencies. Parente2 operates directly on genotype data without the need to phase data prior to IBD inference. We evaluate Parente2’s performance through extensive simulations using real data, and we show that it provides substantially higher accuracy compared to previous state-of-the-art methods while maintaining high computational efficiency. PMID:25273070
An adaptive, formally second order accurate version of the immersed boundary method
NASA Astrophysics Data System (ADS)
Griffith, Boyce E.; Hornung, Richard D.; McQueen, David M.; Peskin, Charles S.
2007-04-01
Like many problems in biofluid mechanics, cardiac mechanics can be modeled as the dynamic interaction of a viscous incompressible fluid (the blood) and a (visco-)elastic structure (the muscular walls and the valves of the heart). The immersed boundary method is a mathematical formulation and numerical approach to such problems that was originally introduced to study blood flow through heart valves, and extensions of this work have yielded a three-dimensional model of the heart and great vessels. In the present work, we introduce a new adaptive version of the immersed boundary method. This adaptive scheme employs the same hierarchical structured grid approach (but a different numerical scheme) as the two-dimensional adaptive immersed boundary method of Roma et al. [A multilevel self adaptive version of the immersed boundary method, Ph.D. Thesis, Courant Institute of Mathematical Sciences, New York University, 1996; An adaptive version of the immersed boundary method, J. Comput. Phys. 153 (2) (1999) 509-534] and is based on a formally second order accurate (i.e., second order accurate for problems with sufficiently smooth solutions) version of the immersed boundary method that we have recently described [B.E. Griffith, C.S. Peskin, On the order of accuracy of the immersed boundary method: higher order convergence rates for sufficiently smooth problems, J. Comput. Phys. 208 (1) (2005) 75-105]. Actual second order convergence rates are obtained for both the uniform and adaptive methods by considering the interaction of a viscous incompressible flow and an anisotropic incompressible viscoelastic shell. We also present initial results from the application of this methodology to the three-dimensional simulation of blood flow in the heart and great vessels. The results obtained by the adaptive method show good qualitative agreement with simulation results obtained by earlier non-adaptive versions of the method, but the flow in the vicinity of the model heart valves
Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method
Sinha, Debalina; Pavanello, Michele
2015-08-28
The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term the Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.
Generalized weighted ratio method for accurate turbidity measurement over a wide range.
Liu, Hongbo; Yang, Ping; Song, Hong; Guo, Yilu; Zhan, Shuyue; Huang, Hui; Wang, Hangzhou; Tao, Bangyi; Mu, Quanquan; Xu, Jing; Li, Dejun; Chen, Ying
2015-12-14
Turbidity measurement is important for water quality assessment, food safety, medicine, ocean monitoring, etc. In this paper, a method that accurately estimates the turbidity over a wide range is proposed, where the turbidity of the sample is represented as a weighted ratio of the scattered light intensities at a series of angles. An improvement in the accuracy is achieved by expanding the structure of the ratio function, thus adding more flexibility to the turbidity-intensity fitting. Experiments have been carried out with an 850 nm laser and a power meter fixed on a turntable to measure the light intensity at different angles. The results show that the relative estimation error of the proposed method is 0.58% on average for a four-angle intensity combination for all test samples with a turbidity ranging from 160 NTU to 4000 NTU. PMID:26699060
Accurate calculation of Coulomb sums: Efficacy of Pade-like methods
Sarkar, B. ); Bhattacharyya, K. )
1993-09-01
The adequacy of numerical sequence accelerative transforms in providing accurate estimates of Coulomb sums is considered, referring particularly to distorted lattices. Performance of diagonal Pade approximants (DPA) in this context is critically assessed. Failure in the case of lattice vacancies is also demonstrated. The method of multiple-point Pade approximants (MPA) has been introduced for slowly convergent sequences and is shown to work well for both regular and distorted lattices, the latter being due either to impurities or vacancies. Viability of the two methods is also compared. In divergent situations with distortions owing to vacancies, a strategy of obtaining reliable results by separate applications of both DPA and MPA at appropriate places is also sketched. Representative calculations involve two basic cubic-lattice sums, one slowly convergent and the other divergent, from which very good quality estimates of Madelung constants for a number of common lattices follow.
Robert, Stéphane; Battie, Yann; Jamon, Damien; Royer, Francois
2007-04-10
Optimal performances of integrated optical devices are obtained by the use of an accurate and reliable characterization method. The parameters of interest, i.e., optical indices and thickness of the waveguide structure, are calculated from effective indices by means of an inversion procedure. We demonstrate how an artificial neural network can achieve such a process. The artificial neural network used is a multilayer perceptron. The first result concerns a simulated anisotropic waveguide. The accuracy in the determination of optical indices and waveguide thickness is 5 x 10(-5) and 4 nm, respectively. Then an experimental application on a silica-titania thin film is performed. In addition, effective indices are measured by m-lines spectroscopy. Finally, a comparison with a classical optimization algorithm demonstrates the robustness of the neural method. PMID:17384718
NASA Technical Reports Server (NTRS)
Yungster, Shaye; Radhakrishnan, Krishnan
1994-01-01
A new fully implicit, time accurate algorithm suitable for chemically reacting, viscous flows in the transonic-to-hypersonic regime is described. The method is based on a class of Total Variation Diminishing (TVD) schemes and uses successive Gauss-Siedel relaxation sweeps. The inversion of large matrices is avoided by partitioning the system into reacting and nonreacting parts, but still maintaining a fully coupled interaction. As a result, the matrices that have to be inverted are of the same size as those obtained with the commonly used point implicit methods. In this paper we illustrate the applicability of the new algorithm to hypervelocity unsteady combustion applications. We present a series of numerical simulations of the periodic combustion instabilities observed in ballistic-range experiments of blunt projectiles flying at subdetonative speeds through hydrogen-air mixtures. The computed frequencies of oscillation are in excellent agreement with experimental data.
Spectroscopic Method for Fast and Accurate Group A Streptococcus Bacteria Detection.
Schiff, Dillon; Aviv, Hagit; Rosenbaum, Efraim; Tischler, Yaakov R
2016-02-16
Rapid and accurate detection of pathogens is paramount to human health. Spectroscopic techniques have been shown to be viable methods for detecting various pathogens. Enhanced methods of Raman spectroscopy can discriminate unique bacterial signatures; however, many of these require precise conditions and do not have in vivo replicability. Common biological detection methods such as rapid antigen detection tests have high specificity but do not have high sensitivity. Here we developed a new method of bacteria detection that is both highly specific and highly sensitive by combining the specificity of antibody staining and the sensitivity of spectroscopic characterization. Bacteria samples, treated with a fluorescent antibody complex specific to Streptococcus pyogenes, were volumetrically normalized according to their Raman bacterial signal intensity and characterized for fluorescence, eliciting a positive result for samples containing Streptococcus pyogenes and a negative result for those without. The normalized fluorescence intensity of the Streptococcus pyogenes gave a signal that is up to 16.4 times higher than that of other bacteria samples for bacteria stained in solution and up to 12.7 times higher in solid state. This method can be very easily replicated for other bacteria species using suitable antibody-dye complexes. In addition, this method shows viability for in vivo detection as it requires minute amounts of bacteria, low laser excitation power, and short integration times in order to achieve high signal. PMID:26752013
NASA Astrophysics Data System (ADS)
Katsuyama, Yutaka; Takebe, Hiroaki; Kurokawa, Koji; Saitoh, Takahiro; Naoi, Satoshi
2001-12-01
We have developed a method that allows Japanese document images to be retrieved more accurately by using OCR character candidate information and a conventional plain text search engine. In this method, the document image is first recognized by normal OCR to produce text. Keyword areas are then estimated from the normal OCR produced text through morphological analysis. A lattice of candidate- character codes is extracted from these areas, and then character strings are extracted from the lattice using a word-matching method in noun areas and a K-th DP-matching method in undefined word areas. Finally, these extracted character strings are added to the normal OCR produced text to improve document retrieval accuracy when u sing a conventional plain text search engine. Experimental results from searches of 49 OHP sheet images revealed that our method has a high recall rate of 98.2%, compared to 90.3% with a conventional method using only normal OCR produced text, while requiring about the same processing time as normal OCR.
[A New Method of Accurately Extracting Spectral Values for Discrete Sampling Points].
Lü, Zhen-zhen; Liu, Guang-ming; Yang, Jin-song
2015-08-01
In the establishment of remote sensing information inversion model, the actual measured data of discrete sampling points and the corresponding spectrum data to pixels of remote sensing image, are used to establish the relation, thus to realize the goal of information retrieval. Accurate extraction of spectrum value is very important to establish the remote sensing inversion mode. Converting target spot layer to ROI (region of interest) and then saving the ROI as ASCII is one of the methods that researchers often used to extract the spectral values. Analyzing the coordinate and spectrum values extracted using original coordinate in ENVI, we found that the extracted and original coordinate were not inconsistent and part of spectrum values not belong to the pixel containing the sampling point. The inversion model based on the above information cannot really reflect relationship between the target properties and spectral values; so that the model is meaningless. We equally divided the pixel into four parts and summed up the law. It was found that only when the sampling points distributed in the upper left corner of pixels, the extracted values were correct. On the basis of the above methods, this paper systematically studied the principle of extraction target coordinate and spectral values, and summarized the rule. A new method for extracting spectral parameters of the pixel that sampling point located in the environment of ENVI software. Firstly, pixel sampling point coordinates for any of the four corner points were extracted by the sample points with original coordinate in ENVI. Secondly, the sampling points were judged in which partition of pixel by comparing the absolute values of difference longitude and latitude of the original and extraction coordinates. Lastly, all points were adjusted to the upper left corner of pixels by symmetry principle and spectrum values were extracted by the same way in the first step. The results indicated that the extracted spectrum
A quantitative method for measuring the quality of history matches
Shaw, T.S.; Knapp, R.M.
1997-08-01
History matching can be an efficient tool for reservoir characterization. A {open_quotes}good{close_quotes} history matching job can generate reliable reservoir parameters. However, reservoir engineers are often frustrated when they try to select a {open_quotes}better{close_quotes} match from a series of history matching runs. Without a quantitative measurement, it is always difficult to tell the difference between a {open_quotes}good{close_quotes} and a {open_quotes}better{close_quotes} matches. For this reason, we need a quantitative method for testing the quality of matches. This paper presents a method for such a purpose. The method uses three statistical indices to (1) test shape conformity, (2) examine bias errors, and (3) measure magnitude of deviation. The shape conformity test insures that the shape of a simulated curve matches that of a historical curve. Examining bias errors assures that model reservoir parameters have been calibrated to that of a real reservoir. Measuring the magnitude of deviation assures that the difference between the model and the real reservoir parameters is minimized. The method was first tested on a hypothetical model and then applied to published field studies. The results showed that the method can efficiently measure the quality of matches. It also showed that the method can serve as a diagnostic tool for calibrating reservoir parameters during history matching.
Quantitative assessment of susceptibility weighted imaging processing methods
Li, Ningzhi; Wang, Wen-Tung; Sati, Pascal; Pham, Dzung L.; Butman, John A.
2013-01-01
Purpose To evaluate different susceptibility weighted imaging (SWI) phase processing methods and parameter selection, thereby improving understanding of potential artifacts, as well as facilitating choice of methodology in clinical settings. Materials and Methods Two major phase processing methods, Homodyne-filtering and phase unwrapping-high pass (HP) filtering, were investigated with various phase unwrapping approaches, filter sizes, and filter types. Magnitude and phase images were acquired from a healthy subject and brain injury patients on a 3T clinical Siemens MRI system. Results were evaluated based on image contrast to noise ratio and presence of processing artifacts. Results When using a relatively small filter size (32 pixels for the matrix size 512 × 512 pixels), all Homodyne-filtering methods were subject to phase errors leading to 2% to 3% masked brain area in lower and middle axial slices. All phase unwrapping-filtering/smoothing approaches demonstrated fewer phase errors and artifacts compared to the Homodyne-filtering approaches. For performing phase unwrapping, Fourier-based methods, although less accurate, were 2–4 orders of magnitude faster than the PRELUDE, Goldstein and Quality-guide methods. Conclusion Although Homodyne-filtering approaches are faster and more straightforward, phase unwrapping followed by HP filtering approaches perform more accurately in a wider variety of acquisition scenarios. PMID:24923594
A comparison of quantitative methods for clinical imaging with hyperpolarized (13)C-pyruvate.
Daniels, Charlie J; McLean, Mary A; Schulte, Rolf F; Robb, Fraser J; Gill, Andrew B; McGlashan, Nicholas; Graves, Martin J; Schwaiger, Markus; Lomas, David J; Brindle, Kevin M; Gallagher, Ferdia A
2016-04-01
Dissolution dynamic nuclear polarization (DNP) enables the metabolism of hyperpolarized (13)C-labelled molecules, such as the conversion of [1-(13)C]pyruvate to [1-(13)C]lactate, to be dynamically and non-invasively imaged in tissue. Imaging of this exchange reaction in animal models has been shown to detect early treatment response and correlate with tumour grade. The first human DNP study has recently been completed, and, for widespread clinical translation, simple and reliable methods are necessary to accurately probe the reaction in patients. However, there is currently no consensus on the most appropriate method to quantify this exchange reaction. In this study, an in vitro system was used to compare several kinetic models, as well as simple model-free methods. Experiments were performed using a clinical hyperpolarizer, a human 3 T MR system, and spectroscopic imaging sequences. The quantitative methods were compared in vivo by using subcutaneous breast tumours in rats to examine the effect of pyruvate inflow. The two-way kinetic model was the most accurate method for characterizing the exchange reaction in vitro, and the incorporation of a Heaviside step inflow profile was best able to describe the in vivo data. The lactate time-to-peak and the lactate-to-pyruvate area under the curve ratio were simple model-free approaches that accurately represented the full reaction, with the time-to-peak method performing indistinguishably from the best kinetic model. Finally, extracting data from a single pixel was a robust and reliable surrogate of the whole region of interest. This work has identified appropriate quantitative methods for future work in the analysis of human hyperpolarized (13)C data. PMID:27414749
A comparison of quantitative methods for clinical imaging with hyperpolarized 13C‐pyruvate
Daniels, Charlie J.; McLean, Mary A.; Schulte, Rolf F.; Robb, Fraser J.; Gill, Andrew B.; McGlashan, Nicholas; Graves, Martin J.; Schwaiger, Markus; Lomas, David J.; Brindle, Kevin M.
2016-01-01
Dissolution dynamic nuclear polarization (DNP) enables the metabolism of hyperpolarized 13C‐labelled molecules, such as the conversion of [1‐13C]pyruvate to [1‐13C]lactate, to be dynamically and non‐invasively imaged in tissue. Imaging of this exchange reaction in animal models has been shown to detect early treatment response and correlate with tumour grade. The first human DNP study has recently been completed, and, for widespread clinical translation, simple and reliable methods are necessary to accurately probe the reaction in patients. However, there is currently no consensus on the most appropriate method to quantify this exchange reaction. In this study, an in vitro system was used to compare several kinetic models, as well as simple model‐free methods. Experiments were performed using a clinical hyperpolarizer, a human 3 T MR system, and spectroscopic imaging sequences. The quantitative methods were compared in vivo by using subcutaneous breast tumours in rats to examine the effect of pyruvate inflow. The two‐way kinetic model was the most accurate method for characterizing the exchange reaction in vitro, and the incorporation of a Heaviside step inflow profile was best able to describe the in vivo data. The lactate time‐to‐peak and the lactate‐to‐pyruvate area under the curve ratio were simple model‐free approaches that accurately represented the full reaction, with the time‐to‐peak method performing indistinguishably from the best kinetic model. Finally, extracting data from a single pixel was a robust and reliable surrogate of the whole region of interest. This work has identified appropriate quantitative methods for future work in the analysis of human hyperpolarized 13C data. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd. PMID:27414749
Caytan, Elsa; Botosoa, Eliot P; Silvestre, Virginie; Robins, Richard J; Akoka, Serge; Remaud, Gérald S
2007-11-01
The stability over time (repeatability) for the determination of site-specific 13C/12C ratios at natural abundance by quantitative 13C NMR spectroscopy has been tested on three probes: enriched bilabeled [1,2-13C2]ethanol; ethanol at natural abundance; and vanillin at natural abundance. It is shown in all three cases that the standard deviation for a series of measurements taken every 2-3 months over periods between 9 and 13 months is equal to or smaller than the standard deviation calculated from 5-10 replicate measurements made on a single sample. The precision which can be achieved using the present analytical 13C NMR protocol is higher than the prerequisite value of 1-2 per thousand for the determination of site-specific 13C/12C ratios at natural abundance (13C-SNIF-NMR). Hence, this technique permits the discrimination of very small variations in 13C/12C ratios between carbon positions, as found in biogenic natural products. This observed stability over time in 13C NMR spectroscopy indicates that further improvements in precision will depend primarily on improved signal-to-noise ratio. PMID:17900175
Golestan Hashemi, Farahnaz Sadat; Rafii, Mohd Y.; Ismail, Mohd Razi; Mohamed, Mahmud Tengku Muda; Rahim, Harun A.; Latif, Mohammad Abdul; Aslani, Farzad
2015-01-01
When a phenotype of interest is associated with an external/internal covariate, covariate inclusion in quantitative trait loci (QTL) analyses can diminish residual variation and subsequently enhance the ability of QTL detection. In the in vitro synthesis of 2-acetyl-1-pyrroline (2AP), the main fragrance compound in rice, the thermal processing during the Maillard-type reaction between proline and carbohydrate reduction produces a roasted, popcorn-like aroma. Hence, for the first time, we included the proline amino acid, an important precursor of 2AP, as a covariate in our QTL mapping analyses to precisely explore the genetic factors affecting natural variation for rice scent. Consequently, two QTLs were traced on chromosomes 4 and 8. They explained from 20% to 49% of the total aroma phenotypic variance. Additionally, by saturating the interval harboring the major QTL using gene-based primers, a putative allele of fgr (major genetic determinant of fragrance) was mapped in the QTL on the 8th chromosome in the interval RM223-SCU015RM (1.63 cM). These loci supported previous studies of different accessions. Such QTLs can be widely used by breeders in crop improvement programs and for further fine mapping. Moreover, no previous studies and findings were found on simultaneous assessment of the relationship among 2AP, proline and fragrance QTLs. Therefore, our findings can help further our understanding of the metabolomic and genetic basis of 2AP biosynthesis in aromatic rice. PMID:26061689
Golestan Hashemi, Farahnaz Sadat; Rafii, Mohd Y; Ismail, Mohd Razi; Mohamed, Mahmud Tengku Muda; Rahim, Harun A; Latif, Mohammad Abdul; Aslani, Farzad
2015-01-01
When a phenotype of interest is associated with an external/internal covariate, covariate inclusion in quantitative trait loci (QTL) analyses can diminish residual variation and subsequently enhance the ability of QTL detection. In the in vitro synthesis of 2-acetyl-1-pyrroline (2AP), the main fragrance compound in rice, the thermal processing during the Maillard-type reaction between proline and carbohydrate reduction produces a roasted, popcorn-like aroma. Hence, for the first time, we included the proline amino acid, an important precursor of 2AP, as a covariate in our QTL mapping analyses to precisely explore the genetic factors affecting natural variation for rice scent. Consequently, two QTLs were traced on chromosomes 4 and 8. They explained from 20% to 49% of the total aroma phenotypic variance. Additionally, by saturating the interval harboring the major QTL using gene-based primers, a putative allele of fgr (major genetic determinant of fragrance) was mapped in the QTL on the 8th chromosome in the interval RM223-SCU015RM (1.63 cM). These loci supported previous studies of different accessions. Such QTLs can be widely used by breeders in crop improvement programs and for further fine mapping. Moreover, no previous studies and findings were found on simultaneous assessment of the relationship among 2AP, proline and fragrance QTLs. Therefore, our findings can help further our understanding of the metabolomic and genetic basis of 2AP biosynthesis in aromatic rice. PMID:26061689
Zhang, Jing; Teixeira da Silva, Jaime A.; Wang, ChunXia; Sun, HongMei
2015-01-01
Lilium is an important commercial market flower bulb. qRT-PCR is an extremely important technique to track gene expression levels. The requirement of suitable reference genes for normalization has become increasingly significant and exigent. The expression of internal control genes in living organisms varies considerably under different experimental conditions. For economically important Lilium, only a limited number of reference genes applied in qRT-PCR have been reported to date. In this study, the expression stability of 12 candidate genes including α-TUB, β-TUB, ACT, eIF, GAPDH, UBQ, UBC, 18S, 60S, AP4, FP, and RH2, in a diverse set of 29 samples representing different developmental processes, three stress treatments (cold, heat, and salt) and different organs, has been evaluated. For different organs, the combination of ACT, GAPDH, and UBQ is appropriate whereas ACT together with AP4, or ACT along with GAPDH is suitable for normalization of leaves and scales at different developmental stages, respectively. In leaves, scales and roots under stress treatments, FP, ACT and AP4, respectively showed the most stable expression. This study provides a guide for the selection of a reference gene under different experimental conditions, and will benefit future research on more accurate gene expression studies in a wide variety of Lilium genotypes. PMID:26509446
An accurate clone-based haplotyping method by overlapping pool sequencing.
Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao
2016-07-01
Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. PMID:27095193
Efficient and accurate numerical methods for the Klein-Gordon-Schroedinger equations
Bao, Weizhu . E-mail: bao@math.nus.edu.sg; Yang, Li . E-mail: yangli@nus.edu.sg
2007-08-10
In this paper, we present efficient, unconditionally stable and accurate numerical methods for approximations of the Klein-Gordon-Schroedinger (KGS) equations with/without damping terms. The key features of our methods are based on: (i) the application of a time-splitting spectral discretization for a Schroedinger-type equation in KGS (ii) the utilization of Fourier pseudospectral discretization for spatial derivatives in the Klein-Gordon equation in KGS (iii) the adoption of solving the ordinary differential equations (ODEs) in phase space analytically under appropriate chosen transmission conditions between different time intervals or applying Crank-Nicolson/leap-frog for linear/nonlinear terms for time derivatives. The numerical methods are either explicit or implicit but can be solved explicitly, unconditionally stable, and of spectral accuracy in space and second-order accuracy in time. Moreover, they are time reversible and time transverse invariant when there is no damping terms in KGS, conserve (or keep the same decay rate of) the wave energy as that in KGS without (or with a linear) damping term, keep the same dynamics of the mean value of the meson field, and give exact results for the plane-wave solution. Extensive numerical tests are presented to confirm the above properties of our numerical methods for KGS. Finally, the methods are applied to study solitary-wave collisions in one dimension (1D), as well as dynamics of a 2D problem in KGS.
An accurate clone-based haplotyping method by overlapping pool sequencing
Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao
2016-01-01
Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. PMID:27095193
A highly accurate method for the determination of mass and center of mass of a spacecraft
NASA Technical Reports Server (NTRS)
Chow, E. Y.; Trubert, M. R.; Egwuatu, A.
1978-01-01
An extremely accurate method for the measurement of mass and the lateral center of mass of a spacecraft has been developed. The method was needed for the Voyager spacecraft mission requirement which limited the uncertainty in the knowledge of lateral center of mass of the spacecraft system weighing 750 kg to be less than 1.0 mm (0.04 in.). The method consists of using three load cells symmetrically located at 120 deg apart on a turntable with respect to the vertical axis of the spacecraft and making six measurements for each load cell. These six measurements are taken by cyclic rotations of the load cell turntable and of the spacecraft, about the vertical axis of the measurement fixture. This method eliminates all alignment, leveling, and load cell calibration errors for the lateral center of mass determination, and permits a statistical best fit of the measurement data. An associated data reduction computer program called MASCM has been written to implement this method and has been used for the Voyager spacecraft.
An Improved Quantitative Analysis Method for Plant Cortical Microtubules
Lu, Yi; Huang, Chenyang; Wang, Jia; Shang, Peng
2014-01-01
The arrangement of plant cortical microtubules can reflect the physiological state of cells. However, little attention has been paid to the image quantitative analysis of plant cortical microtubules so far. In this paper, Bidimensional Empirical Mode Decomposition (BEMD) algorithm was applied in the image preprocessing of the original microtubule image. And then Intrinsic Mode Function 1 (IMF1) image obtained by decomposition was selected to do the texture analysis based on Grey-Level Cooccurrence Matrix (GLCM) algorithm. Meanwhile, in order to further verify its reliability, the proposed texture analysis method was utilized to distinguish different images of Arabidopsis microtubules. The results showed that the effect of BEMD algorithm on edge preserving accompanied with noise reduction was positive, and the geometrical characteristic of the texture was obvious. Four texture parameters extracted by GLCM perfectly reflected the different arrangements between the two images of cortical microtubules. In summary, the results indicate that this method is feasible and effective for the image quantitative analysis of plant cortical microtubules. It not only provides a new quantitative approach for the comprehensive study of the role played by microtubules in cell life activities but also supplies references for other similar studies. PMID:24744684
NASA Astrophysics Data System (ADS)
He, Wantao; Li, Zhongwei; Zhong, Kai; Shi, Yusheng; Zhao, Can; Cheng, Xu
2014-11-01
Fast and precise 3D inspection system is in great demand in modern manufacturing processes. At present, the available sensors have their own pros and cons, and hardly exist an omnipotent sensor to handle the complex inspection task in an accurate and effective way. The prevailing solution is integrating multiple sensors and taking advantages of their strengths. For obtaining a holistic 3D profile, the data from different sensors should be registrated into a coherent coordinate system. However, some complex shape objects own thin wall feather such as blades, the ICP registration method would become unstable. Therefore, it is very important to calibrate the extrinsic parameters of each sensor in the integrated measurement system. This paper proposed an accurate and automatic extrinsic parameter calibration method for blade measurement system integrated by different optical sensors. In this system, fringe projection sensor (FPS) and conoscopic holography sensor (CHS) is integrated into a multi-axis motion platform, and the sensors can be optimally move to any desired position at the object's surface. In order to simple the calibration process, a special calibration artifact is designed according to the characteristics of the two sensors. An automatic registration procedure based on correlation and segmentation is used to realize the artifact datasets obtaining by FPS and CHS rough alignment without any manual operation and data pro-processing, and then the Generalized Gauss-Markoff model is used to estimate the optimization transformation parameters. The experiments show the measurement result of a blade, where several sampled patches are merged into one point cloud, and it verifies the performance of the proposed method.
A Method for Accurate in silico modeling of Ultrasound Transducer Arrays
Guenther, Drake A.; Walker, William F.
2009-01-01
This paper presents a new approach to improve the in silico modeling of ultrasound transducer arrays. While current simulation tools accurately predict the theoretical element spatio-temporal pressure response, transducers do not always behave as theorized. In practice, using the probe's physical dimensions and published specifications in silico, often results in unsatisfactory agreement between simulation and experiment. We describe a general optimization procedure used to maximize the correlation between the observed and simulated spatio-temporal response of a pulsed single element in a commercial ultrasound probe. A linear systems approach is employed to model element angular sensitivity, lens effects, and diffraction phenomena. A numerical deconvolution method is described to characterize the intrinsic electro-mechanical impulse response of the element. Once the response of the element and optimal element characteristics are known, prediction of the pressure response for arbitrary apertures and excitation signals is performed through direct convolution using available tools. We achieve a correlation of 0.846 between the experimental emitted waveform and simulated waveform when using the probe's physical specifications in silico. A far superior correlation of 0.988 is achieved when using the optimized in silico model. Electronic noise appears to be the main effect preventing the realization of higher correlation coefficients. More accurate in silico modeling will improve the evaluation and design of ultrasound transducers as well as aid in the development of sophisticated beamforming strategies. PMID:19041997
2012-01-01
Background Imaging of the human microcirculation in real-time has the potential to detect injuries and illnesses that disturb the microcirculation at earlier stages and may improve the efficacy of resuscitation. Despite advanced imaging techniques to monitor the microcirculation, there are currently no tools for the near real-time analysis of the videos produced by these imaging systems. An automated system tool that can extract microvasculature information and monitor changes in tissue perfusion quantitatively might be invaluable as a diagnostic and therapeutic endpoint for resuscitation. Methods The experimental algorithm automatically extracts microvascular network and quantitatively measures changes in the microcirculation. There are two main parts in the algorithm: video processing and vessel segmentation. Microcirculatory videos are first stabilized in a video processing step to remove motion artifacts. In the vessel segmentation process, the microvascular network is extracted using multiple level thresholding and pixel verification techniques. Threshold levels are selected using histogram information of a set of training video recordings. Pixel-by-pixel differences are calculated throughout the frames to identify active blood vessels and capillaries with flow. Results Sublingual microcirculatory videos are recorded from anesthetized swine at baseline and during hemorrhage using a hand-held Side-stream Dark Field (SDF) imaging device to track changes in the microvasculature during hemorrhage. Automatically segmented vessels in the recordings are analyzed visually and the functional capillary density (FCD) values calculated by the algorithm are compared for both health baseline and hemorrhagic conditions. These results were compared to independently made FCD measurements using a well-known semi-automated method. Results of the fully automated algorithm demonstrated a significant decrease of FCD values. Similar, but more variable FCD values were calculated
Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.
Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin
2015-01-01
Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. PMID:24889823
Aeroacoustic Flow Phenomena Accurately Captured by New Computational Fluid Dynamics Method
NASA Technical Reports Server (NTRS)
Blech, Richard A.
2002-01-01
One of the challenges in the computational fluid dynamics area is the accurate calculation of aeroacoustic phenomena, especially in the presence of shock waves. One such phenomenon is "transonic resonance," where an unsteady shock wave at the throat of a convergent-divergent nozzle results in the emission of acoustic tones. The space-time Conservation-Element and Solution-Element (CE/SE) method developed at the NASA Glenn Research Center can faithfully capture the shock waves, their unsteady motion, and the generated acoustic tones. The CE/SE method is a revolutionary new approach to the numerical modeling of physical phenomena where features with steep gradients (e.g., shock waves, phase transition, etc.) must coexist with those having weaker variations. The CE/SE method does not require the complex interpolation procedures (that allow for the possibility of a shock between grid cells) used by many other methods to transfer information between grid cells. These interpolation procedures can add too much numerical dissipation to the solution process. Thus, while shocks are resolved, weaker waves, such as acoustic waves, are washed out.
Takahashi, F; Endo, A
2007-01-01
A system utilising radiation transport codes has been developed to derive accurate dose distributions in a human body for radiological accidents. A suitable model is quite essential for a numerical analysis. Therefore, two tools were developed to setup a 'problem-dependent' input file, defining a radiation source and an exposed person to simulate the radiation transport in an accident with the Monte Carlo calculation codes-MCNP and MCNPX. Necessary resources are defined by a dialogue method with a generally used personal computer for both the tools. The tools prepare human body and source models described in the input file format of the employed Monte Carlo codes. The tools were validated for dose assessment in comparison with a past criticality accident and a hypothesized exposure. PMID:17510203
Temperature dependent effective potential method for accurate free energy calculations of solids
NASA Astrophysics Data System (ADS)
Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.
2013-03-01
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.
NASA Astrophysics Data System (ADS)
Zacharias, Panagiotis P.; Chatzineofytou, Elpida G.; Spantideas, Sotirios T.; Capsalis, Christos N.
2016-07-01
In the present work, the determination of the magnetic behavior of localized magnetic sources from near-field measurements is examined. The distance power law of the magnetic field fall-off is used in various cases to accurately predict the magnetic signature of an equipment under test (EUT) consisting of multiple alternating current (AC) magnetic sources. Therefore, parameters concerning the location of the observation points (magnetometers) are studied towards this scope. The results clearly show that these parameters are independent of the EUT's size and layout. Additionally, the techniques developed in the present study enable the placing of the magnetometers close to the EUT, thus achieving high signal-to-noise ratio (SNR). Finally, the proposed method is verified by real measurements, using a mobile phone as an EUT.
A method for quantitative wet chemical analysis of urinary calculi.
Larsson, L; Sörbo, B; Tiselius, H G; Ohman, S
1984-06-27
We describe a simple method for quantitative chemical analysis of urinary calculi requiring no specialized equipment. Pulverized calculi are dried over silica gel at room temperature and dissolved in nitric acid, which was the only effective agent for complete dissolution. Calcium, magnesium, ammonium, and phosphate are then determined by conventional methods. Oxalate is determined by a method based on the quenching action of oxalate on the fluorescence of a zirconium-flavonol complex. Uric acid, when treated with nitric acid, is stoichiometrically converted to alloxan, which is determined fluorimetrically with 1,2-phenylenediamine. Similarly, cystine is oxidized by nitric acid to sulfate, which is determined turbidimetrically as barium sulfate. Protein is determined spectrophotometrically as xanthoprotein. The total mass recovery of authentic calculi was 92.2 +/- 6.7 (SD) per cent. The method permits analysis of calculi as small as 1.0 mg. Internal quality control is performed with specially designed control samples. PMID:6086179
Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.; Parks, Jerry M.
2016-07-08
In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalaminmore » in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for CoIII, CoII, and CoI species, respectively, and the second model features saturation of each vacant axial coordination site on CoII and CoI species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co axial ligand binding, leading to substantial errors in predicted
Johnston, Ryne C; Zhou, Jing; Smith, Jeremy C; Parks, Jerry M
2016-08-01
Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co-ligand binding equilibrium constants (Kon/off), pKas, and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co(III), Co(II), and Co(I) species, respectively, and the second model features saturation of each vacant axial coordination site on Co(II) and Co(I) species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co-axial ligand binding, leading to substantial errors in predicted pKas and
Quantitative, Qualitative and Geospatial Methods to Characterize HIV Risk Environments
Conners, Erin E.; West, Brooke S.; Roth, Alexis M.; Meckel-Parker, Kristen G.; Kwan, Mei-Po; Magis-Rodriguez, Carlos; Staines-Orozco, Hugo; Clapp, John D.; Brouwer, Kimberly C.
2016-01-01
Increasingly, ‘place’, including physical and geographical characteristics as well as social meanings, is recognized as an important factor driving individual and community health risks. This is especially true among marginalized populations in low and middle income countries (LMIC), whose environments may also be more difficult to study using traditional methods. In the NIH-funded longitudinal study Mapa de Salud, we employed a novel approach to exploring the risk environment of female sex workers (FSWs) in two Mexico/U.S. border cities, Tijuana and Ciudad Juárez. In this paper we describe the development, implementation, and feasibility of a mix of quantitative and qualitative tools used to capture the HIV risk environments of FSWs in an LMIC setting. The methods were: 1) Participatory mapping; 2) Quantitative interviews; 3) Sex work venue field observation; 4) Time-location-activity diaries; 5) In-depth interviews about daily activity spaces. We found that the mixed-methodology outlined was both feasible to implement and acceptable to participants. These methods can generate geospatial data to assess the role of the environment on drug and sexual risk behaviors among high risk populations. Additionally, the adaptation of existing methods for marginalized populations in resource constrained contexts provides new opportunities for informing public health interventions. PMID:27191846
Quantitative, Qualitative and Geospatial Methods to Characterize HIV Risk Environments.
Conners, Erin E; West, Brooke S; Roth, Alexis M; Meckel-Parker, Kristen G; Kwan, Mei-Po; Magis-Rodriguez, Carlos; Staines-Orozco, Hugo; Clapp, John D; Brouwer, Kimberly C
2016-01-01
Increasingly, 'place', including physical and geographical characteristics as well as social meanings, is recognized as an important factor driving individual and community health risks. This is especially true among marginalized populations in low and middle income countries (LMIC), whose environments may also be more difficult to study using traditional methods. In the NIH-funded longitudinal study Mapa de Salud, we employed a novel approach to exploring the risk environment of female sex workers (FSWs) in two Mexico/U.S. border cities, Tijuana and Ciudad Juárez. In this paper we describe the development, implementation, and feasibility of a mix of quantitative and qualitative tools used to capture the HIV risk environments of FSWs in an LMIC setting. The methods were: 1) Participatory mapping; 2) Quantitative interviews; 3) Sex work venue field observation; 4) Time-location-activity diaries; 5) In-depth interviews about daily activity spaces. We found that the mixed-methodology outlined was both feasible to implement and acceptable to participants. These methods can generate geospatial data to assess the role of the environment on drug and sexual risk behaviors among high risk populations. Additionally, the adaptation of existing methods for marginalized populations in resource constrained contexts provides new opportunities for informing public health interventions. PMID:27191846
Earthquake Rupture Dynamics using Adaptive Mesh Refinement and High-Order Accurate Numerical Methods
NASA Astrophysics Data System (ADS)
Kozdon, J. E.; Wilcox, L.
2013-12-01
Our goal is to develop scalable and adaptive (spatial and temporal) numerical methods for coupled, multiphysics problems using high-order accurate numerical methods. To do so, we are developing an opensource, parallel library known as bfam (available at http://bfam.in). The first application to be developed on top of bfam is an earthquake rupture dynamics solver using high-order discontinuous Galerkin methods and summation-by-parts finite difference methods. In earthquake rupture dynamics, wave propagation in the Earth's crust is coupled to frictional sliding on fault interfaces. This coupling is two-way, required the simultaneous simulation of both processes. The use of laboratory-measured friction parameters requires near-fault resolution that is 4-5 orders of magnitude higher than that needed to resolve the frequencies of interest in the volume. This, along with earlier simulations using a low-order, finite volume based adaptive mesh refinement framework, suggest that adaptive mesh refinement is ideally suited for this problem. The use of high-order methods is motivated by the high level of resolution required off the fault in earlier the low-order finite volume simulations; we believe this need for resolution is a result of the excessive numerical dissipation of low-order methods. In bfam spatial adaptivity is handled using the p4est library and temporal adaptivity will be accomplished through local time stepping. In this presentation we will present the guiding principles behind the library as well as verification of code against the Southern California Earthquake Center dynamic rupture code validation test problems.
Development and evaluation of an improved quantitative 90Y bremsstrahlung SPECT method
Rong, Xing; Du, Yong; Ljungberg, Michael; Rault, Erwann; Vandenberghe, Stefaan; Frey, Eric C.
2012-01-01
Purpose: Yttrium-90 (90Y) is one of the most commonly used radionuclides in targeted radionuclide therapy (TRT). Since it decays with essentially no gamma photon emissions, surrogate radionuclides (e.g., 111In) or imaging agents (e.g., 99mTc MAA) are typically used for treatment planning. It would, however, be useful to image 90Y directly in order to confirm that the distributions measured with these other radionuclides or agents are the same as for the 90Y labeled agents. As a result, there has been a great deal of interest in quantitative imaging of 90Y bremsstrahlung photons using single photon emission computed tomography (SPECT) imaging. The continuous and broad energy distribution of bremsstrahlung photons, however, imposes substantial challenges on accurate quantification of the activity distribution. The aim of this work was to develop and evaluate an improved quantitative 90Y bremsstrahlung SPECT reconstruction method appropriate for these imaging applications. Methods: Accurate modeling of image degrading factors such as object attenuation and scatter and the collimator-detector response is essential to obtain quantitatively accurate images. All of the image degrading factors are energy dependent. Thus, the authors separated the modeling of the bremsstrahlung photons into multiple categories and energy ranges. To improve the accuracy, the authors used a bremsstrahlung energy spectrum previously estimated from experimental measurements and incorporated a model of the distance between 90Y decay location and bremsstrahlung emission location into the SIMIND code used to generate the response functions and kernels used in the model. This improved Monte Carlo bremsstrahlung simulation was validated by comparison to experimentally measured projection data of a 90Y line source. The authors validated the accuracy of the forward projection model for photons in the various categories and energy ranges using the validated Monte Carlo (MC) simulation method. The
Extracting accurate strain measurements in bone mechanics: A critical review of current methods.
Grassi, Lorenzo; Isaksson, Hanna
2015-10-01
Osteoporosis related fractures are a social burden that advocates for more accurate fracture prediction methods. Mechanistic methods, e.g. finite element models, have been proposed as a tool to better predict bone mechanical behaviour and strength. However, there is little consensus about the optimal constitutive law to describe bone as a material. Extracting reliable and relevant strain data from experimental tests is of fundamental importance to better understand bone mechanical properties, and to validate numerical models. Several techniques have been used to measure strain in experimental mechanics, with substantial differences in terms of accuracy, precision, time- and length-scale. Each technique presents upsides and downsides that must be carefully evaluated when designing the experiment. Moreover, additional complexities are often encountered when applying such strain measurement techniques to bone, due to its complex composite structure. This review of literature examined the four most commonly adopted methods for strain measurements (strain gauges, fibre Bragg grating sensors, digital image correlation, and digital volume correlation), with a focus on studies with bone as a substrate material, at the organ and tissue level. For each of them the working principles, a summary of the main applications to bone mechanics at the organ- and tissue-level, and a list of pros and cons are provided. PMID:26099201
An accurate and nondestructive GC method for determination of cocaine on US paper currency.
Zuo, Yuegang; Zhang, Kai; Wu, Jingping; Rego, Christopher; Fritz, John
2008-07-01
The presence of cocaine on US paper currency has been known for a long time. Banknotes become contaminated during the exchange, storage, and abuse of cocaine. The analysis of cocaine on various denominations of US banknotes in the general circulation can provide law enforcement circles and forensic epidemiologists objective and timely information on epidemiology of illicit drug use and on how to differentiate money contaminated in the general circulation from banknotes used in drug transaction. A simple, nondestructive, and accurate capillary gas chromatographic method has been developed for the determination of cocaine on various denominations of US banknotes in this study. The method comprises a fast ultrasonic extraction using water as a solvent followed by a SPE cleanup process with a C(18) cartridge and capillary GC separation, identification, and quantification. This nondestructive analytical method has been successfully applied to determine the cocaine contamination in US paper currency of all denominations. Standard calibration curve was linear over the concentration range from the LOQ (2.00 ng/mL) to 100 microg/mL and the RSD less than 2.0%. Cocaine was detected in 67% of the circulated banknotes collected in Southeastern Massachusetts in amounts ranging from approximately 2 ng to 49.4 microg per note. On average, $5, 10, 20, and 50 denominations contain higher amounts of cocaine than $1 and 100 denominations of US banknotes. PMID:18646272
A Method for Accurate Reconstructions of the Upper Airway Using Magnetic Resonance Images
Xiong, Huahui; Huang, Xiaoqing; Li, Yong; Li, Jianhong; Xian, Junfang; Huang, Yaqi
2015-01-01
Objective The purpose of this study is to provide an optimized method to reconstruct the structure of the upper airway (UA) based on magnetic resonance imaging (MRI) that can faithfully show the anatomical structure with a smooth surface without artificial modifications. Methods MRI was performed on the head and neck of a healthy young male participant in the axial, coronal and sagittal planes to acquire images of the UA. The level set method was used to segment the boundary of the UA. The boundaries in the three scanning planes were registered according to the positions of crossing points and anatomical characteristics using a Matlab program. Finally, the three-dimensional (3D) NURBS (Non-Uniform Rational B-Splines) surface of the UA was constructed using the registered boundaries in all three different planes. Results A smooth 3D structure of the UA was constructed, which captured the anatomical features from the three anatomical planes, particularly the location of the anterior wall of the nasopharynx. The volume and area of every cross section of the UA can be calculated from the constructed 3D model of UA. Conclusions A complete scheme of reconstruction of the UA was proposed, which can be used to measure and evaluate the 3D upper airway accurately. PMID:26066461
Conservative high-order-accurate finite-difference methods for curvilinear grids
NASA Technical Reports Server (NTRS)
Rai, Man M.; Chakrvarthy, Sukumar
1993-01-01
Two fourth-order-accurate finite-difference methods for numerically solving hyperbolic systems of conservation equations on smooth curvilinear grids are presented. The first method uses the differential form of the conservation equations; the second method uses the integral form of the conservation equations. Modifications to these schemes, which are required near boundaries to maintain overall high-order accuracy, are discussed. An analysis that demonstrates the stability of the modified schemes is also provided. Modifications to one of the schemes to make it total variation diminishing (TVD) are also discussed. Results that demonstrate the high-order accuracy of both schemes are included in the paper. In particular, a Ringleb-flow computation demonstrates the high-order accuracy and the stability of the boundary and near-boundary procedures. A second computation of supersonic flow over a cylinder demonstrates the shock-capturing capability of the TVD methodology. An important contribution of this paper is the dear demonstration that higher order accuracy leads to increased computational efficiency.
Frąc, Magdalena; Gryta, Agata; Oszust, Karolina; Kotowicz, Natalia
2016-01-01
The need for finding fungicides against Fusarium is a key step in the chemical plant protection and using appropriate chemical agents. Existing, conventional methods of evaluation of Fusarium isolates resistance to fungicides are costly, time-consuming and potentially environmentally harmful due to usage of high amounts of potentially toxic chemicals. Therefore, the development of fast, accurate and effective detection methods for Fusarium resistance to fungicides is urgently required. MT2 microplates (BiologTM) method is traditionally used for bacteria identification and the evaluation of their ability to utilize different carbon substrates. However, to the best of our knowledge, there is no reports concerning the use of this technical tool to determine fungicides resistance of the Fusarium isolates. For this reason, the objectives of this study are to develop a fast method for Fusarium resistance to fungicides detection and to validate the effectiveness approach between both traditional hole-plate and MT2 microplates assays. In presented study MT2 microplate-based assay was evaluated for potential use as an alternative resistance detection method. This was carried out using three commercially available fungicides, containing following active substances: triazoles (tebuconazole), benzimidazoles (carbendazim) and strobilurins (azoxystrobin), in six concentrations (0, 0.0005, 0.005, 0.05, 0.1, 0.2%), for nine selected Fusarium isolates. In this study, the particular concentrations of each fungicides was loaded into MT2 microplate wells. The wells were inoculated with the Fusarium mycelium suspended in PM4-IF inoculating fluid. Before inoculation the suspension was standardized for each isolates into 75% of transmittance. Traditional hole-plate method was used as a control assay. The fungicides concentrations in control method were the following: 0, 0.0005, 0.005, 0.05, 0.5, 1, 2, 5, 10, 25, and 50%. Strong relationships between MT2 microplate and traditional hole
Frąc, Magdalena; Gryta, Agata; Oszust, Karolina; Kotowicz, Natalia
2016-01-01
The need for finding fungicides against Fusarium is a key step in the chemical plant protection and using appropriate chemical agents. Existing, conventional methods of evaluation of Fusarium isolates resistance to fungicides are costly, time-consuming and potentially environmentally harmful due to usage of high amounts of potentially toxic chemicals. Therefore, the development of fast, accurate and effective detection methods for Fusarium resistance to fungicides is urgently required. MT2 microplates (Biolog(TM)) method is traditionally used for bacteria identification and the evaluation of their ability to utilize different carbon substrates. However, to the best of our knowledge, there is no reports concerning the use of this technical tool to determine fungicides resistance of the Fusarium isolates. For this reason, the objectives of this study are to develop a fast method for Fusarium resistance to fungicides detection and to validate the effectiveness approach between both traditional hole-plate and MT2 microplates assays. In presented study MT2 microplate-based assay was evaluated for potential use as an alternative resistance detection method. This was carried out using three commercially available fungicides, containing following active substances: triazoles (tebuconazole), benzimidazoles (carbendazim) and strobilurins (azoxystrobin), in six concentrations (0, 0.0005, 0.005, 0.05, 0.1, 0.2%), for nine selected Fusarium isolates. In this study, the particular concentrations of each fungicides was loaded into MT2 microplate wells. The wells were inoculated with the Fusarium mycelium suspended in PM4-IF inoculating fluid. Before inoculation the suspension was standardized for each isolates into 75% of transmittance. Traditional hole-plate method was used as a control assay. The fungicides concentrations in control method were the following: 0, 0.0005, 0.005, 0.05, 0.5, 1, 2, 5, 10, 25, and 50%. Strong relationships between MT2 microplate and traditional hole
[Method of quantitative determination of staphylococcal hyaluronidase activity].
Generalov, I I
1998-03-01
The proposed method for measuring hyaluronidase activity of microorganism is based on prevention of hyaluronic acid clot formation with rivanol under the effect of hyaluronidase. This made possible the quantitative and qualitative detection of hyaluronidase activities of different staphylococcus species and strains. The maximum level of the enzyme and highest rate of its detection were typical of St. aureus. Its strains producing hyaluronidase in quantities of at least 0.5 IU are significantly (p < 0.01) more often isolated from medical staff. PMID:9575732
Indirect scaling methods for testing quantitative emotion theories.
Junge, Martin; Reisenzein, Rainer
2013-01-01
Two studies investigated the utility of indirect scaling methods, based on graded pair comparisons, for the testing of quantitative emotion theories. In Study 1, we measured the intensity of relief and disappointment caused by lottery outcomes, and in Study 2, the intensity of disgust evoked by pictures, using both direct intensity ratings and graded pair comparisons. The stimuli were systematically constructed to reflect variables expected to influence the intensity of the emotions according to theoretical models of relief/disappointment and disgust, respectively. Two probabilistic scaling methods were used to estimate scale values from the pair comparison judgements: Additive functional measurement (AFM) and maximum likelihood difference scaling (MLDS). The emotion models were fitted to the direct and indirect intensity measurements using nonlinear regression (Study 1) and analysis of variance (Study 2). Both studies found substantially improved fits of the emotion models for the indirectly determined emotion intensities, with their advantage being evident particularly at the level of individual participants. The results suggest that indirect scaling methods yield more precise measurements of emotion intensity than rating scales and thereby provide stronger tests of emotion theories in general and quantitative emotion theories in particular. PMID:23650936
Dispas, Amandine; Lebrun, Pierre; Ziemons, Eric; Marini, Roland; Rozet, Eric; Hubert, Philippe
2014-08-01
Recently, the number of papers about SFC increased drastically but scientists did not truly focus their work on quantitative performances of this technique. In order to prove the potential of UHPSFC, the present work discussed about the different steps of the analytical life cycle of a method: from development to validation and application. Moreover, the UHPSFC quantitative performances were evaluated in comparison with UHPLC, which is the main technique used for quality control in the pharmaceutical industry and then could be considered as a reference. The methods were developed using Design Space strategy, leading to the optimization of robust method. In this context, when the Design Space optimization shows guarantee of quality, no more robustness study is required prior to the validation. Then, the methods were geometrically transferred in order to reduce the analysis time. The UHPSFC and UHPLC methods were validated based on the total error approach using accuracy profile. Even if UHPLC showed better precision and sensitivity, UHPSFC method is able to give accurate results in a dosing range larger than the 80-120% range required by the European Medicines Agency. Consequently, UHPSFC results are valid and could be used for the control of active substance in a finished pharmaceutical product. Finally, UHPSFC validated method was used to analyse real samples and gave similar results than the reference method (UHPLC). PMID:24513349
A Weight-Averaged Interpolation Method for Coupling Time-Accurate Rarefied and Continuum Flows
NASA Astrophysics Data System (ADS)
Diaz, Steven William
A novel approach to coupling rarefied and continuum flow regimes as a single, hybrid model is introduced. The method borrows from techniques used in the simulation of spray flows to interpolate Lagrangian point-particles onto an Eulerian grid in a weight-averaged sense. A brief overview of traditional methods for modeling both rarefied and continuum domains is given, and a review of the literature regarding rarefied/continuum flow coupling is presented. Details of the theoretical development of the method of weighted interpolation are then described. The method evaluates macroscopic properties at the nodes of a CFD grid via the weighted interpolation of all simulated molecules in a set surrounding the node. The weight factor applied to each simulated molecule is the inverse of the linear distance between it and the given node. During development, the method was applied to several preliminary cases, including supersonic flow over an airfoil, subsonic flow over tandem airfoils, and supersonic flow over a backward facing step; all at low Knudsen numbers. The main thrust of the research centered on the time-accurate expansion of a rocket plume into a near-vacuum. The method proves flexible enough to be used with various flow solvers, demonstrated by the use of Fluent as the continuum solver for the preliminary cases and a NASA-developed Large Eddy Simulation research code, WRLES, for the full lunar model. The method is applicable to a wide range of Mach numbers and is completely grid independent, allowing the rarefied and continuum solvers to be optimized for their respective domains without consideration of the other. The work presented demonstrates the validity, and flexibility of the method of weighted interpolation as a novel concept in the field of hybrid flow coupling. The method marks a significant divergence from current practices in the coupling of rarefied and continuum flow domains and offers a kernel on which to base an ongoing field of research. It has the
A time-accurate adaptive grid method and the numerical simulation of a shock-vortex interaction
NASA Technical Reports Server (NTRS)
Bockelie, Michael J.; Eiseman, Peter R.
1990-01-01
A time accurate, general purpose, adaptive grid method is developed that is suitable for multidimensional steady and unsteady numerical simulations. The grid point movement is performed in a manner that generates smooth grids which resolve the severe solution gradients and the sharp transitions in the solution gradients. The temporal coupling of the adaptive grid and the PDE solver is performed with a grid prediction correction method that is simple to implement and ensures the time accuracy of the grid. Time accurate solutions of the 2-D Euler equations for an unsteady shock vortex interaction demonstrate the ability of the adaptive method to accurately adapt the grid to multiple solution features.
Biological characteristics of crucian by quantitative inspection method
NASA Astrophysics Data System (ADS)
Chu, Mengqi
2015-04-01
Biological characteristics of crucian by quantitative inspection method Through quantitative inspection method , the biological characteristics of crucian was preliminary researched. Crucian , Belongs to Cypriniformes, Cyprinidae, Carassius auratus, is a kind of main plant-eating omnivorous fish,like Gregarious, selection and ranking. Crucian are widely distributed, perennial water all over the country all have production. Determine the indicators of crucian in the experiment, to understand the growth, reproduction situation of crucian in this area . Using the measured data (such as the scale length ,scale size and wheel diameter and so on) and related functional to calculate growth of crucian in any one year.According to the egg shape, color, weight ,etc to determine its maturity, with the mean egg diameter per 20 eggs and the number of eggs per 0.5 grams, to calculate the relative and absolute fecundity of the fish .Measured crucian were female puberty. Based on the relation between the scale diameter and length and the information, linear relationship between crucian scale diameter and length: y=1.530+3.0649. From the data, the fertility and is closely relative to the increase of age. The older, the more mature gonad development. The more amount of eggs. In addition, absolute fecundity increases with the pituitary gland.Through quantitative check crucian bait food intake by the object, reveals the main food, secondary foods, and chance food of crucian ,and understand that crucian degree of be fond of of all kinds of bait organisms.Fish fertility with weight gain, it has the characteristics of species and populations, and at the same tmes influenced by the age of the individual, body length, body weight, environmental conditions (especially the nutrition conditions), and breeding habits, spawning times factors and the size of the egg. After a series of studies of crucian biological character, provide the ecological basis for local crucian's feeding, breeding
Knight, Joseph W; Wang, Xiaopeng; Gallandi, Lukas; Dolgounitcheva, Olga; Ren, Xinguo; Ortiz, J Vincent; Rinke, Patrick; Körzdörfer, Thomas; Marom, Noa
2016-02-01
The performance of different GW methods is assessed for a set of 24 organic acceptors. Errors are evaluated with respect to coupled cluster singles, doubles, and perturbative triples [CCSD(T)] reference data for the vertical ionization potentials (IPs) and electron affinities (EAs), extrapolated to the complete basis set limit. Additional comparisons are made to experimental data, where available. We consider fully self-consistent GW (scGW), partial self-consistency in the Green's function (scGW0), non-self-consistent G0W0 based on several mean-field starting points, and a "beyond GW" second-order screened exchange (SOSEX) correction to G0W0. We also describe the implementation of the self-consistent Coulomb hole with screened exchange method (COHSEX), which serves as one of the mean-field starting points. The best performers overall are G0W0+SOSEX and G0W0 based on an IP-tuned long-range corrected hybrid functional with the former being more accurate for EAs and the latter for IPs. Both provide a balanced treatment of localized vs delocalized states and valence spectra in good agreement with photoemission spectroscopy (PES) experiments. PMID:26731609
Stanley, Jeffrey R.; Adkins, Joshua N.; Slysz, Gordon W.; Monroe, Matthew E.; Purvine, Samuel O.; Karpievitch, Yuliya V.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.
2011-07-15
High-throughput proteomics is rapidly evolving to require high mass measurement accuracy for a variety of different applications. Increased mass measurement accuracy in bottom-up proteomics specifically allows for an improved ability to distinguish and characterize detected MS features, which may in turn be identified by, e.g., matching to entries in a database for both precursor and fragmentation mass identification methods. Many tools exist with which to score the identification of peptides from LC-MS/MS measurements or to assess matches to an accurate mass and time (AMT) tag database, but these two calculations remain distinctly unrelated. Here we present a statistical method, Statistical Tools for AMT tag Confidence (STAC), which extends our previous work incorporating prior probabilities of correct sequence identification from LC-MS/MS, as well as the quality with which LC-MS features match AMT tags, to evaluate peptide identification confidence. Compared to existing tools, we are able to obtain significantly more high-confidence peptide identifications at a given false discovery rate and additionally assign confidence estimates to individual peptide identifications. Freely available software implementations of STAC are available in both command line and as a Windows graphical application.
Obtaining accurate amounts of mercury from mercury compounds via electrolytic methods
Grossman, Mark W.; George, William A.
1987-01-01
A process for obtaining pre-determined, accurate rate amounts of mercury. In one embodiment, predetermined, precise amounts of Hg are separated from HgO and plated onto a cathode wire. The method for doing this involves dissolving a precise amount of HgO which corresponds to a pre-determined amount of Hg desired in an electrolyte solution comprised of glacial acetic acid and H.sub.2 O. The mercuric ions are then electrolytically reduced and plated onto a cathode producing the required pre-determined quantity of Hg. In another embodiment, pre-determined, precise amounts of Hg are obtained from Hg.sub.2 Cl.sub.2. The method for doing this involves dissolving a precise amount of Hg.sub.2 Cl.sub.2 in an electrolyte solution comprised of concentrated HCl and H.sub.2 O. The mercurous ions in solution are then electrolytically reduced and plated onto a cathode wire producing the required, pre-determined quantity of Hg.
Obtaining accurate amounts of mercury from mercury compounds via electrolytic methods
Grossman, M.W.; George, W.A.
1987-07-07
A process is described for obtaining pre-determined, accurate rate amounts of mercury. In one embodiment, predetermined, precise amounts of Hg are separated from HgO and plated onto a cathode wire. The method for doing this involves dissolving a precise amount of HgO which corresponds to a pre-determined amount of Hg desired in an electrolyte solution comprised of glacial acetic acid and H[sub 2]O. The mercuric ions are then electrolytically reduced and plated onto a cathode producing the required pre-determined quantity of Hg. In another embodiment, pre-determined, precise amounts of Hg are obtained from Hg[sub 2]Cl[sub 2]. The method for doing this involves dissolving a precise amount of Hg[sub 2]Cl[sub 2] in an electrolyte solution comprised of concentrated HCl and H[sub 2]O. The mercurous ions in solution are then electrolytically reduced and plated onto a cathode wire producing the required, pre-determined quantity of Hg. 1 fig.
Methods for accurate cold-chain temperature monitoring using digital data-logger thermometers
NASA Astrophysics Data System (ADS)
Chojnacky, M. J.; Miller, W. M.; Strouse, G. F.
2013-09-01
Complete and accurate records of vaccine temperature history are vital to preserving drug potency and patient safety. However, previously published vaccine storage and handling guidelines have failed to indicate a need for continuous temperature monitoring in vaccine storage refrigerators. We evaluated the performance of seven digital data logger models as candidates for continuous temperature monitoring of refrigerated vaccines, based on the following criteria: out-of-box performance and compliance with manufacturer accuracy specifications over the range of use; measurement stability over extended, continuous use; proper setup in a vaccine storage refrigerator so that measurements reflect liquid vaccine temperatures; and practical methods for end-user validation and establishing metrological traceability. Data loggers were tested using ice melting point checks and by comparison to calibrated thermocouples to characterize performance over 0 °C to 10 °C. We also monitored logger performance in a study designed to replicate the range of vaccine storage and environmental conditions encountered at provider offices. Based on the results of this study, the Centers for Disease Control released new guidelines on proper methods for storage, handling, and temperature monitoring of vaccines for participants in its federally-funded Vaccines for Children Program. Improved temperature monitoring practices will ultimately decrease waste from damaged vaccines, improve consumer confidence, and increase effective inoculation rates.
Accurate method to study static volume-pressure relationships in small fetal and neonatal animals.
Suen, H C; Losty, P D; Donahoe, P K; Schnitzer, J J
1994-08-01
We designed an accurate method to study respiratory static volume-pressure relationships in small fetal and neonatal animals on the basis of Archimedes' principle. Our method eliminates the error caused by the compressibility of air (Boyle's law) and is sensitive to a volume change of as little as 1 microliters. Fetal and neonatal rats during the period of rapid lung development from day 19.5 of gestation (term = day 22) to day 3.5 postnatum were studied. The absolute lung volume at a transrespiratory pressure of 30-40 cmH2O increased 28-fold from 0.036 +/- 0.006 (SE) to 0.994 +/- 0.042 ml, the volume per gram of lung increased 14-fold from 0.39 +/- 0.07 to 5.59 +/- 0.66 ml/g, compliance increased 12-fold from 2.3 +/- 0.4 to 27.3 +/- 2.7 microliters/cmH2O, and specific compliance increased 6-fold from 24.9 +/- 4.5 to 152.3 +/- 22.8 microliters.cmH2O-1.g lung-1. This technique, which allowed us to compare changes during late gestation and the early neonatal period in small rodents, can be used to monitor and evaluate pulmonary functional changes after in utero pharmacological therapies in experimentally induced abnormalities such as pulmonary hypoplasia, surfactant deficiency, and congenital diaphragmatic hernia. PMID:8002489
Accurate computation of surface stresses and forces with immersed boundary methods
NASA Astrophysics Data System (ADS)
Goza, Andres; Liska, Sebastian; Morley, Benjamin; Colonius, Tim
2016-09-01
Many immersed boundary methods solve for surface stresses that impose the velocity boundary conditions on an immersed body. These surface stresses may contain spurious oscillations that make them ill-suited for representing the physical surface stresses on the body. Moreover, these inaccurate stresses often lead to unphysical oscillations in the history of integrated surface forces such as the coefficient of lift. While the errors in the surface stresses and forces do not necessarily affect the convergence of the velocity field, it is desirable, especially in fluid-structure interaction problems, to obtain smooth and convergent stress distributions on the surface. To this end, we show that the equation for the surface stresses is an integral equation of the first kind whose ill-posedness is the source of spurious oscillations in the stresses. We also demonstrate that for sufficiently smooth delta functions, the oscillations may be filtered out to obtain physically accurate surface stresses. The filtering is applied as a post-processing procedure, so that the convergence of the velocity field is unaffected. We demonstrate the efficacy of the method by computing stresses and forces that converge to the physical stresses and forces for several test problems.
Methods for accurate estimation of net discharge in a tidal channel
Simpson, M.R.; Bland, R.
2000-01-01
Accurate estimates of net residual discharge in tidally affected rivers and estuaries are possible because of recently developed ultrasonic discharge measurement techniques. Previous discharge estimates using conventional mechanical current meters and methods based on stage/discharge relations or water slope measurements often yielded errors that were as great as or greater than the computed residual discharge. Ultrasonic measurement methods consist of: 1) the use of ultrasonic instruments for the measurement of a representative 'index' velocity used for in situ estimation of mean water velocity and 2) the use of the acoustic Doppler current discharge measurement system to calibrate the index velocity measurement data. Methods used to calibrate (rate) the index velocity to the channel velocity measured using the Acoustic Doppler Current Profiler are the most critical factors affecting the accuracy of net discharge estimation. The index velocity first must be related to mean channel velocity and then used to calculate instantaneous channel discharge. Finally, discharge is low-pass filtered to remove the effects of the tides. An ultrasonic velocity meter discharge-measurement site in a tidally affected region of the Sacramento-San Joaquin Rivers was used to study the accuracy of the index velocity calibration procedure. Calibration data consisting of ultrasonic velocity meter index velocity and concurrent acoustic Doppler discharge measurement data were collected during three time periods. Two sets of data were collected during a spring tide (monthly maximum tidal current) and one of data collected during a neap tide (monthly minimum tidal current). The relative magnitude of instrumental errors, acoustic Doppler discharge measurement errors, and calibration errors were evaluated. Calibration error was found to be the most significant source of error in estimating net discharge. Using a comprehensive calibration method, net discharge estimates developed from the three
NASA Astrophysics Data System (ADS)
Shu, Yu-Chen; Chern, I.-Liang; Chang, Chien C.
2014-10-01
Most elliptic interface solvers become complicated for complex interface problems at those “exceptional points” where there are not enough neighboring interior points for high order interpolation. Such complication increases especially in three dimensions. Usually, the solvers are thus reduced to low order accuracy. In this paper, we classify these exceptional points and propose two recipes to maintain order of accuracy there, aiming at improving the previous coupling interface method [26]. Yet the idea is also applicable to other interface solvers. The main idea is to have at least first order approximations for second order derivatives at those exceptional points. Recipe 1 is to use the finite difference approximation for the second order derivatives at a nearby interior grid point, whenever this is possible. Recipe 2 is to flip domain signatures and introduce a ghost state so that a second-order method can be applied. This ghost state is a smooth extension of the solution at the exceptional point from the other side of the interface. The original state is recovered by a post-processing using nearby states and jump conditions. The choice of recipes is determined by a classification scheme of the exceptional points. The method renders the solution and its gradient uniformly second-order accurate in the entire computed domain. Numerical examples are provided to illustrate the second order accuracy of the presently proposed method in approximating the gradients of the original states for some complex interfaces which we had tested previous in two and three dimensions, and a real molecule (1D63) which is double-helix shape and composed of hundreds of atoms.
Shu, Yu-Chen; Chern, I-Liang; Chang, Chien C.
2014-10-15
Most elliptic interface solvers become complicated for complex interface problems at those “exceptional points” where there are not enough neighboring interior points for high order interpolation. Such complication increases especially in three dimensions. Usually, the solvers are thus reduced to low order accuracy. In this paper, we classify these exceptional points and propose two recipes to maintain order of accuracy there, aiming at improving the previous coupling interface method [26]. Yet the idea is also applicable to other interface solvers. The main idea is to have at least first order approximations for second order derivatives at those exceptional points. Recipe 1 is to use the finite difference approximation for the second order derivatives at a nearby interior grid point, whenever this is possible. Recipe 2 is to flip domain signatures and introduce a ghost state so that a second-order method can be applied. This ghost state is a smooth extension of the solution at the exceptional point from the other side of the interface. The original state is recovered by a post-processing using nearby states and jump conditions. The choice of recipes is determined by a classification scheme of the exceptional points. The method renders the solution and its gradient uniformly second-order accurate in the entire computed domain. Numerical examples are provided to illustrate the second order accuracy of the presently proposed method in approximating the gradients of the original states for some complex interfaces which we had tested previous in two and three dimensions, and a real molecule ( (1D63)) which is double-helix shape and composed of hundreds of atoms.
NASA Technical Reports Server (NTRS)
Constantinescu, G.S.; Lele, S. K.
2000-01-01
The motivation of this work is the ongoing effort at the Center for Turbulence Research (CTR) to use large eddy simulation (LES) techniques to calculate the noise radiated by jet engines. The focus on engine exhaust noise reduction is motivated by the fact that a significant reduction has been achieved over the last decade on the other main sources of acoustic emissions of jet engines, such as the fan and turbomachinery noise, which gives increased priority to jet noise. To be able to propose methods to reduce the jet noise based on results of numerical simulations, one first has to be able to accurately predict the spatio-temporal distribution of the noise sources in the jet. Though a great deal of understanding of the fundamental turbulence mechanisms in high-speed jets was obtained from direct numerical simulations (DNS) at low Reynolds numbers, LES seems to be the only realistic available tool to obtain the necessary near-field information that is required to estimate the acoustic radiation of the turbulent compressible engine exhaust jets. The quality of jet-noise predictions is determined by the accuracy of the numerical method that has to capture the wide range of pressure fluctuations associated with the turbulence in the jet and with the resulting radiated noise, and by the boundary condition treatment and the quality of the mesh. Higher Reynolds numbers and coarser grids put in turn a higher burden on the robustness and accuracy of the numerical method used in this kind of jet LES simulations. As these calculations are often done in cylindrical coordinates, one of the most important requirements for the numerical method is to provide a flow solution that is not contaminated by numerical artifacts. The coordinate singularity is known to be a source of such artifacts. In the present work we use 6th order Pade schemes in the non-periodic directions to discretize the full compressible flow equations. It turns out that the quality of jet-noise predictions
Quantitative methods to direct exploration based on hydrogeologic information
Graettinger, A.J.; Lee, J.; Reeves, H.W.; Dethan, D.
2006-01-01
Quantitatively Directed Exploration (QDE) approaches based on information such as model sensitivity, input data covariance and model output covariance are presented. Seven approaches for directing exploration are developed, applied, and evaluated on a synthetic hydrogeologic site. The QDE approaches evaluate input information uncertainty, subsurface model sensitivity and, most importantly, output covariance to identify the next location to sample. Spatial input parameter values and covariances are calculated with the multivariate conditional probability calculation from a limited number of samples. A variogram structure is used during data extrapolation to describe the spatial continuity, or correlation, of subsurface information. Model sensitivity can be determined by perturbing input data and evaluating output response or, as in this work, sensitivities can be programmed directly into an analysis model. Output covariance is calculated by the First-Order Second Moment (FOSM) method, which combines the covariance of input information with model sensitivity. A groundwater flow example, modeled in MODFLOW-2000, is chosen to demonstrate the seven QDE approaches. MODFLOW-2000 is used to obtain the piezometric head and the model sensitivity simultaneously. The seven QDE approaches are evaluated based on the accuracy of the modeled piezometric head after information from a QDE sample is added. For the synthetic site used in this study, the QDE approach that identifies the location of hydraulic conductivity that contributes the most to the overall piezometric head variance proved to be the best method to quantitatively direct exploration. ?? IWA Publishing 2006.
DREAM: a method for semi-quantitative dermal exposure assessment.
Van-Wendel-de-Joode, Berna; Brouwer, Derk H; Vermeulen, Roel; Van Hemmen, Joop J; Heederik, Dick; Kromhout, Hans
2003-01-01
This paper describes a new method (DREAM) for structured, semi-quantitative dermal exposure assessment for chemical or biological agents that can be used in occupational hygiene or epidemiology. It is anticipated that DREAM could serve as an initial assessment of dermal exposure, amongst others, resulting in a ranking of tasks and subsequently jobs. DREAM consists of an inventory and evaluation part. Two examples of dermal exposure of workers of a car-construction company show that DREAM characterizes tasks and gives insight into exposure mechanisms, forming a basis for systematic exposure reduction. DREAM supplies estimates for exposure levels on the outside clothing layer as well as on skin, and provides insight into the distribution of dermal exposure over the body. Together with the ranking of tasks and people, this provides information for measurement strategies and helps to determine who, where and what to measure. In addition to dermal exposure assessment, the systematic description of dermal exposure pathways helps to prioritize and determine most adequate measurement strategies and methods. DREAM could be a promising approach for structured, semi-quantitative, dermal exposure assessment. PMID:12505908
A gas chromatography-mass spectrometry method for the quantitation of clobenzorex.
Cody, J T; Valtier, S
1999-01-01
Drugs metabolized to amphetamine or methamphetamine are potentially significant concerns in the interpretation of amphetamine-positive urine drug-testing results. One of these compounds, clobenzorex, is an anorectic drug that is available in many countries. Clobenzorex (2-chlorobenzylamphetamine) is metabolized to amphetamine by the body and excreted in the urine. Following administration, the parent compound was detectable for a shorter time than the metabolite amphetamine, which could be detected for days. Because of the potential complication posed to the interpretation of amphetamin-positive drug tests following administration of this drug, the viability of a current amphetamine procedure using liquid-liquid extraction and conversion to the heptafluorobutyryl derivative followed by gas chromatography-mass spectrometry (GC-MS) analysis was evaluated for identification and quantitation of clobenzorex. Qualitative identification of the drug was relatively straightforward. Quantitative analysis proved to be a far more challenging process. Several compounds were evaluated for use as the internal standard in this method, including methamphetamine-d11, fenfluramine, benzphetamine, and diphenylamine. Results using these compounds proved to be less than satisfactory because of poor reproducibility of the quantitative values. Because of its similar chromatographic properties to the parent drug, the compound 3-chlorobenzylamphetamine (3-Cl-clobenzorex) was evaluated in this study as the internal standard for the quantitation of clobenzorex. Precision studies showed 3-Cl-clobenzorex to produce accurate and reliable quantitative results (within-run relative standard deviations [RSDs] < 6.1%, between-run RSDs < 6.0%). The limits of detection and quantitation for this assay were determined to be 1 ng/mL for clobenzorex. PMID:10595847
HPTLC Method for Quantitative Determination of Zopiclone and Its Impurity.
Naguib, Ibrahim A; Abdelrahman, Maha M; El Ghobashy, Mohamed R; Ali, Nesma A
2015-09-01
This study was designed to establish, optimize and validate a sensitive, selective and accurate high-performance thin layer chromatographic (HPTLC) method for determination of zopiclone (ZPC) and its main impurity, 2-amino-5-chloropyridine, one of its degradation products, in raw material and pharmaceutical formulation. The proposed method was applied for analysis of ZPC and its impurity over the concentration range of 0.3-1.4 and 0.05-0.8 µg/band with accuracy of mean percentage recovery 99.92% ± 1.521 and 99.28% ± 2.296, respectively. The method is based on the separation of two components followed by densitometric measurement of the separated peaks at 305 nm. The separation was carried out on silica gel HPTLC F254 plates, using chloroform-methanol-glacial acetic acid (9:1:0.1, by volume) as a developing system. The suggested method was validated according to International Conference on Harmonization guidelines and can be applied for routine analysis in quality control laboratories. The results obtained by the proposed method were statistically compared with the reported method revealing high accuracy and good precision. PMID:25740427
Quach, D.T.; Sakoulas, G.; Nizet, V.; Pogliano, J.; Pogliano, K.
2016-01-01
Successful treatment of bacterial infections requires the timely administration of appropriate antimicrobial therapy. The failure to initiate the correct therapy in a timely fashion results in poor clinical outcomes, longer hospital stays, and higher medical costs. Current approaches to antibiotic susceptibility testing of cultured pathogens have key limitations ranging from long run times to dependence on prior knowledge of genetic mechanisms of resistance. We have developed a rapid antimicrobial susceptibility assay for Staphylococcus aureus based on bacterial cytological profiling (BCP), which uses quantitative fluorescence microscopy to measure antibiotic induced changes in cellular architecture. BCP discriminated between methicillin-susceptible (MSSA) and -resistant (MRSA) clinical isolates of S. aureus (n = 71) within 1–2 h with 100% accuracy. Similarly, BCP correctly distinguished daptomycin susceptible (DS) from daptomycin non-susceptible (DNS) S. aureus strains (n = 20) within 30 min. Among MRSA isolates, BCP further identified two classes of strains that differ in their susceptibility to specific combinations of beta-lactam antibiotics. BCP provides a rapid and flexible alternative to gene-based susceptibility testing methods for S. aureus, and should be readily adaptable to different antibiotics and bacterial species as new mechanisms of resistance or multidrug-resistant pathogens evolve and appear in mainstream clinical practice. PMID:26981574
Quach, D T; Sakoulas, G; Nizet, V; Pogliano, J; Pogliano, K
2016-02-01
Successful treatment of bacterial infections requires the timely administration of appropriate antimicrobial therapy. The failure to initiate the correct therapy in a timely fashion results in poor clinical outcomes, longer hospital stays, and higher medical costs. Current approaches to antibiotic susceptibility testing of cultured pathogens have key limitations ranging from long run times to dependence on prior knowledge of genetic mechanisms of resistance. We have developed a rapid antimicrobial susceptibility assay for Staphylococcus aureus based on bacterial cytological profiling (BCP), which uses quantitative fluorescence microscopy to measure antibiotic induced changes in cellular architecture. BCP discriminated between methicillin-susceptible (MSSA) and -resistant (MRSA) clinical isolates of S. aureus (n = 71) within 1-2 h with 100% accuracy. Similarly, BCP correctly distinguished daptomycin susceptible (DS) from daptomycin non-susceptible (DNS) S. aureus strains (n = 20) within 30 min. Among MRSA isolates, BCP further identified two classes of strains that differ in their susceptibility to specific combinations of beta-lactam antibiotics. BCP provides a rapid and flexible alternative to gene-based susceptibility testing methods for S. aureus, and should be readily adaptable to different antibiotics and bacterial species as new mechanisms of resistance or multidrug-resistant pathogens evolve and appear in mainstream clinical practice. PMID:26981574
Accurate methods for computing inviscid and viscous Kelvin-Helmholtz instability
NASA Astrophysics Data System (ADS)
Chen, Michael J.; Forbes, Lawrence K.
2011-02-01
The Kelvin-Helmholtz instability is modelled for inviscid and viscous fluids. Here, two bounded fluid layers flow parallel to each other with the interface between them growing in an unstable fashion when subjected to a small perturbation. In the various configurations of this problem, and the related problem of the vortex sheet, there are several phenomena associated with the evolution of the interface; notably the formation of a finite time curvature singularity and the ‘roll-up' of the interface. Two contrasting computational schemes will be presented. A spectral method is used to follow the evolution of the interface in the inviscid version of the problem. This allows the interface shape to be computed up to the time that a curvature singularity forms, with several computational difficulties overcome to reach that point. A weakly compressible viscous version of the problem is studied using finite difference techniques and a vorticity-streamfunction formulation. The two versions have comparable, but not identical, initial conditions and so the results exhibit some differences in timing. By including a small amount of viscosity the interface may be followed to the point that it rolls up into a classic ‘cat's-eye' shape. Particular attention was given to computing a consistent initial condition and solving the continuity equation both accurately and efficiently.
Method for accurate sizing of pulmonary vessels from 3D medical images
NASA Astrophysics Data System (ADS)
O'Dell, Walter G.
2015-03-01
Detailed characterization of vascular anatomy, in particular the quantification of changes in the distribution of vessel sizes and of vascular pruning, is essential for the diagnosis and management of a variety of pulmonary vascular diseases and for the care of cancer survivors who have received radiation to the thorax. Clinical estimates of vessel radii are typically based on setting a pixel intensity threshold and counting how many "On" pixels are present across the vessel cross-section. A more objective approach introduced recently involves fitting the image with a library of spherical Gaussian filters and utilizing the size of the best matching filter as the estimate of vessel diameter. However, both these approaches have significant accuracy limitations including mis-match between a Gaussian intensity distribution and that of real vessels. Here we introduce and demonstrate a novel approach for accurate vessel sizing using 3D appearance models of a tubular structure along a curvilinear trajectory in 3D space. The vessel branch trajectories are represented with cubic Hermite splines and the tubular branch surfaces represented as a finite element surface mesh. An iterative parameter adjustment scheme is employed to optimally match the appearance models to a patient's chest X-ray computed tomography (CT) scan to generate estimates for branch radii and trajectories with subpixel resolution. The method is demonstrated on pulmonary vasculature in an adult human CT scan, and on 2D simulated test cases.
Cox, Annie M; Goodwin, Kelly D
2013-08-15
The need for quantitative molecular methods is growing in environmental, food, and medical fields but is hindered by low and variable DNA extraction and by co-extraction of PCR inhibitors. DNA extracts from Enterococcus faecium, seawater, and seawater spiked with E. faecium and Vibrio parahaemolyticus were tested by qPCR for target recovery and inhibition. Conventional and novel methods were tested, including Synchronous Coefficient of Drag Alteration (SCODA) and lysis and purification systems used on an automated genetic sensor (the Environmental Sample Processor, ESP). Variable qPCR target recovery and inhibition were measured, significantly affecting target quantification. An aggressive lysis method that utilized chemical, enzymatic, and mechanical disruption enhanced target recovery compared to commercial kit protocols. SCODA purification did not show marked improvement over commercial spin columns. Overall, data suggested a general need to improve sample preparation and to accurately assess and account for DNA recovery and inhibition in qPCR applications. PMID:23790450
A new method for quantitating total lesion glucose metabolic changes in serial tumor FDG PET studies
Wu, H.M.; Hoh, C.K.; Huang, S.C.; Phelps, M.E.
1994-05-01
Accurate quantitative FDG PET studies have the potential for important applications in clinical oncology for monitoring therapy induced changes in tumor glycolytic rates. Due to a number of technical problems that complicate the use of quantitative PET tumor imaging, methods which can maximize the accuracy and precision of such measurements are advantageous. In this study, we developed and evaluated a method for reducing the errors caused by the conventional single plane, single ROI analysis in parametric images generated from pixel by pixel Patlak graphic analysis (PGA) in FDG PET studies of melanoma patients. We compared this new method to the conventional ROI method. The new processing method involves (1) generating the correlation coefficient (r) constrained Patlak parametric images from dynamic PET data; (2) summing up all the planes which cover the lesion; (3) defining a single ROI which covers the whole lesion in the summing image and determining the total lesion glucose metabolic index (K{sub T}, ml/min/lesion). Although only a single ROI was defined on the summing image, the glucose metabolic index obtained showed negligible difference (<1%) compared to those obtained from multiple ROIs on multiple planes of unconstrained parametric images. When the dynamic PET images were rotated and translated to simulate different patient positionings between scans at different times, the results obtained from the new method showed negligible difference (<2%). In summary, we present a simple but reliable method to quantitatively monitor the total lesion glucose metabolic changes during tumor growth. The method has several advantages over the conventional single ROI, single plane evaluation: (1) less sensitive to the ROI definition; (2) smaller intra- and inter-observer variations and (3) not requiring image registrations of serial scan data.
A novel semi-quantitative method for measuring tissue bleeding.
Vukcevic, G; Volarevic, V; Raicevic, S; Tanaskovic, I; Milicic, B; Vulovic, T; Arsenijevic, S
2014-03-01
In this study, we describe a new semi-quantitative method for measuring the extent of bleeding in pathohistological tissue samples. To test our novel method, we recruited 120 female patients in their first trimester of pregnancy and divided them into three groups of 40. Group I was the control group, in which no dilation was applied. Group II was an experimental group, in which dilation was performed using classical mechanical dilators. Group III was also an experimental group, in which dilation was performed using a hydraulic dilator. Tissue samples were taken from the patients' cervical canals using a Novak's probe via energetic single-step curettage prior to any dilation in Group I and after dilation in Groups II and III. After the tissue samples were prepared, light microscopy was used to obtain microphotographs at 100x magnification. The surfaces affected by bleeding were measured in the microphotographs using the Autodesk AutoCAD 2009 program and its "polylines" function. The lines were used to mark the area around the entire sample (marked A) and to create "polyline" areas around each bleeding area on the sample (marked B). The percentage of the total area affected by bleeding was calculated using the formula: N = Bt x 100 / At where N is the percentage (%) of the tissue sample surface affected by bleeding, At (A total) is the sum of the surfaces of all of the tissue samples and Bt (B total) is the sum of all the surfaces affected by bleeding in all of the tissue samples. This novel semi-quantitative method utilizes the Autodesk AutoCAD 2009 program, which is simple to use and widely available, thereby offering a new, objective and precise approach to estimate the extent of bleeding in tissue samples. PMID:24190861
QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS
Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin
2015-01-01
Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823
Fast, accurate and easy-to-pipeline methods for amplicon sequence processing
NASA Astrophysics Data System (ADS)
Antonielli, Livio; Sessitsch, Angela
2016-04-01
Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.