Sample records for accuracy allowing quantitative

  1. Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

    PubMed Central

    Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

    2011-01-01

    Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

  2. Dependence of quantitative accuracy of CT perfusion imaging on system parameters

    NASA Astrophysics Data System (ADS)

    Li, Ke; Chen, Guang-Hong

    2017-03-01

    Deconvolution is a popular method to calculate parametric perfusion parameters from four dimensional CT perfusion (CTP) source images. During the deconvolution process, the four dimensional space is squeezed into three-dimensional space by removing the temporal dimension, and a prior knowledge is often used to suppress noise associated with the process. These additional complexities confound the understanding about deconvolution-based CTP imaging system and how its quantitative accuracy depends on parameters and sub-operations involved in the image formation process. Meanwhile, there has been a strong clinical need in answering this question, as physicians often rely heavily on the quantitative values of perfusion parameters to make diagnostic decisions, particularly during an emergent clinical situation (e.g. diagnosis of acute ischemic stroke). The purpose of this work was to develop a theoretical framework that quantitatively relates the quantification accuracy of parametric perfusion parameters with CTP acquisition and post-processing parameters. This goal was achieved with the help of a cascaded systems analysis for deconvolution-based CTP imaging systems. Based on the cascaded systems analysis, the quantitative relationship between regularization strength, source image noise, arterial input function, and the quantification accuracy of perfusion parameters was established. The theory could potentially be used to guide developments of CTP imaging technology for better quantification accuracy and lower radiation dose.

  3. Quantitative endoscopy: initial accuracy measurements.

    PubMed

    Truitt, T O; Adelman, R A; Kelly, D H; Willging, J P

    2000-02-01

    The geometric optics of an endoscope can be used to determine the absolute size of an object in an endoscopic field without knowing the actual distance from the object. This study explores the accuracy of a technique that estimates absolute object size from endoscopic images. Quantitative endoscopy involves calibrating a rigid endoscope to produce size estimates from 2 images taken with a known traveled distance between the images. The heights of 12 samples, ranging in size from 0.78 to 11.80 mm, were estimated with this calibrated endoscope. Backup distances of 5 mm and 10 mm were used for comparison. The mean percent error for all estimated measurements when compared with the actual object sizes was 1.12%. The mean errors for 5-mm and 10-mm backup distances were 0.76% and 1.65%, respectively. The mean errors for objects <2 mm and > or =2 mm were 0.94% and 1.18%, respectively. Quantitative endoscopy estimates endoscopic image size to within 5% of the actual object size. This method remains promising for quantitatively evaluating object size from endoscopic images. It does not require knowledge of the absolute distance of the endoscope from the object, rather, only the distance traveled by the endoscope between images.

  4. Diagnostic accuracy of stress perfusion CMR in comparison with quantitative coronary angiography: fully quantitative, semiquantitative, and qualitative assessment.

    PubMed

    Mordini, Federico E; Haddad, Tariq; Hsu, Li-Yueh; Kellman, Peter; Lowrey, Tracy B; Aletras, Anthony H; Bandettini, W Patricia; Arai, Andrew E

    2014-01-01

    This study's primary objective was to determine the sensitivity, specificity, and accuracy of fully quantitative stress perfusion cardiac magnetic resonance (CMR) versus a reference standard of quantitative coronary angiography. We hypothesized that fully quantitative analysis of stress perfusion CMR would have high diagnostic accuracy for identifying significant coronary artery stenosis and exceed the accuracy of semiquantitative measures of perfusion and qualitative interpretation. Relatively few studies apply fully quantitative CMR perfusion measures to patients with coronary disease and comparisons to semiquantitative and qualitative methods are limited. Dual bolus dipyridamole stress perfusion CMR exams were performed in 67 patients with clinical indications for assessment of myocardial ischemia. Stress perfusion images alone were analyzed with a fully quantitative perfusion (QP) method and 3 semiquantitative methods including contrast enhancement ratio, upslope index, and upslope integral. Comprehensive exams (cine imaging, stress/rest perfusion, late gadolinium enhancement) were analyzed qualitatively with 2 methods including the Duke algorithm and standard clinical interpretation. A 70% or greater stenosis by quantitative coronary angiography was considered abnormal. The optimum diagnostic threshold for QP determined by receiver-operating characteristic curve occurred when endocardial flow decreased to <50% of mean epicardial flow, which yielded a sensitivity of 87% and specificity of 93%. The area under the curve for QP was 92%, which was superior to semiquantitative methods: contrast enhancement ratio: 78%; upslope index: 82%; and upslope integral: 75% (p = 0.011, p = 0.019, p = 0.004 vs. QP, respectively). Area under the curve for QP was also superior to qualitative methods: Duke algorithm: 70%; and clinical interpretation: 78% (p < 0.001 and p < 0.001 vs. QP, respectively). Fully quantitative stress perfusion CMR has high diagnostic accuracy for

  5. NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs.

    PubMed

    Morisset, Dany; Dobnik, David; Hamels, Sandrine; Zel, Jana; Gruden, Kristina

    2008-10-01

    We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1-25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification.

  6. NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs

    PubMed Central

    Morisset, Dany; Dobnik, David; Hamels, Sandrine; Žel, Jana; Gruden, Kristina

    2008-01-01

    We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1–25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification. PMID:18710880

  7. Accuracy of quantitative visual soil assessment

    NASA Astrophysics Data System (ADS)

    van Leeuwen, Maricke; Heuvelink, Gerard; Stoorvogel, Jetse; Wallinga, Jakob; de Boer, Imke; van Dam, Jos; van Essen, Everhard; Moolenaar, Simon; Verhoeven, Frank; Stoof, Cathelijne

    2016-04-01

    Visual soil assessment (VSA) is a method to assess soil quality visually, when standing in the field. VSA is increasingly used by farmers, farm organisations and companies, because it is rapid and cost-effective, and because looking at soil provides understanding about soil functioning. Often VSA is regarded as subjective, so there is a need to verify VSA. Also, many VSAs have not been fine-tuned for contrasting soil types. This could lead to wrong interpretation of soil quality and soil functioning when contrasting sites are compared to each other. We wanted to assess accuracy of VSA, while taking into account soil type. The first objective was to test whether quantitative visual field observations, which form the basis in many VSAs, could be validated with standardized field or laboratory measurements. The second objective was to assess whether quantitative visual field observations are reproducible, when used by observers with contrasting backgrounds. For the validation study, we made quantitative visual observations at 26 cattle farms. Farms were located at sand, clay and peat soils in the North Friesian Woodlands, the Netherlands. Quantitative visual observations evaluated were grass cover, number of biopores, number of roots, soil colour, soil structure, number of earthworms, number of gley mottles and soil compaction. Linear regression analysis showed that four out of eight quantitative visual observations could be well validated with standardized field or laboratory measurements. The following quantitative visual observations correlated well with standardized field or laboratory measurements: grass cover with classified images of surface cover; number of roots with root dry weight; amount of large structure elements with mean weight diameter; and soil colour with soil organic matter content. Correlation coefficients were greater than 0.3, from which half of the correlations were significant. For the reproducibility study, a group of 9 soil scientists and 7

  8. Accuracy improvement of quantitative analysis by spatial confinement in laser-induced breakdown spectroscopy.

    PubMed

    Guo, L B; Hao, Z Q; Shen, M; Xiong, W; He, X N; Xie, Z Q; Gao, M; Li, X Y; Zeng, X Y; Lu, Y F

    2013-07-29

    To improve the accuracy of quantitative analysis in laser-induced breakdown spectroscopy, the plasma produced by a Nd:YAG laser from steel targets was confined by a cavity. A number of elements with low concentrations, such as vanadium (V), chromium (Cr), and manganese (Mn), in the steel samples were investigated. After the optimization of the cavity dimension and laser fluence, significant enhancement factors of 4.2, 3.1, and 2.87 in the emission intensity of V, Cr, and Mn lines, respectively, were achieved at a laser fluence of 42.9 J/cm(2) using a hemispherical cavity (diameter: 5 mm). More importantly, the correlation coefficient of the V I 440.85/Fe I 438.35 nm was increased from 0.946 (without the cavity) to 0.981 (with the cavity); and similar results for Cr I 425.43/Fe I 425.08 nm and Mn I 476.64/Fe I 492.05 nm were also obtained. Therefore, it was demonstrated that the accuracy of quantitative analysis with low concentration elements in steel samples was improved, because the plasma became uniform with spatial confinement. The results of this study provide a new pathway for improving the accuracy of quantitative analysis of LIBS.

  9. Contrast-enhanced spectral mammography based on a photon-counting detector: quantitative accuracy and radiation dose

    NASA Astrophysics Data System (ADS)

    Lee, Seungwan; Kang, Sooncheol; Eom, Jisoo

    2017-03-01

    Contrast-enhanced mammography has been used to demonstrate functional information about a breast tumor by injecting contrast agents. However, a conventional technique with a single exposure degrades the efficiency of tumor detection due to structure overlapping. Dual-energy techniques with energy-integrating detectors (EIDs) also cause an increase of radiation dose and an inaccuracy of material decomposition due to the limitations of EIDs. On the other hands, spectral mammography with photon-counting detectors (PCDs) is able to resolve the issues induced by the conventional technique and EIDs using their energy-discrimination capabilities. In this study, the contrast-enhanced spectral mammography based on a PCD was implemented by using a polychromatic dual-energy model, and the proposed technique was compared with the dual-energy technique with an EID in terms of quantitative accuracy and radiation dose. The results showed that the proposed technique improved the quantitative accuracy as well as reduced radiation dose comparing to the dual-energy technique with an EID. The quantitative accuracy of the contrast-enhanced spectral mammography based on a PCD was slightly improved as a function of radiation dose. Therefore, the contrast-enhanced spectral mammography based on a PCD is able to provide useful information for detecting breast tumors and improving diagnostic accuracy.

  10. Accuracy and Precision of Silicon Based Impression Media for Quantitative Areal Texture Analysis

    PubMed Central

    Goodall, Robert H.; Darras, Laurent P.; Purnell, Mark A.

    2015-01-01

    Areal surface texture analysis is becoming widespread across a diverse range of applications, from engineering to ecology. In many studies silicon based impression media are used to replicate surfaces, and the fidelity of replication defines the quality of data collected. However, while different investigators have used different impression media, the fidelity of surface replication has not been subjected to quantitative analysis based on areal texture data. Here we present the results of an analysis of the accuracy and precision with which different silicon based impression media of varying composition and viscosity replicate rough and smooth surfaces. Both accuracy and precision vary greatly between different media. High viscosity media tested show very low accuracy and precision, and most other compounds showed either the same pattern, or low accuracy and high precision, or low precision and high accuracy. Of the media tested, mid viscosity President Jet Regular Body and low viscosity President Jet Light Body (Coltène Whaledent) are the only compounds to show high levels of accuracy and precision on both surface types. Our results show that data acquired from different impression media are not comparable, supporting calls for greater standardisation of methods in areal texture analysis. PMID:25991505

  11. Quantitative phase imaging to improve the diagnostic accuracy of urine cytology.

    PubMed

    Pham, Hoa V; Pantanowitz, Liron; Liu, Yang

    2016-09-01

    A definitive diagnosis of urothelial carcinoma in urine cytology is often challenging and subjective. Many urine cytology samples receive an indeterminate diagnosis. Ancillary techniques such as fluorescence in situ hybridization (FISH) have been used to improve the diagnostic sensitivity, but FISH is not approved as a routine screening test, and the complex fluorescent staining protocol also limits its widespread clinical use. Quantitative phase imaging (QPI) is an emerging technology allowing accurate measurements of the single-cell dry mass. This study was undertaken to explore the ability of QPI to improve the diagnostic accuracy of urine cytology for malignancy. QPI was performed on unstained, ThinPrep-prepared urine cytology slides from 28 patients with 4 categories of cytological diagnoses (negative, atypical, suspicious, and positive for malignancy). The nuclear/cell dry mass, the entropy, and the nucleus-to-cell mass ratio were calculated for several hundred cells for each patient, and they were then correlated with the follow-up diagnoses. The nuclear mass and nuclear mass entropy of urothelial cells showed significant differences between negative and positive groups. These data showed a progressive increase from patients with negative diagnosis, to patients with atypical/suspicious and positive cytologic diagnosis. Most importantly, among the patients in the atypical and suspicious diagnosis, the nuclear mass and its entropy were significantly higher for those patients with a follow-up diagnosis of malignancy than those patients without a subsequent follow-up diagnosis of malignancy. QPI shows potential for improving the diagnostic accuracy of urine cytology, especially for indeterminate cases, and should be further evaluated as an ancillary test for urine cytology. Cancer Cytopathol 2016;124:641-50. © 2016 American Cancer Society. © 2016 American Cancer Society.

  12. Contrast-enhanced small-animal PET/CT in cancer research: strong improvement of diagnostic accuracy without significant alteration of quantitative accuracy and NEMA NU 4-2008 image quality parameters.

    PubMed

    Lasnon, Charline; Quak, Elske; Briand, Mélanie; Gu, Zheng; Louis, Marie-Hélène; Aide, Nicolas

    2013-01-17

    The use of iodinated contrast media in small-animal positron emission tomography (PET)/computed tomography (CT) could improve anatomic referencing and tumor delineation but may introduce inaccuracies in the attenuation correction of the PET images. This study evaluated the diagnostic performance and accuracy of quantitative values in contrast-enhanced small-animal PET/CT (CEPET/CT) as compared to unenhanced small animal PET/CT (UEPET/CT). Firstly, a NEMA NU 4-2008 phantom (filled with 18F-FDG or 18F-FDG plus contrast media) and a homemade phantom, mimicking an abdominal tumor surrounded by water or contrast media, were used to evaluate the impact of iodinated contrast media on the image quality parameters and accuracy of quantitative values for a pertinent-sized target. Secondly, two studies in 22 abdominal tumor-bearing mice and rats were performed. The first animal experiment studied the impact of a dual-contrast media protocol, comprising the intravenous injection of a long-lasting contrast agent mixed with 18F-FDG and the intraperitoneal injection of contrast media, on tumor delineation and the accuracy of quantitative values. The second animal experiment compared the diagnostic performance and quantitative values of CEPET/CT versus UEPET/CT by sacrificing the animals after the tracer uptake period and imaging them before and after intraperitoneal injection of contrast media. There was minimal impact on IQ parameters (%SDunif and spillover ratios in air and water) when the NEMA NU 4-2008 phantom was filled with 18F-FDG plus contrast media. In the homemade phantom, measured activity was similar to true activity (-0.02%) and overestimated by 10.30% when vials were surrounded by water or by an iodine solution, respectively. The first animal experiment showed excellent tumor delineation and a good correlation between small-animal (SA)-PET and ex vivo quantification (r2 = 0.87, P < 0.0001). The second animal experiment showed a good correlation between CEPET/CT and

  13. Homology modeling of a Class A GPCR in the inactive conformation: A quantitative analysis of the correlation between model/template sequence identity and model accuracy.

    PubMed

    Costanzi, Stefano; Skorski, Matthew; Deplano, Alessandro; Habermehl, Brett; Mendoza, Mary; Wang, Keyun; Biederman, Michelle; Dawson, Jessica; Gao, Jia

    2016-11-01

    With the present work we quantitatively studied the modellability of the inactive state of Class A G protein-coupled receptors (GPCRs). Specifically, we constructed models of one of the Class A GPCRs for which structures solved in the inactive state are available, namely the β 2 AR, using as templates each of the other class members for which structures solved in the inactive state are also available. Our results showed a detectable linear correlation between model accuracy and model/template sequence identity. This suggests that the likely accuracy of the homology models that can be built for a given receptor can be generally forecasted on the basis of the available templates. We also probed whether sequence alignments that allow for the presence of gaps within the transmembrane domains to account for structural irregularities afford better models than the classical alignment procedures that do not allow for the presence of gaps within such domains. As our results indicated, although the overall differences are very subtle, the inclusion of internal gaps within the transmembrane domains has a noticeable a beneficial effect on the local structural accuracy of the domain in question. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Performance Evaluation and Quantitative Accuracy of Multipinhole NanoSPECT/CT Scanner for Theranostic Lu-177 Imaging

    NASA Astrophysics Data System (ADS)

    Gupta, Arun; Kim, Kyeong Yun; Hwang, Donghwi; Lee, Min Sun; Lee, Dong Soo; Lee, Jae Sung

    2018-06-01

    SPECT plays important role in peptide receptor targeted radionuclide therapy using theranostic radionuclides such as Lu-177 for the treatment of various cancers. However, SPECT studies must be quantitatively accurate because the reliable assessment of tumor uptake and tumor-to-normal tissue ratios can only be performed using quantitatively accurate images. Hence, it is important to evaluate performance parameters and quantitative accuracy of preclinical SPECT systems for therapeutic radioisotopes before conducting pre- and post-therapy SPECT imaging or dosimetry studies. In this study, we evaluated system performance and quantitative accuracy of NanoSPECT/CT scanner for Lu-177 imaging using point source and uniform phantom studies. We measured recovery coefficient, uniformity, spatial resolution, system sensitivity and calibration factor for mouse whole body standard aperture. We also performed the experiments using Tc-99m to compare the results with that of Lu-177. We found that the recovery coefficient of more than 70% for Lu-177 at the optimum noise level when nine iterations were used. The spatial resolutions of Lu-177 with and without adding uniform background was comparable to that of Tc-99m in axial, radial and tangential directions. System sensitivity measured for Lu-177 was almost three times less than that of Tc-99m.

  15. Quantitative evaluation of contrast-enhanced ultrasound after intravenous administration of a microbubble contrast agent for differentiation of benign and malignant thyroid nodules: assessment of diagnostic accuracy.

    PubMed

    Nemec, Ursula; Nemec, Stefan F; Novotny, Clemens; Weber, Michael; Czerny, Christian; Krestan, Christian R

    2012-06-01

    To investigate the diagnostic accuracy, through quantitative analysis, of contrast-enhanced ultrasound (CEUS), using a microbubble contrast agent, in the differentiation of thyroid nodules. This prospective study enrolled 46 patients with solitary, scintigraphically non-functional thyroid nodules. These patients were scheduled for surgery and underwent preoperative CEUS with pulse-inversion harmonic imaging after intravenous microbubble contrast medium administration. Using histology as a standard of reference, time-intensity curves of benign and malignant nodules were compared by means of peak enhancement and wash-out enhancement relative to the baseline intensity using a mixed model ANOVA. ROC analysis was performed to assess the diagnostic accuracy in the differentiation of benign and malignant nodules on CEUS. The complete CEUS data of 42 patients (31/42 [73.8%] benign and 11/42 [26.2%] malignant nodules) revealed a significant difference (P < 0.001) in enhancement between benign and malignant nodules. Furthermore, based on ROC analysis, CEUS demonstrated sensitivity of 76.9%, specificity of 84.8% and accuracy of 82.6%. Quantitative analysis of CEUS using a microbubble contrast agent allows the differentiation of benign and malignant thyroid nodules and may potentially serve, in addition to grey-scale and Doppler ultrasound, as an adjunctive tool in the assessment of patients with thyroid nodules. • Contrast-enhanced ultrasound (CEUS) helps differentiate between benign and malignant thyroid nodules. • Quantitative CEUS analysis yields sensitivity of 76.9% and specificity of 84.8%. • CEUS may be a potentially useful adjunct in assessing thyroid nodules.

  16. Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

    USGS Publications Warehouse

    Anderson, Ryan; Clegg, Samuel M.; Frydenvang, Jens; Wiens, Roger C.; McLennan, Scott M.; Morris, Richard V.; Ehlmann, Bethany L.; Dyar, M. Darby

    2017-01-01

    Accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response of an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “sub-model” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. The sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.

  17. A quantitative reconstruction software suite for SPECT imaging

    NASA Astrophysics Data System (ADS)

    Namías, Mauro; Jeraj, Robert

    2017-11-01

    Quantitative Single Photon Emission Tomography (SPECT) imaging allows for measurement of activity concentrations of a given radiotracer in vivo. Although SPECT has usually been perceived as non-quantitative by the medical community, the introduction of accurate CT based attenuation correction and scatter correction from hybrid SPECT/CT scanners has enabled SPECT systems to be as quantitative as Positron Emission Tomography (PET) systems. We implemented a software suite to reconstruct quantitative SPECT images from hybrid or dedicated SPECT systems with a separate CT scanner. Attenuation, scatter and collimator response corrections were included in an Ordered Subset Expectation Maximization (OSEM) algorithm. A novel scatter fraction estimation technique was introduced. The SPECT/CT system was calibrated with a cylindrical phantom and quantitative accuracy was assessed with an anthropomorphic phantom and a NEMA/IEC image quality phantom. Accurate activity measurements were achieved at an organ level. This software suite helps increasing quantitative accuracy of SPECT scanners.

  18. Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens

    We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

  19. Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

    DOE PAGES

    Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens; ...

    2016-12-15

    We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

  20. The Shuttle Orbital Maneuvering System P-V-T Propellant Quantity Gaging Accuracy and Leak Detection Allowance for Four Instrumentation Conditions

    NASA Technical Reports Server (NTRS)

    Duhon, D. D.

    1975-01-01

    The shuttle orbital maneuvering system (OMS) pressure-volume-temperature (P-V-T) propellant gaging module computes the quantity of usable OMS propellant remaining based on the real gas P-V-T relationship for the propellant tank pressurant, helium. The OMS P-V-T propellant quantity gaging error was determined for four sets of instrumentation configurations and accuracies with the propellant tank operating in the normal constant pressure mode and in the blowdown mode. The instrumentation inaccuracy allowance for propellant leak detection was also computed for these same four sets of instrumentation. These gaging errors and leak detection allowances are presented in tables designed to permit a direct comparison of the effectiveness of the four instrumentation sets. The results show the magnitudes of the improvements in propellant quantity gaging accuracies and propellant leak detection allowances which can be achieved by employing more accurate pressure and temperature instrumentation.

  1. Reliable gene expression analysis by reverse transcription-quantitative PCR: reporting and minimizing the uncertainty in data accuracy.

    PubMed

    Remans, Tony; Keunen, Els; Bex, Geert Jan; Smeets, Karen; Vangronsveld, Jaco; Cuypers, Ann

    2014-10-01

    Reverse transcription-quantitative PCR (RT-qPCR) has been widely adopted to measure differences in mRNA levels; however, biological and technical variation strongly affects the accuracy of the reported differences. RT-qPCR specialists have warned that, unless researchers minimize this variability, they may report inaccurate differences and draw incorrect biological conclusions. The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines describe procedures for conducting and reporting RT-qPCR experiments. The MIQE guidelines enable others to judge the reliability of reported results; however, a recent literature survey found low adherence to these guidelines. Additionally, even experiments that use appropriate procedures remain subject to individual variation that statistical methods cannot correct. For example, since ideal reference genes do not exist, the widely used method of normalizing RT-qPCR data to reference genes generates background noise that affects the accuracy of measured changes in mRNA levels. However, current RT-qPCR data reporting styles ignore this source of variation. In this commentary, we direct researchers to appropriate procedures, outline a method to present the remaining uncertainty in data accuracy, and propose an intuitive way to select reference genes to minimize uncertainty. Reporting the uncertainty in data accuracy also serves for quality assessment, enabling researchers and peer reviewers to confidently evaluate the reliability of gene expression data. © 2014 American Society of Plant Biologists. All rights reserved.

  2. Accuracy in Rietveld quantitative phase analysis: a comparative study of strictly monochromatic Mo and Cu radiations.

    PubMed

    León-Reina, L; García-Maté, M; Álvarez-Pinazo, G; Santacruz, I; Vallcorba, O; De la Torre, A G; Aranda, M A G

    2016-06-01

    This study reports 78 Rietveld quantitative phase analyses using Cu  K α 1 , Mo  K α 1 and synchrotron radiations. Synchrotron powder diffraction has been used to validate the most challenging analyses. From the results for three series with increasing contents of an analyte (an inorganic crystalline phase, an organic crystalline phase and a glass), it is inferred that Rietveld analyses from high-energy Mo  K α 1 radiation have slightly better accuracies than those obtained from Cu  K α 1 radiation. This behaviour has been established from the results of the calibration graphics obtained through the spiking method and also from Kullback-Leibler distance statistic studies. This outcome is explained, in spite of the lower diffraction power for Mo radiation when compared to Cu radiation, as arising because of the larger volume tested with Mo and also because higher energy allows one to record patterns with fewer systematic errors. The limit of detection (LoD) and limit of quantification (LoQ) have also been established for the studied series. For similar recording times, the LoDs in Cu patterns, ∼0.2 wt%, are slightly lower than those derived from Mo patterns, ∼0.3 wt%. The LoQ for a well crystallized inorganic phase using laboratory powder diffraction was established to be close to 0.10 wt% in stable fits with good precision. However, the accuracy of these analyses was poor with relative errors near to 100%. Only contents higher than 1.0 wt% yielded analyses with relative errors lower than 20%.

  3. Advances in Surface Plasmon Resonance Imaging allowing for quantitative measurement of laterally heterogeneous samples

    NASA Astrophysics Data System (ADS)

    Raegen, Adam; Reiter, Kyle; Clarke, Anthony; Lipkowski, Jacek; Dutcher, John

    2012-02-01

    The Surface Plasmon Resonance (SPR) phenomenon is routinely exploited to qualitatively probe changes to materials on metallic surfaces for use in probes and sensors. Unfortunately, extracting truly quantitative information is usually limited to a select few cases -- uniform absorption/desorption of small biomolecules and films, in which a continuous ``slab'' model is a good approximation. We present advancements in the SPR technique that expand the number of cases for which the technique can provide meaningful results. Use of a custom, angle-scanning SPR imaging system, together with a refined data analysis method, allow for quantitative kinetic measurements of laterally heterogeneous systems. The degradation of cellulose microfibrils and bundles of microfibrils due to the action of cellulolytic enzymes will be presented as an excellent example of the capabilities of the SPR imaging system.

  4. Simulation of FRET dyes allows quantitative comparison against experimental data

    NASA Astrophysics Data System (ADS)

    Reinartz, Ines; Sinner, Claude; Nettels, Daniel; Stucki-Buchli, Brigitte; Stockmar, Florian; Panek, Pawel T.; Jacob, Christoph R.; Nienhaus, Gerd Ulrich; Schuler, Benjamin; Schug, Alexander

    2018-03-01

    Fully understanding biomolecular function requires detailed insight into the systems' structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.

  5. Diagnostic accuracy of semi-automatic quantitative metrics as an alternative to expert reading of CT myocardial perfusion in the CORE320 study.

    PubMed

    Ostovaneh, Mohammad R; Vavere, Andrea L; Mehra, Vishal C; Kofoed, Klaus F; Matheson, Matthew B; Arbab-Zadeh, Armin; Fujisawa, Yasuko; Schuijf, Joanne D; Rochitte, Carlos E; Scholte, Arthur J; Kitagawa, Kakuya; Dewey, Marc; Cox, Christopher; DiCarli, Marcelo F; George, Richard T; Lima, Joao A C

    To determine the diagnostic accuracy of semi-automatic quantitative metrics compared to expert reading for interpretation of computed tomography perfusion (CTP) imaging. The CORE320 multicenter diagnostic accuracy clinical study enrolled patients between 45 and 85 years of age who were clinically referred for invasive coronary angiography (ICA). Computed tomography angiography (CTA), CTP, single photon emission computed tomography (SPECT), and ICA images were interpreted manually in blinded core laboratories by two experienced readers. Additionally, eight quantitative CTP metrics as continuous values were computed semi-automatically from myocardial and blood attenuation and were combined using logistic regression to derive a final quantitative CTP metric score. For the reference standard, hemodynamically significant coronary artery disease (CAD) was defined as a quantitative ICA stenosis of 50% or greater and a corresponding perfusion defect by SPECT. Diagnostic accuracy was determined by area under the receiver operating characteristic curve (AUC). Of the total 377 included patients, 66% were male, median age was 62 (IQR: 56, 68) years, and 27% had prior myocardial infarction. In patient based analysis, the AUC (95% CI) for combined CTA-CTP expert reading and combined CTA-CTP semi-automatic quantitative metrics was 0.87(0.84-0.91) and 0.86 (0.83-0.9), respectively. In vessel based analyses the AUC's were 0.85 (0.82-0.88) and 0.84 (0.81-0.87), respectively. No significant difference in AUC was found between combined CTA-CTP expert reading and CTA-CTP semi-automatic quantitative metrics in patient based or vessel based analyses(p > 0.05 for all). Combined CTA-CTP semi-automatic quantitative metrics is as accurate as CTA-CTP expert reading to detect hemodynamically significant CAD. Copyright © 2018 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

  6. Effect of genetic architecture on the prediction accuracy of quantitative traits in samples of unrelated individuals.

    PubMed

    Morgante, Fabio; Huang, Wen; Maltecca, Christian; Mackay, Trudy F C

    2018-06-01

    Predicting complex phenotypes from genomic data is a fundamental aim of animal and plant breeding, where we wish to predict genetic merits of selection candidates; and of human genetics, where we wish to predict disease risk. While genomic prediction models work well with populations of related individuals and high linkage disequilibrium (LD) (e.g., livestock), comparable models perform poorly for populations of unrelated individuals and low LD (e.g., humans). We hypothesized that low prediction accuracies in the latter situation may occur when the genetics architecture of the trait departs from the infinitesimal and additive architecture assumed by most prediction models. We used simulated data for 10,000 lines based on sequence data from a population of unrelated, inbred Drosophila melanogaster lines to evaluate this hypothesis. We show that, even in very simplified scenarios meant as a stress test of the commonly used Genomic Best Linear Unbiased Predictor (G-BLUP) method, using all common variants yields low prediction accuracy regardless of the trait genetic architecture. However, prediction accuracy increases when predictions are informed by the genetic architecture inferred from mapping the top variants affecting main effects and interactions in the training data, provided there is sufficient power for mapping. When the true genetic architecture is largely or partially due to epistatic interactions, the additive model may not perform well, while models that account explicitly for interactions generally increase prediction accuracy. Our results indicate that accounting for genetic architecture can improve prediction accuracy for quantitative traits.

  7. Simulation-based evaluation of the resolution and quantitative accuracy of temperature-modulated fluorescence tomography.

    PubMed

    Lin, Yuting; Nouizi, Farouk; Kwong, Tiffany C; Gulsen, Gultekin

    2015-09-01

    Conventional fluorescence tomography (FT) can recover the distribution of fluorescent agents within a highly scattering medium. However, poor spatial resolution remains its foremost limitation. Previously, we introduced a new fluorescence imaging technique termed "temperature-modulated fluorescence tomography" (TM-FT), which provides high-resolution images of fluorophore distribution. TM-FT is a multimodality technique that combines fluorescence imaging with focused ultrasound to locate thermo-sensitive fluorescence probes using a priori spatial information to drastically improve the resolution of conventional FT. In this paper, we present an extensive simulation study to evaluate the performance of the TM-FT technique on complex phantoms with multiple fluorescent targets of various sizes located at different depths. In addition, the performance of the TM-FT is tested in the presence of background fluorescence. The results obtained using our new method are systematically compared with those obtained with the conventional FT. Overall, TM-FT provides higher resolution and superior quantitative accuracy, making it an ideal candidate for in vivo preclinical and clinical imaging. For example, a 4 mm diameter inclusion positioned in the middle of a synthetic slab geometry phantom (D:40  mm×W:100  mm) is recovered as an elongated object in the conventional FT (x=4.5  mm; y=10.4  mm), while TM-FT recovers it successfully in both directions (x=3.8  mm; y=4.6  mm). As a result, the quantitative accuracy of the TM-FT is superior because it recovers the concentration of the agent with a 22% error, which is in contrast with the 83% error of the conventional FT.

  8. Simulation-based evaluation of the resolution and quantitative accuracy of temperature-modulated fluorescence tomography

    PubMed Central

    Lin, Yuting; Nouizi, Farouk; Kwong, Tiffany C.; Gulsen, Gultekin

    2016-01-01

    Conventional fluorescence tomography (FT) can recover the distribution of fluorescent agents within a highly scattering medium. However, poor spatial resolution remains its foremost limitation. Previously, we introduced a new fluorescence imaging technique termed “temperature-modulated fluorescence tomography” (TM-FT), which provides high-resolution images of fluorophore distribution. TM-FT is a multimodality technique that combines fluorescence imaging with focused ultrasound to locate thermo-sensitive fluorescence probes using a priori spatial information to drastically improve the resolution of conventional FT. In this paper, we present an extensive simulation study to evaluate the performance of the TM-FT technique on complex phantoms with multiple fluorescent targets of various sizes located at different depths. In addition, the performance of the TM-FT is tested in the presence of background fluorescence. The results obtained using our new method are systematically compared with those obtained with the conventional FT. Overall, TM-FT provides higher resolution and superior quantitative accuracy, making it an ideal candidate for in vivo preclinical and clinical imaging. For example, a 4 mm diameter inclusion positioned in the middle of a synthetic slab geometry phantom (D:40 mm × W :100 mm) is recovered as an elongated object in the conventional FT (x = 4.5 mm; y = 10.4 mm), while TM-FT recovers it successfully in both directions (x = 3.8 mm; y = 4.6 mm). As a result, the quantitative accuracy of the TM-FT is superior because it recovers the concentration of the agent with a 22% error, which is in contrast with the 83% error of the conventional FT. PMID:26368884

  9. Accuracy of the days’ supply and the number of refills allowed recorded in Québec prescription claims databases for inhaled corticosteroids

    PubMed Central

    Blais, Lucie; Vilain, Anne; Kettani, Fatima-Zohra; Forget, Amélie; Lalonde, Geneviève; Beauchesne, Marie-France; Ducharme, Francine M; Lemière, Catherine

    2014-01-01

    Objectives and hypotheses Adherence to inhaled corticosteroids (ICS) is a major issue in asthma. This study aimed to estimate the accuracy of the days’ supply and number of refills allowed, variables recorded in Québec claims databases and used to estimate adherence, and to develop correction factors, if required. We hypothesised that the accuracy of the days’ supply for ICS would be low whereas the accuracy of the number of refills allowed would be high. Setting 40 community pharmacies in Québec (Canada) and a medication registry. Participants We collected data for 1108 ICS original prescriptions stored in the 40 pharmacies (sample 1), and we obtained a second sample of 2676 ICS prescriptions selected from reMed, a medication registry (sample 2). Primary and secondary outcomes We estimated the concordance of the days’ supply and number of refills between Québec claims databases and the original prescription from sample 1. We developed a correction factor for the days’ supply in sample 1 and validated it in sample 2. Analyses were stratified by age: 0–11 and 12–64 years. Results In sample 1, the concordance for the days’ supply was 39.6% (95% CI 37.6% to 41.6%) in those aged 0–11 years and 56% (54.9% to 57.2%) in those aged 12–64 years. The concordance increased to 59.4% (58.2% to 60.5%) in those aged 0–11 years and 74.2% (73.5% to 74.9%) in those aged 12–64 years after applying the correction factors in sample 2. The concordance for the refills allowed was 92.1% (91% to 93.1%) in those aged 0–11 years and 93.1% (92.5% to 93.7%) in those aged 12–64 years in sample 1. Conclusions The accuracy of the days’ supply was moderate among those aged 0–11 years and substantial among those aged 12–64 years after applying the correction factors. The accuracy of the number of refills was almost perfect in both groups. PMID:25432902

  10. Accuracy of a remote quantitative image analysis in the whole slide images.

    PubMed

    Słodkowska, Janina; Markiewicz, Tomasz; Grala, Bartłomiej; Kozłowski, Wojciech; Papierz, Wielisław; Pleskacz, Katarzyna; Murawski, Piotr

    2011-03-30

    The rationale for choosing a remote quantitative method supporting a diagnostic decision requires some empirical studies and knowledge on scenarios including valid telepathology standards. The tumours of the central nervous system [CNS] are graded on the base of the morphological features and the Ki-67 labelling Index [Ki-67 LI]. Various methods have been applied for Ki-67 LI estimation. Recently we have introduced the Computerized Analysis of Medical Images [CAMI] software for an automated Ki-67 LI counting in the digital images. Aims of our study was to explore the accuracy and reliability of a remote assessment of Ki-67 LI with CAMI software applied to the whole slide images [WSI]. The WSI representing CNS tumours: 18 meningiomas and 10 oligodendrogliomas were stored on the server of the Warsaw University of Technology. The digital copies of entire glass slides were created automatically by the Aperio ScanScope CS with objective 20x or 40x. Aperio's Image Scope software provided functionality for a remote viewing of WSI. The Ki-67 LI assessment was carried on within 2 out of 20 selected fields of view (objective 40x) representing the highest labelling areas in each WSI. The Ki-67 LI counting was performed by 3 various methods: 1) the manual reading in the light microscope - LM, 2) the automated counting with CAMI software on the digital images - DI , and 3) the remote quantitation on the WSIs - as WSI method. The quality of WSIs and technical efficiency of the on-line system were analysed. The comparative statistical analysis was performed for the results obtained by 3 methods of Ki-67 LI counting. The preliminary analysis showed that in 18% of WSI the results of Ki-67 LI differed from those obtained in other 2 methods of counting when the quality of the glass slides was below the standard range. The results of our investigations indicate that the remote automated Ki-67 LI analysis performed with the CAMI algorithm on the whole slide images of meningiomas and

  11. Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, Sun Mo, E-mail: Sunmo.Kim@rmp.uhn.on.ca; Haider, Masoom A.; Jaffray, David A.

    quantitative histogram parameters of volume transfer constant [standard deviation (SD), 98th percentile, and range], rate constant (SD), blood volume fraction (mean, SD, 98th percentile, and range), and blood flow (mean, SD, median, 98th percentile, and range) for sampling intervals between 10 and 15 s. Conclusions: The proposed method of PCA filtering combined with the AIF estimation technique allows low frequency scanning for DCE-CT study to reduce patient radiation dose. The results indicate that the method is useful in pixel-by-pixel kinetic analysis of DCE-CT data for patients with cervical cancer.« less

  12. Correlation between average tissue depth data and quantitative accuracy of forensic craniofacial reconstructions measured by geometric surface comparison method.

    PubMed

    Lee, Won-Joon; Wilkinson, Caroline M; Hwang, Hyeon-Shik; Lee, Sang-Mi

    2015-05-01

    Accuracy is the most important factor supporting the reliability of forensic facial reconstruction (FFR) comparing to the corresponding actual face. A number of methods have been employed to evaluate objective accuracy of FFR. Recently, it has been attempted that the degree of resemblance between computer-generated FFR and actual face is measured by geometric surface comparison method. In this study, three FFRs were produced employing live adult Korean subjects and three-dimensional computerized modeling software. The deviations of the facial surfaces between the FFR and the head scan CT of the corresponding subject were analyzed in reverse modeling software. The results were compared with those from a previous study which applied the same methodology as this study except average facial soft tissue depth dataset. Three FFRs of this study that applied updated dataset demonstrated lesser deviation errors between the facial surfaces of the FFR and corresponding subject than those from the previous study. The results proposed that appropriate average tissue depth data are important to increase quantitative accuracy of FFR. © 2015 American Academy of Forensic Sciences.

  13. Quantitative accuracy of the closed-form least-squares solution for targeted SPECT.

    PubMed

    Shcherbinin, S; Celler, A

    2010-10-07

    The aim of this study is to investigate the quantitative accuracy of the closed-form least-squares solution (LSS) for single photon emission computed tomography (SPECT). The main limitation for employing this method in actual clinical reconstructions is the computational cost related to operations with a large-sized system matrix. However, in some clinical situations, the size of the system matrix can be decreased using targeted reconstruction. For example, some oncology SPECT studies are characterized by intense tracer uptakes that are localized in relatively small areas, while the remaining parts of the patient body have only a low activity background. Conventional procedures reconstruct the activity distribution in the whole object, which leads to relatively poor image accuracy/resolution for tumors while computer resources are wasted, trying to rebuild diagnostically useless background. In this study, we apply a concept of targeted reconstruction to SPECT phantom experiments imitating such oncology scans. Our approach includes two major components: (i) disconnection of the entire imaging system of equations and extraction of only those parts that correspond to the targets, i.e., regions of interest (ROI) encompassing active containers/tumors and (ii) generation of the closed-form LSS for each target ROI. We compared these ROI-based LSS with those reconstructed by the conventional MLEM approach. The analysis of the five processed cases from two phantom experiments demonstrated that the LSS approach outperformed MLEM in terms of the noise level inside ROI. On the other hand, MLEM better recovered total activity if the number of iterations was large enough. For the experiment without background activity, the ROI-based LSS led to noticeably better spatial activity distribution inside ROI. However, the distributions pertaining to both approaches were practically identical for the experiment with the concentration ratio 7:1 between the containers and the background.

  14. Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples.

    PubMed

    Zellner, Maria; Babeluk, Rita; Diestinger, Michael; Pirchegger, Petra; Skeledzic, Senada; Oehler, Rudolf

    2008-09-01

    Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.

  15. Reproducibility and Accuracy of Quantitative Myocardial Blood Flow Using 82Rb-PET: Comparison with 13N-Ammonia

    PubMed Central

    Fakhri, Georges El

    2011-01-01

    82Rb cardiac PET allows the assessment of myocardial perfusion using a column generator in clinics that lack a cyclotron. We and others have previously shown that quantitation of myocardial blood flow (MBF) and coronary flow reserve (CFR) is feasible using dynamic 82Rb PET and factor and compartment analyses. The aim of the present work was to determine the intra- and inter-observer variability of MBF estimation using 82Rb PET as well as the reproducibility of our generalized factor + compartment analyses methodology to estimate MBF and assess its accuracy by comparing, in the same subjects, 82Rb estimates of MBF to those obtained using 13N-ammonia. Methods Twenty-two subjects were included in the reproducibility and twenty subjects in the validation study. Patients were injected with 60±5mCi of 82Rb and imaged dynamically for 6 minutes at rest and during dipyridamole stress Left and right ventricular (LV+RV) time-activity curves were estimated by GFADS and used as input to a 2-compartment kinetic analysis that estimates parametric maps of myocardial tissue extraction (K1) and egress (k2), as well as LV+RV contributions (fv,rv). Results Our results show excellent reproducibility of the quantitative dynamic approach itself with coefficients of repeatability of 1.7% for estimation of MBF at rest, 1.4% for MBF at peak stress and 2.8% for CFR estimation. The inter-observer reproducibility between the four observers that participated in this study was also very good with correlation coefficients greater than 0.87 between any two given observers when estimating coronary flow reserve. The reproducibility of MBF in repeated 82Rb studies was good at rest and excellent at peak stress (r2=0.835). Furthermore, the slope of the correlation line was very close to 1 when estimating stress MBF and CFR in repeated 82Rb studies. The correlation between myocardial flow estimates obtained at rest and during peak stress in 82Rb and 13N-ammonia studies was very good at rest (r2

  16. Quantitative underwater 3D motion analysis using submerged video cameras: accuracy analysis and trajectory reconstruction.

    PubMed

    Silvatti, Amanda P; Cerveri, Pietro; Telles, Thiago; Dias, Fábio A S; Baroni, Guido; Barros, Ricardo M L

    2013-01-01

    In this study we aim at investigating the applicability of underwater 3D motion capture based on submerged video cameras in terms of 3D accuracy analysis and trajectory reconstruction. Static points with classical direct linear transform (DLT) solution, a moving wand with bundle adjustment and a moving 2D plate with Zhang's method were considered for camera calibration. As an example of the final application, we reconstructed the hand motion trajectories in different swimming styles and qualitatively compared this with Maglischo's model. Four highly trained male swimmers performed butterfly, breaststroke and freestyle tasks. The middle fingertip trajectories of both hands in the underwater phase were considered. The accuracy (mean absolute error) of the two calibration approaches (wand: 0.96 mm - 2D plate: 0.73 mm) was comparable to out of water results and highly superior to the classical DLT results (9.74 mm). Among all the swimmers, the hands' trajectories of the expert swimmer in the style were almost symmetric and in good agreement with Maglischo's model. The kinematic results highlight symmetry or asymmetry between the two hand sides, intra- and inter-subject variability in terms of the motion patterns and agreement or disagreement with the model. The two outcomes, calibration results and trajectory reconstruction, both move towards the quantitative 3D underwater motion analysis.

  17. Application of linear regression analysis in accuracy assessment of rolling force calculations

    NASA Astrophysics Data System (ADS)

    Poliak, E. I.; Shim, M. K.; Kim, G. S.; Choo, W. Y.

    1998-10-01

    Efficient operation of the computational models employed in process control systems require periodical assessment of the accuracy of their predictions. Linear regression is proposed as a tool which allows separate systematic and random prediction errors from those related to measurements. A quantitative characteristic of the model predictive ability is introduced in addition to standard statistical tests for model adequacy. Rolling force calculations are considered as an example for the application. However, the outlined approach can be used to assess the performance of any computational model.

  18. Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

    PubMed

    Schaab, Christoph; Geiger, Tamar; Stoehr, Gabriele; Cox, Juergen; Mann, Matthias

    2012-03-01

    MS-based proteomics generates rapidly increasing amounts of precise and quantitative information. Analysis of individual proteomic experiments has made great strides, but the crucial ability to compare and store information across different proteome measurements still presents many challenges. For example, it has been difficult to avoid contamination of databases with low quality peptide identifications, to control for the inflation in false positive identifications when combining data sets, and to integrate quantitative data. Although, for example, the contamination with low quality identifications has been addressed by joint analysis of deposited raw data in some public repositories, we reasoned that there should be a role for a database specifically designed for high resolution and quantitative data. Here we describe a novel database termed MaxQB that stores and displays collections of large proteomics projects and allows joint analysis and comparison. We demonstrate the analysis tools of MaxQB using proteome data of 11 different human cell lines and 28 mouse tissues. The database-wide false discovery rate is controlled by adjusting the project specific cutoff scores for the combined data sets. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted. We used MaxQB to calculate the signal reproducibility of the detected peptides for the same proteins across different proteomes. Spearman rank correlation between peptide intensity and detection probability of identified proteins was greater than 0.8 for 64% of the proteome, whereas a minority of proteins have negative correlation. This information can be used to pinpoint false protein identifications, independently of peptide database

  19. Diagnostic performance of semi-quantitative and quantitative stress CMR perfusion analysis: a meta-analysis.

    PubMed

    van Dijk, R; van Assen, M; Vliegenthart, R; de Bock, G H; van der Harst, P; Oudkerk, M

    2017-11-27

    Stress cardiovascular magnetic resonance (CMR) perfusion imaging is a promising modality for the evaluation of coronary artery disease (CAD) due to high spatial resolution and absence of radiation. Semi-quantitative and quantitative analysis of CMR perfusion are based on signal-intensity curves produced during the first-pass of gadolinium contrast. Multiple semi-quantitative and quantitative parameters have been introduced. Diagnostic performance of these parameters varies extensively among studies and standardized protocols are lacking. This study aims to determine the diagnostic accuracy of semi- quantitative and quantitative CMR perfusion parameters, compared to multiple reference standards. Pubmed, WebOfScience, and Embase were systematically searched using predefined criteria (3272 articles). A check for duplicates was performed (1967 articles). Eligibility and relevance of the articles was determined by two reviewers using pre-defined criteria. The primary data extraction was performed independently by two researchers with the use of a predefined template. Differences in extracted data were resolved by discussion between the two researchers. The quality of the included studies was assessed using the 'Quality Assessment of Diagnostic Accuracy Studies Tool' (QUADAS-2). True positives, false positives, true negatives, and false negatives were subtracted/calculated from the articles. The principal summary measures used to assess diagnostic accuracy were sensitivity, specificity, andarea under the receiver operating curve (AUC). Data was pooled according to analysis territory, reference standard and perfusion parameter. Twenty-two articles were eligible based on the predefined study eligibility criteria. The pooled diagnostic accuracy for segment-, territory- and patient-based analyses showed good diagnostic performance with sensitivity of 0.88, 0.82, and 0.83, specificity of 0.72, 0.83, and 0.76 and AUC of 0.90, 0.84, and 0.87, respectively. In per territory

  20. Chemisorption of iodine-125 to gold nanoparticles allows for real-time quantitation and potential use in nanomedicine.

    PubMed

    Walsh, Adrian A

    2017-01-01

    Gold nanoparticles have been available for many years as a research tool in the life sciences due to their electron density and optical properties. New applications are continually being developed, particularly in nanomedicine. One drawback is the need for an easy, real-time quantitation method for gold nanoparticles so that the effects observed in in vitro cell toxicity assays and cell uptake studies can be interpreted quantitatively in terms of nanoparticle loading. One potential method of quantifying gold nanoparticles in real time is by chemisorption of iodine-125, a gamma emitter, to the nanoparticles. This paper revisits the labelling of gold nanoparticles with iodine-125, first described 30 years ago and never fully exploited since. We explore the chemical properties and usefulness in quantifying bio-functionalised gold nanoparticle binding in a quick and simple manner. The gold particles were labelled specifically and quantitatively simply by mixing the two items. The nature of the labelling is chemisorption and is robust, remaining bound over several weeks in a variety of cell culture media. Chemisorption was confirmed as potassium iodide can remove the label whereas sodium chloride and many other buffers had no effect. Particles precoated in polymers or proteins can be labelled just as efficiently allowing for post-labelling experiments in situ rather than using radioactive gold atoms in the production process. We also demonstrate that interparticle exchange of I-125 between different size particles does not appear to take place confirming the affinity of the binding.

  1. Characterization of the relation between CT technical parameters and accuracy of quantification of lung attenuation on quantitative chest CT.

    PubMed

    Trotta, Brian M; Stolin, Alexander V; Williams, Mark B; Gay, Spencer B; Brody, Alan S; Altes, Talissa A

    2007-06-01

    The purpose of this study was to assess the compromise between CT technical parameters and the accuracy of CT quantification of lung attenuation. Materials that simulate water (0 H), healthy lung (-650 H), borderline emphysematous lung (-820 H), and severely emphysematous lung (-1,000 H) were placed at both the base and the apex of the lung of an anthropomorphic phantom and outside the phantom. Transaxial CT images through the samples were obtained while the effective tube current was varied from 440 to 10 mAs, kilovoltage from 140 to 80 kVp, and slice thickness from 0.625 to 10 mm. Mean +/- SD attenuation within the samples and the standard quantitative chest CT measurements, the percentage of pixels with attenuation less than -910 H and 15th percentile of attenuation, were computed. Outside the phantom, variations in CT parameters produced less than 2.0% error in all measurements. Within the anthropomorphic phantom at 30 mAs, error in measurements was much larger, ranging from zero to 200%. Below approximately 80 mAs, mean attenuation became increasingly biased. The effects were most pronounced at the apex of the lungs. Mean attenuation of the borderline emphysematous sample of apex decreased 55 H as the tube current was decreased from 300 to 30 mAs. Both the 15th percentile of attenuation and percentage of pixels with less than -910 H attenuation were more sensitive to variations in effective tube current than was mean attenuation. For example, the -820 H sample should have 0% of pixels less than -910 H, which was true at 400 mA. At 30 mA in the lung apex, however, the measurement was highly inaccurate, 51% of pixels being below this value. Decreased kilovoltage and slice thickness had analogous, but lesser, effects. The accuracy of quantitative chest CT is determined by the CT acquisition parameters. There can be significant decreases in accuracy at less than 80 mAs for thin slices in an anthropomorphic phantom, the most pronounced effects occurring in the lung

  2. Usefulness of quantitative susceptibility mapping for the diagnosis of Parkinson disease.

    PubMed

    Murakami, Y; Kakeda, S; Watanabe, K; Ueda, I; Ogasawara, A; Moriya, J; Ide, S; Futatsuya, K; Sato, T; Okada, K; Uozumi, T; Tsuji, S; Liu, T; Wang, Y; Korogi, Y

    2015-06-01

    Quantitative susceptibility mapping allows overcoming several nonlocal restrictions of susceptibility-weighted and phase imaging and enables quantification of magnetic susceptibility. We compared the diagnostic accuracy of quantitative susceptibility mapping and R2* (1/T2*) mapping to discriminate between patients with Parkinson disease and controls. For 21 patients with Parkinson disease and 21 age- and sex-matched controls, 2 radiologists measured the quantitative susceptibility mapping values and R2* values in 6 brain structures (the thalamus, putamen, caudate nucleus, pallidum, substantia nigra, and red nucleus). The quantitative susceptibility mapping values and R2* values of the substantia nigra were significantly higher in patients with Parkinson disease (P < .01); measurements in other brain regions did not differ significantly between patients and controls. For the discrimination of patients with Parkinson disease from controls, receiver operating characteristic analysis suggested that the optimal cutoff values for the substantia nigra, based on the Youden Index, were >0.210 for quantitative susceptibility mapping and >28.8 for R2*. The sensitivity, specificity, and accuracy of quantitative susceptibility mapping were 90% (19 of 21), 86% (18 of 21), and 88% (37 of 42), respectively; for R2* mapping, they were 81% (17 of 21), 52% (11 of 21), and 67% (28 of 42). Pair-wise comparisons showed that the areas under the receiver operating characteristic curves were significantly larger for quantitative susceptibility mapping than for R2* mapping (0.91 versus 0.69, P < .05). Quantitative susceptibility mapping showed higher diagnostic performance than R2* mapping for the discrimination between patients with Parkinson disease and controls. © 2015 by American Journal of Neuroradiology.

  3. NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

    PubMed Central

    Andreatta, Massimo; Schafer-Nielsen, Claus; Lund, Ole; Buus, Søren; Nielsen, Morten

    2011-01-01

    Recent advances in high-throughput technologies have made it possible to generate both gene and protein sequence data at an unprecedented rate and scale thereby enabling entirely new “omics”-based approaches towards the analysis of complex biological processes. However, the amount and complexity of data that even a single experiment can produce seriously challenges researchers with limited bioinformatics expertise, who need to handle, analyze and interpret the data before it can be understood in a biological context. Thus, there is an unmet need for tools allowing non-bioinformatics users to interpret large data sets. We have recently developed a method, NNAlign, which is generally applicable to any biological problem where quantitative peptide data is available. This method efficiently identifies underlying sequence patterns by simultaneously aligning peptide sequences and identifying motifs associated with quantitative readouts. Here, we provide a web-based implementation of NNAlign allowing non-expert end-users to submit their data (optionally adjusting method parameters), and in return receive a trained method (including a visual representation of the identified motif) that subsequently can be used as prediction method and applied to unknown proteins/peptides. We have successfully applied this method to several different data sets including peptide microarray-derived sets containing more than 100,000 data points. NNAlign is available online at http://www.cbs.dtu.dk/services/NNAlign. PMID:22073191

  4. NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data.

    PubMed

    Andreatta, Massimo; Schafer-Nielsen, Claus; Lund, Ole; Buus, Søren; Nielsen, Morten

    2011-01-01

    Recent advances in high-throughput technologies have made it possible to generate both gene and protein sequence data at an unprecedented rate and scale thereby enabling entirely new "omics"-based approaches towards the analysis of complex biological processes. However, the amount and complexity of data that even a single experiment can produce seriously challenges researchers with limited bioinformatics expertise, who need to handle, analyze and interpret the data before it can be understood in a biological context. Thus, there is an unmet need for tools allowing non-bioinformatics users to interpret large data sets. We have recently developed a method, NNAlign, which is generally applicable to any biological problem where quantitative peptide data is available. This method efficiently identifies underlying sequence patterns by simultaneously aligning peptide sequences and identifying motifs associated with quantitative readouts. Here, we provide a web-based implementation of NNAlign allowing non-expert end-users to submit their data (optionally adjusting method parameters), and in return receive a trained method (including a visual representation of the identified motif) that subsequently can be used as prediction method and applied to unknown proteins/peptides. We have successfully applied this method to several different data sets including peptide microarray-derived sets containing more than 100,000 data points. NNAlign is available online at http://www.cbs.dtu.dk/services/NNAlign.

  5. Accuracy of computed tomographic angiography for stenosis quantification using quantitative coronary angiography or intravascular ultrasound as the gold standard.

    PubMed

    Joshi, Subodh B; Okabe, Teruo; Roswell, Robert O; Weissman, Gaby; Lopez, Cristian F; Lindsay, Joseph; Pichard, Augusto D; Weissman, Neil J; Waksman, Ron; Weigold, Wm Guy

    2009-10-15

    Computed tomographic angiography (CTA) is considered to have limited accuracy for quantifying exact percent diameter stenosis in coronary arteries. However, most studies evaluating CTA use quantitative coronary angiography (QCA) as the gold standard, a technique with its own limitations. We sought to determine whether CTA measurements of stenosis severity correlate better with intravascular ultrasound (IVUS) than with QCA. Luminal dimensions of 67 de novo coronary lesions were measured by CTA, IVUS, and QCA. IVUS was performed when lesion severity by angiography was equivocal. Mean percent diameter stenosis by QCA was 51 +/- 9.8% and mean IVUS minimal luminal area was 3.8 +/- 1.8 mm(2). There was a moderate correlation between CTA minimal luminal area and IVUS minimal luminal area (r(2) = 0.41, p <0.001), but no relation between CTA and QCA measurements of minimal luminal diameter (r(2) = 0.01, p = 0.57) or diameter stenosis (r(2) = 0.02, p = 0.31). There was also no relation between IVUS minimal luminal area and QCA diameter stenosis (r(2) = 0.01, p = 0.50). When lesions with moderate or severe calcification were excluded, the correlation between CTA minimal luminal area and IVUS minimal luminal area was good (r(2) = 0.68, p <0.001). In conclusion, in this cohort of patients with intermediate-grade lesions on cardiac catheterization, absolute measurements of stenosis severity on CTA correlated with IVUS but not with QCA. Our findings suggest that limitations of quantitative coronary angiography as a gold standard need to be considered in studies evaluating the accuracy of coronary CTA.

  6. A custom-built PET phantom design for quantitative imaging of printed distributions.

    PubMed

    Markiewicz, P J; Angelis, G I; Kotasidis, F; Green, M; Lionheart, W R; Reader, A J; Matthews, J C

    2011-11-07

    This note presents a practical approach to a custom-made design of PET phantoms enabling the use of digital radioactive distributions with high quantitative accuracy and spatial resolution. The phantom design allows planar sources of any radioactivity distribution to be imaged in transaxial and axial (sagittal or coronal) planes. Although the design presented here is specially adapted to the high-resolution research tomograph (HRRT), the presented methods can be adapted to almost any PET scanner. Although the presented phantom design has many advantages, a number of practical issues had to be overcome such as positioning of the printed source, calibration, uniformity and reproducibility of printing. A well counter (WC) was used in the calibration procedure to find the nonlinear relationship between digital voxel intensities and the actual measured radioactive concentrations. Repeated printing together with WC measurements and computed radiography (CR) using phosphor imaging plates (IP) were used to evaluate the reproducibility and uniformity of such printing. Results show satisfactory printing uniformity and reproducibility; however, calibration is dependent on the printing mode and the physical state of the cartridge. As a demonstration of the utility of using printed phantoms, the image resolution and quantitative accuracy of reconstructed HRRT images are assessed. There is very good quantitative agreement in the calibration procedure between HRRT, CR and WC measurements. However, the high resolution of CR and its quantitative accuracy supported by WC measurements made it possible to show the degraded resolution of HRRT brain images caused by the partial-volume effect and the limits of iterative image reconstruction.

  7. Rigour in quantitative research.

    PubMed

    Claydon, Leica Sarah

    2015-07-22

    This article which forms part of the research series addresses scientific rigour in quantitative research. It explores the basis and use of quantitative research and the nature of scientific rigour. It examines how the reader may determine whether quantitative research results are accurate, the questions that should be asked to determine accuracy and the checklists that may be used in this process. Quantitative research has advantages in nursing, since it can provide numerical data to help answer questions encountered in everyday practice.

  8. Quantitative optical metrology with CMOS cameras

    NASA Astrophysics Data System (ADS)

    Furlong, Cosme; Kolenovic, Ervin; Ferguson, Curtis F.

    2004-08-01

    Recent advances in laser technology, optical sensing, and computer processing of data, have lead to the development of advanced quantitative optical metrology techniques for high accuracy measurements of absolute shapes and deformations of objects. These techniques provide noninvasive, remote, and full field of view information about the objects of interest. The information obtained relates to changes in shape and/or size of the objects, characterizes anomalies, and provides tools to enhance fabrication processes. Factors that influence selection and applicability of an optical technique include the required sensitivity, accuracy, and precision that are necessary for a particular application. In this paper, sensitivity, accuracy, and precision characteristics in quantitative optical metrology techniques, and specifically in optoelectronic holography (OEH) based on CMOS cameras, are discussed. Sensitivity, accuracy, and precision are investigated with the aid of National Institute of Standards and Technology (NIST) traceable gauges, demonstrating the applicability of CMOS cameras in quantitative optical metrology techniques. It is shown that the advanced nature of CMOS technology can be applied to challenging engineering applications, including the study of rapidly evolving phenomena occurring in MEMS and micromechatronics.

  9. Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.

    PubMed

    Hong, Jungeui; Gresham, David

    2017-11-01

    Quantitative analysis of next-generation sequencing (NGS) data requires discriminating duplicate reads generated by PCR from identical molecules that are of unique origin. Typically, PCR duplicates are identified as sequence reads that align to the same genomic coordinates using reference-based alignment. However, identical molecules can be independently generated during library preparation. Misidentification of these molecules as PCR duplicates can introduce unforeseen biases during analyses. Here, we developed a cost-effective sequencing adapter design by modifying Illumina TruSeq adapters to incorporate a unique molecular identifier (UMI) while maintaining the capacity to undertake multiplexed, single-index sequencing. Incorporation of UMIs into TruSeq adapters (TrUMIseq adapters) enables identification of bona fide PCR duplicates as identically mapped reads with identical UMIs. Using TrUMIseq adapters, we show that accurate removal of PCR duplicates results in improved accuracy of both allele frequency (AF) estimation in heterogeneous populations using DNA sequencing and gene expression quantification using RNA-Seq.

  10. Improvements in Diagnostic Accuracy with Quantitative Dynamic Contrast-Enhanced MRI

    DTIC Science & Technology

    2011-12-01

    Magnetic   Resonance   Imaging  during  the  Menstrual  Cylce:  Perfusion   Imaging  Signal   Enhanceent,  and  Influence  of...acquisition of quantitative images displaying the concentration of contrast media as well as MRI -detectable proton density. To date 21 patients have...truly  quantitative   images  of  a  dynamic  contrast-­‐enhanced  (DCE)   MRI  of  the

  11. Qualitative and quantitative three-dimensional accuracy of a single tooth captured by elastomeric impression materials: an in vitro study.

    PubMed

    Schaefer, Oliver; Schmidt, Monika; Goebel, Roland; Kuepper, Harald

    2012-09-01

    The accuracy of impressions has been described in 1 or 2 dimensions, whereas it is most desirable to evaluate the accuracy of impressions spatially, in 3 dimensions. The purpose of this study was to demonstrate the accuracy and reproducibility of a 3-dimensional (3-D) approach to assessing impression preciseness and to quantitatively comparing the occlusal correctness of gypsum dies made with different impression materials. By using an aluminum replica of a maxillary molar, single-step dual viscosity impressions were made with 1 polyether/vinyl polysiloxane hybrid material (Identium), 1 vinyl polysiloxane (Panasil), and 1 polyether (Impregum) (n=5). Corresponding dies were made of Type IV gypsum and were optically digitized and aligned to the virtual reference of the aluminum tooth. Accuracy was analyzed by computing mean quadratic deviations between the virtual reference and the gypsum dies, while deviations of the dies among one another determined the reproducibility of the method. The virtual reference was adapted to create 15 occlusal contact points. The percentage of contact points deviating within a ±10 µm tolerance limit (PDP(10) = Percentage of Deviating Points within ±10 µm Tolerance) was set as the index for assessing occlusal accuracy. Visual results for the difference from the reference tooth were displayed with colors, whereas mean deviation values as well as mean PDP(10) differences were analyzed with a 1-way ANOVA and Scheffé post hoc comparisons (α=.05). Objective characterization of accuracy showed smooth axial surfaces to be undersized, whereas occlusal surfaces were accurate or enlarged when compared to the original tooth. The accuracy of the gypsum replicas ranged between 3 and 6 µm, while reproducibility results varied from 2 to 4 µm. Mean (SD) PDP(10)-values were: Panasil 91% (±11), Identium 77% (±4) and Impregum 29% (±3). One-way ANOVA detected significant differences among the subjected impression materials (P<.001). The accuracy

  12. NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis.

    PubMed

    Markiewicz, Pawel J; Ehrhardt, Matthias J; Erlandsson, Kjell; Noonan, Philip J; Barnes, Anna; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Ourselin, Sebastien

    2018-01-01

    We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

  13. Improved EPMA Trace Element Accuracy Using a Matrix Iterated Quantitative Blank Correction

    NASA Astrophysics Data System (ADS)

    Donovan, J. J.; Wark, D. A.; Jercinovic, M. J.

    2007-12-01

    At trace element levels below several hundred PPM, accuracy is more often the limiting factor for EPMA quantification rather than precision. Modern EPMA instruments equipped with low noise detectors, counting electronics and large area analyzing crystals can now routinely achieve sensitivities for most elements in the 10 to 100 PPM levels (or even lower). But due to various sample and instrumental artifacts in the x-ray continuum, absolute accuracy is often the limiting factor for ultra trace element quantification. These artifacts have various mechanisms, but are usually attributed to sample artifacts (e.g., sample matrix absorption edges)1, detector artifacts (e.g., Ar or Xe absorption edges) 2 and analyzing crystal artifacts (extended peak tails preventing accurate determination of the true background and ¡§negative peaks¡¨ or ¡§holes¡¨ in the x-ray continuum). The latter being first described3 by Self, et al. and recently documented for the Ti kÑ in quartz geo-thermometer. 4 Ti (ka) Ti (ka) Ti (ka) Ti (ka) Ti (ka) Si () O () Total Average: -.00146 -.00031 -.00180 .00013 .00240 46.7430 53.2563 99.9983 Std Dev: .00069 .00075 .00036 .00190 .00117 .00000 .00168 .00419 The general magnitude of these artifacts can be seen in the above analyses of Ti ka in a synthetic quartz standard. The values for each spectrometer/crystal vary systematically from ¡V18 PPM to + 24 PPM. The exact mechanism for these continuum ¡§holes¡¨ is not known but may be related to secondary lattice diffraction occurring at certain Bragg angles depending on crystal mounting orientation for non-isometric analyzing crystals5. These x-ray continuum artifacts can produce systematic errors at levels up to 100 PPM or more depending on the particular analytical situation. In order to correct for these inaccuracies, a ¡§blank¡¨ correction has been developed that applies a quantitative correction to the measured x-ray intensities during the matrix iteration, by calculating the intensity

  14. Automatic Gleason grading of prostate cancer using quantitative phase imaging and machine learning

    NASA Astrophysics Data System (ADS)

    Nguyen, Tan H.; Sridharan, Shamira; Macias, Virgilia; Kajdacsy-Balla, Andre; Melamed, Jonathan; Do, Minh N.; Popescu, Gabriel

    2017-03-01

    We present an approach for automatic diagnosis of tissue biopsies. Our methodology consists of a quantitative phase imaging tissue scanner and machine learning algorithms to process these data. We illustrate the performance by automatic Gleason grading of prostate specimens. The imaging system operates on the principle of interferometry and, as a result, reports on the nanoscale architecture of the unlabeled specimen. We use these data to train a random forest classifier to learn textural behaviors of prostate samples and classify each pixel in the image into different classes. Automatic diagnosis results were computed from the segmented regions. By combining morphological features with quantitative information from the glands and stroma, logistic regression was used to discriminate regions with Gleason grade 3 versus grade 4 cancer in prostatectomy tissue. The overall accuracy of this classification derived from a receiver operating curve was 82%, which is in the range of human error when interobserver variability is considered. We anticipate that our approach will provide a clinically objective and quantitative metric for Gleason grading, allowing us to corroborate results across instruments and laboratories and feed the computer algorithms for improved accuracy.

  15. Alaska national hydrography dataset positional accuracy assessment study

    USGS Publications Warehouse

    Arundel, Samantha; Yamamoto, Kristina H.; Constance, Eric; Mantey, Kim; Vinyard-Houx, Jeremy

    2013-01-01

    Initial visual assessments Wide range in the quality of fit between features in NHD and these new image sources. No statistical analysis has been performed to actually quantify accuracy Determining absolute accuracy is cost prohibitive (must collect independent, well defined test points) Quantitative analysis of relative positional error is feasible.

  16. Complementary techniques: validation of gene expression data by quantitative real time PCR.

    PubMed

    Provenzano, Maurizio; Mocellin, Simone

    2007-01-01

    Microarray technology can be considered the most powerful tool for screening gene expression profiles of biological samples. After data mining, results need to be validated with highly reliable biotechniques allowing for precise quantitation of transcriptional abundance of identified genes. Quantitative real time PCR (qrt-PCR) technology has recently reached a level of sensitivity, accuracy and practical ease that support its use as a routine bioinstrumentation for gene level measurement. Currently, qrt-PCR is considered by most experts the most appropriate method to confirm or confute microarray-generated data. The knowledge of the biochemical principles underlying qrt-PCR as well as some related technical issues must be beard in mind when using this biotechnology.

  17. Temporal Data Set Reduction Based on D-Optimality for Quantitative FLIM-FRET Imaging.

    PubMed

    Omer, Travis; Intes, Xavier; Hahn, Juergen

    2015-01-01

    Fluorescence lifetime imaging (FLIM) when paired with Förster resonance energy transfer (FLIM-FRET) enables the monitoring of nanoscale interactions in living biological samples. FLIM-FRET model-based estimation methods allow the quantitative retrieval of parameters such as the quenched (interacting) and unquenched (non-interacting) fractional populations of the donor fluorophore and/or the distance of the interactions. The quantitative accuracy of such model-based approaches is dependent on multiple factors such as signal-to-noise ratio and number of temporal points acquired when sampling the fluorescence decays. For high-throughput or in vivo applications of FLIM-FRET, it is desirable to acquire a limited number of temporal points for fast acquisition times. Yet, it is critical to acquire temporal data sets with sufficient information content to allow for accurate FLIM-FRET parameter estimation. Herein, an optimal experimental design approach based upon sensitivity analysis is presented in order to identify the time points that provide the best quantitative estimates of the parameters for a determined number of temporal sampling points. More specifically, the D-optimality criterion is employed to identify, within a sparse temporal data set, the set of time points leading to optimal estimations of the quenched fractional population of the donor fluorophore. Overall, a reduced set of 10 time points (compared to a typical complete set of 90 time points) was identified to have minimal impact on parameter estimation accuracy (≈5%), with in silico and in vivo experiment validations. This reduction of the number of needed time points by almost an order of magnitude allows the use of FLIM-FRET for certain high-throughput applications which would be infeasible if the entire number of time sampling points were used.

  18. Accurate ECG diagnosis of atrial tachyarrhythmias using quantitative analysis: a prospective diagnostic and cost-effectiveness study.

    PubMed

    Krummen, David E; Patel, Mitul; Nguyen, Hong; Ho, Gordon; Kazi, Dhruv S; Clopton, Paul; Holland, Marian C; Greenberg, Scott L; Feld, Gregory K; Faddis, Mitchell N; Narayan, Sanjiv M

    2010-11-01

    Quantitative ECG Analysis. Optimal atrial tachyarrhythmia management is facilitated by accurate electrocardiogram interpretation, yet typical atrial flutter (AFl) may present without sawtooth F-waves or RR regularity, and atrial fibrillation (AF) may be difficult to separate from atypical AFl or rapid focal atrial tachycardia (AT). We analyzed whether improved diagnostic accuracy using a validated analysis tool significantly impacts costs and patient care. We performed a prospective, blinded, multicenter study using a novel quantitative computerized algorithm to identify atrial tachyarrhythmia mechanism from the surface ECG in patients referred for electrophysiology study (EPS). In 122 consecutive patients (age 60 ± 12 years) referred for EPS, 91 sustained atrial tachyarrhythmias were studied. ECGs were also interpreted by 9 physicians from 3 specialties for comparison and to allow healthcare system modeling. Diagnostic accuracy was compared to the diagnosis at EPS. A Markov model was used to estimate the impact of improved arrhythmia diagnosis. We found 13% of typical AFl ECGs had neither sawtooth flutter waves nor RR regularity, and were misdiagnosed by the majority of clinicians (0/6 correctly diagnosed by consensus visual interpretation) but correctly by quantitative analysis in 83% (5/6, P = 0.03). AF diagnosis was also improved through use of the algorithm (92%) versus visual interpretation (primary care: 76%, P < 0.01). Economically, we found that these improvements in diagnostic accuracy resulted in an average cost-savings of $1,303 and 0.007 quality-adjusted-life-years per patient. Typical AFl and AF are frequently misdiagnosed using visual criteria. Quantitative analysis improves diagnostic accuracy and results in improved healthcare costs and patient outcomes. © 2010 Wiley Periodicals, Inc.

  19. UK quantitative WB-DWI technical workgroup: consensus meeting recommendations on optimisation, quality control, processing and analysis of quantitative whole-body diffusion-weighted imaging for cancer.

    PubMed

    Barnes, Anna; Alonzi, Roberto; Blackledge, Matthew; Charles-Edwards, Geoff; Collins, David J; Cook, Gary; Coutts, Glynn; Goh, Vicky; Graves, Martin; Kelly, Charles; Koh, Dow-Mu; McCallum, Hazel; Miquel, Marc E; O'Connor, James; Padhani, Anwar; Pearson, Rachel; Priest, Andrew; Rockall, Andrea; Stirling, James; Taylor, Stuart; Tunariu, Nina; van der Meulen, Jan; Walls, Darren; Winfield, Jessica; Punwani, Shonit

    2018-01-01

    Application of whole body diffusion-weighted MRI (WB-DWI) for oncology are rapidly increasing within both research and routine clinical domains. However, WB-DWI as a quantitative imaging biomarker (QIB) has significantly slower adoption. To date, challenges relating to accuracy and reproducibility, essential criteria for a good QIB, have limited widespread clinical translation. In recognition, a UK workgroup was established in 2016 to provide technical consensus guidelines (to maximise accuracy and reproducibility of WB-MRI QIBs) and accelerate the clinical translation of quantitative WB-DWI applications for oncology. A panel of experts convened from cancer centres around the UK with subspecialty expertise in quantitative imaging and/or the use of WB-MRI with DWI. A formal consensus method was used to obtain consensus agreement regarding best practice. Questions were asked about the appropriateness or otherwise on scanner hardware and software, sequence optimisation, acquisition protocols, reporting, and ongoing quality control programs to monitor precision and accuracy and agreement on quality control. The consensus panel was able to reach consensus on 73% (255/351) items and based on consensus areas made recommendations to maximise accuracy and reproducibly of quantitative WB-DWI studies performed at 1.5T. The panel were unable to reach consensus on the majority of items related to quantitative WB-DWI performed at 3T. This UK Quantitative WB-DWI Technical Workgroup consensus provides guidance on maximising accuracy and reproducibly of quantitative WB-DWI for oncology. The consensus guidance can be used by researchers and clinicians to harmonise WB-DWI protocols which will accelerate clinical translation of WB-DWI-derived QIBs.

  20. On the accuracy of analytical models of impurity segregation during directional melt crystallization and their applicability for quantitative calculations

    NASA Astrophysics Data System (ADS)

    Voloshin, A. E.; Prostomolotov, A. I.; Verezub, N. A.

    2016-11-01

    The paper deals with the analysis of the accuracy of some one-dimensional (1D) analytical models of the axial distribution of impurities in the crystal grown from a melt. The models proposed by Burton-Prim-Slichter, Ostrogorsky-Muller and Garandet with co-authors are considered, these models are compared to the results of a two-dimensional (2D) numerical simulation. Stationary solutions as well as solutions for the initial transient regime obtained using these models are considered. The sources of errors are analyzed, a conclusion is made about the applicability of 1D analytical models for quantitative estimates of impurity incorporation into the crystal sample as well as for the solution of the inverse problems.

  1. Imaging Performance of Quantitative Transmission Ultrasound

    PubMed Central

    Lenox, Mark W.; Wiskin, James; Lewis, Matthew A.; Darrouzet, Stephen; Borup, David; Hsieh, Scott

    2015-01-01

    Quantitative Transmission Ultrasound (QTUS) is a tomographic transmission ultrasound modality that is capable of generating 3D speed-of-sound maps of objects in the field of view. It performs this measurement by propagating a plane wave through the medium from a transmitter on one side of a water tank to a high resolution receiver on the opposite side. This information is then used via inverse scattering to compute a speed map. In addition, the presence of reflection transducers allows the creation of a high resolution, spatially compounded reflection map that is natively coregistered to the speed map. A prototype QTUS system was evaluated for measurement and geometric accuracy as well as for the ability to correctly determine speed of sound. PMID:26604918

  2. Quantitative modeling of the accuracy in registering preoperative patient-specific anatomic models into left atrial cardiac ablation procedures

    PubMed Central

    Rettmann, Maryam E.; Holmes, David R.; Kwartowitz, David M.; Gunawan, Mia; Johnson, Susan B.; Camp, Jon J.; Cameron, Bruce M.; Dalegrave, Charles; Kolasa, Mark W.; Packer, Douglas L.; Robb, Richard A.

    2014-01-01

    Purpose: In cardiac ablation therapy, accurate anatomic guidance is necessary to create effective tissue lesions for elimination of left atrial fibrillation. While fluoroscopy, ultrasound, and electroanatomic maps are important guidance tools, they lack information regarding detailed patient anatomy which can be obtained from high resolution imaging techniques. For this reason, there has been significant effort in incorporating detailed, patient-specific models generated from preoperative imaging datasets into the procedure. Both clinical and animal studies have investigated registration and targeting accuracy when using preoperative models; however, the effect of various error sources on registration accuracy has not been quantitatively evaluated. Methods: Data from phantom, canine, and patient studies are used to model and evaluate registration accuracy. In the phantom studies, data are collected using a magnetically tracked catheter on a static phantom model. Monte Carlo simulation studies were run to evaluate both baseline errors as well as the effect of different sources of error that would be present in a dynamic in vivo setting. Error is simulated by varying the variance parameters on the landmark fiducial, physical target, and surface point locations in the phantom simulation studies. In vivo validation studies were undertaken in six canines in which metal clips were placed in the left atrium to serve as ground truth points. A small clinical evaluation was completed in three patients. Landmark-based and combined landmark and surface-based registration algorithms were evaluated in all studies. In the phantom and canine studies, both target registration error and point-to-surface error are used to assess accuracy. In the patient studies, no ground truth is available and registration accuracy is quantified using point-to-surface error only. Results: The phantom simulation studies demonstrated that combined landmark and surface-based registration improved

  3. RapidEye constellation relative radiometric accuracy measurement using lunar images

    NASA Astrophysics Data System (ADS)

    Steyn, Joe; Tyc, George; Beckett, Keith; Hashida, Yoshi

    2009-09-01

    The RapidEye constellation includes five identical satellites in Low Earth Orbit (LEO). Each satellite has a 5-band (blue, green, red, red-edge and near infrared (NIR)) multispectral imager at 6.5m GSD. A three-axes attitude control system allows pointing the imager of each satellite at the Moon during lunations. It is therefore possible to image the Moon from near identical viewing geometry within a span of 80 minutes with each one of the imagers. Comparing the radiometrically corrected images obtained from each band and each satellite allows a near instantaneous relative radiometric accuracy measurement and determination of relative gain changes between the five imagers. A more traditional terrestrial vicarious radiometric calibration program has also been completed by MDA on RapidEye. The two components of this program provide for spatial radiometric calibration ensuring that detector-to-detector response remains flat, while a temporal radiometric calibration approach has accumulated images of specific dry dessert calibration sites. These images are used to measure the constellation relative radiometric response and make on-ground gain and offset adjustments in order to maintain the relative accuracy of the constellation within +/-2.5%. A quantitative comparison between the gain changes measured by the lunar method and the terrestrial temporal radiometric calibration method is performed and will be presented.

  4. Validation of a Spectral Method for Quantitative Measurement of Color in Protein Drug Solutions.

    PubMed

    Yin, Jian; Swartz, Trevor E; Zhang, Jian; Patapoff, Thomas W; Chen, Bartolo; Marhoul, Joseph; Shih, Norman; Kabakoff, Bruce; Rahimi, Kimia

    2016-01-01

    A quantitative spectral method has been developed to precisely measure the color of protein solutions. In this method, a spectrophotometer is utilized for capturing the visible absorption spectrum of a protein solution, which can then be converted to color values (L*a*b*) that represent human perception of color in a quantitative three-dimensional space. These quantitative values (L*a*b*) allow for calculating the best match of a sample's color to a European Pharmacopoeia reference color solution. In order to qualify this instrument and assay for use in clinical quality control, a technical assessment was conducted to evaluate the assay suitability and precision. Setting acceptance criteria for this study required development and implementation of a unique statistical method for assessing precision in 3-dimensional space. Different instruments, cuvettes, protein solutions, and analysts were compared in this study. The instrument accuracy, repeatability, and assay precision were determined. The instrument and assay are found suitable for use in assessing color of drug substances and drug products and is comparable to the current European Pharmacopoeia visual assessment method. In the biotechnology industry, a visual assessment is the most commonly used method for color characterization, batch release, and stability testing of liquid protein drug solutions. Using this method, an analyst visually determines the color of the sample by choosing the closest match to a standard color series. This visual method can be subjective because it requires an analyst to make a judgment of the best match of color of the sample to the standard color series, and it does not capture data on hue and chroma that would allow for improved product characterization and the ability to detect subtle differences between samples. To overcome these challenges, we developed a quantitative spectral method for color determination that greatly reduces the variability in measuring color and allows

  5. Quantitative performance characterization of three-dimensional noncontact fluorescence molecular tomography

    NASA Astrophysics Data System (ADS)

    Favicchio, Rosy; Psycharakis, Stylianos; Schönig, Kai; Bartsch, Dusan; Mamalaki, Clio; Papamatheakis, Joseph; Ripoll, Jorge; Zacharakis, Giannis

    2016-02-01

    Fluorescent proteins and dyes are routine tools for biological research to describe the behavior of genes, proteins, and cells, as well as more complex physiological dynamics such as vessel permeability and pharmacokinetics. The use of these probes in whole body in vivo imaging would allow extending the range and scope of current biomedical applications and would be of great interest. In order to comply with a wide variety of application demands, in vivo imaging platform requirements span from wide spectral coverage to precise quantification capabilities. Fluorescence molecular tomography (FMT) detects and reconstructs in three dimensions the distribution of a fluorophore in vivo. Noncontact FMT allows fast scanning of an excitation source and noninvasive measurement of emitted fluorescent light using a virtual array detector operating in free space. Here, a rigorous process is defined that fully characterizes the performance of a custom-built horizontal noncontact FMT setup. Dynamic range, sensitivity, and quantitative accuracy across the visible spectrum were evaluated using fluorophores with emissions between 520 and 660 nm. These results demonstrate that high-performance quantitative three-dimensional visible light FMT allowed the detection of challenging mesenteric lymph nodes in vivo and the comparison of spectrally distinct fluorescent reporters in cell culture.

  6. Global, quantitative and dynamic mapping of protein subcellular localization.

    PubMed

    Itzhak, Daniel N; Tyanova, Stefka; Cox, Jürgen; Borner, Georg Hh

    2016-06-09

    Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology.

  7. Confidence estimation for quantitative photoacoustic imaging

    NASA Astrophysics Data System (ADS)

    Gröhl, Janek; Kirchner, Thomas; Maier-Hein, Lena

    2018-02-01

    Quantification of photoacoustic (PA) images is one of the major challenges currently being addressed in PA research. Tissue properties can be quantified by correcting the recorded PA signal with an estimation of the corresponding fluence. Fluence estimation itself, however, is an ill-posed inverse problem which usually needs simplifying assumptions to be solved with state-of-the-art methods. These simplifications, as well as noise and artifacts in PA images reduce the accuracy of quantitative PA imaging (PAI). This reduction in accuracy is often localized to image regions where the assumptions do not hold true. This impedes the reconstruction of functional parameters when averaging over entire regions of interest (ROI). Averaging over a subset of voxels with a high accuracy would lead to an improved estimation of such parameters. To achieve this, we propose a novel approach to the local estimation of confidence in quantitative reconstructions of PA images. It makes use of conditional probability densities to estimate confidence intervals alongside the actual quantification. It encapsulates an estimation of the errors introduced by fluence estimation as well as signal noise. We validate the approach using Monte Carlo generated data in combination with a recently introduced machine learning-based approach to quantitative PAI. Our experiments show at least a two-fold improvement in quantification accuracy when evaluating on voxels with high confidence instead of thresholding signal intensity.

  8. Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering

    PubMed Central

    Kelley, Shana O.; Mirkin, Chad A.; Walt, David R.; Ismagilov, Rustem F.; Toner, Mehmet; Sargent, Edward H.

    2015-01-01

    Rapid progress in identifying disease biomarkers has increased the importance of creating high-performance detection technologies. Over the last decade, the design of many detection platforms has focused on either the nano or micro length scale. Here, we review recent strategies that combine nano- and microscale materials and devices to produce large improvements in detection sensitivity, speed and accuracy, allowing previously undetectable biomarkers to be identified in clinical samples. Microsensors that incorporate nanoscale features can now rapidly detect disease-related nucleic acids expressed in patient samples. New microdevices that separate large clinical samples into nanocompartments allow precise quantitation of analytes, and microfluidic systems that utilize nanoscale binding events can detect rare cancer cells in the bloodstream more accurately than before. These advances will lead to faster and more reliable clinical diagnostic devices. PMID:25466541

  9. Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering

    NASA Astrophysics Data System (ADS)

    Kelley, Shana O.; Mirkin, Chad A.; Walt, David R.; Ismagilov, Rustem F.; Toner, Mehmet; Sargent, Edward H.

    2014-12-01

    Rapid progress in identifying disease biomarkers has increased the importance of creating high-performance detection technologies. Over the last decade, the design of many detection platforms has focused on either the nano or micro length scale. Here, we review recent strategies that combine nano- and microscale materials and devices to produce large improvements in detection sensitivity, speed and accuracy, allowing previously undetectable biomarkers to be identified in clinical samples. Microsensors that incorporate nanoscale features can now rapidly detect disease-related nucleic acids expressed in patient samples. New microdevices that separate large clinical samples into nanocompartments allow precise quantitation of analytes, and microfluidic systems that utilize nanoscale binding events can detect rare cancer cells in the bloodstream more accurately than before. These advances will lead to faster and more reliable clinical diagnostic devices.

  10. Quantitative modeling of the accuracy in registering preoperative patient-specific anatomic models into left atrial cardiac ablation procedures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rettmann, Maryam E., E-mail: rettmann.maryam@mayo.edu; Holmes, David R.; Camp, Jon J.

    2014-02-15

    Purpose: In cardiac ablation therapy, accurate anatomic guidance is necessary to create effective tissue lesions for elimination of left atrial fibrillation. While fluoroscopy, ultrasound, and electroanatomic maps are important guidance tools, they lack information regarding detailed patient anatomy which can be obtained from high resolution imaging techniques. For this reason, there has been significant effort in incorporating detailed, patient-specific models generated from preoperative imaging datasets into the procedure. Both clinical and animal studies have investigated registration and targeting accuracy when using preoperative models; however, the effect of various error sources on registration accuracy has not been quantitatively evaluated. Methods: Datamore » from phantom, canine, and patient studies are used to model and evaluate registration accuracy. In the phantom studies, data are collected using a magnetically tracked catheter on a static phantom model. Monte Carlo simulation studies were run to evaluate both baseline errors as well as the effect of different sources of error that would be present in a dynamicin vivo setting. Error is simulated by varying the variance parameters on the landmark fiducial, physical target, and surface point locations in the phantom simulation studies. In vivo validation studies were undertaken in six canines in which metal clips were placed in the left atrium to serve as ground truth points. A small clinical evaluation was completed in three patients. Landmark-based and combined landmark and surface-based registration algorithms were evaluated in all studies. In the phantom and canine studies, both target registration error and point-to-surface error are used to assess accuracy. In the patient studies, no ground truth is available and registration accuracy is quantified using point-to-surface error only. Results: The phantom simulation studies demonstrated that combined landmark and surface-based registration

  11. Occupational exposure decisions: can limited data interpretation training help improve accuracy?

    PubMed

    Logan, Perry; Ramachandran, Gurumurthy; Mulhausen, John; Hewett, Paul

    2009-06-01

    Accurate exposure assessments are critical for ensuring that potentially hazardous exposures are properly identified and controlled. The availability and accuracy of exposure assessments can determine whether resources are appropriately allocated to engineering and administrative controls, medical surveillance, personal protective equipment and other programs designed to protect workers. A desktop study was performed using videos, task information and sampling data to evaluate the accuracy and potential bias of participants' exposure judgments. Desktop exposure judgments were obtained from occupational hygienists for material handling jobs with small air sampling data sets (0-8 samples) and without the aid of computers. In addition, data interpretation tests (DITs) were administered to participants where they were asked to estimate the 95th percentile of an underlying log-normal exposure distribution from small data sets. Participants were presented with an exposure data interpretation or rule of thumb training which included a simple set of rules for estimating 95th percentiles for small data sets from a log-normal population. DIT was given to each participant before and after the rule of thumb training. Results of each DIT and qualitative and quantitative exposure judgments were compared with a reference judgment obtained through a Bayesian probabilistic analysis of the sampling data to investigate overall judgment accuracy and bias. There were a total of 4386 participant-task-chemical judgments for all data collections: 552 qualitative judgments made without sampling data and 3834 quantitative judgments with sampling data. The DITs and quantitative judgments were significantly better than random chance and much improved by the rule of thumb training. In addition, the rule of thumb training reduced the amount of bias in the DITs and quantitative judgments. The mean DIT % correct scores increased from 47 to 64% after the rule of thumb training (P < 0.001). The

  12. Quantitative characterisation of sedimentary grains

    NASA Astrophysics Data System (ADS)

    Tunwal, Mohit; Mulchrone, Kieran F.; Meere, Patrick A.

    2016-04-01

    Analysis of sedimentary texture helps in determining the formation, transportation and deposition processes of sedimentary rocks. Grain size analysis is traditionally quantitative, whereas grain shape analysis is largely qualitative. A semi-automated approach to quantitatively analyse shape and size of sand sized sedimentary grains is presented. Grain boundaries are manually traced from thin section microphotographs in the case of lithified samples and are automatically identified in the case of loose sediments. Shape and size paramters can then be estimated using a software package written on the Mathematica platform. While automated methodology already exists for loose sediment analysis, the available techniques for the case of lithified samples are limited to cases of high definition thin section microphotographs showing clear contrast between framework grains and matrix. Along with the size of grain, shape parameters such as roundness, angularity, circularity, irregularity and fractal dimension are measured. A new grain shape parameter developed using Fourier descriptors has also been developed. To test this new approach theoretical examples were analysed and produce high quality results supporting the accuracy of the algorithm. Furthermore sandstone samples from known aeolian and fluvial environments from the Dingle Basin, County Kerry, Ireland were collected and analysed. Modern loose sediments from glacial till from County Cork, Ireland and aeolian sediments from Rajasthan, India have also been collected and analysed. A graphical summary of the data is presented and allows for quantitative distinction between samples extracted from different sedimentary environments.

  13. Asynchronous adaptive time step in quantitative cellular automata modeling

    PubMed Central

    Zhu, Hao; Pang, Peter YH; Sun, Yan; Dhar, Pawan

    2004-01-01

    Background The behaviors of cells in metazoans are context dependent, thus large-scale multi-cellular modeling is often necessary, for which cellular automata are natural candidates. Two related issues are involved in cellular automata based multi-cellular modeling: how to introduce differential equation based quantitative computing to precisely describe cellular activity, and upon it, how to solve the heavy time consumption issue in simulation. Results Based on a modified, language based cellular automata system we extended that allows ordinary differential equations in models, we introduce a method implementing asynchronous adaptive time step in simulation that can considerably improve efficiency yet without a significant sacrifice of accuracy. An average speedup rate of 4–5 is achieved in the given example. Conclusions Strategies for reducing time consumption in simulation are indispensable for large-scale, quantitative multi-cellular models, because even a small 100 × 100 × 100 tissue slab contains one million cells. Distributed and adaptive time step is a practical solution in cellular automata environment. PMID:15222901

  14. Global, quantitative and dynamic mapping of protein subcellular localization

    PubMed Central

    Itzhak, Daniel N; Tyanova, Stefka; Cox, Jürgen; Borner, Georg HH

    2016-01-01

    Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology. DOI: http://dx.doi.org/10.7554/eLife.16950.001 PMID:27278775

  15. Air traffic control surveillance accuracy and update rate study

    NASA Technical Reports Server (NTRS)

    Craigie, J. H.; Morrison, D. D.; Zipper, I.

    1973-01-01

    The results of an air traffic control surveillance accuracy and update rate study are presented. The objective of the study was to establish quantitative relationships between the surveillance accuracies, update rates, and the communication load associated with the tactical control of aircraft for conflict resolution. The relationships are established for typical types of aircraft, phases of flight, and types of airspace. Specific cases are analyzed to determine the surveillance accuracies and update rates required to prevent two aircraft from approaching each other too closely.

  16. Diagnostic accuracy of quantitative real-time PCR assay versus clinical and Gram stain identification of bacterial vaginosis.

    PubMed

    Menard, J-P; Mazouni, C; Fenollar, F; Raoult, D; Boubli, L; Bretelle, F

    2010-12-01

    The purpose of this investigation was to determine the diagnostic accuracy of quantitative real-time polymerase chain reaction (PCR) assay in diagnosing bacterial vaginosis versus the standard methods, the Amsel criteria and the Nugent score. The Amsel criteria, the Nugent score, and results from the molecular tool were obtained independently from vaginal samples of 163 pregnant women who reported abnormal vaginal symptoms before 20 weeks gestation. To determine the performance of the molecular tool, we calculated the kappa value, sensitivity, specificity, and positive and negative predictive values. Either or both of the Amsel criteria (≥3 criteria) and the Nugent score (score ≥7) indicated that 25 women (15%) had bacterial vaginosis, and the remaining 138 women did not. DNA levels of Gardnerella vaginalis or Atopobium vaginae exceeded 10(9) copies/mL or 10(8) copies/mL, respectively, in 34 (21%) of the 163 samples. Complete agreement between both reference methods and high concentrations of G. vaginalis and A. vaginae was found in 94.5% of women (154/163 samples, kappa value = 0.81, 95% confidence interval 0.70-0.81). The nine samples with discordant results were categorized as intermediate flora by the Nugent score. The molecular tool predicted bacterial vaginosis with a sensitivity of 100%, a specificity of 93%, a positive predictive value of 73%, and a negative predictive value of 100%. The quantitative real-time PCR assay shows excellent agreement with the results of both reference methods for the diagnosis of bacterial vaginosis.

  17. An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies

    DOE PAGES

    Bilbao, Aivett; Gibbons, Bryson C.; Slysz, Gordon W.; ...

    2017-11-06

    We present that the mass accuracy and peak intensity of ions detected by mass spectrometry (MS) measurements are essential to facilitate compound identification and quantitation. However, high concentration species can yield erroneous results if their ion intensities reach beyond the limits of the detection system, leading to distorted and non-ideal detector response (e.g. saturation), and largely precluding the calculation of accurate m/z and intensity values. Here we present an open source computational method to correct peaks above a defined intensity (saturated) threshold determined by the MS instrumentation such as the analog-to-digital converters or time-to-digital converters used in conjunction with time-of-flightmore » MS. Here, in this method, the isotopic envelope for each observed ion above the saturation threshold is compared to its expected theoretical isotopic distribution. The most intense isotopic peak for which saturation does not occur is then utilized to re-calculate the precursor m/z and correct the intensity, resulting in both higher mass accuracy and greater dynamic range. The benefits of this approach were evaluated with proteomic and lipidomic datasets of varying complexities. After correcting the high concentration species, reduced mass errors and enhanced dynamic range were observed for both simple and complex omic samples. Specifically, the mass error dropped by more than 50% in most cases for highly saturated species and dynamic range increased by 1–2 orders of magnitude for peptides in a blood serum sample.« less

  18. An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bilbao, Aivett; Gibbons, Bryson C.; Slysz, Gordon W.

    The mass accuracy and peak intensity of ions detected by mass spectrometry (MS) measurements are essential to facilitate compound identification and quantitation. However, high concentration species can easily cause problems if their ion intensities reach beyond the limits of the detection system, leading to distorted and non-ideal detector response (e.g. saturation), and largely precluding the calculation of accurate m/z and intensity values. Here we present an open source computational method to correct peaks above a defined intensity (saturated) threshold determined by the MS instrumentation such as the analog-to-digital converters or time-to-digital converters used in conjunction with time-of-flight MS. In thismore » method, the isotopic envelope for each observed ion above the saturation threshold is compared to its expected theoretical isotopic distribution. The most intense isotopic peak for which saturation does not occur is then utilized to re-calculate the precursor m/z and correct the intensity, resulting in both higher mass accuracy and greater dynamic range. The benefits of this approach were evaluated with proteomic and lipidomic datasets of varying complexities. After correcting the high concentration species, reduced mass errors and enhanced dynamic range were observed for both simple and complex omic samples. Specifically, the mass error dropped by more than 50% in most cases with highly saturated species and dynamic range increased by 1-2 orders of magnitude for peptides in a blood serum sample.« less

  19. An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bilbao, Aivett; Gibbons, Bryson C.; Slysz, Gordon W.

    We present that the mass accuracy and peak intensity of ions detected by mass spectrometry (MS) measurements are essential to facilitate compound identification and quantitation. However, high concentration species can yield erroneous results if their ion intensities reach beyond the limits of the detection system, leading to distorted and non-ideal detector response (e.g. saturation), and largely precluding the calculation of accurate m/z and intensity values. Here we present an open source computational method to correct peaks above a defined intensity (saturated) threshold determined by the MS instrumentation such as the analog-to-digital converters or time-to-digital converters used in conjunction with time-of-flightmore » MS. Here, in this method, the isotopic envelope for each observed ion above the saturation threshold is compared to its expected theoretical isotopic distribution. The most intense isotopic peak for which saturation does not occur is then utilized to re-calculate the precursor m/z and correct the intensity, resulting in both higher mass accuracy and greater dynamic range. The benefits of this approach were evaluated with proteomic and lipidomic datasets of varying complexities. After correcting the high concentration species, reduced mass errors and enhanced dynamic range were observed for both simple and complex omic samples. Specifically, the mass error dropped by more than 50% in most cases for highly saturated species and dynamic range increased by 1–2 orders of magnitude for peptides in a blood serum sample.« less

  20. FLIPPER, a combinatorial probe for correlated live imaging and electron microscopy, allows identification and quantitative analysis of various cells and organelles.

    PubMed

    Kuipers, Jeroen; van Ham, Tjakko J; Kalicharan, Ruby D; Veenstra-Algra, Anneke; Sjollema, Klaas A; Dijk, Freark; Schnell, Ulrike; Giepmans, Ben N G

    2015-04-01

    Ultrastructural examination of cells and tissues by electron microscopy (EM) yields detailed information on subcellular structures. However, EM is typically restricted to small fields of view at high magnification; this makes quantifying events in multiple large-area sample sections extremely difficult. Even when combining light microscopy (LM) with EM (correlated LM and EM: CLEM) to find areas of interest, the labeling of molecules is still a challenge. We present a new genetically encoded probe for CLEM, named "FLIPPER", which facilitates quantitative analysis of ultrastructural features in cells. FLIPPER consists of a fluorescent protein (cyan, green, orange, or red) for LM visualization, fused to a peroxidase allowing visualization of targets at the EM level. The use of FLIPPER is straightforward and because the module is completely genetically encoded, cells can be optimally prepared for EM examination. We use FLIPPER to quantify cellular morphology at the EM level in cells expressing a normal and disease-causing point-mutant cell-surface protein called EpCAM (epithelial cell adhesion molecule). The mutant protein is retained in the endoplasmic reticulum (ER) and could therefore alter ER function and morphology. To reveal possible ER alterations, cells were co-transfected with color-coded full-length or mutant EpCAM and a FLIPPER targeted to the ER. CLEM examination of the mixed cell population allowed color-based cell identification, followed by an unbiased quantitative analysis of the ER ultrastructure by EM. Thus, FLIPPER combines bright fluorescent proteins optimized for live imaging with high sensitivity for EM labeling, thereby representing a promising tool for CLEM.

  1. Quantitative analysis of surface characteristics and morphology in Death Valley, California using AIRSAR data

    NASA Technical Reports Server (NTRS)

    Kierein-Young, K. S.; Kruse, F. A.; Lefkoff, A. B.

    1992-01-01

    The Jet Propulsion Laboratory Airborne Synthetic Aperture Radar (JPL-AIRSAR) is used to collect full polarimetric measurements at P-, L-, and C-bands. These data are analyzed using the radar analysis and visualization environment (RAVEN). The AIRSAR data are calibrated using in-scene corner reflectors to allow for quantitative analysis of the radar backscatter. RAVEN is used to extract surface characteristics. Inversion models are used to calculate quantitative surface roughness values and fractal dimensions. These values are used to generate synthetic surface plots that represent the small-scale surface structure of areas in Death Valley. These procedures are applied to a playa, smooth salt-pan, and alluvial fan surfaces in Death Valley. Field measurements of surface roughness are used to verify the accuracy.

  2. Increased genomic prediction accuracy in wheat breeding using a large Australian panel.

    PubMed

    Norman, Adam; Taylor, Julian; Tanaka, Emi; Telfer, Paul; Edwards, James; Martinant, Jean-Pierre; Kuchel, Haydn

    2017-12-01

    Genomic prediction accuracy within a large panel was found to be substantially higher than that previously observed in smaller populations, and also higher than QTL-based prediction. In recent years, genomic selection for wheat breeding has been widely studied, but this has typically been restricted to population sizes under 1000 individuals. To assess its efficacy in germplasm representative of commercial breeding programmes, we used a panel of 10,375 Australian wheat breeding lines to investigate the accuracy of genomic prediction for grain yield, physical grain quality and other physiological traits. To achieve this, the complete panel was phenotyped in a dedicated field trial and genotyped using a custom Axiom TM Affymetrix SNP array. A high-quality consensus map was also constructed, allowing the linkage disequilibrium present in the germplasm to be investigated. Using the complete SNP array, genomic prediction accuracies were found to be substantially higher than those previously observed in smaller populations and also more accurate compared to prediction approaches using a finite number of selected quantitative trait loci. Multi-trait genetic correlations were also assessed at an additive and residual genetic level, identifying a negative genetic correlation between grain yield and protein as well as a positive genetic correlation between grain size and test weight.

  3. Ground Truth Sampling and LANDSAT Accuracy Assessment

    NASA Technical Reports Server (NTRS)

    Robinson, J. W.; Gunther, F. J.; Campbell, W. J.

    1982-01-01

    It is noted that the key factor in any accuracy assessment of remote sensing data is the method used for determining the ground truth, independent of the remote sensing data itself. The sampling and accuracy procedures developed for nuclear power plant siting study are described. The purpose of the sampling procedure was to provide data for developing supervised classifications for two study sites and for assessing the accuracy of that and the other procedures used. The purpose of the accuracy assessment was to allow the comparison of the cost and accuracy of various classification procedures as applied to various data types.

  4. Stroke onset time estimation from multispectral quantitative magnetic resonance imaging in a rat model of focal permanent cerebral ischemia.

    PubMed

    McGarry, Bryony L; Rogers, Harriet J; Knight, Michael J; Jokivarsi, Kimmo T; Sierra, Alejandra; Gröhn, Olli Hj; Kauppinen, Risto A

    2016-08-01

    Quantitative T2 relaxation magnetic resonance imaging allows estimation of stroke onset time. We aimed to examine the accuracy of quantitative T1 and quantitative T2 relaxation times alone and in combination to provide estimates of stroke onset time in a rat model of permanent focal cerebral ischemia and map the spatial distribution of elevated quantitative T1 and quantitative T2 to assess tissue status. Permanent middle cerebral artery occlusion was induced in Wistar rats. Animals were scanned at 9.4T for quantitative T1, quantitative T2, and Trace of Diffusion Tensor (Dav) up to 4 h post-middle cerebral artery occlusion. Time courses of differentials of quantitative T1 and quantitative T2 in ischemic and non-ischemic contralateral brain tissue (ΔT1, ΔT2) and volumes of tissue with elevated T1 and T2 relaxation times (f1, f2) were determined. TTC staining was used to highlight permanent ischemic damage. ΔT1, ΔT2, f1, f2, and the volume of tissue with both elevated quantitative T1 and quantitative T2 (V(Overlap)) increased with time post-middle cerebral artery occlusion allowing stroke onset time to be estimated. V(Overlap) provided the most accurate estimate with an uncertainty of ±25 min. At all times-points regions with elevated relaxation times were smaller than areas with Dav defined ischemia. Stroke onset time can be determined by quantitative T1 and quantitative T2 relaxation times and tissue volumes. Combining quantitative T1 and quantitative T2 provides the most accurate estimate and potentially identifies irreversibly damaged brain tissue. © 2016 World Stroke Organization.

  5. Quantitative hard x-ray phase contrast imaging of micropipes in SiC

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kohn, V. G.; Argunova, T. S.; Je, J. H., E-mail: jhje@postech.ac.kr

    2013-12-15

    Peculiarities of quantitative hard x-ray phase contrast imaging of micropipes in SiC are discussed. The micropipe is assumed as a hollow cylinder with an elliptical cross section. The major and minor diameters can be restored using the least square fitting procedure by comparing the experimental data, i.e. the profile across the micropipe axis, with those calculated based on phase contrast theory. It is shown that one projection image gives an information which does not allow a complete determination of the elliptical cross section, if an orientation of micropipe is not known. Another problem is a weak accuracy in estimating themore » diameters, partly because of using pink synchrotron radiation, which is necessary because a monochromatic beam intensity is not sufficient to reveal the weak contrast from a very small object. The general problems of accuracy in estimating the two diameters using the least square procedure are discussed. Two experimental examples are considered to demonstrate small as well as modest accuracies in estimating the diameters.« less

  6. [The development and validation of the methods for the quantitative determination of sibutramine derivatives in dietary supplements].

    PubMed

    Stern, K I; Malkova, T L

    The objective of the present study was the development and validation of sibutramine demethylated derivatives, desmethyl sibutramine and didesmethyl sibutramine. Gas-liquid chromatography with the flame ionization detector was used for the quantitative determination of the above substances in dietary supplements. The conditions for the chromatographic determination of the analytes in the presence of the reference standard, methyl stearate, were proposed allowing to achieve the efficient separation. The method has the necessary sensitivity, specificity, linearity, accuracy, and precision (on the intra-day and inter-day basis) which suggests its good validation characteristics. The proposed method can be employed in the analytical laboratories for the quantitative determination of sibutramine derivatives in biologically active dietary supplements.

  7. Affordable, automatic quantitative fall risk assessment based on clinical balance scales and Kinect data.

    PubMed

    Colagiorgio, P; Romano, F; Sardi, F; Moraschini, M; Sozzi, A; Bejor, M; Ricevuti, G; Buizza, A; Ramat, S

    2014-01-01

    The problem of a correct fall risk assessment is becoming more and more critical with the ageing of the population. In spite of the available approaches allowing a quantitative analysis of the human movement control system's performance, the clinical assessment and diagnostic approach to fall risk assessment still relies mostly on non-quantitative exams, such as clinical scales. This work documents our current effort to develop a novel method to assess balance control abilities through a system implementing an automatic evaluation of exercises drawn from balance assessment scales. Our aim is to overcome the classical limits characterizing these scales i.e. limited granularity and inter-/intra-examiner reliability, to obtain objective scores and more detailed information allowing to predict fall risk. We used Microsoft Kinect to record subjects' movements while performing challenging exercises drawn from clinical balance scales. We then computed a set of parameters quantifying the execution of the exercises and fed them to a supervised classifier to perform a classification based on the clinical score. We obtained a good accuracy (~82%) and especially a high sensitivity (~83%).

  8. Will it Blend? Visualization and Accuracy Evaluation of High-Resolution Fuzzy Vegetation Maps

    NASA Astrophysics Data System (ADS)

    Zlinszky, A.; Kania, A.

    2016-06-01

    Instead of assigning every map pixel to a single class, fuzzy classification includes information on the class assigned to each pixel but also the certainty of this class and the alternative possible classes based on fuzzy set theory. The advantages of fuzzy classification for vegetation mapping are well recognized, but the accuracy and uncertainty of fuzzy maps cannot be directly quantified with indices developed for hard-boundary categorizations. The rich information in such a map is impossible to convey with a single map product or accuracy figure. Here we introduce a suite of evaluation indices and visualization products for fuzzy maps generated with ensemble classifiers. We also propose a way of evaluating classwise prediction certainty with "dominance profiles" visualizing the number of pixels in bins according to the probability of the dominant class, also showing the probability of all the other classes. Together, these data products allow a quantitative understanding of the rich information in a fuzzy raster map both for individual classes and in terms of variability in space, and also establish the connection between spatially explicit class certainty and traditional accuracy metrics. These map products are directly comparable to widely used hard boundary evaluation procedures, support active learning-based iterative classification and can be applied for operational use.

  9. Meta-analysis of diagnostic accuracy studies in mental health

    PubMed Central

    Takwoingi, Yemisi; Riley, Richard D; Deeks, Jonathan J

    2015-01-01

    Objectives To explain methods for data synthesis of evidence from diagnostic test accuracy (DTA) studies, and to illustrate different types of analyses that may be performed in a DTA systematic review. Methods We described properties of meta-analytic methods for quantitative synthesis of evidence. We used a DTA review comparing the accuracy of three screening questionnaires for bipolar disorder to illustrate application of the methods for each type of analysis. Results The discriminatory ability of a test is commonly expressed in terms of sensitivity (proportion of those with the condition who test positive) and specificity (proportion of those without the condition who test negative). There is a trade-off between sensitivity and specificity, as an increasing threshold for defining test positivity will decrease sensitivity and increase specificity. Methods recommended for meta-analysis of DTA studies --such as the bivariate or hierarchical summary receiver operating characteristic (HSROC) model --jointly summarise sensitivity and specificity while taking into account this threshold effect, as well as allowing for between study differences in test performance beyond what would be expected by chance. The bivariate model focuses on estimation of a summary sensitivity and specificity at a common threshold while the HSROC model focuses on the estimation of a summary curve from studies that have used different thresholds. Conclusions Meta-analyses of diagnostic accuracy studies can provide answers to important clinical questions. We hope this article will provide clinicians with sufficient understanding of the terminology and methods to aid interpretation of systematic reviews and facilitate better patient care. PMID:26446042

  10. [A new method of processing quantitative PCR data].

    PubMed

    Ke, Bing-Shen; Li, Guang-Yun; Chen, Shi-Min; Huang, Xiang-Yan; Chen, Ying-Jian; Xu, Jun

    2003-05-01

    Today standard PCR can't satisfy the need of biotechnique development and clinical research any more. After numerous dynamic research, PE company found there is a linear relation between initial template number and cycling time when the accumulating fluorescent product is detectable.Therefore,they developed a quantitative PCR technique to be used in PE7700 and PE5700. But the error of this technique is too great to satisfy the need of biotechnique development and clinical research. A better quantitative PCR technique is needed. The mathematical model submitted here is combined with the achievement of relative science,and based on the PCR principle and careful analysis of molecular relationship of main members in PCR reaction system. This model describes the function relation between product quantity or fluorescence intensity and initial template number and other reaction conditions, and can reflect the accumulating rule of PCR product molecule accurately. Accurate quantitative PCR analysis can be made use this function relation. Accumulated PCR product quantity can be obtained from initial template number. Using this model to do quantitative PCR analysis,result error is only related to the accuracy of fluorescence intensity or the instrument used. For an example, when the fluorescence intensity is accurate to 6 digits and the template size is between 100 to 1,000,000, the quantitative result accuracy will be more than 99%. The difference of result error is distinct using same condition,same instrument but different analysis method. Moreover,if the PCR quantitative analysis system is used to process data, it will get result 80 times of accuracy than using CT method.

  11. Use of Cell Viability Assay Data Improves the Prediction Accuracy of Conventional Quantitative Structure–Activity Relationship Models of Animal Carcinogenicity

    PubMed Central

    Zhu, Hao; Rusyn, Ivan; Richard, Ann; Tropsha, Alexander

    2008-01-01

    Background To develop efficient approaches for rapid evaluation of chemical toxicity and human health risk of environmental compounds, the National Toxicology Program (NTP) in collaboration with the National Center for Chemical Genomics has initiated a project on high-throughput screening (HTS) of environmental chemicals. The first HTS results for a set of 1,408 compounds tested for their effects on cell viability in six different cell lines have recently become available via PubChem. Objectives We have explored these data in terms of their utility for predicting adverse health effects of the environmental agents. Methods and results Initially, the classification k nearest neighbor (kNN) quantitative structure–activity relationship (QSAR) modeling method was applied to the HTS data only, for a curated data set of 384 compounds. The resulting models had prediction accuracies for training, test (containing 275 compounds together), and external validation (109 compounds) sets as high as 89%, 71%, and 74%, respectively. We then asked if HTS results could be of value in predicting rodent carcinogenicity. We identified 383 compounds for which data were available from both the Berkeley Carcinogenic Potency Database and NTP–HTS studies. We found that compounds classified by HTS as “actives” in at least one cell line were likely to be rodent carcinogens (sensitivity 77%); however, HTS “inactives” were far less informative (specificity 46%). Using chemical descriptors only, kNN QSAR modeling resulted in 62.3% prediction accuracy for rodent carcinogenicity applied to this data set. Importantly, the prediction accuracy of the model was significantly improved (72.7%) when chemical descriptors were augmented by HTS data, which were regarded as biological descriptors. Conclusions Our studies suggest that combining NTP–HTS profiles with conventional chemical descriptors could considerably improve the predictive power of computational approaches in toxicology. PMID

  12. ICan: An Optimized Ion-Current-Based Quantification Procedure with Enhanced Quantitative Accuracy and Sensitivity in Biomarker Discovery

    PubMed Central

    2015-01-01

    The rapidly expanding availability of high-resolution mass spectrometry has substantially enhanced the ion-current-based relative quantification techniques. Despite the increasing interest in ion-current-based methods, quantitative sensitivity, accuracy, and false discovery rate remain the major concerns; consequently, comprehensive evaluation and development in these regards are urgently needed. Here we describe an integrated, new procedure for data normalization and protein ratio estimation, termed ICan, for improved ion-current-based analysis of data generated by high-resolution mass spectrometry (MS). ICan achieved significantly better accuracy and precision, and lower false-positive rate for discovering altered proteins, over current popular pipelines. A spiked-in experiment was used to evaluate the performance of ICan to detect small changes. In this study E. coli extracts were spiked with moderate-abundance proteins from human plasma (MAP, enriched by IgY14-SuperMix procedure) at two different levels to set a small change of 1.5-fold. Forty-five (92%, with an average ratio of 1.71 ± 0.13) of 49 identified MAP protein (i.e., the true positives) and none of the reference proteins (1.0-fold) were determined as significantly altered proteins, with cutoff thresholds of ≥1.3-fold change and p ≤ 0.05. This is the first study to evaluate and prove competitive performance of the ion-current-based approach for assigning significance to proteins with small changes. By comparison, other methods showed remarkably inferior performance. ICan can be broadly applicable to reliable and sensitive proteomic survey of multiple biological samples with the use of high-resolution MS. Moreover, many key features evaluated and optimized here such as normalization, protein ratio determination, and statistical analyses are also valuable for data analysis by isotope-labeling methods. PMID:25285707

  13. Development of quantitative screen for 1550 chemicals with GC-MS.

    PubMed

    Bergmann, Alan J; Points, Gary L; Scott, Richard P; Wilson, Glenn; Anderson, Kim A

    2018-05-01

    With hundreds of thousands of chemicals in the environment, effective monitoring requires high-throughput analytical techniques. This paper presents a quantitative screening method for 1550 chemicals based on statistical modeling of responses with identification and integration performed using deconvolution reporting software. The method was evaluated with representative environmental samples. We tested biological extracts, low-density polyethylene, and silicone passive sampling devices spiked with known concentrations of 196 representative chemicals. A multiple linear regression (R 2  = 0.80) was developed with molecular weight, logP, polar surface area, and fractional ion abundance to predict chemical responses within a factor of 2.5. Linearity beyond the calibration had R 2  > 0.97 for three orders of magnitude. Median limits of quantitation were estimated to be 201 pg/μL (1.9× standard deviation). The number of detected chemicals and the accuracy of quantitation were similar for environmental samples and standard solutions. To our knowledge, this is the most precise method for the largest number of semi-volatile organic chemicals lacking authentic standards. Accessible instrumentation and software make this method cost effective in quantifying a large, customizable list of chemicals. When paired with silicone wristband passive samplers, this quantitative screen will be very useful for epidemiology where binning of concentrations is common. Graphical abstract A multiple linear regression of chemical responses measured with GC-MS allowed quantitation of 1550 chemicals in samples such as silicone wristbands.

  14. Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate.

    PubMed

    Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

    2016-01-01

    Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans , and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations.

  15. Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate

    PubMed Central

    Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

    2016-01-01

    Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations. PMID:28066365

  16. Quantitative assessment of the accuracy of dose calculation using pencil beam and Monte Carlo algorithms and requirements for clinical quality assurance

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ali, Imad, E-mail: iali@ouhsc.edu; Ahmad, Salahuddin

    2013-10-01

    To compare the doses calculated using the BrainLAB pencil beam (PB) and Monte Carlo (MC) algorithms for tumors located in various sites including the lung and evaluate quality assurance procedures required for the verification of the accuracy of dose calculation. The dose-calculation accuracy of PB and MC was also assessed quantitatively with measurement using ionization chamber and Gafchromic films placed in solid water and heterogeneous phantoms. The dose was calculated using PB convolution and MC algorithms in the iPlan treatment planning system from BrainLAB. The dose calculation was performed on the patient's computed tomography images with lesions in various treatmentmore » sites including 5 lungs, 5 prostates, 4 brains, 2 head and necks, and 2 paraspinal tissues. A combination of conventional, conformal, and intensity-modulated radiation therapy plans was used in dose calculation. The leaf sequence from intensity-modulated radiation therapy plans or beam shapes from conformal plans and monitor units and other planning parameters calculated by the PB were identical for calculating dose with MC. Heterogeneity correction was considered in both PB and MC dose calculations. Dose-volume parameters such as V95 (volume covered by 95% of prescription dose), dose distributions, and gamma analysis were used to evaluate the calculated dose by PB and MC. The measured doses by ionization chamber and EBT GAFCHROMIC film in solid water and heterogeneous phantoms were used to quantitatively asses the accuracy of dose calculated by PB and MC. The dose-volume histograms and dose distributions calculated by PB and MC in the brain, prostate, paraspinal, and head and neck were in good agreement with one another (within 5%) and provided acceptable planning target volume coverage. However, dose distributions of the patients with lung cancer had large discrepancies. For a plan optimized with PB, the dose coverage was shown as clinically acceptable, whereas in reality, the MC

  17. Accuracy of the NDI Wave Speech Research System

    ERIC Educational Resources Information Center

    Berry, Jeffrey J.

    2011-01-01

    Purpose: This work provides a quantitative assessment of the positional tracking accuracy of the NDI Wave Speech Research System. Method: Three experiments were completed: (a) static rigid-body tracking across different locations in the electromagnetic field volume, (b) dynamic rigid-body tracking across different locations within the…

  18. Quantitative multi-pinhole small-animal SPECT: uniform versus non-uniform Chang attenuation correction.

    PubMed

    Wu, C; de Jong, J R; Gratama van Andel, H A; van der Have, F; Vastenhouw, B; Laverman, P; Boerman, O C; Dierckx, R A J O; Beekman, F J

    2011-09-21

    Attenuation of photon flux on trajectories between the source and pinhole apertures affects the quantitative accuracy of reconstructed single-photon emission computed tomography (SPECT) images. We propose a Chang-based non-uniform attenuation correction (NUA-CT) for small-animal SPECT/CT with focusing pinhole collimation, and compare the quantitative accuracy with uniform Chang correction based on (i) body outlines extracted from x-ray CT (UA-CT) and (ii) on hand drawn body contours on the images obtained with three integrated optical cameras (UA-BC). Measurements in phantoms and rats containing known activities of isotopes were conducted for evaluation. In (125)I, (201)Tl, (99m)Tc and (111)In phantom experiments, average relative errors comparing to the gold standards measured in a dose calibrator were reduced to 5.5%, 6.8%, 4.9% and 2.8%, respectively, with NUA-CT. In animal studies, these errors were 2.1%, 3.3%, 2.0% and 2.0%, respectively. Differences in accuracy on average between results of NUA-CT, UA-CT and UA-BC were less than 2.3% in phantom studies and 3.1% in animal studies except for (125)I (3.6% and 5.1%, respectively). All methods tested provide reasonable attenuation correction and result in high quantitative accuracy. NUA-CT shows superior accuracy except for (125)I, where other factors may have more impact on the quantitative accuracy than the selected attenuation correction.

  19. A novel iris transillumination grading scale allowing flexible assessment with quantitative image analysis and visual matching.

    PubMed

    Wang, Chen; Brancusi, Flavia; Valivullah, Zaheer M; Anderson, Michael G; Cunningham, Denise; Hedberg-Buenz, Adam; Power, Bradley; Simeonov, Dimitre; Gahl, William A; Zein, Wadih M; Adams, David R; Brooks, Brian

    2018-01-01

    To develop a sensitive scale of iris transillumination suitable for clinical and research use, with the capability of either quantitative analysis or visual matching of images. Iris transillumination photographic images were used from 70 study subjects with ocular or oculocutaneous albinism. Subjects represented a broad range of ocular pigmentation. A subset of images was subjected to image analysis and ranking by both expert and nonexpert reviewers. Quantitative ordering of images was compared with ordering by visual inspection. Images were binned to establish an 8-point scale. Ranking consistency was evaluated using the Kendall rank correlation coefficient (Kendall's tau). Visual ranking results were assessed using Kendall's coefficient of concordance (Kendall's W) analysis. There was a high degree of correlation among the image analysis, expert-based and non-expert-based image rankings. Pairwise comparisons of the quantitative ranking with each reviewer generated an average Kendall's tau of 0.83 ± 0.04 (SD). Inter-rater correlation was also high with Kendall's W of 0.96, 0.95, and 0.95 for nonexpert, expert, and all reviewers, respectively. The current standard for assessing iris transillumination is expert assessment of clinical exam findings. We adapted an image-analysis technique to generate quantitative transillumination values. Quantitative ranking was shown to be highly similar to a ranking produced by both expert and nonexpert reviewers. This finding suggests that the image characteristics used to quantify iris transillumination do not require expert interpretation. Inter-rater rankings were also highly similar, suggesting that varied methods of transillumination ranking are robust in terms of producing reproducible results.

  20. Diagnostic accuracy of an artificial neural network compared with statistical quantitation of myocardial perfusion images: a Japanese multicenter study.

    PubMed

    Nakajima, Kenichi; Kudo, Takashi; Nakata, Tomoaki; Kiso, Keisuke; Kasai, Tokuo; Taniguchi, Yasuyo; Matsuo, Shinro; Momose, Mitsuru; Nakagawa, Masayasu; Sarai, Masayoshi; Hida, Satoshi; Tanaka, Hirokazu; Yokoyama, Kunihiko; Okuda, Koichi; Edenbrandt, Lars

    2017-12-01

    Artificial neural networks (ANN) might help to diagnose coronary artery disease. This study aimed to determine whether the diagnostic accuracy of an ANN-based diagnostic system and conventional quantitation are comparable. The ANN was trained to classify potentially abnormal areas as true or false based on the nuclear cardiology expert interpretation of 1001 gated stress/rest 99m Tc-MIBI images at 12 hospitals. The diagnostic accuracy of the ANN was compared with 364 expert interpretations that served as the gold standard of abnormality for the validation study. Conventional summed stress/rest/difference scores (SSS/SRS/SDS) were calculated and compared with receiver operating characteristics (ROC) analysis. The ANN generated a better area under the ROC curves (AUC) than SSS (0.92 vs. 0.82, p < 0.0001), indicating better identification of stress defects. The ANN also generated a better AUC than SDS (0.90 vs. 0.75, p < 0.0001) for stress-induced ischemia. The AUC for patients with old myocardial infarction based on rest defects was 0.97 (0.91 for SRS, p = 0.0061), and that for patients with and without a history of revascularization based on stress defects was 0.94 and 0.90 (p = 0.0055 and p < 0.0001 vs. SSS, respectively). The SSS/SRS/SDS steeply increased when ANN values (probability of abnormality) were >0.80. The ANN was diagnostically accurate in various clinical settings, including that of patients with previous myocardial infarction and coronary revascularization. The ANN could help to diagnose coronary artery disease.

  1. Accuracy metrics for judging time scale algorithms

    NASA Technical Reports Server (NTRS)

    Douglas, R. J.; Boulanger, J.-S.; Jacques, C.

    1994-01-01

    Time scales have been constructed in different ways to meet the many demands placed upon them for time accuracy, frequency accuracy, long-term stability, and robustness. Usually, no single time scale is optimum for all purposes. In the context of the impending availability of high-accuracy intermittently-operated cesium fountains, we reconsider the question of evaluating the accuracy of time scales which use an algorithm to span interruptions of the primary standard. We consider a broad class of calibration algorithms that can be evaluated and compared quantitatively for their accuracy in the presence of frequency drift and a full noise model (a mixture of white PM, flicker PM, white FM, flicker FM, and random walk FM noise). We present the analytic techniques for computing the standard uncertainty for the full noise model and this class of calibration algorithms. The simplest algorithm is evaluated to find the average-frequency uncertainty arising from the noise of the cesium fountain's local oscillator and from the noise of a hydrogen maser transfer-standard. This algorithm and known noise sources are shown to permit interlaboratory frequency transfer with a standard uncertainty of less than 10(exp -15) for periods of 30-100 days.

  2. A Quantitative Gas Chromatographic Ethanol Determination.

    ERIC Educational Resources Information Center

    Leary, James J.

    1983-01-01

    Describes a gas chromatographic experiment for the quantitative determination of volume percent ethanol in water ethanol solutions. Background information, procedures, and typical results are included. Accuracy and precision of results are both on the order of two percent. (JN)

  3. 3D quantitative analysis of early decomposition changes of the human face.

    PubMed

    Caplova, Zuzana; Gibelli, Daniele Maria; Poppa, Pasquale; Cummaudo, Marco; Obertova, Zuzana; Sforza, Chiarella; Cattaneo, Cristina

    2018-03-01

    Decomposition of the human body and human face is influenced, among other things, by environmental conditions. The early decomposition changes that modify the appearance of the face may hamper the recognition and identification of the deceased. Quantitative assessment of those changes may provide important information for forensic identification. This report presents a pilot 3D quantitative approach of tracking early decomposition changes of a single cadaver in controlled environmental conditions by summarizing the change with weekly morphological descriptions. The root mean square (RMS) value was used to evaluate the changes of the face after death. The results showed a high correlation (r = 0.863) between the measured RMS and the time since death. RMS values of each scan are presented, as well as the average weekly RMS values. The quantification of decomposition changes could improve the accuracy of antemortem facial approximation and potentially could allow the direct comparisons of antemortem and postmortem 3D scans.

  4. Privacy-Preserving Accountable Accuracy Management Systems (PAAMS)

    NASA Astrophysics Data System (ADS)

    Thomas, Roshan K.; Sandhu, Ravi; Bertino, Elisa; Arpinar, Budak; Xu, Shouhuai

    We argue for the design of “Privacy-preserving Accountable Accuracy Management Systems (PAAMS)”. The designs of such systems recognize from the onset that accuracy, accountability, and privacy management are intertwined. As such, these systems have to dynamically manage the tradeoffs between these (often conflicting) objectives. For example, accuracy in such systems can be improved by providing better accountability links between structured and unstructured information. Further, accuracy may be enhanced if access to private information is allowed in controllable and accountable ways. Our proposed approach involves three key elements. First, a model to link unstructured information such as that found in email, image and document repositories with structured information such as that in traditional databases. Second, a model for accuracy management and entity disambiguation by proactively preventing, detecting and tracing errors in information bases. Third, a model to provide privacy-governed operation as accountability and accuracy are managed.

  5. Ultrasensitive, self-calibrated cavity ring-down spectrometer for quantitative trace gas analysis.

    PubMed

    Chen, Bing; Sun, Yu R; Zhou, Ze-Yi; Chen, Jian; Liu, An-Wen; Hu, Shui-Ming

    2014-11-10

    A cavity ring-down spectrometer is built for trace gas detection using telecom distributed feedback (DFB) diode lasers. The longitudinal modes of the ring-down cavity are used as frequency markers without active-locking either the laser or the high-finesse cavity. A control scheme is applied to scan the DFB laser frequency, matching the cavity modes one by one in sequence and resulting in a correct index at each recorded spectral data point, which allows us to calibrate the spectrum with a relative frequency precision of 0.06 MHz. Besides the frequency precision of the spectrometer, a sensitivity (noise-equivalent absorption) of 4×10-11  cm-1  Hz-1/2 has also been demonstrated. A minimum detectable absorption coefficient of 5×10-12  cm-1 has been obtained by averaging about 100 spectra recorded in 2  h. The quantitative accuracy is tested by measuring the CO2 concentrations in N2 samples prepared by the gravimetric method, and the relative deviation is less than 0.3%. The trace detection capability is demonstrated by detecting CO2 of ppbv-level concentrations in a high-purity nitrogen gas sample. Simple structure, high sensitivity, and good accuracy make the instrument very suitable for quantitative trace gas analysis.

  6. Improved accuracies for satellite tracking

    NASA Technical Reports Server (NTRS)

    Kammeyer, P. C.; Fiala, A. D.; Seidelmann, P. K.

    1991-01-01

    A charge coupled device (CCD) camera on an optical telescope which follows the stars can be used to provide high accuracy comparisons between the line of sight to a satellite, over a large range of satellite altitudes, and lines of sight to nearby stars. The CCD camera can be rotated so the motion of the satellite is down columns of the CCD chip, and charge can be moved from row to row of the chip at a rate which matches the motion of the optical image of the satellite across the chip. Measurement of satellite and star images, together with accurate timing of charge motion, provides accurate comparisons of lines of sight. Given lines of sight to stars near the satellite, the satellite line of sight may be determined. Initial experiments with this technique, using an 18 cm telescope, have produced TDRS-4 observations which have an rms error of 0.5 arc second, 100 m at synchronous altitude. Use of a mosaic of CCD chips, each having its own rate of charge motion, in the focal place of a telescope would allow point images of a geosynchronous satellite and of stars to be formed simultaneously in the same telescope. The line of sight of such a satellite could be measured relative to nearby star lines of sight with an accuracy of approximately 0.03 arc second. Development of a star catalog with 0.04 arc second rms accuracy and perhaps ten stars per square degree would allow determination of satellite lines of sight with 0.05 arc second rms absolute accuracy, corresponding to 10 m at synchronous altitude. Multiple station time transfers through a communications satellite can provide accurate distances from the satellite to the ground stations. Such observations can, if calibrated for delays, determine satellite orbits to an accuracy approaching 10 m rms.

  7. Multistrip western blotting to increase quantitative data output.

    PubMed

    Kiyatkin, Anatoly; Aksamitiene, Edita

    2009-01-01

    The qualitative and quantitative measurements of protein abundance and modification states are essential in understanding their functions in diverse cellular processes. Typical western blotting, though sensitive, is prone to produce substantial errors and is not readily adapted to high-throughput technologies. Multistrip western blotting is a modified immunoblotting procedure based on simultaneous electrophoretic transfer of proteins from multiple strips of polyacrylamide gels to a single membrane sheet. In comparison with the conventional technique, Multistrip western blotting increases the data output per single blotting cycle up to tenfold, allows concurrent monitoring of up to nine different proteins from the same loading of the sample, and substantially improves the data accuracy by reducing immunoblotting-derived signal errors. This approach enables statistically reliable comparison of different or repeated sets of data, and therefore is beneficial to apply in biomedical diagnostics, systems biology, and cell signaling research.

  8. Accuracy increase of self-compensator

    NASA Astrophysics Data System (ADS)

    Zhambalova, S. Ts; Vinogradova, A. A.

    2018-03-01

    In this paper, the authors consider a self-compensation system and a method for increasing its accuracy, without compromising the condition of the information theory of measuring devices. The result can be achieved using the pulse control of the tracking system in the dead zone (the zone of the proportional section of the amplifier's characteristic). Pulse control allows one to increase the control power, but the input signal of the amplifier is infinitesimal. To do this, the authors use the conversion scheme for the input quantity. It is also possible to reduce the dead band, but the system becomes unstable. The amount of information received from the instrument, correcting circuits complicates the system, and, reducing the feedback coefficient dramatically, reduces the speed. Thanks to this, without compromising the measurement condition, the authors increase the accuracy of the self-compensation system. The implementation technique allows increasing the power of the input signal by many orders of magnitude.

  9. Quantitative fluorescence angiography for neurosurgical interventions.

    PubMed

    Weichelt, Claudia; Duscha, Philipp; Steinmeier, Ralf; Meyer, Tobias; Kuß, Julia; Cimalla, Peter; Kirsch, Matthias; Sobottka, Stephan B; Koch, Edmund; Schackert, Gabriele; Morgenstern, Ute

    2013-06-01

    Present methods for quantitative measurement of cerebral perfusion during neurosurgical operations require additional technology for measurement, data acquisition, and processing. This study used conventional fluorescence video angiography--as an established method to visualize blood flow in brain vessels--enhanced by a quantifying perfusion software tool. For these purposes, the fluorescence dye indocyanine green is given intravenously, and after activation by a near-infrared light source the fluorescence signal is recorded. Video data are analyzed by software algorithms to allow quantification of the blood flow. Additionally, perfusion is measured intraoperatively by a reference system. Furthermore, comparing reference measurements using a flow phantom were performed to verify the quantitative blood flow results of the software and to validate the software algorithm. Analysis of intraoperative video data provides characteristic biological parameters. These parameters were implemented in the special flow phantom for experimental validation of the developed software algorithms. Furthermore, various factors that influence the determination of perfusion parameters were analyzed by means of mathematical simulation. Comparing patient measurement, phantom experiment, and computer simulation under certain conditions (variable frame rate, vessel diameter, etc.), the results of the software algorithms are within the range of parameter accuracy of the reference methods. Therefore, the software algorithm for calculating cortical perfusion parameters from video data presents a helpful intraoperative tool without complex additional measurement technology.

  10. Using quantitative disease dynamics as a tool for guiding response to avian influenza in poultry in the United States of America☆

    PubMed Central

    Pepin, K.M.; Spackman, E.; Brown, J.D.; Pabilonia, K.L.; Garber, L.P.; Weaver, J.T.; Kennedy, D.A.; Patyk, K.A.; Huyvaert, K.P.; Miller, R.S.; Franklin, A.B.; Pedersen, K.; Bogich, T.L.; Rohani, P.; Shriner, S.A.; Webb, C.T.; Riley, S.

    2014-01-01

    Wild birds are the primary source of genetic diversity for influenza A viruses that eventually emerge in poultry and humans. Much progress has been made in the descriptive ecology of avian influenza viruses (AIVs), but contributions are less evident from quantitative studies (e.g., those including disease dynamic models). Transmission between host species, individuals and flocks has not been measured with sufficient accuracy to allow robust quantitative evaluation of alternate control protocols. We focused on the United States of America (USA) as a case study for determining the state of our quantitative knowledge of potential AIV emergence processes from wild hosts to poultry. We identified priorities for quantitative research that would build on existing tools for responding to AIV in poultry and concluded that the following knowledge gaps can be addressed with current empirical data: (1) quantification of the spatio-temporal relationships between AIV prevalence in wild hosts and poultry populations, (2) understanding how the structure of different poultry sectors impacts within-flock transmission, (3) determining mechanisms and rates of between-farm spread, and (4) validating current policy-decision tools with data. The modeling studies we recommend will improve our mechanistic understanding of potential AIV transmission patterns in USA poultry, leading to improved measures of accuracy and reduced uncertainty when evaluating alternative control strategies. PMID:24462191

  11. Using quantitative disease dynamics as a tool for guiding response to avian influenza in poultry in the United States of America.

    PubMed

    Pepin, K M; Spackman, E; Brown, J D; Pabilonia, K L; Garber, L P; Weaver, J T; Kennedy, D A; Patyk, K A; Huyvaert, K P; Miller, R S; Franklin, A B; Pedersen, K; Bogich, T L; Rohani, P; Shriner, S A; Webb, C T; Riley, S

    2014-03-01

    Wild birds are the primary source of genetic diversity for influenza A viruses that eventually emerge in poultry and humans. Much progress has been made in the descriptive ecology of avian influenza viruses (AIVs), but contributions are less evident from quantitative studies (e.g., those including disease dynamic models). Transmission between host species, individuals and flocks has not been measured with sufficient accuracy to allow robust quantitative evaluation of alternate control protocols. We focused on the United States of America (USA) as a case study for determining the state of our quantitative knowledge of potential AIV emergence processes from wild hosts to poultry. We identified priorities for quantitative research that would build on existing tools for responding to AIV in poultry and concluded that the following knowledge gaps can be addressed with current empirical data: (1) quantification of the spatio-temporal relationships between AIV prevalence in wild hosts and poultry populations, (2) understanding how the structure of different poultry sectors impacts within-flock transmission, (3) determining mechanisms and rates of between-farm spread, and (4) validating current policy-decision tools with data. The modeling studies we recommend will improve our mechanistic understanding of potential AIV transmission patterns in USA poultry, leading to improved measures of accuracy and reduced uncertainty when evaluating alternative control strategies. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  12. [Quantitative surface analysis of Pt-Co, Cu-Au and Cu-Ag alloy films by XPS and AES].

    PubMed

    Li, Lian-Zhong; Zhuo, Shang-Jun; Shen, Ru-Xiang; Qian, Rong; Gao, Jie

    2013-11-01

    In order to improve the quantitative analysis accuracy of AES, We associated XPS with AES and studied the method to reduce the error of AES quantitative analysis, selected Pt-Co, Cu-Au and Cu-Ag binary alloy thin-films as the samples, used XPS to correct AES quantitative analysis results by changing the auger sensitivity factors to make their quantitative analysis results more similar. Then we verified the accuracy of the quantitative analysis of AES when using the revised sensitivity factors by other samples with different composition ratio, and the results showed that the corrected relative sensitivity factors can reduce the error in quantitative analysis of AES to less than 10%. Peak defining is difficult in the form of the integral spectrum of AES analysis since choosing the starting point and ending point when determining the characteristic auger peak intensity area with great uncertainty, and to make analysis easier, we also processed data in the form of the differential spectrum, made quantitative analysis on the basis of peak to peak height instead of peak area, corrected the relative sensitivity factors, and verified the accuracy of quantitative analysis by the other samples with different composition ratio. The result showed that the analytical error in quantitative analysis of AES reduced to less than 9%. It showed that the accuracy of AES quantitative analysis can be highly improved by the way of associating XPS with AES to correct the auger sensitivity factors since the matrix effects are taken into account. Good consistency was presented, proving the feasibility of this method.

  13. Larger core size has superior technical and analytical accuracy in bladder tissue microarray.

    PubMed

    Eskaros, Adel Rh; Egloff, Shanna A Arnold; Boyd, Kelli L; Richardson, Joyce E; Hyndman, M Eric; Zijlstra, Andries

    2017-03-01

    The construction of tissue microarrays (TMAs) with cores from a large number of paraffin-embedded tissues (donors) into a single paraffin block (recipient) is an effective method of analyzing samples from many patient specimens simultaneously. For the TMA to be successful, the cores within it must capture the correct histologic areas from the donor blocks (technical accuracy) and maintain concordance with the tissue of origin (analytical accuracy). This can be particularly challenging for tissues with small histological features such as small islands of carcinoma in situ (CIS), thin layers of normal urothelial lining of the bladder, or cancers that exhibit intratumor heterogeneity. In an effort to create a comprehensive TMA of a bladder cancer patient cohort that accurately represents the tumor heterogeneity and captures the small features of normal and CIS, we determined how core size (0.6 vs 1.0 mm) impacted the technical and analytical accuracy of the TMA. The larger 1.0 mm core exhibited better technical accuracy for all tissue types at 80.9% (normal), 94.2% (tumor), and 71.4% (CIS) compared with 58.6%, 85.9%, and 63.8% for 0.6 mm cores. Although the 1.0 mm core provided better tissue capture, increasing the number of replicates from two to three allowed with the 0.6 mm core compensated for this reduced technical accuracy. However, quantitative image analysis of proliferation using both Ki67+ immunofluorescence counts and manual mitotic counts demonstrated that the 1.0 mm core size also exhibited significantly greater analytical accuracy (P=0.004 and 0.035, respectively, r 2 =0.979 and 0.669, respectively). Ultimately, our findings demonstrate that capturing two or more 1.0 mm cores for TMA construction provides superior technical and analytical accuracy over the smaller 0.6 mm cores, especially for tissues harboring small histological features or substantial heterogeneity.

  14. The hidden KPI registration accuracy.

    PubMed

    Shorrosh, Paul

    2011-09-01

    Determining the registration accuracy rate is fundamental to improving revenue cycle key performance indicators. A registration quality assurance (QA) process allows errors to be corrected before bills are sent and helps registrars learn from their mistakes. Tools are available to help patient access staff who perform registration QA manually.

  15. Evaluation of in vivo quantification accuracy of the Ingenuity-TF PET/MR

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Maus, Jens, E-mail: j.maus@hzdr.de; Schramm, Georg; Hofheinz, Frank

    2015-10-15

    Purpose: The quantitative accuracy of standardized uptake values (SUVs) and tracer kinetic uptake parameters in patient investigations strongly depends on accurate determination of regional activity concentrations in positron emission tomography (PET) data. This determination rests on the assumption that the given scanner calibration is valid in vivo. In a previous study, we introduced a method to test this assumption. This method allows to identify discrepancies in quantitative accuracy in vivo by comparison of activity concentrations of urine samples measured in a well-counter with activity concentrations extracted from PET images of the bladder. In the present study, we have applied thismore » method to the Philips Ingenuity-TF PET/MR since at the present stage, absolute quantitative accuracy of combined PET/MR systems is still under investigation. Methods: Twenty one clinical whole-body F18-FDG scans were included in this study. The bladder region was imaged as the last bed position and urine samples were collected afterward. PET images were reconstructed including MR-based attenuation correction with and without truncation compensation and 3D regions-of-interest (ROIs) of the bladder were delineated by three observers. To exclude partial volume effects, ROIs were concentrically shrunk by 8–10 mm. Then, activity concentrations were determined in the PET images for the bladder and for the urine by measuring the samples in a calibrated well-counter. In addition, linearity measurements of SUV vs singles rate and measurements of the stability of the coincidence rate of “true” events of the PET/MR system were performed over a period of 4 months. Results: The measured in vivo activity concentrations were significantly lower in PET/MR than in the well-counter with a ratio of the former to the latter of 0.756 ± 0.060 (mean ± std. dev.), a range of 0.604–0.858, and a P value of 3.9 ⋅ 10{sup −14}. While the stability measurements of the coincidence rate

  16. Maximizing the quantitative accuracy and reproducibility of Förster resonance energy transfer measurement for screening by high throughput widefield microscopy

    PubMed Central

    Schaufele, Fred

    2013-01-01

    Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) provides insights into the proximities and orientations of FPs as surrogates of the biochemical interactions and structures of the factors to which the FPs are genetically fused. As powerful as FRET methods are, technical issues have impeded their broad adoption in the biologic sciences. One hurdle to accurate and reproducible FRET microscopy measurement stems from variable fluorescence backgrounds both within a field and between different fields. Those variations introduce errors into the precise quantification of fluorescence levels on which the quantitative accuracy of FRET measurement is highly dependent. This measurement error is particularly problematic for screening campaigns since minimal well-to-well variation is necessary to faithfully identify wells with altered values. High content screening depends also upon maximizing the numbers of cells imaged, which is best achieved by low magnification high throughput microscopy. But, low magnification introduces flat-field correction issues that degrade the accuracy of background correction to cause poor reproducibility in FRET measurement. For live cell imaging, fluorescence of cell culture media in the fluorescence collection channels for the FPs commonly used for FRET analysis is a high source of background error. These signal-to-noise problems are compounded by the desire to express proteins at biologically meaningful levels that may only be marginally above the strong fluorescence background. Here, techniques are presented that correct for background fluctuations. Accurate calculation of FRET is realized even from images in which a non-flat background is 10-fold higher than the signal. PMID:23927839

  17. Analysis of deformable image registration accuracy using computational modeling

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhong Hualiang; Kim, Jinkoo; Chetty, Indrin J.

    2010-03-15

    Computer aided modeling of anatomic deformation, allowing various techniques and protocols in radiation therapy to be systematically verified and studied, has become increasingly attractive. In this study the potential issues in deformable image registration (DIR) were analyzed based on two numerical phantoms: One, a synthesized, low intensity gradient prostate image, and the other a lung patient's CT image data set. Each phantom was modeled with region-specific material parameters with its deformation solved using a finite element method. The resultant displacements were used to construct a benchmark to quantify the displacement errors of the Demons and B-Spline-based registrations. The results showmore » that the accuracy of these registration algorithms depends on the chosen parameters, the selection of which is closely associated with the intensity gradients of the underlying images. For the Demons algorithm, both single resolution (SR) and multiresolution (MR) registrations required approximately 300 iterations to reach an accuracy of 1.4 mm mean error in the lung patient's CT image (and 0.7 mm mean error averaged in the lung only). For the low gradient prostate phantom, these algorithms (both SR and MR) required at least 1600 iterations to reduce their mean errors to 2 mm. For the B-Spline algorithms, best performance (mean errors of 1.9 mm for SR and 1.6 mm for MR, respectively) on the low gradient prostate was achieved using five grid nodes in each direction. Adding more grid nodes resulted in larger errors. For the lung patient's CT data set, the B-Spline registrations required ten grid nodes in each direction for highest accuracy (1.4 mm for SR and 1.5 mm for MR). The numbers of iterations or grid nodes required for optimal registrations depended on the intensity gradients of the underlying images. In summary, the performance of the Demons and B-Spline registrations have been quantitatively evaluated using numerical phantoms. The results show that

  18. Temporal lobe epilepsy: quantitative MR volumetry in detection of hippocampal atrophy.

    PubMed

    Farid, Nikdokht; Girard, Holly M; Kemmotsu, Nobuko; Smith, Michael E; Magda, Sebastian W; Lim, Wei Y; Lee, Roland R; McDonald, Carrie R

    2012-08-01

    To determine the ability of fully automated volumetric magnetic resonance (MR) imaging to depict hippocampal atrophy (HA) and to help correctly lateralize the seizure focus in patients with temporal lobe epilepsy (TLE). This study was conducted with institutional review board approval and in compliance with HIPAA regulations. Volumetric MR imaging data were analyzed for 34 patients with TLE and 116 control subjects. Structural volumes were calculated by using U.S. Food and Drug Administration-cleared software for automated quantitative MR imaging analysis (NeuroQuant). Results of quantitative MR imaging were compared with visual detection of atrophy, and, when available, with histologic specimens. Receiver operating characteristic analyses were performed to determine the optimal sensitivity and specificity of quantitative MR imaging for detecting HA and asymmetry. A linear classifier with cross validation was used to estimate the ability of quantitative MR imaging to help lateralize the seizure focus. Quantitative MR imaging-derived hippocampal asymmetries discriminated patients with TLE from control subjects with high sensitivity (86.7%-89.5%) and specificity (92.2%-94.1%). When a linear classifier was used to discriminate left versus right TLE, hippocampal asymmetry achieved 94% classification accuracy. Volumetric asymmetries of other subcortical structures did not improve classification. Compared with invasive video electroencephalographic recordings, lateralization accuracy was 88% with quantitative MR imaging and 85% with visual inspection of volumetric MR imaging studies but only 76% with visual inspection of clinical MR imaging studies. Quantitative MR imaging can depict the presence and laterality of HA in TLE with accuracy rates that may exceed those achieved with visual inspection of clinical MR imaging studies. Thus, quantitative MR imaging may enhance standard visual analysis, providing a useful and viable means for translating volumetric analysis into

  19. High dose microCT does not contribute towards improved microPET/CT image quantitative accuracy and can limit longitudinal scanning of small animals

    NASA Astrophysics Data System (ADS)

    McDougald, Wendy A.; Collins, Richard; Green, Mark; Tavares, Adriana A. S.

    2017-10-01

    Obtaining accurate quantitative measurements in preclinical Positron Emission Tomography/Computed Tomography (PET/CT) imaging is of paramount importance in biomedical research and helps supporting efficient translation of preclinical results to the clinic. The purpose of this study was two-fold: (1) to investigate the effects of different CT acquisition protocols on PET/CT image quality and data quantification; and (2) to evaluate the absorbed dose associated with varying CT parameters. Methods: An air/water quality control CT phantom, tissue equivalent material phantom, an in-house 3D printed phantom and an image quality PET/CT phantom were imaged using a Mediso nanoPET/CT scanner. Collected data was analyzed using PMOD software, VivoQuant software and National Electric Manufactures Association (NEMA) software implemented by Mediso. Measured Hounsfield Unit (HU) in collected CT images were compared to the known HU values and image noise was quantified. PET recovery coefficients (RC), uniformity and quantitative bias were also measured. Results: Only less than 2% and 1% of CT acquisition protocols yielded water HU values < -80 and air HU values < -840, respectively. Four out of eleven CT protocols resulted in more than 100 mGy absorbed dose. Different CT protocols did not impact PET uniformity and RC, and resulted in <4% overall bias relative to expected radioactive concentration. Conclusion: Preclinical CT protocols with increased exposure times can result in high absorbed doses to the small animals. These should be avoided, as they do not contributed towards improved microPET/CT image quantitative accuracy and could limit longitudinal scanning of small animals.

  20. Metrologies for quantitative nanomechanical testing and quality control in semiconductor manufacturing

    NASA Astrophysics Data System (ADS)

    Pratt, Jon R.; Kramar, John A.; Newell, David B.; Smith, Douglas T.

    2005-05-01

    If nanomechanical testing is to evolve into a tool for process and quality control in semiconductor fabrication, great advances in throughput, repeatability, and accuracy of the associated instruments and measurements will be required. A recent grant awarded by the NIST Advanced Technology Program seeks to address the throughput issue by developing a high-speed AFM-based platform for quantitative nanomechanical measurements. The following paper speaks to the issue of quantitative accuracy by presenting an overview of various standards and techniques under development at NIST and other national metrology institutes (NMIs) that can provide a metrological basis for nanomechanical testing. The infrastructure we describe places firm emphasis on traceability to the International System of Units, paving the way for truly quantitative, rather than qualitative, physical property testing.

  1. Frontally eluted components procedure with thin layer chromatography as a mode of sample preparation for high performance liquid chromatography quantitation of acetaminophen in biological matrix.

    PubMed

    Klimek-Turek, A; Sikora, M; Rybicki, M; Dzido, T H

    2016-03-04

    A new concept of using thin-layer chromatography to sample preparation for the quantitative determination of solute/s followed by instrumental techniques is presented Thin-layer chromatography (TLC) is used to completely separate acetaminophen and its internal standard from other components (matrix) and to form a single spot/zone containing them at the solvent front position (after the final stage of the thin-layer chromatogram development). The location of the analytes and internal standard in the solvent front zone allows their easy extraction followed by quantitation by HPLC. The exctraction procedure of the solute/s and internal standard can proceed from whole solute frontal zone or its part without lowering in accuracy of quantitative analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Radiologic-Pathologic Analysis of Contrast-enhanced and Diffusion-weighted MR Imaging in Patients with HCC after TACE: Diagnostic Accuracy of 3D Quantitative Image Analysis

    PubMed Central

    Chapiro, Julius; Wood, Laura D.; Lin, MingDe; Duran, Rafael; Cornish, Toby; Lesage, David; Charu, Vivek; Schernthaner, Rüdiger; Wang, Zhijun; Tacher, Vania; Savic, Lynn Jeanette; Kamel, Ihab R.

    2014-01-01

    standard error [RSEresidual standard error] = 6.38 and 6.33 for quantitative EASLEuropean Association for the Study of the Liver and quantitative ADCapparent diffusion coefficient, respectively), when compared with non-3Dthree-dimensional techniques (RSEresidual standard error = 12.18 for visual assessment). Conclusion This radiologic-pathologic correlation study demonstrates the diagnostic accuracy of 3Dthree-dimensional quantitative MR imaging techniques in identifying pathologically measured tumor necrosis in HCChepatocellular carcinoma lesions treated with TACEtransarterial chemoembolization. © RSNA, 2014 Online supplemental material is available for this article. PMID:25028783

  3. Nonlinear optical microscopy: use of second harmonic generation and two-photon microscopy for automated quantitative liver fibrosis studies.

    PubMed

    Sun, Wanxin; Chang, Shi; Tai, Dean C S; Tan, Nancy; Xiao, Guangfa; Tang, Huihuan; Yu, Hanry

    2008-01-01

    Liver fibrosis is associated with an abnormal increase in an extracellular matrix in chronic liver diseases. Quantitative characterization of fibrillar collagen in intact tissue is essential for both fibrosis studies and clinical applications. Commonly used methods, histological staining followed by either semiquantitative or computerized image analysis, have limited sensitivity, accuracy, and operator-dependent variations. The fibrillar collagen in sinusoids of normal livers could be observed through second-harmonic generation (SHG) microscopy. The two-photon excited fluorescence (TPEF) images, recorded simultaneously with SHG, clearly revealed the hepatocyte morphology. We have systematically optimized the parameters for the quantitative SHG/TPEF imaging of liver tissue and developed fully automated image analysis algorithms to extract the information of collagen changes and cell necrosis. Subtle changes in the distribution and amount of collagen and cell morphology are quantitatively characterized in SHG/TPEF images. By comparing to traditional staining, such as Masson's trichrome and Sirius red, SHG/TPEF is a sensitive quantitative tool for automated collagen characterization in liver tissue. Our system allows for enhanced detection and quantification of sinusoidal collagen fibers in fibrosis research and clinical diagnostics.

  4. Assessing genomic selection prediction accuracy in a dynamic barley breeding

    USDA-ARS?s Scientific Manuscript database

    Genomic selection is a method to improve quantitative traits in crops and livestock by estimating breeding values of selection candidates using phenotype and genome-wide marker data sets. Prediction accuracy has been evaluated through simulation and cross-validation, however validation based on prog...

  5. Portable smartphone based quantitative phase microscope

    NASA Astrophysics Data System (ADS)

    Meng, Xin; Tian, Xiaolin; Yu, Wei; Kong, Yan; Jiang, Zhilong; Liu, Fei; Xue, Liang; Liu, Cheng; Wang, Shouyu

    2018-01-01

    To realize portable device with high contrast imaging capability, we designed a quantitative phase microscope using transport of intensity equation method based on a smartphone. The whole system employs an objective and an eyepiece as imaging system and a cost-effective LED as illumination source. A 3-D printed cradle is used to align these components. Images of different focal planes are captured by manual focusing, followed by calculation of sample phase via a self-developed Android application. To validate its accuracy, we first tested the device by measuring a random phase plate with known phases, and then red blood cell smear, Pap smear, broad bean epidermis sections and monocot root were also measured to show its performance. Owing to its advantages as accuracy, high-contrast, cost-effective and portability, the portable smartphone based quantitative phase microscope is a promising tool which can be future adopted in remote healthcare and medical diagnosis.

  6. Edge technique lidar for high accuracy, high spatial resolution wind measurement in the Planetary Boundary Layer

    NASA Technical Reports Server (NTRS)

    Korb, C. L.; Gentry, Bruce M.

    1995-01-01

    The goal of the Army Research Office (ARO) Geosciences Program is to measure the three dimensional wind field in the planetary boundary layer (PBL) over a measurement volume with a 50 meter spatial resolution and with measurement accuracies of the order of 20 cm/sec. The objective of this work is to develop and evaluate a high vertical resolution lidar experiment using the edge technique for high accuracy measurement of the atmospheric wind field to meet the ARO requirements. This experiment allows the powerful capabilities of the edge technique to be quantitatively evaluated. In the edge technique, a laser is located on the steep slope of a high resolution spectral filter. This produces large changes in measured signal for small Doppler shifts. A differential frequency technique renders the Doppler shift measurement insensitive to both laser and filter frequency jitter and drift. The measurement is also relatively insensitive to the laser spectral width for widths less than the width of the edge filter. Thus, the goal is to develop a system which will yield a substantial improvement in the state of the art of wind profile measurement in terms of both vertical resolution and accuracy and which will provide a unique capability for atmospheric wind studies.

  7. Heat-Treatment-Responsive Proteins in Different Developmental Stages of Tomato Pollen Detected by Targeted Mass Accuracy Precursor Alignment (tMAPA).

    PubMed

    Chaturvedi, Palak; Doerfler, Hannes; Jegadeesan, Sridharan; Ghatak, Arindam; Pressman, Etan; Castillejo, Maria Angeles; Wienkoop, Stefanie; Egelhofer, Volker; Firon, Nurit; Weckwerth, Wolfram

    2015-11-06

    Recently, we have developed a quantitative shotgun proteomics strategy called mass accuracy precursor alignment (MAPA). The MAPA algorithm uses high mass accuracy to bin mass-to-charge (m/z) ratios of precursor ions from LC-MS analyses, determines their intensities, and extracts a quantitative sample versus m/z ratio data alignment matrix from a multitude of samples. Here, we introduce a novel feature of this algorithm that allows the extraction and alignment of proteotypic peptide precursor ions or any other target peptide from complex shotgun proteomics data for accurate quantification of unique proteins. This strategy circumvents the problem of confusing the quantification of proteins due to indistinguishable protein isoforms by a typical shotgun proteomics approach. We applied this strategy to a comparison of control and heat-treated tomato pollen grains at two developmental stages, post-meiotic and mature. Pollen is a temperature-sensitive tissue involved in the reproductive cycle of plants and plays a major role in fruit setting and yield. By LC-MS-based shotgun proteomics, we identified more than 2000 proteins in total for all different tissues. By applying the targeted MAPA data-processing strategy, 51 unique proteins were identified as heat-treatment-responsive protein candidates. The potential function of the identified candidates in a specific developmental stage is discussed.

  8. Measures of model performance based on the log accuracy ratio

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Morley, Steven Karl; Brito, Thiago Vasconcelos; Welling, Daniel T.

    Quantitative assessment of modeling and forecasting of continuous quantities uses a variety of approaches. We review existing literature describing metrics for forecast accuracy and bias, concentrating on those based on relative errors and percentage errors. Of these accuracy metrics, the mean absolute percentage error (MAPE) is one of the most common across many fields and has been widely applied in recent space science literature and we highlight the benefits and drawbacks of MAPE and proposed alternatives. We then introduce the log accuracy ratio, and derive from it two metrics: the median symmetric accuracy; and the symmetric signed percentage bias. Robustmore » methods for estimating the spread of a multiplicative linear model using the log accuracy ratio are also presented. The developed metrics are shown to be easy to interpret, robust, and to mitigate the key drawbacks of their more widely-used counterparts based on relative errors and percentage errors. Their use is illustrated with radiation belt electron flux modeling examples.« less

  9. Measures of model performance based on the log accuracy ratio

    DOE PAGES

    Morley, Steven Karl; Brito, Thiago Vasconcelos; Welling, Daniel T.

    2018-01-03

    Quantitative assessment of modeling and forecasting of continuous quantities uses a variety of approaches. We review existing literature describing metrics for forecast accuracy and bias, concentrating on those based on relative errors and percentage errors. Of these accuracy metrics, the mean absolute percentage error (MAPE) is one of the most common across many fields and has been widely applied in recent space science literature and we highlight the benefits and drawbacks of MAPE and proposed alternatives. We then introduce the log accuracy ratio, and derive from it two metrics: the median symmetric accuracy; and the symmetric signed percentage bias. Robustmore » methods for estimating the spread of a multiplicative linear model using the log accuracy ratio are also presented. The developed metrics are shown to be easy to interpret, robust, and to mitigate the key drawbacks of their more widely-used counterparts based on relative errors and percentage errors. Their use is illustrated with radiation belt electron flux modeling examples.« less

  10. Accuracy Assessment of Coastal Topography Derived from Uav Images

    NASA Astrophysics Data System (ADS)

    Long, N.; Millescamps, B.; Pouget, F.; Dumon, A.; Lachaussée, N.; Bertin, X.

    2016-06-01

    To monitor coastal environments, Unmanned Aerial Vehicle (UAV) is a low-cost and easy to use solution to enable data acquisition with high temporal frequency and spatial resolution. Compared to Light Detection And Ranging (LiDAR) or Terrestrial Laser Scanning (TLS), this solution produces Digital Surface Model (DSM) with a similar accuracy. To evaluate the DSM accuracy on a coastal environment, a campaign was carried out with a flying wing (eBee) combined with a digital camera. Using the Photoscan software and the photogrammetry process (Structure From Motion algorithm), a DSM and an orthomosaic were produced. Compared to GNSS surveys, the DSM accuracy is estimated. Two parameters are tested: the influence of the methodology (number and distribution of Ground Control Points, GCPs) and the influence of spatial image resolution (4.6 cm vs 2 cm). The results show that this solution is able to reproduce the topography of a coastal area with a high vertical accuracy (< 10 cm). The georeferencing of the DSM require a homogeneous distribution and a large number of GCPs. The accuracy is correlated with the number of GCPs (use 19 GCPs instead of 10 allows to reduce the difference of 4 cm); the required accuracy should be dependant of the research problematic. Last, in this particular environment, the presence of very small water surfaces on the sand bank does not allow to improve the accuracy when the spatial resolution of images is decreased.

  11. An approach for quantitative image quality analysis for CT

    NASA Astrophysics Data System (ADS)

    Rahimi, Amir; Cochran, Joe; Mooney, Doug; Regensburger, Joe

    2016-03-01

    An objective and standardized approach to assess image quality of Compute Tomography (CT) systems is required in a wide variety of imaging processes to identify CT systems appropriate for a given application. We present an overview of the framework we have developed to help standardize and to objectively assess CT image quality for different models of CT scanners used for security applications. Within this framework, we have developed methods to quantitatively measure metrics that should correlate with feature identification, detection accuracy and precision, and image registration capabilities of CT machines and to identify strengths and weaknesses in different CT imaging technologies in transportation security. To that end we have designed, developed and constructed phantoms that allow for systematic and repeatable measurements of roughly 88 image quality metrics, representing modulation transfer function, noise equivalent quanta, noise power spectra, slice sensitivity profiles, streak artifacts, CT number uniformity, CT number consistency, object length accuracy, CT number path length consistency, and object registration. Furthermore, we have developed a sophisticated MATLAB based image analysis tool kit to analyze CT generated images of phantoms and report these metrics in a format that is standardized across the considered models of CT scanners, allowing for comparative image quality analysis within a CT model or between different CT models. In addition, we have developed a modified sparse principal component analysis (SPCA) method to generate a modified set of PCA components as compared to the standard principal component analysis (PCA) with sparse loadings in conjunction with Hotelling T2 statistical analysis method to compare, qualify, and detect faults in the tested systems.

  12. Monitoring of protease catalyzed reactions by quantitative MALDI MS using metal labeling.

    PubMed

    Gregorius, Barbara; Jakoby, Thomas; Schaumlöffel, Dirk; Tholey, Andreas

    2013-05-21

    Quantitative mass spectrometry is a powerful tool for the determination of enzyme activities as it does not require labeled substrates and simultaneously allows for the identification of reaction products. However, major restrictions are the limited number of samples which can be measured in parallel due to the need for isotope labeled internal standards. Here we describe the use of metal labeling of peptides for the setup of multiplexed enzyme activity assays. After proteolytic reaction, using the protease trypsin, remaining substrates and peptide products formed in the reaction were labeled with metal chelators complexing rare earth metal ions. Labeled peptides were quantified with high accuracy and over a wide dynamic range (at least 2 orders of magnitude) using MALDI MS in case of simple peptide mixtures or by LC-MALDI MS for complex substrate mixtures and used for the monitoring of time-dependent product formation and substrate consumption. Due to multiplexing capabilities and accuracy, the presented approach will be useful for the determination of enzyme activities with a wide range of biochemical and biotechnological applications.

  13. Analytical robustness of quantitative NIR chemical imaging for Islamic paper characterization

    NASA Astrophysics Data System (ADS)

    Mahgoub, Hend; Gilchrist, John R.; Fearn, Thomas; Strlič, Matija

    2017-07-01

    Recently, spectral imaging techniques such as Multispectral (MSI) and Hyperspectral Imaging (HSI) have gained importance in the field of heritage conservation. This paper explores the analytical robustness of quantitative chemical imaging for Islamic paper characterization by focusing on the effect of different measurement and processing parameters, i.e. acquisition conditions and calibration on the accuracy of the collected spectral data. This will provide a better understanding of the technique that can provide a measure of change in collections through imaging. For the quantitative model, special calibration target was devised using 105 samples from a well-characterized reference Islamic paper collection. Two material properties were of interest: starch sizing and cellulose degree of polymerization (DP). Multivariate data analysis methods were used to develop discrimination and regression models which were used as an evaluation methodology for the metrology of quantitative NIR chemical imaging. Spectral data were collected using a pushbroom HSI scanner (Gilden Photonics Ltd) in the 1000-2500 nm range with a spectral resolution of 6.3 nm using a mirror scanning setup and halogen illumination. Data were acquired at different measurement conditions and acquisition parameters. Preliminary results showed the potential of the evaluation methodology to show that measurement parameters such as the use of different lenses and different scanning backgrounds may not have a great influence on the quantitative results. Moreover, the evaluation methodology allowed for the selection of the best pre-treatment method to be applied to the data.

  14. Discovering the Quantity of Quality: Scoring "Regional Identity" for Quantitative Research

    ERIC Educational Resources Information Center

    Miller, Daniel A.

    2008-01-01

    The variationist paradigm in sociolinguistics is at a disadvantage when dealing with variables that are traditionally treated qualitatively, e.g., "identity". This study essays to level the accuracy and descriptive value of qualitative research in a quantitative setting by rendering such a variable quantitatively accessible. To this end,…

  15. A low-cost tracked C-arm (TC-arm) upgrade system for versatile quantitative intraoperative imaging.

    PubMed

    Amiri, Shahram; Wilson, David R; Masri, Bassam A; Anglin, Carolyn

    2014-07-01

    C-arm fluoroscopy is frequently used in clinical applications as a low-cost and mobile real-time qualitative assessment tool. C-arms, however, are not widely accepted for applications involving quantitative assessments, mainly due to the lack of reliable and low-cost position tracking methods, as well as adequate calibration and registration techniques. The solution suggested in this work is a tracked C-arm (TC-arm) which employs a low-cost sensor tracking module that can be retrofitted to any conventional C-arm for tracking the individual joints of the device. Registration and offline calibration methods were developed that allow accurate tracking of the gantry and determination of the exact intrinsic and extrinsic parameters of the imaging system for any acquired fluoroscopic image. The performance of the system was evaluated in comparison to an Optotrak[Formula: see text] motion tracking system and by a series of experiments on accurately built ball-bearing phantoms. Accuracies of the system were determined for 2D-3D registration, three-dimensional landmark localization, and for generating panoramic stitched views in simulated intraoperative applications. The system was able to track the center point of the gantry with an accuracy of [Formula: see text] mm or better. Accuracies of 2D-3D registrations were [Formula: see text] mm and [Formula: see text]. Three-dimensional landmark localization had an accuracy of [Formula: see text] of the length (or [Formula: see text] mm) on average, depending on whether the landmarks were located along, above, or across the table. The overall accuracies of the two-dimensional measurements conducted on stitched panoramic images of the femur and lumbar spine were 2.5 [Formula: see text] 2.0 % [Formula: see text] and [Formula: see text], respectively. The TC-arm system has the potential to achieve sophisticated quantitative fluoroscopy assessment capabilities using an existing C-arm imaging system. This technology may be useful to

  16. Quantitative Myocardial Perfusion Imaging Versus Visual Analysis in Diagnosing Myocardial Ischemia: A CE-MARC Substudy.

    PubMed

    Biglands, John D; Ibraheem, Montasir; Magee, Derek R; Radjenovic, Aleksandra; Plein, Sven; Greenwood, John P

    2018-05-01

    This study sought to compare the diagnostic accuracy of visual and quantitative analyses of myocardial perfusion cardiovascular magnetic resonance against a reference standard of quantitative coronary angiography. Visual analysis of perfusion cardiovascular magnetic resonance studies for assessing myocardial perfusion has been shown to have high diagnostic accuracy for coronary artery disease. However, only a few small studies have assessed the diagnostic accuracy of quantitative myocardial perfusion. This retrospective study included 128 patients randomly selected from the CE-MARC (Clinical Evaluation of Magnetic Resonance Imaging in Coronary Heart Disease) study population such that the distribution of risk factors and disease status was proportionate to the full population. Visual analysis results of cardiovascular magnetic resonance perfusion images, by consensus of 2 expert readers, were taken from the original study reports. Quantitative myocardial blood flow estimates were obtained using Fermi-constrained deconvolution. The reference standard for myocardial ischemia was a quantitative coronary x-ray angiogram stenosis severity of ≥70% diameter in any coronary artery of >2 mm diameter, or ≥50% in the left main stem. Diagnostic performance was calculated using receiver-operating characteristic curve analysis. The area under the curve for visual analysis was 0.88 (95% confidence interval: 0.81 to 0.95) with a sensitivity of 81.0% (95% confidence interval: 69.1% to 92.8%) and specificity of 86.0% (95% confidence interval: 78.7% to 93.4%). For quantitative stress myocardial blood flow the area under the curve was 0.89 (95% confidence interval: 0.83 to 0.96) with a sensitivity of 87.5% (95% confidence interval: 77.3% to 97.7%) and specificity of 84.5% (95% confidence interval: 76.8% to 92.3%). There was no statistically significant difference between the diagnostic performance of quantitative and visual analyses (p = 0.72). Incorporating rest myocardial

  17. Temporal Lobe Epilepsy: Quantitative MR Volumetry in Detection of Hippocampal Atrophy

    PubMed Central

    Farid, Nikdokht; Girard, Holly M.; Kemmotsu, Nobuko; Smith, Michael E.; Magda, Sebastian W.; Lim, Wei Y.; Lee, Roland R.

    2012-01-01

    Purpose: To determine the ability of fully automated volumetric magnetic resonance (MR) imaging to depict hippocampal atrophy (HA) and to help correctly lateralize the seizure focus in patients with temporal lobe epilepsy (TLE). Materials and Methods: This study was conducted with institutional review board approval and in compliance with HIPAA regulations. Volumetric MR imaging data were analyzed for 34 patients with TLE and 116 control subjects. Structural volumes were calculated by using U.S. Food and Drug Administration–cleared software for automated quantitative MR imaging analysis (NeuroQuant). Results of quantitative MR imaging were compared with visual detection of atrophy, and, when available, with histologic specimens. Receiver operating characteristic analyses were performed to determine the optimal sensitivity and specificity of quantitative MR imaging for detecting HA and asymmetry. A linear classifier with cross validation was used to estimate the ability of quantitative MR imaging to help lateralize the seizure focus. Results: Quantitative MR imaging–derived hippocampal asymmetries discriminated patients with TLE from control subjects with high sensitivity (86.7%–89.5%) and specificity (92.2%–94.1%). When a linear classifier was used to discriminate left versus right TLE, hippocampal asymmetry achieved 94% classification accuracy. Volumetric asymmetries of other subcortical structures did not improve classification. Compared with invasive video electroencephalographic recordings, lateralization accuracy was 88% with quantitative MR imaging and 85% with visual inspection of volumetric MR imaging studies but only 76% with visual inspection of clinical MR imaging studies. Conclusion: Quantitative MR imaging can depict the presence and laterality of HA in TLE with accuracy rates that may exceed those achieved with visual inspection of clinical MR imaging studies. Thus, quantitative MR imaging may enhance standard visual analysis, providing a

  18. Preliminary research on eddy current bobbin quantitative test for heat exchange tube in nuclear power plant

    NASA Astrophysics Data System (ADS)

    Qi, Pan; Shao, Wenbin; Liao, Shusheng

    2016-02-01

    For quantitative defects detection research on heat transfer tube in nuclear power plants (NPP), two parts of work are carried out based on the crack as the main research objects. (1) Production optimization of calibration tube. Firstly, ASME, RSEM and homemade crack calibration tubes are applied to quantitatively analyze the defects depth on other designed crack test tubes, and then the judgment with quantitative results under crack calibration tube with more accuracy is given. Base on that, weight analysis of influence factors for crack depth quantitative test such as crack orientation, length, volume and so on can be undertaken, which will optimize manufacture technology of calibration tubes. (2) Quantitative optimization of crack depth. Neural network model with multi-calibration curve adopted to optimize natural crack test depth generated in in-service tubes shows preliminary ability to improve quantitative accuracy.

  19. Flow cytometric immunobead assay for quantitative detection of platelet autoantibodies in immune thrombocytopenia patients.

    PubMed

    Zhai, Juping; Ding, Mengyuan; Yang, Tianjie; Zuo, Bin; Weng, Zhen; Zhao, Yunxiao; He, Jun; Wu, Qingyu; Ruan, Changgeng; He, Yang

    2017-10-23

    Platelet autoantibody detection is critical for immune thrombocytopenia (ITP) diagnosis and prognosis. Therefore, we aimed to establish a quantitative flow cytometric immunobead assay (FCIA) for ITP platelet autoantibodies evaluation. Capture microbeads coupled with anti-GPIX, -GPIb, -GPIIb, -GPIIIa and P-selectin antibodies were used to bind the platelet-bound autoantibodies complex generated from plasma samples of 250 ITP patients, 163 non-ITP patients and 243 healthy controls, a fluorescein isothiocyanate (FITC)-conjugated secondary antibody was the detector reagent and mean fluorescence intensity (MFI) signals were recorded by flow cytometry. Intra- and inter-assay variations of the quantitative FCIA assay were assessed. Comparisons of the specificity, sensitivity and accuracy between quantitative and qualitative FCIA or monoclonal antibody immobilization of platelet antigen (MAIPA) assay were performed. Finally, treatment process was monitored by our quantitative FCIA in 8 newly diagnosed ITPs. The coefficient of variations (CV) of the quantitative FCIA assay were respectively 9.4, 3.8, 5.4, 5.1 and 5.8% for anti-GPIX, -GPIb, -GPIIIa, -GPIIb and -P-selectin autoantibodies. Elevated levels of autoantibodies against platelet glycoproteins GPIX, GPIb, GPIIIa, GPIIb and P-selectin were detected by our quantitative FCIA in ITP patients compared to non-ITP patients or healthy controls. The sensitivity, specificity and accuracy of our quantitative assay were respectively 73.13, 81.98 and 78.65% when combining all 5 autoantibodies, while the sensitivity, specificity and accuracy of MAIPA assay were respectively 41.46, 90.41 and 72.81%. A quantitative FCIA assay was established. Reduced levels of platelet autoantibodies could be confirmed by our quantitative FCIA in ITP patients after corticosteroid treatment. Our quantitative assay is not only good for ITP diagnosis but also for ITP treatment monitoring.

  20. Diagnostic accuracy of semi-quantitative and quantitative culture techniques for the diagnosis of catheter-related infections in newborns and molecular typing of isolated microorganisms.

    PubMed

    Riboli, Danilo Flávio Moraes; Lyra, João César; Silva, Eliane Pessoa; Valadão, Luisa Leite; Bentlin, Maria Regina; Corrente, José Eduardo; Rugolo, Ligia Maria Suppo de Souza; da Cunha, Maria de Lourdes Ribeiro de Souza

    2014-05-22

    Catheter-related bloodstream infections (CR-BSIs) have become the most common cause of healthcare-associated bloodstream infections in neonatal intensive care units (ICUs). Microbiological evidence implicating catheters as the source of bloodstream infection is necessary to establish the diagnosis of CR-BSIs. Semi-quantitative culture is used to determine the presence of microorganisms on the external catheter surface, whereas quantitative culture also isolates microorganisms present inside the catheter. The main objective of this study was to determine the sensitivity and specificity of these two techniques for the diagnosis of CR-BSIs in newborns from a neonatal ICU. In addition, PFGE was used for similarity analysis of the microorganisms isolated from catheters and blood cultures. Semi-quantitative and quantitative methods were used for the culture of catheter tips obtained from newborns. Strains isolated from catheter tips and blood cultures which exhibited the same antimicrobial susceptibility profile were included in the study as positive cases of CR-BSI. PFGE of the microorganisms isolated from catheters and blood cultures was performed for similarity analysis and detection of clones in the ICU. A total of 584 catheter tips from 399 patients seen between November 2005 and June 2012 were analyzed. Twenty-nine cases of CR-BSI were confirmed. Coagulase-negative staphylococci (CoNS) were the most frequently isolated microorganisms, including S. epidermidis as the most prevalent species (65.5%), followed by S. haemolyticus (10.3%), yeasts (10.3%), K. pneumoniae (6.9%), S. aureus (3.4%), and E. coli (3.4%). The sensitivity of the semi-quantitative and quantitative techniques was 72.7% and 59.3%, respectively, and specificity was 95.7% and 94.4%. The diagnosis of CR-BSIs based on PFGE analysis of similarity between strains isolated from catheter tips and blood cultures showed 82.6% sensitivity and 100% specificity. The semi-quantitative culture method showed higher

  1. Accuracy of nursing diagnoses for identifying domestic violence against children.

    PubMed

    Apostólico, Maíra Rosa; Egry, Emiko Yoshikawa; Fornari, Lucimara Fabiana; Gessner, Rafaela

    2017-01-01

    Objective Identify nursing diagnoses involving a hypothetical situation of domestic violence against a child and the respective degrees of accuracy. Method An exploratory, evaluative, case study was conducted using a quantitative and qualitative approach, with data collected using an online instrument from 26 nurses working in the Municipal Health Network, between June and August 2010, in Curitiba, and also during the first half of 2014 in São Paulo. Both of these cities are in Brazil. Nursing diagnoses and interventions from the International Classification of Nursing Practices in Collective Health were provided, and accuracy was verified using the Nursing Diagnosis Accuracy Scale. Results Thirty-nine nursing diagnoses were identified, 27 of which were common to both cities. Of these, 15 were scored at the null level of accuracy, 11 at high accuracy and 1 at medium accuracy. Conclusion The difficulty the nurses had in defining diagnoses may be associated with the fact that nursing care generally focuses on clinical problems, and signs expressing situations of domestic violence against children go unnoticed. The results demonstrated the difficulty of participants in selecting the appropriate nursing diagnosis for the case in question.

  2. Quantitative evaluation of hidden defects in cast iron components using ultrasound activated lock-in vibrothermography.

    PubMed

    Montanini, R; Freni, F; Rossi, G L

    2012-09-01

    This paper reports one of the first experimental results on the application of ultrasound activated lock-in vibrothermography for quantitative assessment of buried flaws in complex cast parts. The use of amplitude modulated ultrasonic heat generation allowed selective response of defective areas within the part, as the defect itself is turned into a local thermal wave emitter. Quantitative evaluation of hidden damages was accomplished by estimating independently both the area and the depth extension of the buried flaws, while x-ray 3D computed tomography was used as reference for sizing accuracy assessment. To retrieve flaw's area, a simple yet effective histogram-based phase image segmentation algorithm with automatic pixels classification has been developed. A clear correlation was found between the thermal (phase) signature measured by the infrared camera on the target surface and the actual mean cross-section area of the flaw. Due to the very fast cycle time (<30 s/part), the method could potentially be applied for 100% quality control of casting components.

  3. Quantitative Measurement of Local Infrared Absorption and Dielectric Function with Tip-Enhanced Near-Field Microscopy.

    PubMed

    Govyadinov, Alexander A; Amenabar, Iban; Huth, Florian; Carney, P Scott; Hillenbrand, Rainer

    2013-05-02

    Scattering-type scanning near-field optical microscopy (s-SNOM) and Fourier transform infrared nanospectroscopy (nano-FTIR) are emerging tools for nanoscale chemical material identification. Here, we push s-SNOM and nano-FTIR one important step further by enabling them to quantitatively measure local dielectric constants and infrared absorption. Our technique is based on an analytical model, which allows for a simple inversion of the near-field scattering problem. It yields the dielectric permittivity and absorption of samples with 2 orders of magnitude improved spatial resolution compared to far-field measurements and is applicable to a large class of samples including polymers and biological matter. We verify the capabilities by determining the local dielectric permittivity of a PMMA film from nano-FTIR measurements, which is in excellent agreement with far-field ellipsometric data. We further obtain local infrared absorption spectra with unprecedented accuracy in peak position and shape, which is the key to quantitative chemometrics on the nanometer scale.

  4. Quantitative accuracy of the simplified strong ion equation to predict serum pH in dogs.

    PubMed

    Cave, N J; Koo, S T

    2015-01-01

    Electrochemical approach to the assessment of acid-base states should provide a better mechanistic explanation of the metabolic component than methods that consider only pH and carbon dioxide. Simplified strong ion equation (SSIE), using published dog-specific values, would predict the measured serum pH of diseased dogs. Ten dogs, hospitalized for various reasons. Prospective study of a convenience sample of a consecutive series of dogs admitted to the Massey University Veterinary Teaching Hospital (MUVTH), from which serum biochemistry and blood gas analyses were performed at the same time. Serum pH was calculated (Hcal+) using the SSIE, and published values for the concentration and dissociation constant for the nonvolatile weak acids (Atot and Ka ), and subsequently Hcal+ was compared with the dog's actual pH (Hmeasured+). To determine the source of discordance between Hcal+ and Hmeasured+, the calculations were repeated using a series of substituted values for Atot and Ka . The Hcal+ did not approximate the Hmeasured+ for any dog (P = 0.499, r(2) = 0.068), and was consistently more basic. Substituted values Atot and Ka did not significantly improve the accuracy (r(2) = 0.169 to <0.001). Substituting the effective SID (Atot-[HCO3-]) produced a strong association between Hcal+ and Hmeasured+ (r(2) = 0.977). Using the simplified strong ion equation and the published values for Atot and Ka does not appear to provide a quantitative explanation for the acid-base status of dogs. Efficacy of substituting the effective SID in the simplified strong ion equation suggests the error lies in calculating the SID. Copyright © 2015 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

  5. Analytic Guided-Search Model of Human Performance Accuracy in Target- Localization Search Tasks

    NASA Technical Reports Server (NTRS)

    Eckstein, Miguel P.; Beutter, Brent R.; Stone, Leland S.

    2000-01-01

    Current models of human visual search have extended the traditional serial/parallel search dichotomy. Two successful models for predicting human visual search are the Guided Search model and the Signal Detection Theory model. Although these models are inherently different, it has been difficult to compare them because the Guided Search model is designed to predict response time, while Signal Detection Theory models are designed to predict performance accuracy. Moreover, current implementations of the Guided Search model require the use of Monte-Carlo simulations, a method that makes fitting the model's performance quantitatively to human data more computationally time consuming. We have extended the Guided Search model to predict human accuracy in target-localization search tasks. We have also developed analytic expressions that simplify simulation of the model to the evaluation of a small set of equations using only three free parameters. This new implementation and extension of the Guided Search model will enable direct quantitative comparisons with human performance in target-localization search experiments and with the predictions of Signal Detection Theory and other search accuracy models.

  6. Regulation of Memory Accuracy with Multiple Answers: The Plurality Option

    ERIC Educational Resources Information Center

    Luna, Karlos; Higham, Philip A.; Martin-Luengo, Beatriz

    2011-01-01

    We report two experiments that investigated the regulation of memory accuracy with a new regulatory mechanism: the plurality option. This mechanism is closely related to the grain-size option but involves control over the number of alternatives contained in an answer rather than the quantitative boundaries of a single answer. Participants were…

  7. Sensitivity, accuracy, and precision issues in opto-electronic holography based on fiber optics and high-spatial- and high-digitial-resolution cameras

    NASA Astrophysics Data System (ADS)

    Furlong, Cosme; Yokum, Jeffrey S.; Pryputniewicz, Ryszard J.

    2002-06-01

    Sensitivity, accuracy, and precision characteristics in quantitative optical metrology techniques, and specifically in optoelectronic holography based on fiber optics and high-spatial and high-digital resolution cameras, are discussed in this paper. It is shown that sensitivity, accuracy, and precision dependent on both, the effective determination of optical phase and the effective characterization of the illumination-observation conditions. Sensitivity, accuracy, and precision are investigated with the aid of National Institute of Standards and Technology (NIST) traceable gages, demonstrating the applicability of quantitative optical metrology techniques to satisfy constantly increasing needs for the study and development of emerging technologies.

  8. Quantitative comparison of OSEM and penalized likelihood image reconstruction using relative difference penalties for clinical PET

    NASA Astrophysics Data System (ADS)

    Ahn, Sangtae; Ross, Steven G.; Asma, Evren; Miao, Jun; Jin, Xiao; Cheng, Lishui; Wollenweber, Scott D.; Manjeshwar, Ravindra M.

    2015-08-01

    Ordered subset expectation maximization (OSEM) is the most widely used algorithm for clinical PET image reconstruction. OSEM is usually stopped early and post-filtered to control image noise and does not necessarily achieve optimal quantitation accuracy. As an alternative to OSEM, we have recently implemented a penalized likelihood (PL) image reconstruction algorithm for clinical PET using the relative difference penalty with the aim of improving quantitation accuracy without compromising visual image quality. Preliminary clinical studies have demonstrated visual image quality including lesion conspicuity in images reconstructed by the PL algorithm is better than or at least as good as that in OSEM images. In this paper we evaluate lesion quantitation accuracy of the PL algorithm with the relative difference penalty compared to OSEM by using various data sets including phantom data acquired with an anthropomorphic torso phantom, an extended oval phantom and the NEMA image quality phantom; clinical data; and hybrid clinical data generated by adding simulated lesion data to clinical data. We focus on mean standardized uptake values and compare them for PL and OSEM using both time-of-flight (TOF) and non-TOF data. The results demonstrate improvements of PL in lesion quantitation accuracy compared to OSEM with a particular improvement in cold background regions such as lungs.

  9. Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

    PubMed Central

    Edwards, Stefan M.; Sørensen, Izel F.; Sarup, Pernille; Mackay, Trudy F. C.; Sørensen, Peter

    2016-01-01

    Predicting individual quantitative trait phenotypes from high-resolution genomic polymorphism data is important for personalized medicine in humans, plant and animal breeding, and adaptive evolution. However, this is difficult for populations of unrelated individuals when the number of causal variants is low relative to the total number of polymorphisms and causal variants individually have small effects on the traits. We hypothesized that mapping molecular polymorphisms to genomic features such as genes and their gene ontology categories could increase the accuracy of genomic prediction models. We developed a genomic feature best linear unbiased prediction (GFBLUP) model that implements this strategy and applied it to three quantitative traits (startle response, starvation resistance, and chill coma recovery) in the unrelated, sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel. Our results indicate that subsetting markers based on genomic features increases the predictive ability relative to the standard genomic best linear unbiased prediction (GBLUP) model. Both models use all markers, but GFBLUP allows differential weighting of the individual genetic marker relationships, whereas GBLUP weighs the genetic marker relationships equally. Simulation studies show that it is possible to further increase the accuracy of genomic prediction for complex traits using this model, provided the genomic features are enriched for causal variants. Our GFBLUP model using prior information on genomic features enriched for causal variants can increase the accuracy of genomic predictions in populations of unrelated individuals and provides a formal statistical framework for leveraging and evaluating information across multiple experimental studies to provide novel insights into the genetic architecture of complex traits. PMID:27235308

  10. Monte Carlo evaluation of accuracy and noise properties of two scatter correction methods for /sup 201/Tl cardiac SPECT

    NASA Astrophysics Data System (ADS)

    Narita, Y.; Iida, H.; Ebert, S.; Nakamura, T.

    1997-12-01

    Two independent scatter correction techniques, transmission dependent convolution subtraction (TDCS) and triple-energy window (TEW) method, were evaluated in terms of quantitative accuracy and noise properties using Monte Carlo simulation (EGS4). Emission projections (primary, scatter and scatter plus primary) were simulated for three numerical phantoms for /sup 201/Tl. Data were reconstructed with ordered-subset EM algorithm including noise-less transmission data based attenuation correction. Accuracy of TDCS and TEW scatter corrections were assessed by comparison with simulated true primary data. The uniform cylindrical phantom simulation demonstrated better quantitative accuracy with TDCS than with TEW (-2.0% vs. 16.7%) and better S/N (6.48 vs. 5.05). A uniform ring myocardial phantom simulation demonstrated better homogeneity with TDCS than TEW in the myocardium; i.e., anterior-to-posterior wall count ratios were 0.99 and 0.76 with TDCS and TEW, respectively. For the MCAT phantom, TDCS provided good visual and quantitative agreement with simulated true primary image without noticeably increasing the noise after scatter correction. Overall TDCS proved to be more accurate and less noisy than TEW, facilitating quantitative assessment of physiological functions with SPECT.

  11. Quantitative Large-Scale Three-Dimensional Imaging of Human Kidney Biopsies: A Bridge to Precision Medicine in Kidney Disease.

    PubMed

    Winfree, Seth; Dagher, Pierre C; Dunn, Kenneth W; Eadon, Michael T; Ferkowicz, Michael; Barwinska, Daria; Kelly, Katherine J; Sutton, Timothy A; El-Achkar, Tarek M

    2018-06-05

    Kidney biopsy remains the gold standard for uncovering the pathogenesis of acute and chronic kidney diseases. However, the ability to perform high resolution, quantitative, molecular and cellular interrogation of this precious tissue is still at a developing stage compared to other fields such as oncology. Here, we discuss recent advances in performing large-scale, three-dimensional (3D), multi-fluorescence imaging of kidney biopsies and quantitative analysis referred to as 3D tissue cytometry. This approach allows the accurate measurement of specific cell types and their spatial distribution in a thick section spanning the entire length of the biopsy. By uncovering specific disease signatures, including rare occurrences, and linking them to the biology in situ, this approach will enhance our understanding of disease pathogenesis. Furthermore, by providing accurate quantitation of cellular events, 3D cytometry may improve the accuracy of prognosticating the clinical course and response to therapy. Therefore, large-scale 3D imaging and cytometry of kidney biopsy is poised to become a bridge towards personalized medicine for patients with kidney disease. © 2018 S. Karger AG, Basel.

  12. Four-hour quantitative real-time polymerase chain reaction-based comprehensive chromosome screening and accumulating evidence of accuracy, safety, predictive value, and clinical efficacy.

    PubMed

    Treff, Nathan R; Scott, Richard T

    2013-03-15

    Embryonic comprehensive chromosomal euploidy may represent a powerful biomarker to improve the success of IVF. However, there are a number of aneuploidy screening strategies to consider, including different technologic platforms with which to interrogate the embryonic DNA, and different embryonic developmental stages from which DNA can be analyzed. Although there are advantages and disadvantages associated with each strategy, a series of experiments producing evidence of accuracy, safety, clinical predictive value, and clinical efficacy indicate that trophectoderm biopsy and quantitative real-time polymerase chain reaction (qPCR)-based comprehensive chromosome screening (CCS) may represent a useful strategy to improve the success of IVF. This Biomarkers in Reproductive Medicine special issue review summarizes the accumulated experience with the development and clinical application of a 4-hour blastocyst qPCR-based CCS technology. Copyright © 2013 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  13. Quantitative comparison of the application accuracy between NDI and IGT tracking systems

    NASA Astrophysics Data System (ADS)

    Li, Qinghang; Zamorano, Lucia J.; Jiang, Charlie Z. W.; Gong, JianXing; Diaz, Fernando

    1999-07-01

    The application accuracy is a crucial factor for the stereotactic surgical localization system in which space digitization system is one of the most important part of equipment. In this study we compared the application accuracy of using the OPTOTRAK space digitization system (OPTOTRAK 3020, Northern Digital, Waterloo, CAN) and FlashPoint Model 3000 and 5000 3-D digitizer systems (FlashPoint Model 3000 and 5000, Image Guided Surgery Technology Inc., Boulder, CO 80301, USA) for interactive localization of intracranial lesions. A phantom was mounted with the implantable frameless marker system (Fischer- Leibinger, Freiburg, Germany) which randomly distributed markers on the surface of the phantom. The target point was digitized and the coordinates were recorded and compared with reference points. The differences from the reference points were used as the deviation from the `true point'. The mean square root was calculated to show the sum of vectors. A paired t-test was used to analyze results. The results of the phantom showed that the mean square roots were 0.76 +/- 0.54 mm for the OPTOTRAK system and 1.23 +/- 0.53 mm for FlashPoint Model 3000 3-D digitizer system and 1.00 +/- 0.42 mm for FlashPoint Model 3000 3-D digitizer system in the 1 mm sections of CT scan. This preliminary results showed that there is no significant difference between two tracking systems. Both of them can be used for image guided surgery procedure.

  14. Rational calculation accuracy in acousto-optical matrix-vector processor

    NASA Astrophysics Data System (ADS)

    Oparin, V. V.; Tigin, Dmitry V.

    1994-01-01

    The high speed of parallel computations for a comparatively small-size processor and acceptable power consumption makes the usage of acousto-optic matrix-vector multiplier (AOMVM) attractive for processing of large amounts of information in real time. The limited accuracy of computations is an essential disadvantage of such a processor. The reduced accuracy requirements allow for considerable simplification of the AOMVM architecture and the reduction of the demands on its components.

  15. Oufti: An integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

    PubMed Central

    Paintdakhi, Ahmad; Parry, Bradley; Campos, Manuel; Irnov, Irnov; Elf, Johan; Surovtsev, Ivan; Jacobs-Wagner, Christine

    2016-01-01

    Summary With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re-emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today’s single-cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand-alone, open-source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non-diffraction-limited fluorescence signals, and is scalable for high-throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis, and post-processing analysis, makes the software broadly accessible to users irrespective of their computational skills. PMID:26538279

  16. High accuracy electronic material level sensor

    DOEpatents

    McEwan, T.E.

    1997-03-11

    The High Accuracy Electronic Material Level Sensor (electronic dipstick) is a sensor based on time domain reflectometry (TDR) of very short electrical pulses. Pulses are propagated along a transmission line or guide wire that is partially immersed in the material being measured; a launcher plate is positioned at the beginning of the guide wire. Reflected pulses are produced at the material interface due to the change in dielectric constant. The time difference of the reflections at the launcher plate and at the material interface are used to determine the material level. Improved performance is obtained by the incorporation of: (1) a high accuracy time base that is referenced to a quartz crystal, (2) an ultrawideband directional sampler to allow operation without an interconnect cable between the electronics module and the guide wire, (3) constant fraction discriminators (CFDs) that allow accurate measurements regardless of material dielectric constants, and reduce or eliminate errors induced by triple-transit or ``ghost`` reflections on the interconnect cable. These improvements make the dipstick accurate to better than 0.1%. 4 figs.

  17. High accuracy electronic material level sensor

    DOEpatents

    McEwan, Thomas E.

    1997-01-01

    The High Accuracy Electronic Material Level Sensor (electronic dipstick) is a sensor based on time domain reflectometry (TDR) of very short electrical pulses. Pulses are propagated along a transmission line or guide wire that is partially immersed in the material being measured; a launcher plate is positioned at the beginning of the guide wire. Reflected pulses are produced at the material interface due to the change in dielectric constant. The time difference of the reflections at the launcher plate and at the material interface are used to determine the material level. Improved performance is obtained by the incorporation of: 1) a high accuracy time base that is referenced to a quartz crystal, 2) an ultrawideband directional sampler to allow operation without an interconnect cable between the electronics module and the guide wire, 3) constant fraction discriminators (CFDs) that allow accurate measurements regardless of material dielectric constants, and reduce or eliminate errors induced by triple-transit or "ghost" reflections on the interconnect cable. These improvements make the dipstick accurate to better than 0.1%.

  18. Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions.

    PubMed

    Doshi, Urmi; Hamelberg, Donald

    2012-11-13

    In enhanced sampling techniques, the precision of the reweighted ensemble properties is often decreased due to large variation in statistical weights and reduction in the effective sampling size. To abate this reweighting problem, here, we propose a general accelerated molecular dynamics (aMD) approach in which only the rotatable dihedrals are subjected to aMD (RaMD), unlike the typical implementation wherein all dihedrals are boosted (all-aMD). Nonrotatable and improper dihedrals are marginally important to conformational changes or the different rotameric states. Not accelerating them avoids the sharp increases in the potential energies due to small deviations from their minimum energy conformations and leads to improvement in the precision of RaMD. We present benchmark studies on two model dipeptides, Ace-Ala-Nme and Ace-Trp-Nme, simulated with normal MD, all-aMD, and RaMD. We carry out a systematic comparison between the performances of both forms of aMD using a theory that allows quantitative estimation of the effective number of sampled points and the associated uncertainty. Our results indicate that, for the same level of acceleration and simulation length, as used in all-aMD, RaMD results in significantly less loss in the effective sample size and, hence, increased accuracy in the sampling of φ-ψ space. RaMD yields an accuracy comparable to that of all-aMD, from simulation lengths 5 to 1000 times shorter, depending on the peptide and the acceleration level. Such improvement in speed and accuracy over all-aMD is highly remarkable, suggesting RaMD as a promising method for sampling larger biomolecules.

  19. Quantitative data standardization of X-ray based densitometry methods

    NASA Astrophysics Data System (ADS)

    Sergunova, K. A.; Petraikin, A. V.; Petrjajkin, F. A.; Akhmad, K. S.; Semenov, D. S.; Potrakhov, N. N.

    2018-02-01

    In the present work is proposed the design of special liquid phantom for assessing the accuracy of quantitative densitometric data. Also are represented the dependencies between the measured bone mineral density values and the given values for different X-ray based densitometry techniques. Shown linear graphs make it possible to introduce correction factors to increase the accuracy of BMD measurement by QCT, DXA and DECT methods, and to use them for standardization and comparison of measurements.

  20. Spinal intra-operative three-dimensional navigation with infra-red tool tracking: correlation between clinical and absolute engineering accuracy

    NASA Astrophysics Data System (ADS)

    Guha, Daipayan; Jakubovic, Raphael; Gupta, Shaurya; Yang, Victor X. D.

    2017-02-01

    Computer-assisted navigation (CAN) may guide spinal surgeries, reliably reducing screw breach rates. Definitions of screw breach, if reported, vary widely across studies. Absolute quantitative error is theoretically a more precise and generalizable metric of navigation accuracy, but has been computed variably and reported in fewer than 25% of clinical studies of CAN-guided pedicle screw accuracy. We reviewed a prospectively-collected series of 209 pedicle screws placed with CAN guidance to characterize the correlation between clinical pedicle screw accuracy, based on postoperative imaging, and absolute quantitative navigation accuracy. We found that acceptable screw accuracy was achieved for significantly fewer screws based on 2mm grade vs. Heary grade, particularly in the lumbar spine. Inter-rater agreement was good for the Heary classification and moderate for the 2mm grade, significantly greater among radiologists than surgeon raters. Mean absolute translational/angular accuracies were 1.75mm/3.13° and 1.20mm/3.64° in the axial and sagittal planes, respectively. There was no correlation between clinical and absolute navigation accuracy, in part because surgeons appear to compensate for perceived translational navigation error by adjusting screw medialization angle. Future studies of navigation accuracy should therefore report absolute translational and angular errors. Clinical screw grades based on post-operative imaging, if reported, may be more reliable if performed in multiple by radiologist raters.

  1. The Accuracy and Precision of Flow Measurements Using Phase Contrast Techniques

    NASA Astrophysics Data System (ADS)

    Tang, Chao

    Quantitative volume flow rate measurements using the magnetic resonance imaging technique are studied in this dissertation because the volume flow rates have a special interest in the blood supply of the human body. The method of quantitative volume flow rate measurements is based on the phase contrast technique, which assumes a linear relationship between the phase and flow velocity of spins. By measuring the phase shift of nuclear spins and integrating velocity across the lumen of the vessel, we can determine the volume flow rate. The accuracy and precision of volume flow rate measurements obtained using the phase contrast technique are studied by computer simulations and experiments. The various factors studied include (1) the partial volume effect due to voxel dimensions and slice thickness relative to the vessel dimensions; (2) vessel angulation relative to the imaging plane; (3) intravoxel phase dispersion; (4) flow velocity relative to the magnitude of the flow encoding gradient. The partial volume effect is demonstrated to be the major obstacle to obtaining accurate flow measurements for both laminar and plug flow. Laminar flow can be measured more accurately than plug flow in the same condition. Both the experiment and simulation results for laminar flow show that, to obtain the accuracy of volume flow rate measurements to within 10%, at least 16 voxels are needed to cover the vessel lumen. The accuracy of flow measurements depends strongly on the relative intensity of signal from stationary tissues. A correction method is proposed to compensate for the partial volume effect. The correction method is based on a small phase shift approximation. After the correction, the errors due to the partial volume effect are compensated, allowing more accurate results to be obtained. An automatic program based on the correction method is developed and implemented on a Sun workstation. The correction method is applied to the simulation and experiment results. The

  2. Surrogate matrix and surrogate analyte approaches for definitive quantitation of endogenous biomolecules.

    PubMed

    Jones, Barry R; Schultz, Gary A; Eckstein, James A; Ackermann, Bradley L

    2012-10-01

    Quantitation of biomarkers by LC-MS/MS is complicated by the presence of endogenous analytes. This challenge is most commonly overcome by calibration using an authentic standard spiked into a surrogate matrix devoid of the target analyte. A second approach involves use of a stable-isotope-labeled standard as a surrogate analyte to allow calibration in the actual biological matrix. For both methods, parallelism between calibration standards and the target analyte in biological matrix must be demonstrated in order to ensure accurate quantitation. In this communication, the surrogate matrix and surrogate analyte approaches are compared for the analysis of five amino acids in human plasma: alanine, valine, methionine, leucine and isoleucine. In addition, methodology based on standard addition is introduced, which enables a robust examination of parallelism in both surrogate analyte and surrogate matrix methods prior to formal validation. Results from additional assays are presented to introduce the standard-addition methodology and to highlight the strengths and weaknesses of each approach. For the analysis of amino acids in human plasma, comparable precision and accuracy were obtained by the surrogate matrix and surrogate analyte methods. Both assays were well within tolerances prescribed by regulatory guidance for validation of xenobiotic assays. When stable-isotope-labeled standards are readily available, the surrogate analyte approach allows for facile method development. By comparison, the surrogate matrix method requires greater up-front method development; however, this deficit is offset by the long-term advantage of simplified sample analysis.

  3. An evaluation of information retrieval accuracy with simulated OCR output

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Croft, W.B.; Harding, S.M.; Taghva, K.

    Optical Character Recognition (OCR) is a critical part of many text-based applications. Although some commercial systems use the output from OCR devices to index documents without editing, there is very little quantitative data on the impact of OCR errors on the accuracy of a text retrieval system. Because of the difficulty of constructing test collections to obtain this data, we have carried out evaluation using simulated OCR output on a variety of databases. The results show that high quality OCR devices have little effect on the accuracy of retrieval, but low quality devices used with databases of short documents canmore » result in significant degradation.« less

  4. Objective breast tissue image classification using Quantitative Transmission ultrasound tomography

    NASA Astrophysics Data System (ADS)

    Malik, Bilal; Klock, John; Wiskin, James; Lenox, Mark

    2016-12-01

    Quantitative Transmission Ultrasound (QT) is a powerful and emerging imaging paradigm which has the potential to perform true three-dimensional image reconstruction of biological tissue. Breast imaging is an important application of QT and allows non-invasive, non-ionizing imaging of whole breasts in vivo. Here, we report the first demonstration of breast tissue image classification in QT imaging. We systematically assess the ability of the QT images’ features to differentiate between normal breast tissue types. The three QT features were used in Support Vector Machines (SVM) classifiers, and classification of breast tissue as either skin, fat, glands, ducts or connective tissue was demonstrated with an overall accuracy of greater than 90%. Finally, the classifier was validated on whole breast image volumes to provide a color-coded breast tissue volume. This study serves as a first step towards a computer-aided detection/diagnosis platform for QT.

  5. Wavelength Selection Method Based on Differential Evolution for Precise Quantitative Analysis Using Terahertz Time-Domain Spectroscopy.

    PubMed

    Li, Zhi; Chen, Weidong; Lian, Feiyu; Ge, Hongyi; Guan, Aihong

    2017-12-01

    Quantitative analysis of component mixtures is an important application of terahertz time-domain spectroscopy (THz-TDS) and has attracted broad interest in recent research. Although the accuracy of quantitative analysis using THz-TDS is affected by a host of factors, wavelength selection from the sample's THz absorption spectrum is the most crucial component. The raw spectrum consists of signals from the sample and scattering and other random disturbances that can critically influence the quantitative accuracy. For precise quantitative analysis using THz-TDS, the signal from the sample needs to be retained while the scattering and other noise sources are eliminated. In this paper, a novel wavelength selection method based on differential evolution (DE) is investigated. By performing quantitative experiments on a series of binary amino acid mixtures using THz-TDS, we demonstrate the efficacy of the DE-based wavelength selection method, which yields an error rate below 5%.

  6. Adaptive sensor-based ultra-high accuracy solar concentrator tracker

    NASA Astrophysics Data System (ADS)

    Brinkley, Jordyn; Hassanzadeh, Ali

    2017-09-01

    Conventional solar trackers use information of the sun's position, either by direct sensing or by GPS. Our method uses the shading of the receiver. This, coupled with nonimaging optics design allows us to achieve ultra-high concentration. Incorporating a sensor based shadow tracking method with a two stage concentration solar hybrid parabolic trough allows the system to maintain high concentration with acute accuracy.

  7. Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xie, Fang; Liu, Tao; Qian, Weijun

    2011-07-22

    Liquid chromatography-mass spectrometry (LC-MS)-based quantitative proteomics has become increasingly applied for a broad range of biological applications due to growing capabilities for broad proteome coverage and good accuracy in quantification. Herein, we review the current LC-MS-based quantification methods with respect to their advantages and limitations, and highlight their potential applications.

  8. Spectral performance of a whole-body research photon counting detector CT: quantitative accuracy in derived image sets

    NASA Astrophysics Data System (ADS)

    Leng, Shuai; Zhou, Wei; Yu, Zhicong; Halaweish, Ahmed; Krauss, Bernhard; Schmidt, Bernhard; Yu, Lifeng; Kappler, Steffen; McCollough, Cynthia

    2017-09-01

    Photon-counting computed tomography (PCCT) uses a photon counting detector to count individual photons and allocate them to specific energy bins by comparing photon energy to preset thresholds. This enables simultaneous multi-energy CT with a single source and detector. Phantom studies were performed to assess the spectral performance of a research PCCT scanner by assessing the accuracy of derived images sets. Specifically, we assessed the accuracy of iodine quantification in iodine map images and of CT number accuracy in virtual monoenergetic images (VMI). Vials containing iodine with five known concentrations were scanned on the PCCT scanner after being placed in phantoms representing the attenuation of different size patients. For comparison, the same vials and phantoms were also scanned on 2nd and 3rd generation dual-source, dual-energy scanners. After material decomposition, iodine maps were generated, from which iodine concentration was measured for each vial and phantom size and compared with the known concentration. Additionally, VMIs were generated and CT number accuracy was compared to the reference standard, which was calculated based on known iodine concentration and attenuation coefficients at each keV obtained from the U.S. National Institute of Standards and Technology (NIST). Results showed accurate iodine quantification (root mean square error of 0.5 mgI/cc) and accurate CT number of VMIs (percentage error of 8.9%) using the PCCT scanner. The overall performance of the PCCT scanner, in terms of iodine quantification and VMI CT number accuracy, was comparable to that of EID-based dual-source, dual-energy scanners.

  9. Accuracy in inference of nursing diagnoses in heart failure patients.

    PubMed

    Pereira, Juliana de Melo Vellozo; Cavalcanti, Ana Carla Dantas; Lopes, Marcos Venícios de Oliveira; da Silva, Valéria Gonçalves; de Souza, Rosana Oliveira; Gonçalves, Ludmila Cuzatis

    2015-01-01

    Heart failure (HF) is a common cause of hospitalization and requires accuracy in clinical judgment and appropriate nursing diagnoses. to determine the accuracy of nursing diagnoses of fatigue, intolerance to activity and decreased cardiac output in hospitalized HF patients. descriptive study applied to nurses with experience in NANDA-I and/or HF nursing diagnoses. Evaluation and accuracy were determined by calculating efficacy (E), false negative (FN), false positive (FP) and trend (T) measures. Nurses who showed acceptable inspection for two diagnoses were selected. the nursing diagnosis of fatigue was the most commonly mistaken diagnosis identified by the nursing evaluators. the search for improving diagnostic accuracy reaffirms the need for continuous and specific training to improve the diagnosis capability of nurses. the training allowed the exercise of clinical judgment and better accuracy of nurses.

  10. Quantitative analysis of SMEX'02 AIRSAR data for soil moisture inversion

    NASA Technical Reports Server (NTRS)

    Zyl, J. J. van; Njoku, E.; Jackson, T.

    2003-01-01

    This paper discusses in detail the characteristics of the AIRSAR data acquired, and provides an initial quantitative assessment of the accuracy of the radar inversion algorithms under these vegetated conditions.

  11. A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

    PubMed Central

    Morales-Navarrete, Hernán; Segovia-Miranda, Fabián; Klukowski, Piotr; Meyer, Kirstin; Nonaka, Hidenori; Marsico, Giovanni; Chernykh, Mikhail; Kalaidzidis, Alexander; Zerial, Marino; Kalaidzidis, Yannis

    2015-01-01

    A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness. DOI: http://dx.doi.org/10.7554/eLife.11214.001 PMID:26673893

  12. Short communication: Evaluation of the PREP10 energy-, protein-, and amino acid-allowable milk equations in comparison with the National Research Council model.

    PubMed

    White, Robin R; McGill, Tyler; Garnett, Rebecca; Patterson, Robert J; Hanigan, Mark D

    2017-04-01

    The objective of this work was to evaluate the precision and accuracy of the milk yield predictions made by the PREP10 model in comparison to those from the National Research Council (NRC) Nutrient Requirements of Dairy Cattle. The PREP10 model is a ration-balancing system that allows protein use efficiency to vary with production level. The model also has advanced AA supply and requirement calculations that enable estimation of AA-allowable milk (Milk AA ) based on 10 essential AA. A literature data set of 374 treatment means was collected and used to quantitatively evaluate the estimates of protein-allowable milk (Milk MP ) and energy-allowable milk yields from the NRC and PREP10 models. The PREP10 Milk AA prediction was also evaluated, as were both models' estimates of milk based on the most-limiting nutrient or the mean of the estimated milk yields. For most milk estimates compared, the PREP10 model had reduced root mean squared prediction error (RMSPE), improved concordance correlation coefficient, and reduced mean and slope bias in comparison to the NRC model. In particular, utilizing the variable protein use efficiency for milk production notably improved the estimate of Milk MP when compared with NRC. The PREP10 Milk MP estimate had an RMSPE of 18.2% (NRC = 25.7%), concordance correlation coefficient of 0.82% (NRC = 0.64), slope bias of -0.14 kg/kg of predicted milk (NRC = -0.34 kg/kg), and mean bias of -0.63 kg (NRC = -2.85 kg). The PREP10 estimate of Milk AA had slightly elevated RMSPE and mean and slope bias when compared with Milk MP . The PREP10 estimate of Milk AA was not advantageous when compared with Milk MP , likely because AA use efficiency for milk was constant whereas MP use was variable. Future work evaluating variable AA use efficiencies for milk production is likely to improve accuracy and precision of models of allowable milk. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  13. Cued Speech Transliteration: Effects of Speaking Rate and Lag Time on Production Accuracy

    PubMed Central

    Tessler, Morgan P.

    2016-01-01

    Many deaf and hard-of-hearing children rely on interpreters to access classroom communication. Although the exact level of access provided by interpreters in these settings is unknown, it is likely to depend heavily on interpreter accuracy (portion of message correctly produced by the interpreter) and the factors that govern interpreter accuracy. In this study, the accuracy of 12 Cued Speech (CS) transliterators with varying degrees of experience was examined at three different speaking rates (slow, normal, fast). Accuracy was measured with a high-resolution, objective metric in order to facilitate quantitative analyses of the effect of each factor on accuracy. Results showed that speaking rate had a large negative effect on accuracy, caused primarily by an increase in omitted cues, whereas the effect of lag time on accuracy, also negative, was quite small and explained just 3% of the variance. Increased experience level was generally associated with increased accuracy; however, high levels of experience did not guarantee high levels of accuracy. Finally, the overall accuracy of the 12 transliterators, 54% on average across all three factors, was low enough to raise serious concerns about the quality of CS transliteration services that (at least some) children receive in educational settings. PMID:27221370

  14. Quantitative study of FORC diagrams in thermally corrected Stoner- Wohlfarth nanoparticles systems

    NASA Astrophysics Data System (ADS)

    De Biasi, E.; Curiale, J.; Zysler, R. D.

    2016-12-01

    The use of FORC diagrams is becoming increasingly popular among researchers devoted to magnetism and magnetic materials. However, a thorough interpretation of this kind of diagrams, in order to achieve quantitative information, requires an appropriate model of the studied system. For that reason most of the FORC studies are used for a qualitative analysis. In magnetic systems thermal fluctuations "blur" the signatures of the anisotropy, volume and particle interactions distributions, therefore thermal effects in nanoparticles systems conspire against a proper interpretation and analysis of these diagrams. Motivated by this fact, we have quantitatively studied the degree of accuracy of the information extracted from FORC diagrams for the special case of single-domain thermal corrected Stoner- Wohlfarth (easy axes along the external field orientation) nanoparticles systems. In this work, the starting point is an analytical model that describes the behavior of a magnetic nanoparticles system as a function of field, anisotropy, temperature and measurement time. In order to study the quantitative degree of accuracy of our model, we built FORC diagrams for different archetypical cases of magnetic nanoparticles. Our results show that from the quantitative information obtained from the diagrams, under the hypotheses of the proposed model, is possible to recover the features of the original system with accuracy above 95%. This accuracy is improved at low temperatures and also it is possible to access to the anisotropy distribution directly from the FORC coercive field profile. Indeed, our simulations predict that the volume distribution plays a secondary role being the mean value and its deviation the only important parameters. Therefore it is possible to obtain an accurate result for the inversion and interaction fields despite the features of the volume distribution.

  15. Response moderation models for conditional dependence between response time and response accuracy.

    PubMed

    Bolsinova, Maria; Tijmstra, Jesper; Molenaar, Dylan

    2017-05-01

    It is becoming more feasible and common to register response times in the application of psychometric tests. Researchers thus have the opportunity to jointly model response accuracy and response time, which provides users with more relevant information. The most common choice is to use the hierarchical model (van der Linden, 2007, Psychometrika, 72, 287), which assumes conditional independence between response time and accuracy, given a person's speed and ability. However, this assumption may be violated in practice if, for example, persons vary their speed or differ in their response strategies, leading to conditional dependence between response time and accuracy and confounding measurement. We propose six nested hierarchical models for response time and accuracy that allow for conditional dependence, and discuss their relationship to existing models. Unlike existing approaches, the proposed hierarchical models allow for various forms of conditional dependence in the model and allow the effect of continuous residual response time on response accuracy to be item-specific, person-specific, or both. Estimation procedures for the models are proposed, as well as two information criteria that can be used for model selection. Parameter recovery and usefulness of the information criteria are investigated using simulation, indicating that the procedure works well and is likely to select the appropriate model. Two empirical applications are discussed to illustrate the different types of conditional dependence that may occur in practice and how these can be captured using the proposed hierarchical models. © 2016 The British Psychological Society.

  16. Targeted Quantitation of Proteins by Mass Spectrometry

    PubMed Central

    2013-01-01

    Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement. PMID:23517332

  17. Targeted quantitation of proteins by mass spectrometry.

    PubMed

    Liebler, Daniel C; Zimmerman, Lisa J

    2013-06-04

    Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement.

  18. Increased Accuracy of Ligand Sensing by Receptor Internalization and Lateral Receptor Diffusion

    NASA Astrophysics Data System (ADS)

    Aquino, Gerardo; Endres, Robert

    2010-03-01

    Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as overcounting of the same ligand molecules is reduced. A similar role may be played by receptor diffusion om the cell membrane. Fast, lateral receptor diffusion is known to be relevant in neurotransmission initiated by release of neurotransmitter glutamate in the synaptic cleft between neurons. By binding ligand and removal by diffusion from the region of release of the neurotransmitter, diffusing receptors can be reasonably expected to reduce the local overcounting of the same ligand molecules in the region of signaling. By extending simple ligand-receptor models to out-of-equilibrium thermodynamics, we show that both receptor internalization and lateral diffusion increase the accuracy with which cells can measure ligand concentrations in the external environment. We confirm this with our model and give quantitative predictions for experimental parameters values. We give quantitative predictions, which compare favorably to experimental data of real receptors.

  19. Quantitative Evaluation of a Planetary Renderer for Terrain Relative Navigation

    NASA Astrophysics Data System (ADS)

    Amoroso, E.; Jones, H.; Otten, N.; Wettergreen, D.; Whittaker, W.

    2016-11-01

    A ray-tracing computer renderer tool is presented based on LOLA and LROC elevation models and is quantitatively compared to LRO WAC and NAC images for photometric accuracy. We investigated using rendered images for terrain relative navigation.

  20. Living cell dry mass measurement using quantitative phase imaging with quadriwave lateral shearing interferometry: an accuracy and sensitivity discussion.

    PubMed

    Aknoun, Sherazade; Savatier, Julien; Bon, Pierre; Galland, Frédéric; Abdeladim, Lamiae; Wattellier, Benoit; Monneret, Serge

    2015-01-01

    Single-cell dry mass measurement is used in biology to follow cell cycle, to address effects of drugs, or to investigate cell metabolism. Quantitative phase imaging technique with quadriwave lateral shearing interferometry (QWLSI) allows measuring cell dry mass. The technique is very simple to set up, as it is integrated in a camera-like instrument. It simply plugs onto a standard microscope and uses a white light illumination source. Its working principle is first explained, from image acquisition to automated segmentation algorithm and dry mass quantification. Metrology of the whole process, including its sensitivity, repeatability, reliability, sources of error, over different kinds of samples and under different experimental conditions, is developed. We show that there is no influence of magnification or spatial light coherence on dry mass measurement; effect of defocus is more critical but can be calibrated. As a consequence, QWLSI is a well-suited technique for fast, simple, and reliable cell dry mass study, especially for live cells.

  1. Magnetic Resonance Imaging of Intracranial Hypotension: Diagnostic Value of Combined Qualitative Signs and Quantitative Metrics.

    PubMed

    Aslan, Kerim; Gunbey, Hediye Pinar; Tomak, Leman; Ozmen, Zafer; Incesu, Lutfi

    The aim of this study was to investigate whether the use of combination quantitative metrics (mamillopontine distance [MPD], pontomesencephalic angle, and mesencephalon anterior-posterior/medial-lateral diameter ratios) with qualitative signs (dural enhancement, subdural collections/hematoma, venous engorgement, pituitary gland enlargements, and tonsillar herniations) provides a more accurate diagnosis of intracranial hypotension (IH). The quantitative metrics and qualitative signs of 34 patients and 34 control subjects were assessed by 2 independent observers. Receiver operating characteristic (ROC) curve was used to evaluate the diagnostic performance of quantitative metrics and qualitative signs, and for the diagnosis of IH, optimum cutoff values of quantitative metrics were found with ROC analysis. Combined ROC curve was measured for the quantitative metrics, and qualitative signs combinations in determining diagnostic accuracy and sensitivity, specificity, and positive and negative predictive values were found, and the best model combination was formed. Whereas MPD and pontomesencephalic angle were significantly lower in patients with IH when compared with the control group (P < 0.001), mesencephalon anterior-posterior/medial-lateral diameter ratio was significantly higher (P < 0.001). For qualitative signs, the highest individual distinctive power was dural enhancement with area under the ROC curve (AUC) of 0.838. For quantitative metrics, the highest individual distinctive power was MPD with AUC of 0.947. The best accuracy in the diagnosis of IH was obtained by combination of dural enhancement, venous engorgement, and MPD with an AUC of 1.00. This study showed that the combined use of dural enhancement, venous engorgement, and MPD had diagnostic accuracy of 100 % for the diagnosis of IH. Therefore, a more accurate IH diagnosis can be provided with combination of quantitative metrics with qualitative signs.

  2. X-ray Phase Contrast Allows Three Dimensional, Quantitative Imaging of Hydrogel Implants

    DOE PAGES

    Appel, Alyssa A.; Larson, Jeffrey C.; Jiang, Bin; ...

    2015-10-20

    Three dimensional imaging techniques are needed for the evaluation and assessment of biomaterials used for tissue engineering and drug delivery applications. Hydrogels are a particularly popular class of materials for medical applications but are difficult to image in tissue using most available imaging modalities. Imaging techniques based on X-ray Phase Contrast (XPC) have shown promise for tissue engineering applications due to their ability to provide image contrast based on multiple X-ray properties. In this manuscript we describe results using XPC to image a model hydrogel and soft tissue structure. Porous fibrin loaded poly(ethylene glycol) hydrogels were synthesized and implanted inmore » a rodent subcutaneous model. Samples were explanted and imaged with an analyzer-based XPC technique and processed and stained for histology for comparison. Both hydrogel and soft tissues structures could be identified in XPC images. Structure in skeletal muscle adjacent could be visualized and invading fibrovascular tissue could be quantified. In quantitative results, there were no differences between XPC and the gold-standard histological measurements. These results provide evidence of the significant potential of techniques based on XPC for 3D imaging of hydrogel structure and local tissue response.« less

  3. The impact of 3D volume of interest definition on accuracy and precision of activity estimation in quantitative SPECT and planar processing methods

    NASA Astrophysics Data System (ADS)

    He, Bin; Frey, Eric C.

    2010-06-01

    Accurate and precise estimation of organ activities is essential for treatment planning in targeted radionuclide therapy. We have previously evaluated the impact of processing methodology, statistical noise and variability in activity distribution and anatomy on the accuracy and precision of organ activity estimates obtained with quantitative SPECT (QSPECT) and planar (QPlanar) processing. Another important factor impacting the accuracy and precision of organ activity estimates is accuracy of and variability in the definition of organ regions of interest (ROI) or volumes of interest (VOI). The goal of this work was thus to systematically study the effects of VOI definition on the reliability of activity estimates. To this end, we performed Monte Carlo simulation studies using randomly perturbed and shifted VOIs to assess the impact on organ activity estimates. The 3D NCAT phantom was used with activities that modeled clinically observed 111In ibritumomab tiuxetan distributions. In order to study the errors resulting from misdefinitions due to manual segmentation errors, VOIs of the liver and left kidney were first manually defined. Each control point was then randomly perturbed to one of the nearest or next-nearest voxels in three ways: with no, inward or outward directional bias, resulting in random perturbation, erosion or dilation, respectively, of the VOIs. In order to study the errors resulting from the misregistration of VOIs, as would happen, e.g. in the case where the VOIs were defined using a misregistered anatomical image, the reconstructed SPECT images or projections were shifted by amounts ranging from -1 to 1 voxels in increments of with 0.1 voxels in both the transaxial and axial directions. The activity estimates from the shifted reconstructions or projections were compared to those from the originals, and average errors were computed for the QSPECT and QPlanar methods, respectively. For misregistration, errors in organ activity estimations were

  4. Motion correction for improving the accuracy of dual-energy myocardial perfusion CT imaging

    NASA Astrophysics Data System (ADS)

    Pack, Jed D.; Yin, Zhye; Xiong, Guanglei; Mittal, Priya; Dunham, Simon; Elmore, Kimberly; Edic, Peter M.; Min, James K.

    2016-03-01

    Coronary Artery Disease (CAD) is the leading cause of death globally [1]. Modern cardiac computed tomography angiography (CCTA) is highly effective at identifying and assessing coronary blockages associated with CAD. The diagnostic value of this anatomical information can be substantially increased in combination with a non-invasive, low-dose, correlative, quantitative measure of blood supply to the myocardium. While CT perfusion has shown promise of providing such indications of ischemia, artifacts due to motion, beam hardening, and other factors confound clinical findings and can limit quantitative accuracy. In this paper, we investigate the impact of applying a novel motion correction algorithm to correct for motion in the myocardium. This motion compensation algorithm (originally designed to correct for the motion of the coronary arteries in order to improve CCTA images) has been shown to provide substantial improvements in both overall image quality and diagnostic accuracy of CCTA. We have adapted this technique for application beyond the coronary arteries and present an assessment of its impact on image quality and quantitative accuracy within the context of dual-energy CT perfusion imaging. We conclude that motion correction is a promising technique that can help foster the routine clinical use of dual-energy CT perfusion. When combined, the anatomical information of CCTA and the hemodynamic information from dual-energy CT perfusion should facilitate better clinical decisions about which patients would benefit from treatments such as stent placement, drug therapy, or surgery and help other patients avoid the risks and costs associated with unnecessary, invasive, diagnostic coronary angiography procedures.

  5. Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry.

    PubMed

    Pfammatter, Sibylle; Bonneil, Eric; Thibault, Pierre

    2016-12-02

    Quantitative proteomics using isobaric reagent tandem mass tags (TMT) or isobaric tags for relative and absolute quantitation (iTRAQ) provides a convenient approach to compare changes in protein abundance across multiple samples. However, the analysis of complex protein digests by isobaric labeling can be undermined by the relative large proportion of co-selected peptide ions that lead to distorted reporter ion ratios and affect the accuracy and precision of quantitative measurements. Here, we investigated the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS) in proteomic experiments to reduce sample complexity and improve protein quantification using TMT isobaric labeling. LC-FAIMS-MS/MS analyses of human and yeast protein digests led to significant reductions in interfering ions, which increased the number of quantifiable peptides by up to 68% while significantly improving the accuracy of abundance measurements compared to that with conventional LC-MS/MS. The improvement in quantitative measurements using FAIMS is further demonstrated for the temporal profiling of protein abundance of HEK293 cells following heat shock treatment.

  6. The influence of biological and technical factors on quantitative analysis of amyloid PET: Points to consider and recommendations for controlling variability in longitudinal data.

    PubMed

    Schmidt, Mark E; Chiao, Ping; Klein, Gregory; Matthews, Dawn; Thurfjell, Lennart; Cole, Patricia E; Margolin, Richard; Landau, Susan; Foster, Norman L; Mason, N Scott; De Santi, Susan; Suhy, Joyce; Koeppe, Robert A; Jagust, William

    2015-09-01

    In vivo imaging of amyloid burden with positron emission tomography (PET) provides a means for studying the pathophysiology of Alzheimer's and related diseases. Measurement of subtle changes in amyloid burden requires quantitative analysis of image data. Reliable quantitative analysis of amyloid PET scans acquired at multiple sites and over time requires rigorous standardization of acquisition protocols, subject management, tracer administration, image quality control, and image processing and analysis methods. We review critical points in the acquisition and analysis of amyloid PET, identify ways in which technical factors can contribute to measurement variability, and suggest methods for mitigating these sources of noise. Improved quantitative accuracy could reduce the sample size necessary to detect intervention effects when amyloid PET is used as a treatment end point and allow more reliable interpretation of change in amyloid burden and its relationship to clinical course. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Semantic focusing allows fully automated single-layer slide scanning of cervical cytology slides.

    PubMed

    Lahrmann, Bernd; Valous, Nektarios A; Eisenmann, Urs; Wentzensen, Nicolas; Grabe, Niels

    2013-01-01

    Liquid-based cytology (LBC) in conjunction with Whole-Slide Imaging (WSI) enables the objective and sensitive and quantitative evaluation of biomarkers in cytology. However, the complex three-dimensional distribution of cells on LBC slides requires manual focusing, long scanning-times, and multi-layer scanning. Here, we present a solution that overcomes these limitations in two steps: first, we make sure that focus points are only set on cells. Secondly, we check the total slide focus quality. From a first analysis we detected that superficial dust can be separated from the cell layer (thin layer of cells on the glass slide) itself. Then we analyzed 2,295 individual focus points from 51 LBC slides stained for p16 and Ki67. Using the number of edges in a focus point image, specific color values and size-inclusion filters, focus points detecting cells could be distinguished from focus points on artifacts (accuracy 98.6%). Sharpness as total focus quality of a virtual LBC slide is computed from 5 sharpness features. We trained a multi-parameter SVM classifier on 1,600 images. On an independent validation set of 3,232 cell images we achieved an accuracy of 94.8% for classifying images as focused. Our results show that single-layer scanning of LBC slides is possible and how it can be achieved. We assembled focus point analysis and sharpness classification into a fully automatic, iterative workflow, free of user intervention, which performs repetitive slide scanning as necessary. On 400 LBC slides we achieved a scanning-time of 13.9±10.1 min with 29.1±15.5 focus points. In summary, the integration of semantic focus information into whole-slide imaging allows automatic high-quality imaging of LBC slides and subsequent biomarker analysis.

  8. Single-exposure quantitative phase imaging in color-coded LED microscopy.

    PubMed

    Lee, Wonchan; Jung, Daeseong; Ryu, Suho; Joo, Chulmin

    2017-04-03

    We demonstrate single-shot quantitative phase imaging (QPI) in a platform of color-coded LED microscopy (cLEDscope). The light source in a conventional microscope is replaced by a circular LED pattern that is trisected into subregions with equal area, assigned to red, green, and blue colors. Image acquisition with a color image sensor and subsequent computation based on weak object transfer functions allow for the QPI of a transparent specimen. We also provide a correction method for color-leakage, which may be encountered in implementing our method with consumer-grade LEDs and image sensors. Most commercially available LEDs and image sensors do not provide spectrally isolated emissions and pixel responses, generating significant error in phase estimation in our method. We describe the correction scheme for this color-leakage issue, and demonstrate improved phase measurement accuracy. The computational model and single-exposure QPI capability of our method are presented by showing images of calibrated phase samples and cellular specimens.

  9. Quantitative evaluation of software packages for single-molecule localization microscopy.

    PubMed

    Sage, Daniel; Kirshner, Hagai; Pengo, Thomas; Stuurman, Nico; Min, Junhong; Manley, Suliana; Unser, Michael

    2015-08-01

    The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution microscopy and present a comprehensive evaluation of localization software packages. Our philosophy is to evaluate each package as a whole, thus maintaining the integrity of the software. We prepared synthetic data that represent three-dimensional structures modeled after biological components, taking excitation parameters, noise sources, point-spread functions and pixelation into account. We then asked developers to run their software on our data; most responded favorably, allowing us to present a broad picture of the methods available. We evaluated their results using quantitative and user-interpretable criteria: detection rate, accuracy, quality of image reconstruction, resolution, software usability and computational resources. These metrics reflect the various tradeoffs of SMLM software packages and help users to choose the software that fits their needs.

  10. A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation.

    PubMed

    Zhao, Huaying; Ghirlando, Rodolfo; Alfonso, Carlos; Arisaka, Fumio; Attali, Ilan; Bain, David L; Bakhtina, Marina M; Becker, Donald F; Bedwell, Gregory J; Bekdemir, Ahmet; Besong, Tabot M D; Birck, Catherine; Brautigam, Chad A; Brennerman, William; Byron, Olwyn; Bzowska, Agnieszka; Chaires, Jonathan B; Chaton, Catherine T; Cölfen, Helmut; Connaghan, Keith D; Crowley, Kimberly A; Curth, Ute; Daviter, Tina; Dean, William L; Díez, Ana I; Ebel, Christine; Eckert, Debra M; Eisele, Leslie E; Eisenstein, Edward; England, Patrick; Escalante, Carlos; Fagan, Jeffrey A; Fairman, Robert; Finn, Ron M; Fischle, Wolfgang; de la Torre, José García; Gor, Jayesh; Gustafsson, Henning; Hall, Damien; Harding, Stephen E; Cifre, José G Hernández; Herr, Andrew B; Howell, Elizabeth E; Isaac, Richard S; Jao, Shu-Chuan; Jose, Davis; Kim, Soon-Jong; Kokona, Bashkim; Kornblatt, Jack A; Kosek, Dalibor; Krayukhina, Elena; Krzizike, Daniel; Kusznir, Eric A; Kwon, Hyewon; Larson, Adam; Laue, Thomas M; Le Roy, Aline; Leech, Andrew P; Lilie, Hauke; Luger, Karolin; Luque-Ortega, Juan R; Ma, Jia; May, Carrie A; Maynard, Ernest L; Modrak-Wojcik, Anna; Mok, Yee-Foong; Mücke, Norbert; Nagel-Steger, Luitgard; Narlikar, Geeta J; Noda, Masanori; Nourse, Amanda; Obsil, Tomas; Park, Chad K; Park, Jin-Ku; Pawelek, Peter D; Perdue, Erby E; Perkins, Stephen J; Perugini, Matthew A; Peterson, Craig L; Peverelli, Martin G; Piszczek, Grzegorz; Prag, Gali; Prevelige, Peter E; Raynal, Bertrand D E; Rezabkova, Lenka; Richter, Klaus; Ringel, Alison E; Rosenberg, Rose; Rowe, Arthur J; Rufer, Arne C; Scott, David J; Seravalli, Javier G; Solovyova, Alexandra S; Song, Renjie; Staunton, David; Stoddard, Caitlin; Stott, Katherine; Strauss, Holger M; Streicher, Werner W; Sumida, John P; Swygert, Sarah G; Szczepanowski, Roman H; Tessmer, Ingrid; Toth, Ronald T; Tripathy, Ashutosh; Uchiyama, Susumu; Uebel, Stephan F W; Unzai, Satoru; Gruber, Anna Vitlin; von Hippel, Peter H; Wandrey, Christine; Wang, Szu-Huan; Weitzel, Steven E; Wielgus-Kutrowska, Beata; Wolberger, Cynthia; Wolff, Martin; Wright, Edward; Wu, Yu-Sung; Wubben, Jacinta M; Schuck, Peter

    2015-01-01

    Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.

  11. A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation

    PubMed Central

    Zhao, Huaying; Ghirlando, Rodolfo; Alfonso, Carlos; Arisaka, Fumio; Attali, Ilan; Bain, David L.; Bakhtina, Marina M.; Becker, Donald F.; Bedwell, Gregory J.; Bekdemir, Ahmet; Besong, Tabot M. D.; Birck, Catherine; Brautigam, Chad A.; Brennerman, William; Byron, Olwyn; Bzowska, Agnieszka; Chaires, Jonathan B.; Chaton, Catherine T.; Cölfen, Helmut; Connaghan, Keith D.; Crowley, Kimberly A.; Curth, Ute; Daviter, Tina; Dean, William L.; Díez, Ana I.; Ebel, Christine; Eckert, Debra M.; Eisele, Leslie E.; Eisenstein, Edward; England, Patrick; Escalante, Carlos; Fagan, Jeffrey A.; Fairman, Robert; Finn, Ron M.; Fischle, Wolfgang; de la Torre, José García; Gor, Jayesh; Gustafsson, Henning; Hall, Damien; Harding, Stephen E.; Cifre, José G. Hernández; Herr, Andrew B.; Howell, Elizabeth E.; Isaac, Richard S.; Jao, Shu-Chuan; Jose, Davis; Kim, Soon-Jong; Kokona, Bashkim; Kornblatt, Jack A.; Kosek, Dalibor; Krayukhina, Elena; Krzizike, Daniel; Kusznir, Eric A.; Kwon, Hyewon; Larson, Adam; Laue, Thomas M.; Le Roy, Aline; Leech, Andrew P.; Lilie, Hauke; Luger, Karolin; Luque-Ortega, Juan R.; Ma, Jia; May, Carrie A.; Maynard, Ernest L.; Modrak-Wojcik, Anna; Mok, Yee-Foong; Mücke, Norbert; Nagel-Steger, Luitgard; Narlikar, Geeta J.; Noda, Masanori; Nourse, Amanda; Obsil, Tomas; Park, Chad K.; Park, Jin-Ku; Pawelek, Peter D.; Perdue, Erby E.; Perkins, Stephen J.; Perugini, Matthew A.; Peterson, Craig L.; Peverelli, Martin G.; Piszczek, Grzegorz; Prag, Gali; Prevelige, Peter E.; Raynal, Bertrand D. E.; Rezabkova, Lenka; Richter, Klaus; Ringel, Alison E.; Rosenberg, Rose; Rowe, Arthur J.; Rufer, Arne C.; Scott, David J.; Seravalli, Javier G.; Solovyova, Alexandra S.; Song, Renjie; Staunton, David; Stoddard, Caitlin; Stott, Katherine; Strauss, Holger M.; Streicher, Werner W.; Sumida, John P.; Swygert, Sarah G.; Szczepanowski, Roman H.; Tessmer, Ingrid; Toth, Ronald T.; Tripathy, Ashutosh; Uchiyama, Susumu; Uebel, Stephan F. W.; Unzai, Satoru; Gruber, Anna Vitlin; von Hippel, Peter H.; Wandrey, Christine; Wang, Szu-Huan; Weitzel, Steven E.; Wielgus-Kutrowska, Beata; Wolberger, Cynthia; Wolff, Martin; Wright, Edward; Wu, Yu-Sung; Wubben, Jacinta M.; Schuck, Peter

    2015-01-01

    Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies. PMID:25997164

  12. Accuracy and precision of 3 intraoral scanners and accuracy of conventional impressions: A novel in vivo analysis method.

    PubMed

    Nedelcu, R; Olsson, P; Nyström, I; Rydén, J; Thor, A

    2018-02-01

    To evaluate a novel methodology using industrial scanners as a reference, and assess in vivo accuracy of 3 intraoral scanners (IOS) and conventional impressions. Further, to evaluate IOS precision in vivo. Four reference-bodies were bonded to the buccal surfaces of upper premolars and incisors in five subjects. After three reference-scans, ATOS Core 80 (ATOS), subjects were scanned three times with three IOS systems: 3M True Definition (3M), CEREC Omnicam (OMNI) and Trios 3 (TRIOS). One conventional impression (IMPR) was taken, 3M Impregum Penta Soft, and poured models were digitized with laboratory scanner 3shape D1000 (D1000). Best-fit alignment of reference-bodies and 3D Compare Analysis was performed. Precision of ATOS and D1000 was assessed for quantitative evaluation and comparison. Accuracy of IOS and IMPR were analyzed using ATOS as reference. Precision of IOS was evaluated through intra-system comparison. Precision of ATOS reference scanner (mean 0.6 μm) and D1000 (mean 0.5 μm) was high. Pairwise multiple comparisons of reference-bodies located in different tooth positions displayed a statistically significant difference of accuracy between two scanner-groups: 3M and TRIOS, over OMNI (p value range 0.0001 to 0.0006). IMPR did not show any statistically significant difference to IOS. However, deviations of IOS and IMPR were within a similar magnitude. No statistical difference was found for IOS precision. The methodology can be used for assessing accuracy of IOS and IMPR in vivo in up to five units bilaterally from midline. 3M and TRIOS had a higher accuracy than OMNI. IMPR overlapped both groups. Intraoral scanners can be used as a replacement for conventional impressions when restoring up to ten units without extended edentulous spans. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  13. Anatomical reconstructions of pediatric airways from endoscopic images: a pilot study of the accuracy of quantitative endoscopy.

    PubMed

    Meisner, Eric M; Hager, Gregory D; Ishman, Stacey L; Brown, David; Tunkel, David E; Ishii, Masaru

    2013-11-01

    To evaluate the accuracy of three-dimensional (3D) airway reconstructions obtained using quantitative endoscopy (QE). We developed this novel technique to reconstruct precise 3D representations of airway geometries from endoscopic video streams. This method, based on machine vision methodologies, uses a post-processing step of the standard videos obtained during routine laryngoscopy and bronchoscopy. We hypothesize that this method is precise and will generate assessment of airway size and shape similar to those obtained using computed tomography (CT). This study was approved by the institutional review board (IRB). We analyzed video sequences from pediatric patients receiving rigid bronchoscopy. We generated 3D scaled airway models of the subglottis, trachea, and carina using QE. These models were compared to 3D airway models generated from CT. We used the CT data as the gold standard measure of airway size, and used a mixed linear model to estimate the average error in cross-sectional area and effective diameter for QE. The average error in cross sectional area (area sliced perpendicular to the long axis of the airway) was 7.7 mm(2) (variance 33.447 mm(4)). The average error in effective diameter was 0.38775 mm (variance 2.45 mm(2)), approximately 9% error. Our pilot study suggests that QE can be used to generate precise 3D reconstructions of airways. This technique is atraumatic, does not require ionizing radiation, and integrates easily into standard airway assessment protocols. We conjecture that this technology will be useful for staging airway disease and assessing surgical outcomes. Copyright © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

  14. EyeTribe Tracker Data Accuracy Evaluation and Its Interconnection with Hypothesis Software for Cartographic Purposes.

    PubMed

    Popelka, Stanislav; Stachoň, Zdeněk; Šašinka, Čeněk; Doležalová, Jitka

    2016-01-01

    The mixed research design is a progressive methodological discourse that combines the advantages of quantitative and qualitative methods. Its possibilities of application are, however, dependent on the efficiency with which the particular research techniques are used and combined. The aim of the paper is to introduce the possible combination of Hypothesis with EyeTribe tracker. The Hypothesis is intended for quantitative data acquisition and the EyeTribe is intended for qualitative (eye-tracking) data recording. In the first part of the paper, Hypothesis software is described. The Hypothesis platform provides an environment for web-based computerized experiment design and mass data collection. Then, evaluation of the accuracy of data recorded by EyeTribe tracker was performed with the use of concurrent recording together with the SMI RED 250 eye-tracker. Both qualitative and quantitative results showed that data accuracy is sufficient for cartographic research. In the third part of the paper, a system for connecting EyeTribe tracker and Hypothesis software is presented. The interconnection was performed with the help of developed web application HypOgama. The created system uses open-source software OGAMA for recording the eye-movements of participants together with quantitative data from Hypothesis. The final part of the paper describes the integrated research system combining Hypothesis and EyeTribe.

  15. EyeTribe Tracker Data Accuracy Evaluation and Its Interconnection with Hypothesis Software for Cartographic Purposes

    PubMed Central

    Stachoň, Zdeněk; Šašinka, Čeněk; Doležalová, Jitka

    2016-01-01

    The mixed research design is a progressive methodological discourse that combines the advantages of quantitative and qualitative methods. Its possibilities of application are, however, dependent on the efficiency with which the particular research techniques are used and combined. The aim of the paper is to introduce the possible combination of Hypothesis with EyeTribe tracker. The Hypothesis is intended for quantitative data acquisition and the EyeTribe is intended for qualitative (eye-tracking) data recording. In the first part of the paper, Hypothesis software is described. The Hypothesis platform provides an environment for web-based computerized experiment design and mass data collection. Then, evaluation of the accuracy of data recorded by EyeTribe tracker was performed with the use of concurrent recording together with the SMI RED 250 eye-tracker. Both qualitative and quantitative results showed that data accuracy is sufficient for cartographic research. In the third part of the paper, a system for connecting EyeTribe tracker and Hypothesis software is presented. The interconnection was performed with the help of developed web application HypOgama. The created system uses open-source software OGAMA for recording the eye-movements of participants together with quantitative data from Hypothesis. The final part of the paper describes the integrated research system combining Hypothesis and EyeTribe. PMID:27087805

  16. Quantitative Imaging Biomarkers of NAFLD

    PubMed Central

    Kinner, Sonja; Reeder, Scott B.

    2016-01-01

    Conventional imaging modalities, including ultrasonography (US), computed tomography (CT), and magnetic resonance (MR), play an important role in the diagnosis and management of patients with nonalcoholic fatty liver disease (NAFLD) by allowing noninvasive diagnosis of hepatic steatosis. However, conventional imaging modalities are limited as biomarkers of NAFLD for various reasons. Multi-parametric quantitative MRI techniques overcome many of the shortcomings of conventional imaging and allow comprehensive and objective evaluation of NAFLD. MRI can provide unconfounded biomarkers of hepatic fat, iron, and fibrosis in a single examination—a virtual biopsy has become a clinical reality. In this article, we will review the utility and limitation of conventional US, CT, and MR imaging for the diagnosis NAFLD. Recent advances in imaging biomarkers of NAFLD are also discussed with an emphasis in multi-parametric quantitative MRI. PMID:26848588

  17. Cued Speech Transliteration: Effects of Speaking Rate and Lag Time on Production Accuracy.

    PubMed

    Krause, Jean C; Tessler, Morgan P

    2016-10-01

    Many deaf and hard-of-hearing children rely on interpreters to access classroom communication. Although the exact level of access provided by interpreters in these settings is unknown, it is likely to depend heavily on interpreter accuracy (portion of message correctly produced by the interpreter) and the factors that govern interpreter accuracy. In this study, the accuracy of 12 Cued Speech (CS) transliterators with varying degrees of experience was examined at three different speaking rates (slow, normal, fast). Accuracy was measured with a high-resolution, objective metric in order to facilitate quantitative analyses of the effect of each factor on accuracy. Results showed that speaking rate had a large negative effect on accuracy, caused primarily by an increase in omitted cues, whereas the effect of lag time on accuracy, also negative, was quite small and explained just 3% of the variance. Increased experience level was generally associated with increased accuracy; however, high levels of experience did not guarantee high levels of accuracy. Finally, the overall accuracy of the 12 transliterators, 54% on average across all three factors, was low enough to raise serious concerns about the quality of CS transliteration services that (at least some) children receive in educational settings. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. Quantitative assessment of cancer cell morphology and motility using telecentric digital holographic microscopy and machine learning.

    PubMed

    Lam, Van K; Nguyen, Thanh C; Chung, Byung M; Nehmetallah, George; Raub, Christopher B

    2018-03-01

    The noninvasive, fast acquisition of quantitative phase maps using digital holographic microscopy (DHM) allows tracking of rapid cellular motility on transparent substrates. On two-dimensional surfaces in vitro, MDA-MB-231 cancer cells assume several morphologies related to the mode of migration and substrate stiffness, relevant to mechanisms of cancer invasiveness in vivo. The quantitative phase information from DHM may accurately classify adhesive cancer cell subpopulations with clinical relevance. To test this, cells from the invasive breast cancer MDA-MB-231 cell line were cultured on glass, tissue-culture treated polystyrene, and collagen hydrogels, and imaged with DHM followed by epifluorescence microscopy after staining F-actin and nuclei. Trends in cell phase parameters were tracked on the different substrates, during cell division, and during matrix adhesion, relating them to F-actin features. Support vector machine learning algorithms were trained and tested using parameters from holographic phase reconstructions and cell geometric features from conventional phase images, and used to distinguish between elongated and rounded cell morphologies. DHM was able to distinguish between elongated and rounded morphologies of MDA-MB-231 cells with 94% accuracy, compared to 83% accuracy using cell geometric features from conventional brightfield microscopy. This finding indicates the potential of DHM to detect and monitor cancer cell morphologies relevant to cell cycle phase status, substrate adhesion, and motility. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

  19. Quantitative Clinical Diagnostic Analysis of Acetone in Human Blood by HPLC: A Metabolomic Search for Acetone as Indicator

    PubMed Central

    Akgul Kalkan, Esin; Sahiner, Mehtap; Ulker Cakir, Dilek; Alpaslan, Duygu; Yilmaz, Selehattin

    2016-01-01

    Using high-performance liquid chromatography (HPLC) and 2,4-dinitrophenylhydrazine (2,4-DNPH) as a derivatizing reagent, an analytical method was developed for the quantitative determination of acetone in human blood. The determination was carried out at 365 nm using an ultraviolet-visible (UV-Vis) diode array detector (DAD). For acetone as its 2,4-dinitrophenylhydrazone derivative, a good separation was achieved with a ThermoAcclaim C18 column (15 cm × 4.6 mm × 3 μm) at retention time (t R) 12.10 min and flowrate of 1 mL min−1 using a (methanol/acetonitrile) water elution gradient. The methodology is simple, rapid, sensitive, and of low cost, exhibits good reproducibility, and allows the analysis of acetone in biological fluids. A calibration curve was obtained for acetone using its standard solutions in acetonitrile. Quantitative analysis of acetone in human blood was successfully carried out using this calibration graph. The applied method was validated in parameters of linearity, limit of detection and quantification, accuracy, and precision. We also present acetone as a useful tool for the HPLC-based metabolomic investigation of endogenous metabolism and quantitative clinical diagnostic analysis. PMID:27298750

  20. Evaluation of airway protection: Quantitative timing measures versus penetration/aspiration score.

    PubMed

    Kendall, Katherine A

    2017-10-01

    Quantitative measures of swallowing function may improve the reliability and accuracy of modified barium swallow (MBS) study interpretation. Quantitative study analysis has not been widely instituted, however, secondary to concerns about the time required to make measures and a lack of research demonstrating impact on MBS interpretation. This study compares the accuracy of the penetration/aspiration (PEN/ASP) scale (an observational visual-perceptual assessment tool) to quantitative measures of airway closure timing relative to the arrival of the bolus at the upper esophageal sphincter in identifying a failure of airway protection during deglutition. Retrospective review of clinical swallowing data from a university-based outpatient clinic. Swallowing data from 426 patients were reviewed. Patients with normal PEN/ASP scores were identified, and the results of quantitative airway closure timing measures for three liquid bolus sizes were evaluated. The incidence of significant airway closure delay with and without a normal PEN/ASP score was determined. Inter-rater reliability for the quantitative measures was calculated. In patients with a normal PEN/ASP score, 33% demonstrated a delay in airway closure on at least one swallow during the MBS study. There was no correlation between PEN/ASP score and airway closure delay. Inter-rater reliability for the quantitative measure of airway closure timing was nearly perfect (intraclass correlation coefficient = 0.973). The use of quantitative measures of swallowing function, in conjunction with traditional visual perceptual methods of MBS study interpretation, improves the identification of airway closure delay, and hence, potential aspiration risk, even when no penetration or aspiration is apparent on the MBS study. 4. Laryngoscope, 127:2314-2318, 2017. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  1. Comparative Performance of Reagents and Platforms for Quantitation of Cytomegalovirus DNA by Digital PCR

    PubMed Central

    Gu, Z.; Sam, S. S.; Sun, Y.; Tang, L.; Pounds, S.; Caliendo, A. M.

    2016-01-01

    A potential benefit of digital PCR is a reduction in result variability across assays and platforms. Three sets of PCR reagents were tested on two digital PCR systems (Bio-Rad and RainDance), using three different sets of PCR reagents for quantitation of cytomegalovirus (CMV). Both commercial quantitative viral standards and 16 patient samples (n = 16) were tested. Quantitative accuracy (compared to nominal values) and variability were determined based on viral standard testing results. Quantitative correlation and variability were assessed with pairwise comparisons across all reagent-platform combinations for clinical plasma sample results. The three reagent sets, when used to assay quantitative standards on the Bio-Rad system, all showed a high degree of accuracy, low variability, and close agreement with one another. When used on the RainDance system, one of the three reagent sets appeared to have a much better correlation to nominal values than did the other two. Quantitative results for patient samples showed good correlation in most pairwise comparisons, with some showing poorer correlations when testing samples with low viral loads. Digital PCR is a robust method for measuring CMV viral load. Some degree of result variation may be seen, depending on platform and reagents used; this variation appears to be greater in samples with low viral load values. PMID:27535685

  2. Pharmacometabolomics Informs Quantitative Radiomics for Glioblastoma Diagnostic Innovation.

    PubMed

    Katsila, Theodora; Matsoukas, Minos-Timotheos; Patrinos, George P; Kardamakis, Dimitrios

    2017-08-01

    Applications of omics systems biology technologies have enormous promise for radiology and diagnostics in surgical fields. In this context, the emerging fields of radiomics (a systems scale approach to radiology using a host of technologies, including omics) and pharmacometabolomics (use of metabolomics for patient and disease stratification and guiding precision medicine) offer much synergy for diagnostic innovation in surgery, particularly in neurosurgery. This synthesis of omics fields and applications is timely because diagnostic accuracy in central nervous system tumors still challenges decision-making. Considering the vast heterogeneity in brain tumors, disease phenotypes, and interindividual variability in surgical and chemotherapy outcomes, we believe that diagnostic accuracy can be markedly improved by quantitative radiomics coupled to pharmacometabolomics and related health information technologies while optimizing economic costs of traditional diagnostics. In this expert review, we present an innovation analysis on a systems-level multi-omics approach toward diagnostic accuracy in central nervous system tumors. For this, we suggest that glioblastomas serve as a useful application paradigm. We performed a literature search on PubMed for articles published in English between 2006 and 2016. We used the search terms "radiomics," "glioblastoma," "biomarkers," "pharmacogenomics," "pharmacometabolomics," "pharmacometabonomics/pharmacometabolomics," "collaborative informatics," and "precision medicine." A list of the top 4 insights we derived from this literature analysis is presented in this study. For example, we found that (i) tumor grading needs to be better refined, (ii) diagnostic precision should be improved, (iii) standardization in radiomics is lacking, and (iv) quantitative radiomics needs to prove clinical implementation. We conclude with an interdisciplinary call to the metabolomics, pharmacy/pharmacology, radiology, and surgery communities that

  3. The accuracy of Genomic Selection in Norwegian red cattle assessed by cross-validation.

    PubMed

    Luan, Tu; Woolliams, John A; Lien, Sigbjørn; Kent, Matthew; Svendsen, Morten; Meuwissen, Theo H E

    2009-11-01

    Genomic Selection (GS) is a newly developed tool for the estimation of breeding values for quantitative traits through the use of dense markers covering the whole genome. For a successful application of GS, accuracy of the prediction of genomewide breeding value (GW-EBV) is a key issue to consider. Here we investigated the accuracy and possible bias of GW-EBV prediction, using real bovine SNP genotyping (18,991 SNPs) and phenotypic data of 500 Norwegian Red bulls. The study was performed on milk yield, fat yield, protein yield, first lactation mastitis traits, and calving ease. Three methods, best linear unbiased prediction (G-BLUP), Bayesian statistics (BayesB), and a mixture model approach (MIXTURE), were used to estimate marker effects, and their accuracy and bias were estimated by using cross-validation. The accuracies of the GW-EBV prediction were found to vary widely between 0.12 and 0.62. G-BLUP gave overall the highest accuracy. We observed a strong relationship between the accuracy of the prediction and the heritability of the trait. GW-EBV prediction for production traits with high heritability achieved higher accuracy and also lower bias than health traits with low heritability. To achieve a similar accuracy for the health traits probably more records will be needed.

  4. Quantitative analysis of professionally trained versus untrained voices.

    PubMed

    Siupsinskiene, Nora

    2003-01-01

    The aim of this study was to compare healthy trained and untrained voices as well as healthy and dysphonic trained voices in adults using combined voice range profile and aerodynamic tests, to define the normal range limiting values of quantitative voice parameters and to select the most informative quantitative voice parameters for separation between healthy and dysphonic trained voices. Three groups of persons were evaluated. One hundred eighty six healthy volunteers were divided into two groups according to voice training: non-professional speakers group consisted of 106 untrained voices persons (36 males and 70 females) and professional speakers group--of 80 trained voices persons (21 males and 59 females). Clinical group consisted of 103 dysphonic professional speakers (23 males and 80 females) with various voice disorders. Eighteen quantitative voice parameters from combined voice range profile (VRP) test were analyzed: 8 of voice range profile, 8 of speaking voice, overall vocal dysfunction degree and coefficient of sound, and aerodynamic maximum phonation time. Analysis showed that healthy professional speakers demonstrated expanded vocal abilities in comparison to healthy non-professional speakers. Quantitative voice range profile parameters- pitch range, high frequency limit, area of high frequencies and coefficient of sound differed significantly between healthy professional and non-professional voices, and were more informative than speaking voice or aerodynamic parameters in showing the voice training. Logistic stepwise regression revealed that VRP area in high frequencies was sufficient to discriminate between healthy and dysphonic professional speakers for male subjects (overall discrimination accuracy--81.8%) and combination of three quantitative parameters (VRP high frequency limit, maximum voice intensity and slope of speaking curve) for female subjects (overall model discrimination accuracy--75.4%). We concluded that quantitative voice assessment

  5. Principles of Quantitative MR Imaging with Illustrated Review of Applicable Modular Pulse Diagrams.

    PubMed

    Mills, Andrew F; Sakai, Osamu; Anderson, Stephan W; Jara, Hernan

    2017-01-01

    Continued improvements in diagnostic accuracy using magnetic resonance (MR) imaging will require development of methods for tissue analysis that complement traditional qualitative MR imaging studies. Quantitative MR imaging is based on measurement and interpretation of tissue-specific parameters independent of experimental design, compared with qualitative MR imaging, which relies on interpretation of tissue contrast that results from experimental pulse sequence parameters. Quantitative MR imaging represents a natural next step in the evolution of MR imaging practice, since quantitative MR imaging data can be acquired using currently available qualitative imaging pulse sequences without modifications to imaging equipment. The article presents a review of the basic physical concepts used in MR imaging and how quantitative MR imaging is distinct from qualitative MR imaging. Subsequently, the article reviews the hierarchical organization of major applicable pulse sequences used in this article, with the sequences organized into conventional, hybrid, and multispectral sequences capable of calculating the main tissue parameters of T1, T2, and proton density. While this new concept offers the potential for improved diagnostic accuracy and workflow, awareness of this extension to qualitative imaging is generally low. This article reviews the basic physical concepts in MR imaging, describes commonly measured tissue parameters in quantitative MR imaging, and presents the major available pulse sequences used for quantitative MR imaging, with a focus on the hierarchical organization of these sequences. © RSNA, 2017.

  6. Accuracy of the Medication Adherence Report Scale (MARS-5) as a quantitative measure of adherence to inhalation medication in patients with COPD.

    PubMed

    Tommelein, Eline; Mehuys, Els; Van Tongelen, Inge; Brusselle, Guy; Boussery, Koen

    2014-05-01

    Self-report is considered most suitable to measure medication adherence in routine clinical practice. However, accuracy of self-report as a quantitative measure of adherence is not well documented. To assess the accuracy of a self-report measure of adherence (Medication Adherence Report Scale [MARS-5]) for identifying nonadherent users of inhalation medication among patients with chronic obstructive pulmonary disease (COPD), compared with medication refill adherence (MRA) as reference. We used baseline data from the Pharmaceutical Care for Patients with COPD (PHARMACOP)-trial (n = 734). Patients with incomplete MARS-5 and/or incomplete pharmacy refill records were excluded (n = 121). Internal consistency of MARS-5 (Crohnbach α) and Spearman rank correlation (ρ) with MRA were calculated. Different thresholds for nonadherence were used to calculate sensitivity, specificity, and positive predictive value (PPV), compared with dichotomized MRA (MRA ≥80% = adherent). A receiver operating characteristic (ROC) curve was plotted to determine the goodness of test. 613 patients were included in the analysis. The mean adherence score by MARS-5 (range = 5-25) was 23.5 (SD = 2.6); mean adherence by MRA was 83.4% (SD = 23.8%). Internal consistency of MARS-5 was high (α = 0.77). Continuous MARS-5 scores correlated poorly with continuous MRA scores (ρ = 0.10; P = 0.011). When lowering the nonadherence threshold stepwise from 25 to 20, MARS-5 did not reach sufficient sensitivity (53% to 13%), specificity (57% to 94%), and PPV (42% to 57%) to detect nonadherers compared with dichotomized MRA. ROC curve plotting resulted in an area under the curve value of 0.56 (95% CI = 0.521-0.616; P = 0.005). Self-reported adherence measured by MARS-5 is inaccurate in identifying nonadherence to inhalation medication in patients with COPD.

  7. Effects of calibration methods on quantitative material decomposition in photon-counting spectral computed tomography using a maximum a posteriori estimator.

    PubMed

    Curtis, Tyler E; Roeder, Ryan K

    2017-10-01

    Advances in photon-counting detectors have enabled quantitative material decomposition using multi-energy or spectral computed tomography (CT). Supervised methods for material decomposition utilize an estimated attenuation for each material of interest at each photon energy level, which must be calibrated based upon calculated or measured values for known compositions. Measurements using a calibration phantom can advantageously account for system-specific noise, but the effect of calibration methods on the material basis matrix and subsequent quantitative material decomposition has not been experimentally investigated. Therefore, the objective of this study was to investigate the influence of the range and number of contrast agent concentrations within a modular calibration phantom on the accuracy of quantitative material decomposition in the image domain. Gadolinium was chosen as a model contrast agent in imaging phantoms, which also contained bone tissue and water as negative controls. The maximum gadolinium concentration (30, 60, and 90 mM) and total number of concentrations (2, 4, and 7) were independently varied to systematically investigate effects of the material basis matrix and scaling factor calibration on the quantitative (root mean squared error, RMSE) and spatial (sensitivity and specificity) accuracy of material decomposition. Images of calibration and sample phantoms were acquired using a commercially available photon-counting spectral micro-CT system with five energy bins selected to normalize photon counts and leverage the contrast agent k-edge. Material decomposition of gadolinium, calcium, and water was performed for each calibration method using a maximum a posteriori estimator. Both the quantitative and spatial accuracy of material decomposition were most improved by using an increased maximum gadolinium concentration (range) in the basis matrix calibration; the effects of using a greater number of concentrations were relatively small in

  8. Studying learning in the healthcare setting: the potential of quantitative diary methods.

    PubMed

    Ciere, Yvette; Jaarsma, Debbie; Visser, Annemieke; Sanderman, Robbert; Snippe, Evelien; Fleer, Joke

    2015-08-01

    Quantitative diary methods are longitudinal approaches that involve the repeated measurement of aspects of peoples' experience of daily life. In this article, we outline the main characteristics and applications of quantitative diary methods and discuss how their use may further research in the field of medical education. Quantitative diary methods offer several methodological advantages, such as measuring aspects of learning with great detail, accuracy and authenticity. Moreover, they enable researchers to study how and under which conditions learning in the health care setting occurs and in which way learning can be promoted. Hence, quantitative diary methods may contribute to theory development and the optimization of teaching methods in medical education.

  9. Fundus autofluorescence imaging: systematic review of test accuracy for the diagnosis and monitoring of retinal conditions.

    PubMed

    Frampton, G K; Kalita, N; Payne, L; Colquitt, J L; Loveman, E; Downes, S M; Lotery, A J

    2017-07-01

    We conducted a systematic review of the accuracy of fundus autofluorescence (FAF) imaging for diagnosing and monitoring retinal conditions. Searches in November 2014 identified English language references. Sources included MEDLINE, EMBASE, the Cochrane Library, Web of Science, and MEDION databases; reference lists of retrieved studies; and internet pages of relevant organisations, meetings, and trial registries. For inclusion, studies had to report FAF imaging accuracy quantitatively. Studies were critically appraised using QUADAS risk of bias criteria. Two reviewers conducted all review steps. From 2240 unique references identified, eight primary research studies met the inclusion criteria. These investigated diagnostic accuracy of FAF imaging for choroidal neovascularisation (one study), reticular pseudodrusen (three studies), cystoid macular oedema (two studies), and diabetic macular oedema (two studies). Diagnostic sensitivity of FAF imaging ranged from 32 to 100% and specificity from 34 to 100%. However, owing to methodological limitations, including high and/or unclear risks of bias, none of these studies provides conclusive evidence of the diagnostic accuracy of FAF imaging. Study heterogeneity precluded meta-analysis. In most studies, the patient spectrum was not reflective of those who would present in clinical practice and no studies adequately reported whether FAF images were interpreted consistently. No studies of monitoring accuracy were identified. An update in October 2016, based on MEDLINE and internet searches, identified four new studies but did not alter our conclusions. Robust quantitative evidence on the accuracy of FAF imaging and how FAF images are interpreted is lacking. We provide recommendations to address this.

  10. Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements

    PubMed Central

    Coltharp, Carla; Kessler, Rene P.; Xiao, Jie

    2012-01-01

    Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (tThresh and dThresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and

  11. MR Fingerprinting for Rapid Quantitative Abdominal Imaging

    PubMed Central

    Chen, Yong; Jiang, Yun; Pahwa, Shivani; Ma, Dan; Lu, Lan; Twieg, Michael D.; Wright, Katherine L.; Seiberlich, Nicole; Griswold, Mark A.

    2016-01-01

    Purpose To develop a magnetic resonance (MR) “fingerprinting” technique for quantitative abdominal imaging. Materials and Methods This HIPAA-compliant study had institutional review board approval, and informed consent was obtained from all subjects. To achieve accurate quantification in the presence of marked B0 and B1 field inhomogeneities, the MR fingerprinting framework was extended by using a two-dimensional fast imaging with steady-state free precession, or FISP, acquisition and a Bloch-Siegert B1 mapping method. The accuracy of the proposed technique was validated by using agarose phantoms. Quantitative measurements were performed in eight asymptomatic subjects and in six patients with 20 focal liver lesions. A two-tailed Student t test was used to compare the T1 and T2 results in metastatic adenocarcinoma with those in surrounding liver parenchyma and healthy subjects. Results Phantom experiments showed good agreement with standard methods in T1 and T2 after B1 correction. In vivo studies demonstrated that quantitative T1, T2, and B1 maps can be acquired within a breath hold of approximately 19 seconds. T1 and T2 measurements were compatible with those in the literature. Representative values included the following: liver, 745 msec ± 65 (standard deviation) and 31 msec ± 6; renal medulla, 1702 msec ± 205 and 60 msec ± 21; renal cortex, 1314 msec ± 77 and 47 msec ± 10; spleen, 1232 msec ± 92 and 60 msec ± 19; skeletal muscle, 1100 msec ± 59 and 44 msec ± 9; and fat, 253 msec ± 42 and 77 msec ± 16, respectively. T1 and T2 in metastatic adenocarcinoma were 1673 msec ± 331 and 43 msec ± 13, respectively, significantly different from surrounding liver parenchyma relaxation times of 840 msec ± 113 and 28 msec ± 3 (P < .0001 and P < .01) and those in hepatic parenchyma in healthy volunteers (745 msec ± 65 and 31 msec ± 6, P < .0001 and P = .021, respectively). Conclusion A rapid technique for quantitative abdominal imaging was developed that

  12. MR Fingerprinting for Rapid Quantitative Abdominal Imaging.

    PubMed

    Chen, Yong; Jiang, Yun; Pahwa, Shivani; Ma, Dan; Lu, Lan; Twieg, Michael D; Wright, Katherine L; Seiberlich, Nicole; Griswold, Mark A; Gulani, Vikas

    2016-04-01

    To develop a magnetic resonance (MR) "fingerprinting" technique for quantitative abdominal imaging. This HIPAA-compliant study had institutional review board approval, and informed consent was obtained from all subjects. To achieve accurate quantification in the presence of marked B0 and B1 field inhomogeneities, the MR fingerprinting framework was extended by using a two-dimensional fast imaging with steady-state free precession, or FISP, acquisition and a Bloch-Siegert B1 mapping method. The accuracy of the proposed technique was validated by using agarose phantoms. Quantitative measurements were performed in eight asymptomatic subjects and in six patients with 20 focal liver lesions. A two-tailed Student t test was used to compare the T1 and T2 results in metastatic adenocarcinoma with those in surrounding liver parenchyma and healthy subjects. Phantom experiments showed good agreement with standard methods in T1 and T2 after B1 correction. In vivo studies demonstrated that quantitative T1, T2, and B1 maps can be acquired within a breath hold of approximately 19 seconds. T1 and T2 measurements were compatible with those in the literature. Representative values included the following: liver, 745 msec ± 65 (standard deviation) and 31 msec ± 6; renal medulla, 1702 msec ± 205 and 60 msec ± 21; renal cortex, 1314 msec ± 77 and 47 msec ± 10; spleen, 1232 msec ± 92 and 60 msec ± 19; skeletal muscle, 1100 msec ± 59 and 44 msec ± 9; and fat, 253 msec ± 42 and 77 msec ± 16, respectively. T1 and T2 in metastatic adenocarcinoma were 1673 msec ± 331 and 43 msec ± 13, respectively, significantly different from surrounding liver parenchyma relaxation times of 840 msec ± 113 and 28 msec ± 3 (P < .0001 and P < .01) and those in hepatic parenchyma in healthy volunteers (745 msec ± 65 and 31 msec ± 6, P < .0001 and P = .021, respectively). A rapid technique for quantitative abdominal imaging was developed that allows simultaneous quantification of multiple tissue

  13. Impact of high 131I-activities on quantitative 124I-PET

    NASA Astrophysics Data System (ADS)

    Braad, P. E. N.; Hansen, S. B.; Høilund-Carlsen, P. F.

    2015-07-01

    Peri-therapeutic 124 I-PET/CT is of interest as guidance for radioiodine therapy. Unfortunately, image quality is complicated by dead time effects and increased random coincidence rates from high 131 I-activities. A series of phantom experiments with clinically relevant 124 I/131 I-activities were performed on a clinical PET/CT-system. Noise equivalent count rate (NECR) curves and quantitation accuracy were determined from repeated scans performed over several weeks on a decaying NEMA NU-2 1994 cylinder phantom initially filled with 25 MBq 124 I and 1250 MBq 131 I. Six spherical inserts with diameters 10-37 mm were filled with 124 I (0.45 MBq ml-1 ) and 131 I (22 MBq ml-1 ) and placed inside the background of the NEMA/IEC torso phantom. Contrast recovery, background variability and the accuracy of scatter and attenuation corrections were assessed at sphere-to-background activity ratios of 20, 10 and 5. Results were compared to pure 124 I-acquisitions. The quality of 124 I-PET images in the presence of high 131 I-activities was good and image quantification unaffected except at very high count rates. Quantitation accuracy and contrast recovery were uninfluenced at 131 I-activities below 1000 MBq, whereas image noise was slightly increased. The NECR peaked at 550 MBq of 131 I, where it was 2.8 times lower than without 131 I in the phantom. Quantitative peri-therapeutic 124 I-PET is feasible.

  14. Validation of the Mass-Extraction-Window for Quantitative Methods Using Liquid Chromatography High Resolution Mass Spectrometry.

    PubMed

    Glauser, Gaétan; Grund, Baptiste; Gassner, Anne-Laure; Menin, Laure; Henry, Hugues; Bromirski, Maciej; Schütz, Frédéric; McMullen, Justin; Rochat, Bertrand

    2016-03-15

    A paradigm shift is underway in the field of quantitative liquid chromatography-mass spectrometry (LC-MS) analysis thanks to the arrival of recent high-resolution mass spectrometers (HRMS). The capability of HRMS to perform sensitive and reliable quantifications of a large variety of analytes in HR-full scan mode is showing that it is now realistic to perform quantitative and qualitative analysis with the same instrument. Moreover, HR-full scan acquisition offers a global view of sample extracts and allows retrospective investigations as virtually all ionized compounds are detected with a high sensitivity. In time, the versatility of HRMS together with the increasing need for relative quantification of hundreds of endogenous metabolites should promote a shift from triple-quadrupole MS to HRMS. However, a current "pitfall" in quantitative LC-HRMS analysis is the lack of HRMS-specific guidance for validated quantitative analyses. Indeed, false positive and false negative HRMS detections are rare, albeit possible, if inadequate parameters are used. Here, we investigated two key parameters for the validation of LC-HRMS quantitative analyses: the mass accuracy (MA) and the mass-extraction-window (MEW) that is used to construct the extracted-ion-chromatograms. We propose MA-parameters, graphs, and equations to calculate rational MEW width for the validation of quantitative LC-HRMS methods. MA measurements were performed on four different LC-HRMS platforms. Experimentally determined MEW values ranged between 5.6 and 16.5 ppm and depended on the HRMS platform, its working environment, the calibration procedure, and the analyte considered. The proposed procedure provides a fit-for-purpose MEW determination and prevents false detections.

  15. The Accuracy of Student Self-Assessments of English-Chinese Bidirectional Interpretation: A Longitudinal Quantitative Study

    ERIC Educational Resources Information Center

    Han, Chao; Riazi, Mehdi

    2018-01-01

    The accuracy of self-assessment has long been examined empirically in higher education research, producing a substantial body of literature that casts light on numerous potential moderators. However, despite the growing popularity of self-assessment in interpreter training and education, very limited evidence-based research has been initiated to…

  16. Collection of quantitative chemical release field data.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Demirgian, J.; Macha, S.; Loyola Univ.

    1999-01-01

    Detection and quantitation of chemicals in the environment requires Fourier-transform infrared (FTIR) instruments that are properly calibrated and tested. This calibration and testing requires field testing using matrices that are representative of actual instrument use conditions. Three methods commonly used for developing calibration files and training sets in the field are a closed optical cell or chamber, a large-scale chemical release, and a small-scale chemical release. There is no best method. The advantages and limitations of each method should be considered in evaluating field results. Proper calibration characterizes the sensitivity of an instrument, its ability to detect a component inmore » different matrices, and the quantitative accuracy and precision of the results.« less

  17. Multistrip Western blotting: a tool for comparative quantitative analysis of multiple proteins.

    PubMed

    Aksamitiene, Edita; Hoek, Jan B; Kiyatkin, Anatoly

    2015-01-01

    The qualitative and quantitative measurements of protein abundance and modification states are essential in understanding their functions in diverse cellular processes. Typical Western blotting, though sensitive, is prone to produce substantial errors and is not readily adapted to high-throughput technologies. Multistrip Western blotting is a modified immunoblotting procedure based on simultaneous electrophoretic transfer of proteins from multiple strips of polyacrylamide gels to a single membrane sheet. In comparison with the conventional technique, Multistrip Western blotting increases data output per single blotting cycle up to tenfold; allows concurrent measurement of up to nine different total and/or posttranslationally modified protein expression obtained from the same loading of the sample; and substantially improves the data accuracy by reducing immunoblotting-derived signal errors. This approach enables statistically reliable comparison of different or repeated sets of data and therefore is advantageous to apply in biomedical diagnostics, systems biology, and cell signaling research.

  18. Automated Quantitative Nuclear Cardiology Methods

    PubMed Central

    Motwani, Manish; Berman, Daniel S.; Germano, Guido; Slomka, Piotr J.

    2016-01-01

    Quantitative analysis of SPECT and PET has become a major part of nuclear cardiology practice. Current software tools can automatically segment the left ventricle, quantify function, establish myocardial perfusion maps and estimate global and local measures of stress/rest perfusion – all with minimal user input. State-of-the-art automated techniques have been shown to offer high diagnostic accuracy for detecting coronary artery disease, as well as predict prognostic outcomes. This chapter briefly reviews these techniques, highlights several challenges and discusses the latest developments. PMID:26590779

  19. Accurate virus quantitation using a Scanning Transmission Electron Microscopy (STEM) detector in a scanning electron microscope.

    PubMed

    Blancett, Candace D; Fetterer, David P; Koistinen, Keith A; Morazzani, Elaine M; Monninger, Mitchell K; Piper, Ashley E; Kuehl, Kathleen A; Kearney, Brian J; Norris, Sarah L; Rossi, Cynthia A; Glass, Pamela J; Sun, Mei G

    2017-10-01

    A method for accurate quantitation of virus particles has long been sought, but a perfect method still eludes the scientific community. Electron Microscopy (EM) quantitation is a valuable technique because it provides direct morphology information and counts of all viral particles, whether or not they are infectious. In the past, EM negative stain quantitation methods have been cited as inaccurate, non-reproducible, and with detection limits that were too high to be useful. To improve accuracy and reproducibility, we have developed a method termed Scanning Transmission Electron Microscopy - Virus Quantitation (STEM-VQ), which simplifies sample preparation and uses a high throughput STEM detector in a Scanning Electron Microscope (SEM) coupled with commercially available software. In this paper, we demonstrate STEM-VQ with an alphavirus stock preparation to present the method's accuracy and reproducibility, including a comparison of STEM-VQ to viral plaque assay and the ViroCyt Virus Counter. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  20. Comparative study of contrast-enhanced ultrasound qualitative and quantitative analysis for identifying benign and malignant breast tumor lumps.

    PubMed

    Liu, Jian; Gao, Yun-Hua; Li, Ding-Dong; Gao, Yan-Chun; Hou, Ling-Mi; Xie, Ting

    2014-01-01

    To compare the value of contrast-enhanced ultrasound (CEUS) qualitative and quantitative analysis in the identification of breast tumor lumps. Qualitative and quantitative indicators of CEUS for 73 cases of breast tumor lumps were retrospectively analyzed by univariate and multivariate approaches. Logistic regression was applied and ROC curves were drawn for evaluation and comparison. The CEUS qualitative indicator-generated regression equation contained three indicators, namely enhanced homogeneity, diameter line expansion and peak intensity grading, which demonstrated prediction accuracy for benign and malignant breast tumor lumps of 91.8%; the quantitative indicator-generated regression equation only contained one indicator, namely the relative peak intensity, and its prediction accuracy was 61.5%. The corresponding areas under the ROC curve for qualitative and quantitative analyses were 91.3% and 75.7%, respectively, which exhibited a statistically significant difference by the Z test (P<0.05). The ability of CEUS qualitative analysis to identify breast tumor lumps is better than with quantitative analysis.

  1. Quantitative analysis of peel-off degree for printed electronics

    NASA Astrophysics Data System (ADS)

    Park, Janghoon; Lee, Jongsu; Sung, Ki-Hak; Shin, Kee-Hyun; Kang, Hyunkyoo

    2018-02-01

    We suggest a facile methodology of peel-off degree evaluation by image processing on printed electronics. The quantification of peeled and printed areas was performed using open source programs. To verify the accuracy of methods, we manually removed areas from the printed circuit that was measured, resulting in 96.3% accuracy. The sintered patterns showed a decreasing tendency in accordance with the increase in the energy density of an infrared lamp, and the peel-off degree increased. Thus, the comparison between both results was presented. Finally, the correlation between performance characteristics was determined by quantitative analysis.

  2. A New Algorithm Using Cross-Assignment for Label-Free Quantitation with LC/LTQ-FT MS

    PubMed Central

    Andreev, Victor P.; Li, Lingyun; Cao, Lei; Gu, Ye; Rejtar, Tomas; Wu, Shiaw-Lin; Karger, Barry L.

    2008-01-01

    A new algorithm is described for label-free quantitation of relative protein abundances across multiple complex proteomic samples. Q-MEND is based on the denoising and peak picking algorithm, MEND, previously developed in our laboratory. Q-MEND takes advantage of the high resolution and mass accuracy of the hybrid LTQFT MS mass spectrometer (or other high resolution mass spectrometers, such as a Q-TOF MS). The strategy, termed “cross-assignment”, is introduced to increase substantially the number of quantitated proteins. In this approach, all MS/MS identifications for the set of analyzed samples are combined into a master ID list, and then each LC/MS run is searched for the features that can be assigned to a specific identification from that master list. The reliability of quantitation is enhanced by quantitating separately all peptide charge states, along with a scoring procedure to filter out less reliable peptide abundance measurements. The effectiveness of Q-MEND is illustrated in the relative quantitative analysis of E.coli samples spiked with known amounts of non-E.coli protein digests. A mean quantitation accuracy of 7% and mean precision of 15% is demonstrated. Q-MEND can perform relative quantitation of a set of LC/MS datasets without manual intervention and can generate files compatible with the Guidelines for Proteomic Data Publication. PMID:17441747

  3. A new algorithm using cross-assignment for label-free quantitation with LC-LTQ-FT MS.

    PubMed

    Andreev, Victor P; Li, Lingyun; Cao, Lei; Gu, Ye; Rejtar, Tomas; Wu, Shiaw-Lin; Karger, Barry L

    2007-06-01

    A new algorithm is described for label-free quantitation of relative protein abundances across multiple complex proteomic samples. Q-MEND is based on the denoising and peak picking algorithm, MEND, previously developed in our laboratory. Q-MEND takes advantage of the high resolution and mass accuracy of the hybrid LTQ-FT MS mass spectrometer (or other high-resolution mass spectrometers, such as a Q-TOF MS). The strategy, termed "cross-assignment", is introduced to increase substantially the number of quantitated proteins. In this approach, all MS/MS identifications for the set of analyzed samples are combined into a master ID list, and then each LC-MS run is searched for the features that can be assigned to a specific identification from that master list. The reliability of quantitation is enhanced by quantitating separately all peptide charge states, along with a scoring procedure to filter out less reliable peptide abundance measurements. The effectiveness of Q-MEND is illustrated in the relative quantitative analysis of Escherichia coli samples spiked with known amounts of non-E. coli protein digests. A mean quantitation accuracy of 7% and mean precision of 15% is demonstrated. Q-MEND can perform relative quantitation of a set of LC-MS data sets without manual intervention and can generate files compatible with the Guidelines for Proteomic Data Publication.

  4. Towards quantitative classification of folded proteins in terms of elementary functions.

    PubMed

    Hu, Shuangwei; Krokhotin, Andrei; Niemi, Antti J; Peng, Xubiao

    2011-04-01

    A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a classification scheme that describes a protein starting from its well-organized secondary structures and often involves direct human involvement, with an atomary-level physics-based approach where a protein is fundamentally nothing more than an ensemble of mutually interacting carbon, hydrogen, oxygen, and nitrogen atoms. In order to bridge these two complementary approaches to proteins, conceptually novel tools need to be introduced. Here we explain how an approach toward geometric characterization of entire folded proteins can be based on a single explicit elementary function that is familiar from nonlinear physical systems where it is known as the kink soliton. Our approach enables the conversion of hierarchical structural information into a quantitative form that allows for a folded protein to be characterized in terms of a small number of global parameters that are in principle computable from atomary-level considerations. As an example we describe in detail how the native fold of the myoglobin 1M6C emerges from a combination of kink solitons with a very high atomary-level accuracy. We also verify that our approach describes longer loops and loops connecting α helices with β strands, with the same overall accuracy. ©2011 American Physical Society

  5. Speed-accuracy trade-off in a trajectory-constrained self-feeding task: a quantitative index of unsuppressed motor noise in children with dystonia

    PubMed Central

    Lunardini, Francesca; Bertucco, Matteo; Casellato, Claudia; Bhanpuri, Nasir; Pedrocchi, Alessandra; Sanger, Terence D.

    2015-01-01

    Motor speed and accuracy are both affected in childhood dystonia. Thus, deriving a speed-accuracy function is an important metric for assessing motor impairments in dystonia. Previous work in dystonia studied the speed-accuracy trade-off during point-to-point tasks. To achieve a more relevant measurement of functional abilities in dystonia, the present study investigates upper-limb kinematics and electromyographic activity of 8 children with dystonia and 8 healthy children during a trajectory-constrained child-relevant task that emulates self-feeding with a spoon and requires continuous monitoring of accuracy. The speed-accuracy trade-off is examined by changing the spoon size to create different accuracy demands. Results demonstrate that the trajectory-constrained speed-accuracy relation is present in both groups, but it is altered in dystonia in terms of increased slope and offset towards longer movement times. Findings are consistent with the hypothesis of increased signal-dependent noise in dystonia, which may partially explain the slow and variable movements observed in dystonia. PMID:25895910

  6. Quantitative fluorescence tomography using a trimodality system: in vivo validation

    PubMed Central

    Lin, Yuting; Barber, William C.; Iwanczyk, Jan S.; Roeck, Werner W.; Nalcioglu, Orhan; Gulsen, Gultekin

    2010-01-01

    A fully integrated trimodality fluorescence, diffuse optical, and x-ray computed tomography (FT∕DOT∕XCT) system for small animal imaging is reported in this work. The main purpose of this system is to obtain quantitatively accurate fluorescence concentration images using a multimodality approach. XCT offers anatomical information, while DOT provides the necessary background optical property map to improve FT image accuracy. The quantitative accuracy of this trimodality system is demonstrated in vivo. In particular, we show that a 2-mm-diam fluorescence inclusion located 8 mm deep in a nude mouse can only be localized when functional a priori information from DOT is available. However, the error in the recovered fluorophore concentration is nearly 87%. On the other hand, the fluorophore concentration can be accurately recovered within 2% error when both DOT functional and XCT structural a priori information are utilized together to guide and constrain the FT reconstruction algorithm. PMID:20799770

  7. Analysis on detection accuracy of binocular photoelectric instrument optical axis parallelism digital calibration instrument

    NASA Astrophysics Data System (ADS)

    Ying, Jia-ju; Yin, Jian-ling; Wu, Dong-sheng; Liu, Jie; Chen, Yu-dan

    2017-11-01

    Low-light level night vision device and thermal infrared imaging binocular photoelectric instrument are used widely. The maladjustment of binocular instrument ocular axises parallelism will cause the observer the symptom such as dizziness, nausea, when use for a long time. Binocular photoelectric equipment digital calibration instrument is developed for detecting ocular axises parallelism. And the quantitative value of optical axis deviation can be quantitatively measured. As a testing instrument, the precision must be much higher than the standard of test instrument. Analyzes the factors that influence the accuracy of detection. Factors exist in each testing process link which affect the precision of the detecting instrument. They can be divided into two categories, one category is factors which directly affect the position of reticle image, the other category is factors which affect the calculation the center of reticle image. And the Synthesize error is calculated out. And further distribute the errors reasonably to ensure the accuracy of calibration instruments.

  8. A GATE evaluation of the sources of error in quantitative {sup 90}Y PET

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Strydhorst, Jared, E-mail: jared.strydhorst@gmail.

    Purpose: Accurate reconstruction of the dose delivered by {sup 90}Y microspheres using a postembolization PET scan would permit the establishment of more accurate dose–response relationships for treatment of hepatocellular carcinoma with {sup 90}Y. However, the quality of the PET data obtained is compromised by several factors, including poor count statistics and a very high random fraction. This work uses Monte Carlo simulations to investigate what impact factors other than low count statistics have on the quantification of {sup 90}Y PET. Methods: PET acquisitions of two phantoms—a NEMA PET phantom and the NEMA IEC PET body phantom-containing either {sup 90}Y ormore » {sup 18}F were simulated using GATE. Simulated projections were created with subsets of the simulation data allowing the contributions of random, scatter, and LSO background to be independently evaluated. The simulated projections were reconstructed using the commercial software for the simulated scanner, and the quantitative accuracy of the reconstruction and the contrast recovery of the reconstructed images were evaluated. Results: The quantitative accuracy of the {sup 90}Y reconstructions were not strongly influenced by the high random fraction present in the projection data, and the activity concentration was recovered to within 5% of the known value. The contrast recovery measured for simulated {sup 90}Y data was slightly poorer than that for simulated {sup 18}F data with similar count statistics. However, the degradation was not strongly linked to any particular factor. Using a more restricted energy range to reduce the random fraction in the projections had no significant effect. Conclusions: Simulations of {sup 90}Y PET confirm that quantitative {sup 90}Y is achievable with the same approach as that used for {sup 18}F, and that there is likely very little margin for improvement by attempting to model aspects unique to {sup 90}Y, such as the much higher random fraction or the presence of

  9. Accuracy Assessment of Professional Grade Unmanned Systems for High Precision Airborne Mapping

    NASA Astrophysics Data System (ADS)

    Mostafa, M. M. R.

    2017-08-01

    Recently, sophisticated multi-sensor systems have been implemented on-board modern Unmanned Aerial Systems. This allows for producing a variety of mapping products for different mapping applications. The resulting accuracies match the traditional well engineered manned systems. This paper presents the results of a geometric accuracy assessment project for unmanned systems equipped with multi-sensor systems for direct georeferencing purposes. There are a number of parameters that either individually or collectively affect the quality and accuracy of a final airborne mapping product. This paper focuses on identifying and explaining these parameters and their mutual interaction and correlation. Accuracy Assessment of the final ground object positioning accuracy is presented through real-world 8 flight missions that were flown in Quebec, Canada. The achievable precision of map production is addressed in some detail.

  10. Illusory expectations can affect retrieval-monitoring accuracy.

    PubMed

    McDonough, Ian M; Gallo, David A

    2012-03-01

    The present study investigated how expectations, even when illusory, can affect the accuracy of memory decisions. Participants studied words presented in large or small font for subsequent memory tests. Replicating prior work, judgments of learning indicated that participants expected to remember large words better than small words, even though memory for these words was equivalent on a standard test of recognition memory and subjective judgments. Critically, we also included tests that instructed participants to selectively search memory for either large or small words, thereby allowing different memorial expectations to contribute to performance. On these tests we found reduced false recognition when searching memory for large words relative to small words, such that the size illusion paradoxically affected accuracy measures (d' scores) in the absence of actual memory differences. Additional evidence for the role of illusory expectations was that (a) the accuracy effect was obtained only when participants searched memory for the aspect of the stimuli corresponding to illusory expectations (size instead of color) and (b) the accuracy effect was eliminated on a forced-choice test that prevented the influence of memorial expectations. These findings demonstrate the critical role of memorial expectations in the retrieval-monitoring process. 2012 APA, all rights reserved

  11. [Effect of algorithms for calibration set selection on quantitatively determining asiaticoside content in Centella total glucosides by near infrared spectroscopy].

    PubMed

    Zhan, Xue-yan; Zhao, Na; Lin, Zhao-zhou; Wu, Zhi-sheng; Yuan, Rui-juan; Qiao, Yan-jiang

    2014-12-01

    The appropriate algorithm for calibration set selection was one of the key technologies for a good NIR quantitative model. There are different algorithms for calibration set selection, such as Random Sampling (RS) algorithm, Conventional Selection (CS) algorithm, Kennard-Stone(KS) algorithm and Sample set Portioning based on joint x-y distance (SPXY) algorithm, et al. However, there lack systematic comparisons between two algorithms of the above algorithms. The NIR quantitative models to determine the asiaticoside content in Centella total glucosides were established in the present paper, of which 7 indexes were classified and selected, and the effects of CS algorithm, KS algorithm and SPXY algorithm for calibration set selection on the accuracy and robustness of NIR quantitative models were investigated. The accuracy indexes of NIR quantitative models with calibration set selected by SPXY algorithm were significantly different from that with calibration set selected by CS algorithm or KS algorithm, while the robustness indexes, such as RMSECV and |RMSEP-RMSEC|, were not significantly different. Therefore, SPXY algorithm for calibration set selection could improve the predicative accuracy of NIR quantitative models to determine asiaticoside content in Centella total glucosides, and have no significant effect on the robustness of the models, which provides a reference to determine the appropriate algorithm for calibration set selection when NIR quantitative models are established for the solid system of traditional Chinese medcine.

  12. Potassium-based algorithm allows correction for the hematocrit bias in quantitative analysis of caffeine and its major metabolite in dried blood spots.

    PubMed

    De Kesel, Pieter M M; Capiau, Sara; Stove, Veronique V; Lambert, Willy E; Stove, Christophe P

    2014-10-01

    Although dried blood spot (DBS) sampling is increasingly receiving interest as a potential alternative to traditional blood sampling, the impact of hematocrit (Hct) on DBS results is limiting its final breakthrough in routine bioanalysis. To predict the Hct of a given DBS, potassium (K(+)) proved to be a reliable marker. The aim of this study was to evaluate whether application of an algorithm, based upon predicted Hct or K(+) concentrations as such, allowed correction for the Hct bias. Using validated LC-MS/MS methods, caffeine, chosen as a model compound, was determined in whole blood and corresponding DBS samples with a broad Hct range (0.18-0.47). A reference subset (n = 50) was used to generate an algorithm based on K(+) concentrations in DBS. Application of the developed algorithm on an independent test set (n = 50) alleviated the assay bias, especially at lower Hct values. Before correction, differences between DBS and whole blood concentrations ranged from -29.1 to 21.1%. The mean difference, as obtained by Bland-Altman comparison, was -6.6% (95% confidence interval (CI), -9.7 to -3.4%). After application of the algorithm, differences between corrected and whole blood concentrations lay between -19.9 and 13.9% with a mean difference of -2.1% (95% CI, -4.5 to 0.3%). The same algorithm was applied to a separate compound, paraxanthine, which was determined in 103 samples (Hct range, 0.17-0.47), yielding similar results. In conclusion, a K(+)-based algorithm allows correction for the Hct bias in the quantitative analysis of caffeine and its metabolite paraxanthine.

  13. Detection of Prostate Cancer: Quantitative Multiparametric MR Imaging Models Developed Using Registered Correlative Histopathology.

    PubMed

    Metzger, Gregory J; Kalavagunta, Chaitanya; Spilseth, Benjamin; Bolan, Patrick J; Li, Xiufeng; Hutter, Diane; Nam, Jung W; Johnson, Andrew D; Henriksen, Jonathan C; Moench, Laura; Konety, Badrinath; Warlick, Christopher A; Schmechel, Stephen C; Koopmeiners, Joseph S

    2016-06-01

    Purpose To develop multiparametric magnetic resonance (MR) imaging models to generate a quantitative, user-independent, voxel-wise composite biomarker score (CBS) for detection of prostate cancer by using coregistered correlative histopathologic results, and to compare performance of CBS-based detection with that of single quantitative MR imaging parameters. Materials and Methods Institutional review board approval and informed consent were obtained. Patients with a diagnosis of prostate cancer underwent multiparametric MR imaging before surgery for treatment. All MR imaging voxels in the prostate were classified as cancer or noncancer on the basis of coregistered histopathologic data. Predictive models were developed by using more than one quantitative MR imaging parameter to generate CBS maps. Model development and evaluation of quantitative MR imaging parameters and CBS were performed separately for the peripheral zone and the whole gland. Model accuracy was evaluated by using the area under the receiver operating characteristic curve (AUC), and confidence intervals were calculated with the bootstrap procedure. The improvement in classification accuracy was evaluated by comparing the AUC for the multiparametric model and the single best-performing quantitative MR imaging parameter at the individual level and in aggregate. Results Quantitative T2, apparent diffusion coefficient (ADC), volume transfer constant (K(trans)), reflux rate constant (kep), and area under the gadolinium concentration curve at 90 seconds (AUGC90) were significantly different between cancer and noncancer voxels (P < .001), with ADC showing the best accuracy (peripheral zone AUC, 0.82; whole gland AUC, 0.74). Four-parameter models demonstrated the best performance in both the peripheral zone (AUC, 0.85; P = .010 vs ADC alone) and whole gland (AUC, 0.77; P = .043 vs ADC alone). Individual-level analysis showed statistically significant improvement in AUC in 82% (23 of 28) and 71% (24 of 34

  14. Speed-Accuracy Trade-Off in a Trajectory-Constrained Self-Feeding Task: A Quantitative Index of Unsuppressed Motor Noise in Children With Dystonia.

    PubMed

    Lunardini, Francesca; Bertucco, Matteo; Casellato, Claudia; Bhanpuri, Nasir; Pedrocchi, Alessandra; Sanger, Terence D

    2015-10-01

    Motor speed and accuracy are both affected in childhood dystonia. Thus, deriving a speed-accuracy function is an important metric for assessing motor impairments in dystonia. Previous work in dystonia studied the speed-accuracy trade-off during point-to-point tasks. To achieve a more relevant measurement of functional abilities in dystonia, the present study investigates upper-limb kinematics and electromyographic activity of 8 children with dystonia and 8 healthy children during a trajectory-constrained child-relevant task that emulates self-feeding with a spoon and requires continuous monitoring of accuracy. The speed-accuracy trade-off is examined by changing the spoon size to create different accuracy demands. Results demonstrate that the trajectory-constrained speed-accuracy relation is present in both groups, but it is altered in dystonia in terms of increased slope and offset toward longer movement times. Findings are consistent with the hypothesis of increased signal-dependent noise in dystonia, which may partially explain the slow and variable movements observed in dystonia. © The Author(s) 2015.

  15. Quantitative structure-activity relationship (QSAR) for insecticides: development of predictive in vivo insecticide activity models.

    PubMed

    Naik, P K; Singh, T; Singh, H

    2009-07-01

    Quantitative structure-activity relationship (QSAR) analyses were performed independently on data sets belonging to two groups of insecticides, namely the organophosphates and carbamates. Several types of descriptors including topological, spatial, thermodynamic, information content, lead likeness and E-state indices were used to derive quantitative relationships between insecticide activities and structural properties of chemicals. A systematic search approach based on missing value, zero value, simple correlation and multi-collinearity tests as well as the use of a genetic algorithm allowed the optimal selection of the descriptors used to generate the models. The QSAR models developed for both organophosphate and carbamate groups revealed good predictability with r(2) values of 0.949 and 0.838 as well as [image omitted] values of 0.890 and 0.765, respectively. In addition, a linear correlation was observed between the predicted and experimental LD(50) values for the test set data with r(2) of 0.871 and 0.788 for both the organophosphate and carbamate groups, indicating that the prediction accuracy of the QSAR models was acceptable. The models were also tested successfully from external validation criteria. QSAR models developed in this study should help further design of novel potent insecticides.

  16. Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method.

    PubMed

    Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

    2014-02-01

    To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Both assays provided good linearity, accuracy, reproducibility and selectivity for determination of γ-oryzanol. The TLC-densitometric and TLC-image analysis methods provided a similar reproducibility, accuracy and selectivity for the quantitative determination of γ-oryzanol in cold pressed rice bran oil. A statistical comparison of the quantitative determinations of γ-oryzanol in samples did not show any statistically significant difference between TLC-densitometric and TLC-image analysis methods. As both methods were found to be equal, they therefore can be used for the determination of γ-oryzanol in cold pressed rice bran oil.

  17. Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method

    PubMed Central

    Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

    2014-01-01

    Objective To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. Methods TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Results Both assays provided good linearity, accuracy, reproducibility and selectivity for determination of γ-oryzanol. Conclusions The TLC-densitometric and TLC-image analysis methods provided a similar reproducibility, accuracy and selectivity for the quantitative determination of γ-oryzanol in cold pressed rice bran oil. A statistical comparison of the quantitative determinations of γ-oryzanol in samples did not show any statistically significant difference between TLC-densitometric and TLC-image analysis methods. As both methods were found to be equal, they therefore can be used for the determination of γ-oryzanol in cold pressed rice bran oil. PMID:25182282

  18. Testing the accuracy of clustering redshifts with simulations

    NASA Astrophysics Data System (ADS)

    Scottez, V.; Benoit-Lévy, A.; Coupon, J.; Ilbert, O.; Mellier, Y.

    2018-03-01

    We explore the accuracy of clustering-based redshift inference within the MICE2 simulation. This method uses the spatial clustering of galaxies between a spectroscopic reference sample and an unknown sample. This study give an estimate of the reachable accuracy of this method. First, we discuss the requirements for the number objects in the two samples, confirming that this method does not require a representative spectroscopic sample for calibration. In the context of next generation of cosmological surveys, we estimated that the density of the Quasi Stellar Objects in BOSS allows us to reach 0.2 per cent accuracy in the mean redshift. Secondly, we estimate individual redshifts for galaxies in the densest regions of colour space ( ˜ 30 per cent of the galaxies) without using the photometric redshifts procedure. The advantage of this procedure is threefold. It allows: (i) the use of cluster-zs for any field in astronomy, (ii) the possibility to combine photo-zs and cluster-zs to get an improved redshift estimation, (iii) the use of cluster-z to define tomographic bins for weak lensing. Finally, we explore this last option and build five cluster-z selected tomographic bins from redshift 0.2 to 1. We found a bias on the mean redshift estimate of 0.002 per bin. We conclude that cluster-z could be used as a primary redshift estimator by next generation of cosmological surveys.

  19. Quantitative proteomics in biological research.

    PubMed

    Wilm, Matthias

    2009-10-01

    Proteomics has enabled the direct investigation of biological material, at first through the analysis of individual proteins, then of lysates from cell cultures, and finally of extracts from tissues and biopsies from entire organisms. Its latest manifestation - quantitative proteomics - allows deeper insight into biological systems. This article reviews the different methods used to extract quantitative information from mass spectra. It follows the technical developments aimed toward global proteomics, the attempt to characterize every expressed protein in a cell by at least one peptide. When applications of the technology are discussed, the focus is placed on yeast biology. In particular, differential quantitative proteomics, the comparison between an experiment and its control, is very discriminating for proteins involved in the process being studied. When trying to understand biological processes on a molecular level, differential quantitative proteomics tends to give a clearer picture than global transcription analyses. As a result, MS has become an even more indispensable tool for biochemically motivated biological research.

  20. Precision and Accuracy Parameters in Structured Light 3-D Scanning

    NASA Astrophysics Data System (ADS)

    Eiríksson, E. R.; Wilm, J.; Pedersen, D. B.; Aanæs, H.

    2016-04-01

    Structured light systems are popular in part because they can be constructed from off-the-shelf low cost components. In this paper we quantitatively show how common design parameters affect precision and accuracy in such systems, supplying a much needed guide for practitioners. Our quantitative measure is the established VDI/VDE 2634 (Part 2) guideline using precision made calibration artifacts. Experiments are performed on our own structured light setup, consisting of two cameras and a projector. We place our focus on the influence of calibration design parameters, the calibration procedure and encoding strategy and present our findings. Finally, we compare our setup to a state of the art metrology grade commercial scanner. Our results show that comparable, and in some cases better, results can be obtained using the parameter settings determined in this study.

  1. Quantitative secondary electron imaging for work function extraction at atomic level and layer identification of graphene

    PubMed Central

    Zhou, Yangbo; Fox, Daniel S; Maguire, Pierce; O’Connell, Robert; Masters, Robert; Rodenburg, Cornelia; Wu, Hanchun; Dapor, Maurizio; Chen, Ying; Zhang, Hongzhou

    2016-01-01

    Two-dimensional (2D) materials usually have a layer-dependent work function, which require fast and accurate detection for the evaluation of their device performance. A detection technique with high throughput and high spatial resolution has not yet been explored. Using a scanning electron microscope, we have developed and implemented a quantitative analytical technique which allows effective extraction of the work function of graphene. This technique uses the secondary electron contrast and has nanometre-resolved layer information. The measurement of few-layer graphene flakes shows the variation of work function between graphene layers with a precision of less than 10 meV. It is expected that this technique will prove extremely useful for researchers in a broad range of fields due to its revolutionary throughput and accuracy. PMID:26878907

  2. Improving the quantitative accuracy of optical-emission computed tomography by incorporating an attenuation correction: application to HIF1 imaging

    NASA Astrophysics Data System (ADS)

    Kim, E.; Bowsher, J.; Thomas, A. S.; Sakhalkar, H.; Dewhirst, M.; Oldham, M.

    2008-10-01

    Optical computed tomography (optical-CT) and optical-emission computed tomography (optical-ECT) are new techniques for imaging the 3D structure and function (including gene expression) of whole unsectioned tissue samples. This work presents a method of improving the quantitative accuracy of optical-ECT by correcting for the 'self'-attenuation of photons emitted within the sample. The correction is analogous to a method commonly applied in single-photon-emission computed tomography reconstruction. The performance of the correction method was investigated by application to a transparent cylindrical gelatin phantom, containing a known distribution of attenuation (a central ink-doped gelatine core) and a known distribution of fluorescing fibres. Attenuation corrected and uncorrected optical-ECT images were reconstructed on the phantom to enable an evaluation of the effectiveness of the correction. Significant attenuation artefacts were observed in the uncorrected images where the central fibre appeared ~24% less intense due to greater attenuation from the surrounding ink-doped gelatin. This artefact was almost completely removed in the attenuation-corrected image, where the central fibre was within ~4% of the others. The successful phantom test enabled application of attenuation correction to optical-ECT images of an unsectioned human breast xenograft tumour grown subcutaneously on the hind leg of a nude mouse. This tumour cell line had been genetically labelled (pre-implantation) with fluorescent reporter genes such that all viable tumour cells expressed constitutive red fluorescent protein and hypoxia-inducible factor 1 transcription-produced green fluorescent protein. In addition to the fluorescent reporter labelling of gene expression, the tumour microvasculature was labelled by a light-absorbing vasculature contrast agent delivered in vivo by tail-vein injection. Optical-CT transmission images yielded high-resolution 3D images of the absorbing contrast agent, and

  3. Regulation of memory accuracy with multiple answers: the plurality option.

    PubMed

    Luna, Karlos; Higham, Philip A; Martín-Luengo, Beatriz

    2011-06-01

    We report two experiments that investigated the regulation of memory accuracy with a new regulatory mechanism: the plurality option. This mechanism is closely related to the grain-size option but involves control over the number of alternatives contained in an answer rather than the quantitative boundaries of a single answer. Participants were presented with a slideshow depicting a robbery (Experiment 1) or a murder (Experiment 2), and their memory was tested with five-alternative multiple-choice questions. For each question, participants were asked to generate two answers: a single answer consisting of one alternative and a plural answer consisting of the single answer and two other alternatives. Each answer was rated for confidence (Experiment 1) or for the likelihood of being correct (Experiment 2), and one of the answers was selected for reporting. Results showed that participants used the plurality option to regulate accuracy, selecting single answers when their accuracy and confidence were high, but opting for plural answers when they were low. Although accuracy was higher for selected plural than for selected single answers, the opposite pattern was evident for confidence or likelihood ratings. This dissociation between confidence and accuracy for selected answers was the result of marked overconfidence in single answers coupled with underconfidence in plural answers. We hypothesize that these results can be attributed to overly dichotomous metacognitive beliefs about personal knowledge states that cause subjective confidence to be extreme.

  4. Reduced Set of Virulence Genes Allows High Accuracy Prediction of Bacterial Pathogenicity in Humans

    PubMed Central

    Iraola, Gregorio; Vazquez, Gustavo; Spangenberg, Lucía; Naya, Hugo

    2012-01-01

    Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. In this work we determined presence/absence patterns of different virulence-related genes among more than finished bacterial genomes from both human pathogenic and non-pathogenic strains, belonging to different taxonomic groups (i.e: Actinobacteria, Gammaproteobacteria, Firmicutes, etc.). An accuracy of 95% using a cross-fold validation scheme with in-fold feature selection is obtained when classifying human pathogens and non-pathogens. A reduced subset of highly informative genes () is presented and applied to an external validation set. The statistical model was implemented in the BacFier v1.0 software (freely available at ), that displays not only the prediction (pathogen/non-pathogen) and an associated probability for pathogenicity, but also the presence/absence vector for the analyzed genes, so it is possible to decipher the subset of virulence genes responsible for the classification on the analyzed genome. Furthermore, we discuss the biological relevance for bacterial pathogenesis of the core set of genes, corresponding to eight functional categories, all with evident and documented association with the phenotypes of interest. Also, we analyze which functional categories of virulence genes were more distinctive for pathogenicity in each taxonomic group, which seems to be a completely new kind of information and could lead to important evolutionary conclusions. PMID:22916122

  5. Technical Note: Quantitative accuracy evaluation for spectral images from a detector-based spectral CT scanner using an iodine phantom.

    PubMed

    Duan, Xinhui; Arbique, Gary; Guild, Jeffrey; Xi, Yin; Anderson, Jon

    2018-05-01

    The purpose of this study was to evaluate the quantitative accuracy of spectral images from a detector-based spectral CT scanner using a phantom with iodine-loaded inserts. A 40-cm long-body phantom with seven iodine inserts (2-20 mg/ml of iodine) was used in the study. The inserts could be placed at 5.5 or 10.5 cm from the phantom axis. The phantom was scanned five times for each insert configuration using 120 kVp tube voltage. A set of iodine, virtual noncontrast, effective atomic number, and virtual monoenergetic spectral CT images were generated and measurements were made for all the iodine rods. Measured values were compared with reference values calculated from the chemical composition information provided by the phantom manufacturer. Radiation dose from the spectral CT was compared to a conventional CT using a CTDI (32 cm) phantom. Good agreement between measurements and reference values was achieved for all types of spectral images. The differences ranged from -0.46 to 0.1 mg/ml for iodine concentration, -9.95 to 6.41 HU for virtual noncontrast images, 0.12 to 0.35 for effective Z images, and -17.7 to 55.7 HU for virtual monoenergetic images. For a similar CTDIvol, image noise from the conventional CT was 10% lower than the spectral CT. The detector-based spectral CT can achieve accurate spectral measurements on iodine concentration, virtual non-contrast images, effective atomic numbers, and virtual monoenergetic images. © 2018 American Association of Physicists in Medicine.

  6. Quantitating Organoleptic Volatile Phenols in Smoke-Exposed Vitis vinifera Berries.

    PubMed

    Noestheden, Matthew; Thiessen, Katelyn; Dennis, Eric G; Tiet, Ben; Zandberg, Wesley F

    2017-09-27

    Accurate methods for quantitating volatile phenols (i.e., guaiacol, syringol, 4-ethylphenol, etc.) in smoke-exposed Vitis vinifera berries prior to fermentation are needed to predict the likelihood of perceptible smoke taint following vinification. Reported here is a complete, cross-validated analytical workflow to accurately quantitate free and glycosidically bound volatile phenols in smoke-exposed berries using liquid-liquid extraction, acid-mediated hydrolysis, and gas chromatography-tandem mass spectrometry. The reported workflow addresses critical gaps in existing methods for volatile phenols that impact quantitative accuracy, most notably the effect of injection port temperature and the variability in acid-mediated hydrolytic procedures currently used. Addressing these deficiencies will help the wine industry make accurate, informed decisions when producing wines from smoke-exposed berries.

  7. Improving decision speed, accuracy and group cohesion through early information gathering in house-hunting ants.

    PubMed

    Stroeymeyt, Nathalie; Giurfa, Martin; Franks, Nigel R

    2010-09-29

    Successful collective decision-making depends on groups of animals being able to make accurate choices while maintaining group cohesion. However, increasing accuracy and/or cohesion usually decreases decision speed and vice-versa. Such trade-offs are widespread in animal decision-making and result in various decision-making strategies that emphasize either speed or accuracy, depending on the context. Speed-accuracy trade-offs have been the object of many theoretical investigations, but these studies did not consider the possible effects of previous experience and/or knowledge of individuals on such trade-offs. In this study, we investigated how previous knowledge of their environment may affect emigration speed, nest choice and colony cohesion in emigrations of the house-hunting ant Temnothorax albipennis, a collective decision-making process subject to a classical speed-accuracy trade-off. Colonies allowed to explore a high quality nest site for one week before they were forced to emigrate found that nest and accepted it faster than emigrating naïve colonies. This resulted in increased speed in single choice emigrations and higher colony cohesion in binary choice emigrations. Additionally, colonies allowed to explore both high and low quality nest sites for one week prior to emigration remained more cohesive, made more accurate decisions and emigrated faster than emigrating naïve colonies. These results show that colonies gather and store information about available nest sites while their nest is still intact, and later retrieve and use this information when they need to emigrate. This improves colony performance. Early gathering of information for later use is therefore an effective strategy allowing T. albipennis colonies to improve simultaneously all aspects of the decision-making process--i.e. speed, accuracy and cohesion--and partly circumvent the speed-accuracy trade-off classically observed during emigrations. These findings should be taken into account

  8. Effects of accuracy motivation and anchoring on metacomprehension judgment and accuracy.

    PubMed

    Zhao, Qin

    2012-01-01

    The current research investigates how accuracy motivation impacts anchoring and adjustment in metacomprehension judgment and how accuracy motivation and anchoring affect metacomprehension accuracy. Participants were randomly assigned to one of six conditions produced by the between-subjects factorial design involving accuracy motivation (incentive or no) and peer performance anchor (95%, 55%, or no). Two studies showed that accuracy motivation did not impact anchoring bias, but the adjustment-from-anchor process occurred. Accuracy incentive increased anchor-judgment gap for the 95% anchor but not for the 55% anchor, which induced less certainty about the direction of adjustment. The findings offer support to the integrative theory of anchoring. Additionally, the two studies revealed a "power struggle" between accuracy motivation and anchoring in influencing metacomprehension accuracy. Accuracy motivation could improve metacomprehension accuracy in spite of anchoring effect, but if anchoring effect is too strong, it could overpower the motivation effect. The implications of the findings were discussed.

  9. Combining cow and bull reference populations to increase accuracy of genomic prediction and genome-wide association studies.

    PubMed

    Calus, M P L; de Haas, Y; Veerkamp, R F

    2013-10-01

    Genomic selection holds the promise to be particularly beneficial for traits that are difficult or expensive to measure, such that access to phenotypes on large daughter groups of bulls is limited. Instead, cow reference populations can be generated, potentially supplemented with existing information from the same or (highly) correlated traits available on bull reference populations. The objective of this study, therefore, was to develop a model to perform genomic predictions and genome-wide association studies based on a combined cow and bull reference data set, with the accuracy of the phenotypes differing between the cow and bull genomic selection reference populations. The developed bivariate Bayesian stochastic search variable selection model allowed for an unbalanced design by imputing residuals in the residual updating scheme for all missing records. The performance of this model is demonstrated on a real data example, where the analyzed trait, being milk fat or protein yield, was either measured only on a cow or a bull reference population, or recorded on both. Our results were that the developed bivariate Bayesian stochastic search variable selection model was able to analyze 2 traits, even though animals had measurements on only 1 of 2 traits. The Bayesian stochastic search variable selection model yielded consistently higher accuracy for fat yield compared with a model without variable selection, both for the univariate and bivariate analyses, whereas the accuracy of both models was very similar for protein yield. The bivariate model identified several additional quantitative trait loci peaks compared with the single-trait models on either trait. In addition, the bivariate models showed a marginal increase in accuracy of genomic predictions for the cow traits (0.01-0.05), although a greater increase in accuracy is expected as the size of the bull population increases. Our results emphasize that the chosen value of priors in Bayesian genomic prediction

  10. 40 CFR 35.2025 - Allowance and advance of allowance.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... advance of allowance. (a) Allowance. Step 2+3 and Step 3 grant agreements will include an allowance for facilities planning and design of the project and Step 7 agreements will include an allowance for facility... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Allowance and advance of allowance. 35...

  11. High-Precision Pinpointing of Luminescent Targets in Encoder-Assisted Scanning Microscopy Allowing High-Speed Quantitative Analysis.

    PubMed

    Zheng, Xianlin; Lu, Yiqing; Zhao, Jiangbo; Zhang, Yuhai; Ren, Wei; Liu, Deming; Lu, Jie; Piper, James A; Leif, Robert C; Liu, Xiaogang; Jin, Dayong

    2016-01-19

    Compared with routine microscopy imaging of a few analytes at a time, rapid scanning through the whole sample area of a microscope slide to locate every single target object offers many advantages in terms of simplicity, speed, throughput, and potential for robust quantitative analysis. Existing techniques that accommodate solid-phase samples incorporating individual micrometer-sized targets generally rely on digital microscopy and image analysis, with intrinsically low throughput and reliability. Here, we report an advanced on-the-fly stage scanning method to achieve high-precision target location across the whole slide. By integrating X- and Y-axis linear encoders to a motorized stage as the virtual "grids" that provide real-time positional references, we demonstrate an orthogonal scanning automated microscopy (OSAM) technique which can search a coverslip area of 50 × 24 mm(2) in just 5.3 min and locate individual 15 μm lanthanide luminescent microspheres with standard deviations of 1.38 and 1.75 μm in X and Y directions. Alongside implementation of an autofocus unit that compensates the tilt of a slide in the Z-axis in real time, we increase the luminescence detection efficiency by 35% with an improved coefficient of variation. We demonstrate the capability of advanced OSAM for robust quantification of luminescence intensities and lifetimes for a variety of micrometer-scale luminescent targets, specifically single down-shifting and upconversion microspheres, crystalline microplates, and color-barcoded microrods, as well as quantitative suspension array assays of biotinylated-DNA functionalized upconversion nanoparticles.

  12. Accuracy of alpha amylase in diagnosing microaspiration in intubated critically-ill patients.

    PubMed

    Dewavrin, Florent; Zerimech, Farid; Boyer, Alexandre; Maboudou, Patrice; Balduyck, Malika; Duhamel, Alain; Nseir, Saad

    2014-01-01

    Amylase concentration in respiratory secretions was reported to be a potentially useful marker for aspiration and pneumonia. The aim of this study was to determine accuracy of α-amylase in diagnosing microaspiration in critically ill patients. Retrospective analysis of prospectively collected data collected in a medical ICU. All patients requiring mechanical ventilation for at least 48 h, and included in a previous randomized controlled trial were eligible for this study, provided that at least one tracheal aspirate was available for α-amylase measurement. As part of the initial trial, pepsin was quantitatively measured in all tracheal aspirates during a 48-h period. All tracheal aspirates were frozen, allowing subsequent measurement of α-amylase for the purpose of the current study. Microaspiration was defined as the presence of at least one positive tracheal aspirate for pepsin (>200 ng.mL-1). Abundant microaspiration was defined as the presence of pepsin at significant level in >74% of tracheal aspirates. Amylase was measured in 1055 tracheal aspirates, collected from 109 patients. Using mean α-amylase level per patient, accuracy of α-amylase in diagnosing microaspiration was moderate (area under the receiver operator curve 0.72±0.05 [95%CI 0.61-0.83], for an α-amylase value of 1685 UI.L-1). However, when α-amylase levels, coming from all samples, were taken into account, area under the receiver operator curve was 0.56±0.05 [0.53-0.60]. Mean α-amylase level, and percentage of tracheal aspirates positive for α-amylase were significantly higher in patients with microaspiration, and in patients with abundant microaspiration compared with those with no microaspiration; and similar in patients with microaspiration compared with those with abundant microaspiration. α-amylase and pepsin were significantly correlated (r2 = 0.305, p = 0.001). Accuracy of mean α-amylase in diagnosing microaspiration is moderate. Further, when all α-amylase levels

  13. Sample and data processing considerations for the NIST quantitative infrared database

    NASA Astrophysics Data System (ADS)

    Chu, Pamela M.; Guenther, Franklin R.; Rhoderick, George C.; Lafferty, Walter J.; Phillips, William

    1999-02-01

    Fourier-transform infrared (FT-IR) spectrometry has become a useful real-time in situ analytical technique for quantitative gas phase measurements. In fact, the U.S. Environmental Protection Agency (EPA) has recently approved open-path FT-IR monitoring for the determination of hazardous air pollutants (HAP) identified in EPA's Clean Air Act of 1990. To support infrared based sensing technologies, the National Institute of Standards and Technology (NIST) is currently developing a standard quantitative spectral database of the HAPs based on gravimetrically prepared standard samples. The procedures developed to ensure the quantitative accuracy of the reference data are discussed, including sample preparation, residual sample contaminants, data processing considerations, and estimates of error.

  14. Analysis of machining accuracy during free form surface milling simulation for different milling strategies

    NASA Astrophysics Data System (ADS)

    Matras, A.; Kowalczyk, R.

    2014-11-01

    The analysis results of machining accuracy after the free form surface milling simulations (based on machining EN AW- 7075 alloys) for different machining strategies (Level Z, Radial, Square, Circular) are presented in the work. Particular milling simulations were performed using CAD/CAM Esprit software. The accuracy of obtained allowance is defined as a difference between the theoretical surface of work piece element (the surface designed in CAD software) and the machined surface after a milling simulation. The difference between two surfaces describes a value of roughness, which is as the result of tool shape mapping on the machined surface. Accuracy of the left allowance notifies in direct way a surface quality after the finish machining. Described methodology of usage CAD/CAM software can to let improve a time design of machining process for a free form surface milling by a 5-axis CNC milling machine with omitting to perform the item on a milling machine in order to measure the machining accuracy for the selected strategies and cutting data.

  15. Seven-Year Clinical Surveillance Program Demonstrates Consistent MARD Accuracy Performance of a Blood Glucose Test Strip.

    PubMed

    Setford, Steven; Grady, Mike; Mackintosh, Stephen; Donald, Robert; Levy, Brian

    2018-05-01

    MARD (mean absolute relative difference) is increasingly used to describe performance of glucose monitoring systems, providing a single-value quantitative measure of accuracy and allowing comparisons between different monitoring systems. This study reports MARDs for the OneTouch Verio® glucose meter clinical data set of 80 258 data points (671 individual batches) gathered as part of a 7.5-year self-surveillance program Methods: Test strips were routinely sampled from randomly selected manufacturer's production batches and sent to one of 3 clinic sites for clinical accuracy assessment using fresh capillary blood from patients with diabetes, using both the meter system and standard laboratory reference instrument. Evaluation of the distribution of strip batch MARD yielded a mean value of 5.05% (range: 3.68-6.43% at ±1.96 standard deviations from mean). The overall MARD for all clinic data points (N = 80 258) was also 5.05%, while a mean bias of 1.28 was recorded. MARD by glucose level was found to be consistent, yielding a maximum value of 4.81% at higher glucose (≥100 mg/dL) and a mean absolute difference (MAD) of 5.60 mg/dL at low glucose (<100 mg/dL). MARD by year of manufacture varied from 4.67-5.42% indicating consistent accuracy performance over the surveillance period. This 7.5-year surveillance program showed that this meter system exhibits consistently low MARD by batch, glucose level and year, indicating close agreement with established reference methods whilste exhibiting lower MARD values than continuous glucose monitoring (CGM) systems and providing users with confidence in the performance when transitioning to each new strip batch.

  16. Speckle noise reduction in quantitative optical metrology techniques by application of the discrete wavelet transformation

    NASA Astrophysics Data System (ADS)

    Furlong, Cosme; Pryputniewicz, Ryszard J.

    2002-06-01

    Effective suppression of speckle noise content in interferometric data images can help in improving accuracy and resolution of the results obtained with interferometric optical metrology techniques. In this paper, novel speckle noise reduction algorithms based on the discrete wavelet transformation are presented. The algorithms proceed by: (a) estimating the noise level contained in the interferograms of interest, (b) selecting wavelet families, (c) applying the wavelet transformation using the selected families, (d) wavelet thresholding, and (e) applying the inverse wavelet transformation, producing denoised interferograms. The algorithms are applied to the different stages of the processing procedures utilized for generation of quantitative speckle correlation interferometry data of fiber-optic based opto-electronic holography (FOBOEH) techniques, allowing identification of optimal processing conditions. It is shown that wavelet algorithms are effective for speckle noise reduction while preserving image features otherwise faded with other algorithms.

  17. [Quantitative Analysis of Heavy Metals in Water with LIBS Based on Signal-to-Background Ratio].

    PubMed

    Hu, Li; Zhao, Nan-jing; Liu, Wen-qing; Fang, Li; Zhang, Da-hai; Wang, Yin; Meng, De Shuo; Yu, Yang; Ma, Ming-jun

    2015-07-01

    There are many influence factors in the precision and accuracy of the quantitative analysis with LIBS technology. According to approximately the same characteristics trend of background spectrum and characteristic spectrum along with the change of temperature through in-depth analysis, signal-to-background ratio (S/B) measurement and regression analysis could compensate the spectral line intensity changes caused by system parameters such as laser power, spectral efficiency of receiving. Because the measurement dates were limited and nonlinear, we used support vector machine (SVM) for regression algorithm. The experimental results showed that the method could improve the stability and the accuracy of quantitative analysis of LIBS, and the relative standard deviation and average relative error of test set respectively were 4.7% and 9.5%. Data fitting method based on signal-to-background ratio(S/B) is Less susceptible to matrix elements and background spectrum etc, and provides data processing reference for real-time online LIBS quantitative analysis technology.

  18. A comparative proteomics method for multiple samples based on a 18O-reference strategy and a quantitation and identification-decoupled strategy.

    PubMed

    Wang, Hongbin; Zhang, Yongqian; Gui, Shuqi; Zhang, Yong; Lu, Fuping; Deng, Yulin

    2017-08-15

    Comparisons across large numbers of samples are frequently necessary in quantitative proteomics. Many quantitative methods used in proteomics are based on stable isotope labeling, but most of these are only useful for comparing two samples. For up to eight samples, the iTRAQ labeling technique can be used. For greater numbers of samples, the label-free method has been used, but this method was criticized for low reproducibility and accuracy. An ingenious strategy has been introduced, comparing each sample against a 18 O-labeled reference sample that was created by pooling equal amounts of all samples. However, it is necessary to use proportion-known protein mixtures to investigate and evaluate this new strategy. Another problem for comparative proteomics of multiple samples is the poor coincidence and reproducibility in protein identification results across samples. In present study, a method combining 18 O-reference strategy and a quantitation and identification-decoupled strategy was investigated with proportion-known protein mixtures. The results obviously demonstrated that the 18 O-reference strategy had greater accuracy and reliability than other previously used comparison methods based on transferring comparison or label-free strategies. By the decoupling strategy, the quantification data acquired by LC-MS and the identification data acquired by LC-MS/MS are matched and correlated to identify differential expressed proteins, according to retention time and accurate mass. This strategy made protein identification possible for all samples using a single pooled sample, and therefore gave a good reproducibility in protein identification across multiple samples, and allowed for optimizing peptide identification separately so as to identify more proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Computational motor control: feedback and accuracy.

    PubMed

    Guigon, Emmanuel; Baraduc, Pierre; Desmurget, Michel

    2008-02-01

    Speed/accuracy trade-off is a ubiquitous phenomenon in motor behaviour, which has been ascribed to the presence of signal-dependent noise (SDN) in motor commands. Although this explanation can provide a quantitative account of many aspects of motor variability, including Fitts' law, the fact that this law is frequently violated, e.g. during the acquisition of new motor skills, remains unexplained. Here, we describe a principled approach to the influence of noise on motor behaviour, in which motor variability results from the interplay between sensory and motor execution noises in an optimal feedback-controlled system. In this framework, we first show that Fitts' law arises due to signal-dependent motor noise (SDN(m)) when sensory (proprioceptive) noise is low, e.g. under visual feedback. Then we show that the terminal variability of non-visually guided movement can be explained by the presence of signal-dependent proprioceptive noise. Finally, we show that movement accuracy can be controlled by opposite changes in signal-dependent sensory (SDN(s)) and SDN(m), a phenomenon that could be ascribed to muscular co-contraction. As the model also explains kinematics, kinetics, muscular and neural characteristics of reaching movements, it provides a unified framework to address motor variability.

  20. Millisecond accuracy video display using OpenGL under Linux.

    PubMed

    Stewart, Neil

    2006-02-01

    To measure people's reaction times to the nearest millisecond, it is necessary to know exactly when a stimulus is displayed. This article describes how to display stimuli with millisecond accuracy on a normal CRT monitor, using a PC running Linux. A simple C program is presented to illustrate how this may be done within X Windows using the OpenGL rendering system. A test of this system is reported that demonstrates that stimuli may be consistently displayed with millisecond accuracy. An algorithm is presented that allows the exact time of stimulus presentation to be deduced, even if there are relatively large errors in measuring the display time.

  1. Large-scale label-free quantitative proteomics of the pea aphid-Buchnera symbiosis.

    PubMed

    Poliakov, Anton; Russell, Calum W; Ponnala, Lalit; Hoops, Harold J; Sun, Qi; Douglas, Angela E; van Wijk, Klaas J

    2011-06-01

    Many insects are nutritionally dependent on symbiotic microorganisms that have tiny genomes and are housed in specialized host cells called bacteriocytes. The obligate symbiosis between the pea aphid Acyrthosiphon pisum and the γ-proteobacterium Buchnera aphidicola (only 584 predicted proteins) is particularly amenable for molecular analysis because the genomes of both partners have been sequenced. To better define the symbiotic relationship between this aphid and Buchnera, we used large-scale, high accuracy tandem mass spectrometry (nanoLC-LTQ-Orbtrap) to identify aphid and Buchnera proteins in the whole aphid body, purified bacteriocytes, isolated Buchnera cells and the residual bacteriocyte fraction. More than 1900 aphid and 400 Buchnera proteins were identified. All enzymes in amino acid metabolism annotated in the Buchnera genome were detected, reflecting the high (68%) coverage of the proteome and supporting the core function of Buchnera in the aphid symbiosis. Transporters mediating the transport of predicted metabolites were present in the bacteriocyte. Label-free spectral counting combined with hierarchical clustering, allowed to define the quantitative distribution of a subset of these proteins across both symbiotic partners, yielding no evidence for the selective transfer of protein among the partners in either direction. This is the first quantitative proteome analysis of bacteriocyte symbiosis, providing a wealth of information about molecular function of both the host cell and bacterial symbiont.

  2. High accuracy wavelength calibration for a scanning visible spectrometer.

    PubMed

    Scotti, Filippo; Bell, Ronald E

    2010-10-01

    Spectroscopic applications for plasma velocity measurements often require wavelength accuracies ≤0.2 Å. An automated calibration, which is stable over time and environmental conditions without the need to recalibrate after each grating movement, was developed for a scanning spectrometer to achieve high wavelength accuracy over the visible spectrum. This method fits all relevant spectrometer parameters using multiple calibration spectra. With a stepping-motor controlled sine drive, an accuracy of ∼0.25 Å has been demonstrated. With the addition of a high resolution (0.075 arc  sec) optical encoder on the grating stage, greater precision (∼0.005 Å) is possible, allowing absolute velocity measurements within ∼0.3 km/s. This level of precision requires monitoring of atmospheric temperature and pressure and of grating bulk temperature to correct for changes in the refractive index of air and the groove density, respectively.

  3. Quantitative assessment of emphysema from whole lung CT scans: comparison with visual grading

    NASA Astrophysics Data System (ADS)

    Keller, Brad M.; Reeves, Anthony P.; Apanosovich, Tatiyana V.; Wang, Jianwei; Yankelevitz, David F.; Henschke, Claudia I.

    2009-02-01

    Emphysema is a disease of the lungs that destroys the alveolar air sacs and induces long-term respiratory dysfunction. CT scans allow for imaging of the anatomical basis of emphysema and for visual assessment by radiologists of the extent present in the lungs. Several measures have been introduced for the quantification of the extent of disease directly from CT data in order to add to the qualitative assessments made by radiologists. In this paper we compare emphysema index, mean lung density, histogram percentiles, and the fractal dimension to visual grade in order to evaluate the predictability of radiologist visual scoring of emphysema from low-dose CT scans through quantitative scores, in order to determine which measures can be useful as surrogates for visual assessment. All measures were computed over nine divisions of the lung field (whole lung, individual lungs, and upper/middle/lower thirds of each lung) for each of 148 low-dose, whole lung scans. In addition, a visual grade of each section was also given by an expert radiologist. One-way ANOVA and multinomial logistic regression were used to determine the ability of the measures to predict visual grade from quantitative score. We found that all measures were able to distinguish between normal and severe grades (p<0.01), and between mild/moderate and all other grades (p<0.05). However, no measure was able to distinguish between mild and moderate cases. Approximately 65% prediction accuracy was achieved from using quantitative score to predict visual grade, with 73% if mild and moderate cases are considered as a single class.

  4. Tuning plasmons layer-by-layer for quantitative colloidal sensing with surface-enhanced Raman spectroscopy.

    PubMed

    Anderson, William J; Nowinska, Kamila; Hutter, Tanya; Mahajan, Sumeet; Fischlechner, Martin

    2018-04-19

    Surface-enhanced Raman spectroscopy (SERS) is well known for its high sensitivity that emerges due to the plasmonic enhancement of electric fields typically on gold and silver nanostructures. However, difficulties associated with the preparation of nanostructured substrates with uniform and reproducible features limit reliability and quantitation using SERS measurements. In this work we use layer-by-layer (LbL) self-assembly to incorporate multiple functional building blocks of collaborative assemblies of nanoparticles on colloidal spheres to fabricate SERS sensors. Gold nanoparticles (AuNPs) are packaged in discrete layers, effectively 'freezing nano-gaps', on spherical colloidal cores to achieve multifunctionality and reproducible sensing. Coupling between layers tunes the plasmon resonance for optimum SERS signal generation to achieve a 10 nM limit of detection. Significantly, using the layer-by-layer construction, SERS-active AuNP layers are spaced out and thus optically isolated. This uniquely allows the creation of an internal standard within each colloidal sensor to enable highly reproducible self-calibrated sensing. By using 4-mercaptobenzoic acid (4-MBA) as the internal standard adenine concentrations are quantified to an accuracy of 92.6-99.5%. Our versatile approach paves the way for rationally designed yet quantitative colloidal SERS sensors and their use in a variety of sensing applications.

  5. Effects of disease severity distribution on the performance of quantitative diagnostic methods and proposal of a novel 'V-plot' methodology to display accuracy values.

    PubMed

    Petraco, Ricardo; Dehbi, Hakim-Moulay; Howard, James P; Shun-Shin, Matthew J; Sen, Sayan; Nijjer, Sukhjinder S; Mayet, Jamil; Davies, Justin E; Francis, Darrel P

    2018-01-01

    Diagnostic accuracy is widely accepted by researchers and clinicians as an optimal expression of a test's performance. The aim of this study was to evaluate the effects of disease severity distribution on values of diagnostic accuracy as well as propose a sample-independent methodology to calculate and display accuracy of diagnostic tests. We evaluated the diagnostic relationship between two hypothetical methods to measure serum cholesterol (Chol rapid and Chol gold ) by generating samples with statistical software and (1) keeping the numerical relationship between methods unchanged and (2) changing the distribution of cholesterol values. Metrics of categorical agreement were calculated (accuracy, sensitivity and specificity). Finally, a novel methodology to display and calculate accuracy values was presented (the V-plot of accuracies). No single value of diagnostic accuracy can be used to describe the relationship between tests, as accuracy is a metric heavily affected by the underlying sample distribution. Our novel proposed methodology, the V-plot of accuracies, can be used as a sample-independent measure of a test performance against a reference gold standard.

  6. Clinical evaluation and treatment accuracy in diabetic macular edema using navigated laser photocoagulator NAVILAS.

    PubMed

    Kozak, Igor; Oster, Stephen F; Cortes, Marco A; Dowell, Dennis; Hartmann, Kathrin; Kim, Jae Suk; Freeman, William R

    2011-06-01

    To evaluate the clinical use and accuracy of a new retinal navigating laser technology that integrates a scanning slit fundus camera system with fluorescein angiography (FA), color, red-free, and infrared imaging capabilities with a computer steerable therapeutic 532-nm laser. Interventional case series. Eighty-six eyes of 61 patients with diabetic retinopathy and macular edema treated by NAVILAS. The imaging included digital color fundus photographs and FA. The planning included graphically marking future treatment sites (microaneurysms for single-spot focal treatment and areas of diffuse leakage for grid pattern photocoagulation) on the acquired images. The preplanned treatment was visible and overlaid on the live fundus image during the actual photocoagulation. The NAVILAS automatically advances the aiming beam location from one planned treatment site to the next after each photocoagulation spot until all sites are treated. Aiming beam stabilization compensated for patient's eye movements. The pretreatment FA with the treatment plan was overlaid on top of the posttreatment color fundus images with the actual laser burns. This allowed treatment accuracy to be calculated. Independent observers evaluated the images to determine if the retinal opacification after treatment overlapped the targeted microaneurysm. Safety and accuracy of laser photocoagulation. The images were of very good quality compared with standard fundus cameras, allowing careful delineation of target areas on FA. Toggling from infrared, to monochromatic, to color view allowed evaluation and adjustment of burn intensity during treatment. There were no complications during or after photocoagulation treatment. An analysis of accuracy of 400 random focal targeted spots found that the NAVILAS achieved a microaneurysm hit rate of 92% when the placement of the treatment circle was centered by the operating surgeon on the microaneurysm. The accuracy for the control group analyzing 100 focal spots was

  7. "Small Talk": Developing Fluency, Accuracy, and Complexity in Speaking

    ERIC Educational Resources Information Center

    Hunter, James

    2012-01-01

    A major issue that continues to challenge language teachers is how to ensure that learners develop accuracy and complexity in their speaking, as well as fluency. Teachers know that too much corrective feedback (CF) can make learners reluctant to speak, while not enough may allow their errors to become entrenched. Furthermore, there is controversy…

  8. Cost and accuracy of advanced breeding trial designs in apple

    PubMed Central

    Harshman, Julia M; Evans, Kate M; Hardner, Craig M

    2016-01-01

    Trialing advanced candidates in tree fruit crops is expensive due to the long-term nature of the planting and labor-intensive evaluations required to make selection decisions. How closely the trait evaluations approximate the true trait value needs balancing with the cost of the program. Designs of field trials of advanced apple candidates in which reduced number of locations, the number of years and the number of harvests per year were modeled to investigate the effect on the cost and accuracy in an operational breeding program. The aim was to find designs that would allow evaluation of the most additional candidates while sacrificing the least accuracy. Critical percentage difference, response to selection, and correlated response were used to examine changes in accuracy of trait evaluations. For the quality traits evaluated, accuracy and response to selection were not substantially reduced for most trial designs. Risk management influences the decision to change trial design, and some designs had greater risk associated with them. Balancing cost and accuracy with risk yields valuable insight into advanced breeding trial design. The methods outlined in this analysis would be well suited to other horticultural crop breeding programs. PMID:27019717

  9. Quantitative characterization of nanoscale polycrystalline magnets with electron magnetic circular dichroism.

    PubMed

    Muto, Shunsuke; Rusz, Ján; Tatsumi, Kazuyoshi; Adam, Roman; Arai, Shigeo; Kocevski, Vancho; Oppeneer, Peter M; Bürgler, Daniel E; Schneider, Claus M

    2014-01-01

    Electron magnetic circular dichroism (EMCD) allows the quantitative, element-selective determination of spin and orbital magnetic moments, similar to its well-established X-ray counterpart, X-ray magnetic circular dichroism (XMCD). As an advantage over XMCD, EMCD measurements are made using transmission electron microscopes, which are routinely operated at sub-nanometre resolution, thereby potentially allowing nanometre magnetic characterization. However, because of the low intensity of the EMCD signal, it has not yet been possible to obtain quantitative information from EMCD signals at the nanoscale. Here we demonstrate a new approach to EMCD measurements that considerably enhances the outreach of the technique. The statistical analysis introduced here yields robust quantitative EMCD signals. Moreover, we demonstrate that quantitative magnetic information can be routinely obtained using electron beams of only a few nanometres in diameter without imposing any restriction regarding the crystalline order of the specimen.

  10. A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification.

    PubMed

    Tu, Chengjian; Shen, Shichen; Sheng, Quanhu; Shyr, Yu; Qu, Jun

    2017-01-30

    Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the less confident peptides that were previously filtered out using the standard target-decoy search strategy. The filtered-out MS/MS spectra matched to confidently-identified proteins were recovered, and the peptide-spectrum-match FDR were re-calculated and controlled at a confident level of FDR≤1%, while protein FDR maintained at ~1%. We evaluated the performance of this strategy in both spectral count- and ion current-based methods. >60% increase of total quantified spectra/peptides was respectively achieved for analyzing a spike-in sample set and a public dataset from CPTAC. Incorporating the peptide retrieval strategy significantly improved the quantitative accuracy and precision, especially for low-abundance proteins (e.g. one-hit proteins). Moreover, the capacity of confidently discovering significantly-altered proteins was also enhanced substantially, as demonstrated with two spike-in datasets. In summary, improved quantitative performance was achieved by this peptide recovery strategy without compromising confidence of protein identification, which can be readily implemented in a broad range of quantitative proteomics techniques including label-free or labeling approaches. We hypothesize that more quantifiable spectra and peptides in a protein, even including less confident peptides, could help reduce variations and improve protein quantification. Hence the peptide retrieval strategy was developed and evaluated in two spike-in sample sets with different LC-MS/MS variations using both MS1- and MS2-based quantitative approach. The list of confidently identified proteins using the standard target-decoy search strategy was fixed and more spectra/peptides with less

  11. The Impact of Pushed Output on Accuracy and Fluency of Iranian EFL Learners' Speaking

    ERIC Educational Resources Information Center

    Sadeghi Beniss, Aram Reza; Edalati Bazzaz, Vahid

    2014-01-01

    The current study attempted to establish baseline quantitative data on the impacts of pushed output on two components of speaking (i.e., accuracy and fluency). To achieve this purpose, 30 female EFL learners were selected from a whole population pool of 50 based on the standard test of IELTS interview and were randomly assigned into an…

  12. Monitoring the injured brain: registered, patient specific atlas models to improve accuracy of recovered brain saturation values

    NASA Astrophysics Data System (ADS)

    Clancy, Michael; Belli, Antonio; Davies, David; Lucas, Samuel J. E.; Su, Zhangjie; Dehghani, Hamid

    2015-07-01

    The subject of superficial contamination and signal origins remains a widely debated topic in the field of Near Infrared Spectroscopy (NIRS), yet the concept of using the technology to monitor an injured brain, in a clinical setting, poses additional challenges concerning the quantitative accuracy of recovered parameters. Using high density diffuse optical tomography probes, quantitatively accurate parameters from different layers (skin, bone and brain) can be recovered from subject specific reconstruction models. This study assesses the use of registered atlas models for situations where subject specific models are not available. Data simulated from subject specific models were reconstructed using the 8 registered atlas models implementing a regional (layered) parameter recovery in NIRFAST. A 3-region recovery based on the atlas model yielded recovered brain saturation values which were accurate to within 4.6% (percentage error) of the simulated values, validating the technique. The recovered saturations in the superficial regions were not quantitatively accurate. These findings highlight differences in superficial (skin and bone) layer thickness between the subject and atlas models. This layer thickness mismatch was propagated through the reconstruction process decreasing the parameter accuracy.

  13. Accuracy of lineaments mapping from space

    NASA Technical Reports Server (NTRS)

    Short, Nicholas M.

    1989-01-01

    The use of Landsat and other space imaging systems for lineaments detection is analyzed in terms of their effectiveness in recognizing and mapping fractures and faults, and the results of several studies providing a quantitative assessment of lineaments mapping accuracies are discussed. The cases under investigation include a Landsat image of the surface overlying a part of the Anadarko Basin of Oklahoma, the Landsat images and selected radar imagery of major lineaments systems distributed over much of Canadian Shield, and space imagery covering a part of the East African Rift in Kenya. It is demonstrated that space imagery can detect a significant portion of a region's fracture pattern, however, significant fractions of faults and fractures recorded on a field-produced geological map are missing from the imagery as it is evident in the Kenya case.

  14. Quantification Bias Caused by Plasmid DNA Conformation in Quantitative Real-Time PCR Assay

    PubMed Central

    Lin, Chih-Hui; Chen, Yu-Chieh; Pan, Tzu-Ming

    2011-01-01

    Quantitative real-time PCR (qPCR) is the gold standard for the quantification of specific nucleic acid sequences. However, a serious concern has been revealed in a recent report: supercoiled plasmid standards cause significant over-estimation in qPCR quantification. In this study, we investigated the effect of plasmid DNA conformation on the quantification of DNA and the efficiency of qPCR. Our results suggest that plasmid DNA conformation has significant impact on the accuracy of absolute quantification by qPCR. DNA standard curves shifted significantly among plasmid standards with different DNA conformations. Moreover, the choice of DNA measurement method and plasmid DNA conformation may also contribute to the measurement error of DNA standard curves. Due to the multiple effects of plasmid DNA conformation on the accuracy of qPCR, efforts should be made to assure the highest consistency of plasmid standards for qPCR. Thus, we suggest that the conformation, preparation, quantification, purification, handling, and storage of standard plasmid DNA should be described and defined in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) to assure the reproducibility and accuracy of qPCR absolute quantification. PMID:22194997

  15. Accuracy in the estimation of quantitative minimal area from the diversity/area curve.

    PubMed

    Vives, Sergi; Salicrú, Miquel

    2005-05-01

    The problem of representativity is fundamental in ecological studies. A qualitative minimal area that gives a good representation of species pool [C.M. Bouderesque, Methodes d'etude qualitative et quantitative du benthos (en particulier du phytobenthos), Tethys 3(1) (1971) 79] can be discerned from a quantitative minimal area which reflects the structural complexity of community [F.X. Niell, Sobre la biologia de Ascophyllum nosodum (L.) Le Jolis en Galicia, Invest. Pesq. 43 (1979) 501]. This suggests that the populational diversity can be considered as the value of the horizontal asymptote corresponding to the curve sample diversity/biomass [F.X. Niell, Les applications de l'index de Shannon a l'etude de la vegetation interdidale, Soc. Phycol. Fr. Bull. 19 (1974) 238]. In this study we develop a expression to determine minimal areas and use it to obtain certain information about the community structure based on diversity/area curve graphs. This expression is based on the functional relationship between the expected value of the diversity and the sample size used to estimate it. In order to establish the quality of the estimation process, we obtained the confidence intervals as a particularization of the functional (h-phi)-entropies proposed in [M. Salicru, M.L. Menendez, D. Morales, L. Pardo, Asymptotic distribution of (h,phi)-entropies, Commun. Stat. (Theory Methods) 22 (7) (1993) 2015]. As an example used to demonstrate the possibilities of this method, and only for illustrative purposes, data about a study on the rocky intertidal seawed populations in the Ria of Vigo (N.W. Spain) are analyzed [F.X. Niell, Estudios sobre la estructura, dinamica y produccion del Fitobentos intermareal (Facies rocosa) de la Ria de Vigo. Ph.D. Mem. University of Barcelona, Barcelona, 1979].

  16. "Score the Core" Web-based pathologist training tool improves the accuracy of breast cancer IHC4 scoring.

    PubMed

    Engelberg, Jesse A; Retallack, Hanna; Balassanian, Ronald; Dowsett, Mitchell; Zabaglo, Lila; Ram, Arishneel A; Apple, Sophia K; Bishop, John W; Borowsky, Alexander D; Carpenter, Philip M; Chen, Yunn-Yi; Datnow, Brian; Elson, Sarah; Hasteh, Farnaz; Lin, Fritz; Moatamed, Neda A; Zhang, Yanhong; Cardiff, Robert D

    2015-11-01

    Hormone receptor status is an integral component of decision-making in breast cancer management. IHC4 score is an algorithm that combines hormone receptor, HER2, and Ki-67 status to provide a semiquantitative prognostic score for breast cancer. High accuracy and low interobserver variance are important to ensure the score is accurately calculated; however, few previous efforts have been made to measure or decrease interobserver variance. We developed a Web-based training tool, called "Score the Core" (STC) using tissue microarrays to train pathologists to visually score estrogen receptor (using the 300-point H score), progesterone receptor (percent positive), and Ki-67 (percent positive). STC used a reference score calculated from a reproducible manual counting method. Pathologists in the Athena Breast Health Network and pathology residents at associated institutions completed the exercise. By using STC, pathologists improved their estrogen receptor H score and progesterone receptor and Ki-67 proportion assessment and demonstrated a good correlation between pathologist and reference scores. In addition, we collected information about pathologist performance that allowed us to compare individual pathologists and measures of agreement. Pathologists' assessment of the proportion of positive cells was closer to the reference than their assessment of the relative intensity of positive cells. Careful training and assessment should be used to ensure the accuracy of breast biomarkers. This is particularly important as breast cancer diagnostics become increasingly quantitative and reproducible. Our training tool is a novel approach for pathologist training that can serve as an important component of ongoing quality assessment and can improve the accuracy of breast cancer prognostic biomarkers. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers

    PubMed Central

    Meng, He; Andresen, Kurt; van Noort, John

    2015-01-01

    Single-molecule techniques allow for picoNewton manipulation and nanometer accuracy measurements of single chromatin fibers. However, the complexity of the data, the heterogeneity of the composition of individual fibers and the relatively large fluctuations in extension of the fibers complicate a structural interpretation of such force-extension curves. Here we introduce a statistical mechanics model that quantitatively describes the extension of individual fibers in response to force on a per nucleosome basis. Four nucleosome conformations can be distinguished when pulling a chromatin fiber apart. A novel, transient conformation is introduced that coexists with single wrapped nucleosomes between 3 and 7 pN. Comparison of force-extension curves between single nucleosomes and chromatin fibers shows that embedding nucleosomes in a fiber stabilizes the nucleosome by 10 kBT. Chromatin fibers with 20- and 50-bp linker DNA follow a different unfolding pathway. These results have implications for accessibility of DNA in fully folded and partially unwrapped chromatin fibers and are vital for understanding force unfolding experiments on nucleosome arrays. PMID:25779043

  18. High-accuracy direct aerial platform orientation with tightly coupled GPS/INS system.

    DOT National Transportation Integrated Search

    2004-09-01

    Obtaining sensor orientation by direct measurements is a rapidly emerging mapping technology. Modern GPS and INS systems allow for the direct determination of platform position and orientation at an unprecedented accuracy. In airborne surveying, airc...

  19. Accuracy of Satellite Optical Observations and Precise Orbit Determination

    NASA Astrophysics Data System (ADS)

    Shakun, L.; Koshkin, N.; Korobeynikova, E.; Strakhova, S.; Dragomiretsky, V.; Ryabov, A.; Melikyants, S.; Golubovskaya, T.; Terpan, S.

    The monitoring of low-orbit space objects (LEO-objects) is performed in the Astronomical Observatory of Odessa I.I. Mechnikov National University (Ukraine) for many years. Decades-long archives of these observations are accessible within Ukrainian network of optical observers (UMOS). In this work, we give an example of orbit determination for the satellite with the 1500-km height of orbit based on angular observations in our observatory (Int. No. 086). For estimation of the measurement accuracy and accuracy of determination and propagation of satellite position, we analyze the observations of Ajisai satellite with the well-determined orbit. This allows making justified conclusions not only about random errors of separate measurements, but also to analyze the presence of systematic errors, including external ones to the measurement process. We have shown that the accuracy of one measurement has the standard deviation about 1 arcsec across the track and 1.4 arcsec along the track and systematical shifts in measurements of one track do not exceed 0.45 arcsec. Ajisai position in the interval of the orbit fitting is predicted with accuracy better than 30 m along the orbit and better than 10 m across the orbit for any its point.

  20. Climate Change Accuracy: Requirements and Economic Value

    NASA Astrophysics Data System (ADS)

    Wielicki, B. A.; Cooke, R.; Mlynczak, M. G.; Lukashin, C.; Thome, K. J.; Baize, R. R.

    2014-12-01

    Higher than normal accuracy is required to rigorously observe decadal climate change. But what level is needed? How can this be quantified? This presentation will summarize a new more rigorous and quantitative approach to determining the required accuracy for climate change observations (Wielicki et al., 2013, BAMS). Most current global satellite observations cannot meet this accuracy level. A proposed new satellite mission to resolve this challenge is CLARREO (Climate Absolute Radiance and Refractivity Observatory). CLARREO is designed to achieve advances of a factor of 10 for reflected solar spectra and a factor of 3 to 5 for thermal infrared spectra (Wielicki et al., Oct. 2013 BAMS). The CLARREO spectrometers are designed to serve as SI traceable benchmarks for the Global Satellite Intercalibration System (GSICS) and to greatly improve the utility of a wide range of LEO and GEO infrared and reflected solar passive satellite sensors for climate change observations (e.g. CERES, MODIS, VIIIRS, CrIS, IASI, Landsat, SPOT, etc). Providing more accurate decadal change trends can in turn lead to more rapid narrowing of key climate science uncertainties such as cloud feedback and climate sensitivity. A study has been carried out to quantify the economic benefits of such an advance as part of a rigorous and complete climate observing system. The study concludes that the economic value is $12 Trillion U.S. dollars in Net Present Value for a nominal discount rate of 3% (Cooke et al. 2013, J. Env. Sys. Dec.). A brief summary of these two studies and their implications for the future of climate science will be presented.

  1. A quantitative comparison of corrective and perfective maintenance

    NASA Technical Reports Server (NTRS)

    Henry, Joel; Cain, James

    1994-01-01

    This paper presents a quantitative comparison of corrective and perfective software maintenance activities. The comparison utilizes basic data collected throughout the maintenance process. The data collected are extensive and allow the impact of both types of maintenance to be quantitatively evaluated and compared. Basic statistical techniques test relationships between and among process and product data. The results show interesting similarities and important differences in both process and product characteristics.

  2. Quantitative AOP-based predictions for two aromatase inhibitors evaluating the influence of bioaccumulation on prediction accuracy

    EPA Science Inventory

    The adverse outcome pathway (AOP) framework can be used to support the use of mechanistic toxicology data as a basis for risk assessment. For certain risk contexts this includes defining, quantitative linkages between the molecular initiating event (MIE) and subsequent key events...

  3. Commissioning Procedures for Mechanical Precision and Accuracy in a Dedicated LINAC

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ballesteros-Zebadua, P.; Larrga-Gutierrez, J. M.; Garcia-Garduno, O. A.

    2008-08-11

    Mechanical precision measurements are fundamental procedures for the commissioning of a dedicated LINAC. At our Radioneurosurgery Unit, these procedures can be suitable as quality assurance routines that allow the verification of the equipment geometrical accuracy and precision. In this work mechanical tests were performed for gantry and table rotation, obtaining mean associated uncertainties of 0.3 mm and 0.71 mm, respectively. Using an anthropomorphic phantom and a series of localized surface markers, isocenter accuracy showed to be smaller than 0.86 mm for radiosurgery procedures and 0.95 mm for fractionated treatments with mask. All uncertainties were below tolerances. The highest contribution tomore » mechanical variations is due to table rotation, so it is important to correct variations using a localization frame with printed overlays. Mechanical precision knowledge would allow to consider the statistical errors in the treatment planning volume margins.« less

  4. Quantitative analysis of single-molecule superresolution images

    PubMed Central

    Coltharp, Carla; Yang, Xinxing; Xiao, Jie

    2014-01-01

    This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10 – 50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images. PMID:25179006

  5. 42 CFR 61.9 - Payments: Stipends; dependency allowances; travel allowances.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 1 2014-10-01 2014-10-01 false Payments: Stipends; dependency allowances; travel... FELLOWSHIPS, INTERNSHIPS, TRAINING FELLOWSHIPS Regular Fellowships § 61.9 Payments: Stipends; dependency allowances; travel allowances. Payments for stipends, dependency allowances, and the travel allowances...

  6. 42 CFR 61.9 - Payments: Stipends; dependency allowances; travel allowances.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 1 2012-10-01 2012-10-01 false Payments: Stipends; dependency allowances; travel... FELLOWSHIPS, INTERNSHIPS, TRAINING FELLOWSHIPS Regular Fellowships § 61.9 Payments: Stipends; dependency allowances; travel allowances. Payments for stipends, dependency allowances, and the travel allowances...

  7. 42 CFR 61.9 - Payments: Stipends; dependency allowances; travel allowances.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 1 2011-10-01 2011-10-01 false Payments: Stipends; dependency allowances; travel... FELLOWSHIPS, INTERNSHIPS, TRAINING FELLOWSHIPS Regular Fellowships § 61.9 Payments: Stipends; dependency allowances; travel allowances. Payments for stipends, dependency allowances, and the travel allowances...

  8. 42 CFR 61.9 - Payments: Stipends; dependency allowances; travel allowances.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 1 2013-10-01 2013-10-01 false Payments: Stipends; dependency allowances; travel... FELLOWSHIPS, INTERNSHIPS, TRAINING FELLOWSHIPS Regular Fellowships § 61.9 Payments: Stipends; dependency allowances; travel allowances. Payments for stipends, dependency allowances, and the travel allowances...

  9. 42 CFR 61.9 - Payments: Stipends; dependency allowances; travel allowances.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 1 2010-10-01 2010-10-01 false Payments: Stipends; dependency allowances; travel... FELLOWSHIPS, INTERNSHIPS, TRAINING FELLOWSHIPS Regular Fellowships § 61.9 Payments: Stipends; dependency allowances; travel allowances. Payments for stipends, dependency allowances, and the travel allowances...

  10. SVM-Based Synthetic Fingerprint Discrimination Algorithm and Quantitative Optimization Strategy

    PubMed Central

    Chen, Suhang; Chang, Sheng; Huang, Qijun; He, Jin; Wang, Hao; Huang, Qiangui

    2014-01-01

    Synthetic fingerprints are a potential threat to automatic fingerprint identification systems (AFISs). In this paper, we propose an algorithm to discriminate synthetic fingerprints from real ones. First, four typical characteristic factors—the ridge distance features, global gray features, frequency feature and Harris Corner feature—are extracted. Then, a support vector machine (SVM) is used to distinguish synthetic fingerprints from real fingerprints. The experiments demonstrate that this method can achieve a recognition accuracy rate of over 98% for two discrete synthetic fingerprint databases as well as a mixed database. Furthermore, a performance factor that can evaluate the SVM's accuracy and efficiency is presented, and a quantitative optimization strategy is established for the first time. After the optimization of our synthetic fingerprint discrimination task, the polynomial kernel with a training sample proportion of 5% is the optimized value when the minimum accuracy requirement is 95%. The radial basis function (RBF) kernel with a training sample proportion of 15% is a more suitable choice when the minimum accuracy requirement is 98%. PMID:25347063

  11. Quantitative measurement of marginal disintegration of ceramic inlays.

    PubMed

    Hayashi, Mikako; Tsubakimoto, Yuko; Takeshige, Fumio; Ebisu, Shigeyuki

    2004-01-01

    The objectives of this study include establishing a method for quantitative measurement of marginal change in ceramic inlays and clarifying their marginal disintegration in vivo. An accurate CCD optical laser scanner system was used for morphological measurement of the marginal change of ceramic inlays. The accuracy of the CCD measurement was assessed by comparing it with microscopic measurement. Replicas of 15 premolars restored with Class II ceramic inlays at the time of placement and eight years after restoration were used for morphological measurement by means of the CCD laser scanner system. Occlusal surfaces of the restored teeth were scanned and cross-sections of marginal areas were computed with software. Marginal change was defined as the area enclosed by two profiles obtained by superimposing two cross-sections of the same location at two different times and expressing the maximum depth and mean area of the area enclosed. The accuracy of this method of measurement was 4.3 +/- 3.2 microm in distance and 2.0 +/- 0.6% in area. Quantitative marginal changes for the eight-year period were 10 x 10 microm in depth and 50 x 10(3) microm2 in area at the functional cusp area and 7 x 10 microm in depth and 28 x 10(3) microm2 in area at the non-functional cusp area. Marginal disintegration at the functional cusp area was significantly greater than at the non-functional cusp area (Wilcoxon signed-ranks test, p < 0.05). This study constitutes a quantitative measurement of in vivo deterioration in marginal adaptation of ceramic inlays and indicates that occlusal force may accelerate marginal disintegration.

  12. Quantitative evaluation of Alzheimer's disease

    NASA Astrophysics Data System (ADS)

    Duchesne, S.; Frisoni, G. B.

    2009-02-01

    We propose a single, quantitative metric called the disease evaluation factor (DEF) and assess its efficiency at estimating disease burden in normal, control subjects (CTRL) and probable Alzheimer's disease (AD) patients. The study group consisted in 75 patients with a diagnosis of probable AD and 75 age-matched normal CTRL without neurological or neuropsychological deficit. We calculated a reference eigenspace of MRI appearance from reference data, in which our CTRL and probable AD subjects were projected. We then calculated the multi-dimensional hyperplane separating the CTRL and probable AD groups. The DEF was estimated via a multidimensional weighted distance of eigencoordinates for a given subject and the CTRL group mean, along salient principal components forming the separating hyperplane. We used quantile plots, Kolmogorov-Smirnov and χ2 tests to compare the DEF values and test that their distribution was normal. We used a linear discriminant test to separate CTRL from probable AD based on the DEF factor, and reached an accuracy of 87%. A quantitative biomarker in AD would act as an important surrogate marker of disease status and progression.

  13. Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method.

    PubMed

    Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

    2018-04-01

    Isotope ratio monitoring by 13 C NMR spectrometry (irm- 13 C NMR) provides the complete 13 C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13 C natural abundance values (50‰), irm- 13 C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13 C NMR. Until now, the conventional strategy to determine the position-specific abundance x i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13 C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13 C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1 H NMR pulse sequence (named DWET) with a 13 C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T 1 , which forms a serious limitation for irm- 13 C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T 1 variations. Their performance is evaluated on the determination of the 13 C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm- 13 C NMR since it is now possible to perform

  14. Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

    NASA Astrophysics Data System (ADS)

    Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

    2018-04-01

    Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high

  15. Effects of disease severity distribution on the performance of quantitative diagnostic methods and proposal of a novel ‘V-plot’ methodology to display accuracy values

    PubMed Central

    Dehbi, Hakim-Moulay; Howard, James P; Shun-Shin, Matthew J; Sen, Sayan; Nijjer, Sukhjinder S; Mayet, Jamil; Davies, Justin E; Francis, Darrel P

    2018-01-01

    Background Diagnostic accuracy is widely accepted by researchers and clinicians as an optimal expression of a test’s performance. The aim of this study was to evaluate the effects of disease severity distribution on values of diagnostic accuracy as well as propose a sample-independent methodology to calculate and display accuracy of diagnostic tests. Methods and findings We evaluated the diagnostic relationship between two hypothetical methods to measure serum cholesterol (Cholrapid and Cholgold) by generating samples with statistical software and (1) keeping the numerical relationship between methods unchanged and (2) changing the distribution of cholesterol values. Metrics of categorical agreement were calculated (accuracy, sensitivity and specificity). Finally, a novel methodology to display and calculate accuracy values was presented (the V-plot of accuracies). Conclusion No single value of diagnostic accuracy can be used to describe the relationship between tests, as accuracy is a metric heavily affected by the underlying sample distribution. Our novel proposed methodology, the V-plot of accuracies, can be used as a sample-independent measure of a test performance against a reference gold standard. PMID:29387424

  16. Calibration methods influence quantitative material decomposition in photon-counting spectral CT

    NASA Astrophysics Data System (ADS)

    Curtis, Tyler E.; Roeder, Ryan K.

    2017-03-01

    Photon-counting detectors and nanoparticle contrast agents can potentially enable molecular imaging and material decomposition in computed tomography (CT). Material decomposition has been investigated using both simulated and acquired data sets. However, the effect of calibration methods on material decomposition has not been systematically investigated. Therefore, the objective of this study was to investigate the influence of the range and number of contrast agent concentrations within a modular calibration phantom on quantitative material decomposition. A commerciallyavailable photon-counting spectral micro-CT (MARS Bioimaging) was used to acquire images with five energy bins selected to normalize photon counts and leverage the contrast agent k-edge. Material basis matrix values were determined using multiple linear regression models and material decomposition was performed using a maximum a posteriori estimator. The accuracy of quantitative material decomposition was evaluated by the root mean squared error (RMSE), specificity, sensitivity, and area under the curve (AUC). An increased maximum concentration (range) in the calibration significantly improved RMSE, specificity and AUC. The effects of an increased number of concentrations in the calibration were not statistically significant for the conditions in this study. The overall results demonstrated that the accuracy of quantitative material decomposition in spectral CT is significantly influenced by calibration methods, which must therefore be carefully considered for the intended diagnostic imaging application.

  17. Quantitative measurement of MLC leaf displacements using an electronic portal image device

    NASA Astrophysics Data System (ADS)

    Yang, Yong; Xing, Lei

    2004-04-01

    The success of an IMRT treatment relies on the positioning accuracy of the MLC (multileaf collimator) leaves for both step-and-shoot and dynamic deliveries. In practice, however, there exists no effective and quantitative means for routine MLC QA and this has become one of the bottleneck problems in IMRT implementation. In this work we present an electronic portal image device (EPID) based method for fast and accurate measurement of MLC leaf positions at arbitrary locations within the 40 cm × 40 cm radiation field. The new technique utilizes the fact that the integral signal in a small region of interest (ROI) is a sensitive and reliable indicator of the leaf displacement. In this approach, the integral signal at a ROI was expressed as a weighted sum of the contributions from the displacements of the leaf above the point and the adjacent leaves. The weighting factors or linear coefficients of the system equations were determined by fitting the integral signal data for a group of pre-designed MLC leaf sequences to the known leaf displacements that were intentionally introduced during the creation of the leaf sequences. Once the calibration is done, the system can be used for routine MLC leaf positioning QA to detect possible leaf errors. A series of tests was carried out to examine the functionality and accuracy of the technique. Our results show that the proposed technique is potentially superior to the conventional edge-detecting approach in two aspects: (i) it deals with the problem in a systematic approach and allows us to take into account the influence of the adjacent MLC leaves effectively; and (ii) it may improve the signal-to-noise ratio and is thus capable of quantitatively measuring extremely small leaf positional displacements. Our results indicate that the technique can detect a leaf positional error as small as 0.1 mm at an arbitrary point within the field in the absence of EPID set-up error and 0.3 mm when the uncertainty is considered. Given its

  18. Development and application of a quantitative multiplexed small GTPase activity assay using targeted proteomics.

    PubMed

    Zhang, Cheng-Cheng; Li, Ru; Jiang, Honghui; Lin, Shujun; Rogalski, Jason C; Liu, Kate; Kast, Juergen

    2015-02-06

    Small GTPases are a family of key signaling molecules that are ubiquitously expressed in various types of cells. Their activity is often analyzed by western blot, which is limited by its multiplexing capability, the quality of isoform-specific antibodies, and the accuracy of quantification. To overcome these issues, a quantitative multiplexed small GTPase activity assay has been developed. Using four different binding domains, this assay allows the binding of up to 12 active small GTPase isoforms simultaneously in a single experiment. To accurately quantify the closely related small GTPase isoforms, a targeted proteomic approach, i.e., selected/multiple reaction monitoring, was developed, and its functionality and reproducibility were validated. This assay was successfully applied to human platelets and revealed time-resolved coactivation of multiple small GTPase isoforms in response to agonists and differential activation of these isoforms in response to inhibitor treatment. This widely applicable approach can be used for signaling pathway studies and inhibitor screening in many cellular systems.

  19. Differential diagnosis of lung carcinoma with three-dimensional quantitative molecular vibrational imaging

    NASA Astrophysics Data System (ADS)

    Gao, Liang; Hammoudi, Ahmad A.; Li, Fuhai; Thrall, Michael J.; Cagle, Philip T.; Chen, Yuanxin; Yang, Jian; Xia, Xiaofeng; Fan, Yubo; Massoud, Yehia; Wang, Zhiyong; Wong, Stephen T. C.

    2012-06-01

    The advent of molecularly targeted therapies requires effective identification of the various cell types of non-small cell lung carcinomas (NSCLC). Currently, cell type diagnosis is performed using small biopsies or cytology specimens that are often insufficient for molecular testing after morphologic analysis. Thus, the ability to rapidly recognize different cancer cell types, with minimal tissue consumption, would accelerate diagnosis and preserve tissue samples for subsequent molecular testing in targeted therapy. We report a label-free molecular vibrational imaging framework enabling three-dimensional (3-D) image acquisition and quantitative analysis of cellular structures for identification of NSCLC cell types. This diagnostic imaging system employs superpixel-based 3-D nuclear segmentation for extracting such disease-related features as nuclear shape, volume, and cell-cell distance. These features are used to characterize cancer cell types using machine learning. Using fresh unstained tissue samples derived from cell lines grown in a mouse model, the platform showed greater than 97% accuracy for diagnosis of NSCLC cell types within a few minutes. As an adjunct to subsequent histology tests, our novel system would allow fast delineation of cancer cell types with minimum tissue consumption, potentially facilitating on-the-spot diagnosis, while preserving specimens for additional tests. Furthermore, 3-D measurements of cellular structure permit evaluation closer to the native state of cells, creating an alternative to traditional 2-D histology specimen evaluation, potentially increasing accuracy in diagnosing cell type of lung carcinomas.

  20. Implications of Polishing Techniques in Quantitative X-Ray Microanalysis

    PubMed Central

    Rémond, Guy; Nockolds, Clive; Phillips, Matthew; Roques-Carmes, Claude

    2002-01-01

    Specimen preparation using abrasives results in surface and subsurface mechanical (stresses, strains), geometrical (roughness), chemical (contaminants, reaction products) and physical modifications (structure, texture, lattice defects). The mechanisms involved in polishing with abrasives are presented to illustrate the effects of surface topography, surface and subsurface composition and induced lattice defects on the accuracy of quantitative x-ray microanalysis of mineral materials with the electron probe microanalyzer (EPMA). PMID:27446758

  1. Quantitative characterization of color Doppler images: reproducibility, accuracy, and limitations.

    PubMed

    Delorme, S; Weisser, G; Zuna, I; Fein, M; Lorenz, A; van Kaick, G

    1995-01-01

    A computer-based quantitative analysis for color Doppler images of complex vascular formations is presented. The red-green-blue-signal from an Acuson XP10 is frame-grabbed and digitized. By matching each image pixel with the color bar, color pixels are identified and assigned to the corresponding flow velocity (color value). Data analysis consists of delineation of a region of interest and calculation of the relative number of color pixels in this region (color pixel density) as well as the mean color value. The mean color value was compared to flow velocities in a flow phantom. The thyroid and carotid artery in a volunteer were repeatedly examined by a single examiner to assess intra-observer variability. The thyroids in five healthy controls were examined by three experienced physicians to assess the extent of inter-observer variability and observer bias. The correlation between the mean color value and flow velocity ranged from 0.94 to 0.96 for a range of velocities determined by pulse repetition frequency. The average deviation of the mean color value from the flow velocity was 22% to 41%, depending on the selected pulse repetition frequency (range of deviations, -46% to +66%). Flow velocity was underestimated with inadequately low pulse repetition frequency, or inadequately high reject threshold. An overestimation occurred with inadequately high pulse repetition frequency. The highest intra-observer variability was 22% (relative standard deviation) for the color pixel density, and 9.1% for the mean color value. The inter-observer variation was approximately 30% for the color pixel density, and 20% for the mean color value. In conclusion, computer assisted image analysis permits an objective description of color Doppler images. However, the user must be aware that image acquisition under in vivo conditions as well as physical and instrumental factors may considerably influence the results.

  2. Cleavage Entropy as Quantitative Measure of Protease Specificity

    PubMed Central

    Fuchs, Julian E.; von Grafenstein, Susanne; Huber, Roland G.; Margreiter, Michael A.; Spitzer, Gudrun M.; Wallnoefer, Hannes G.; Liedl, Klaus R.

    2013-01-01

    A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity. PMID:23637583

  3. Evaluating the decision accuracy and speed of clinical data visualizations.

    PubMed

    Pieczkiewicz, David S; Finkelstein, Stanley M

    2010-01-01

    Clinicians face an increasing volume of biomedical data. Assessing the efficacy of systems that enable accurate and timely clinical decision making merits corresponding attention. This paper discusses the multiple-reader multiple-case (MRMC) experimental design and linear mixed models as means of assessing and comparing decision accuracy and latency (time) for decision tasks in which clinician readers must interpret visual displays of data. These tools can assess and compare decision accuracy and latency (time). These experimental and statistical techniques, used extensively in radiology imaging studies, offer a number of practical and analytic advantages over more traditional quantitative methods such as percent-correct measurements and ANOVAs, and are recommended for their statistical efficiency and generalizability. An example analysis using readily available, free, and commercial statistical software is provided as an appendix. While these techniques are not appropriate for all evaluation questions, they can provide a valuable addition to the evaluative toolkit of medical informatics research.

  4. Bio-knowledge based filters improve residue-residue contact prediction accuracy.

    PubMed

    Wozniak, P P; Pelc, J; Skrzypecki, M; Vriend, G; Kotulska, M

    2018-05-29

    Residue-residue contact prediction through direct coupling analysis has reached impressive accuracy, but yet higher accuracy will be needed to allow for routine modelling of protein structures. One way to improve the prediction accuracy is to filter predicted contacts using knowledge about the particular protein of interest or knowledge about protein structures in general. We focus on the latter and discuss a set of filters that can be used to remove false positive contact predictions. Each filter depends on one or a few cut-off parameters for which the filter performance was investigated. Combining all filters while using default parameters resulted for a test-set of 851 protein domains in the removal of 29% of the predictions of which 92% were indeed false positives. All data and scripts are available from http://comprec-lin.iiar.pwr.edu.pl/FPfilter/. malgorzata.kotulska@pwr.edu.pl. Supplementary data are available at Bioinformatics online.

  5. Quantitative fetal fibronectin and cervical length to predict preterm birth in asymptomatic women with previous cervical surgery.

    PubMed

    Vandermolen, Brooke I; Hezelgrave, Natasha L; Smout, Elizabeth M; Abbott, Danielle S; Seed, Paul T; Shennan, Andrew H

    2016-10-01

    Quantitative fetal fibronectin testing has demonstrated accuracy for prediction of spontaneous preterm birth in asymptomatic women with a history of preterm birth. Predictive accuracy in women with previous cervical surgery (a potentially different risk mechanism) is not known. We sought to compare the predictive accuracy of cervicovaginal fluid quantitative fetal fibronectin and cervical length testing in asymptomatic women with previous cervical surgery to that in women with 1 previous preterm birth. We conducted a prospective blinded secondary analysis of a larger observational study of cervicovaginal fluid quantitative fetal fibronectin concentration in asymptomatic women measured with a Hologic 10Q system (Hologic, Marlborough, MA). Prediction of spontaneous preterm birth (<30, <34, and <37 weeks) with cervicovaginal fluid quantitative fetal fibronectin concentration in primiparous women who had undergone at least 1 invasive cervical procedure (n = 473) was compared with prediction in women who had previous spontaneous preterm birth, preterm prelabor rupture of membranes, or late miscarriage (n = 821). Relationship with cervical length was explored. The rate of spontaneous preterm birth <34 weeks in the cervical surgery group was 3% compared with 9% in previous spontaneous preterm birth group. Receiver operating characteristic curves comparing quantitative fetal fibronectin for prediction at all 3 gestational end points were comparable between the cervical surgery and previous spontaneous preterm birth groups (34 weeks: area under the curve, 0.78 [95% confidence interval 0.64-0.93] vs 0.71 [95% confidence interval 0.64-0.78]; P = .39). Prediction of spontaneous preterm birth using cervical length compared with quantitative fetal fibronectin for prediction of preterm birth <34 weeks of gestation offered similar prediction (area under the curve, 0.88 [95% confidence interval 0.79-0.96] vs 0.77 [95% confidence interval 0.62-0.92], P = .12 in the cervical

  6. Improvement of the accuracy of noise measurements by the two-amplifier correlation method.

    PubMed

    Pellegrini, B; Basso, G; Fiori, G; Macucci, M; Maione, I A; Marconcini, P

    2013-10-01

    We present a novel method for device noise measurement, based on a two-channel cross-correlation technique and a direct "in situ" measurement of the transimpedance of the device under test (DUT), which allows improved accuracy with respect to what is available in the literature, in particular when the DUT is a nonlinear device. Detailed analytical expressions for the total residual noise are derived, and an experimental investigation of the increased accuracy provided by the method is performed.

  7. Development and evaluation of a model-based downscatter compensation method for quantitative I-131 SPECT

    PubMed Central

    Song, Na; Du, Yong; He, Bin; Frey, Eric C.

    2011-01-01

    Purpose: The radionuclide 131I has found widespread use in targeted radionuclide therapy (TRT), partly due to the fact that it emits photons that can be imaged to perform treatment planning or posttherapy dose verification as well as beta rays that are suitable for therapy. In both the treatment planning and dose verification applications, it is necessary to estimate the activity distribution in organs or tumors at several time points. In vivo estimates of the 131I activity distribution at each time point can be obtained from quantitative single-photon emission computed tomography (QSPECT) images and organ activity estimates can be obtained either from QSPECT images or quantification of planar projection data. However, in addition to the photon used for imaging, 131I decay results in emission of a number of other higher-energy photons with significant abundances. These higher-energy photons can scatter in the body, collimator, or detector and be counted in the 364 keV photopeak energy window, resulting in reduced image contrast and degraded quantitative accuracy; these photons are referred to as downscatter. The goal of this study was to develop and evaluate a model-based downscatter compensation method specifically designed for the compensation of high-energy photons emitted by 131I and detected in the imaging energy window. Methods: In the evaluation study, we used a Monte Carlo simulation (MCS) code that had previously been validated for other radionuclides. Thus, in preparation for the evaluation study, we first validated the code for 131I imaging simulation by comparison with experimental data. Next, we assessed the accuracy of the downscatter model by comparing downscatter estimates with MCS results. Finally, we combined the downscatter model with iterative reconstruction-based compensation for attenuation (A) and scatter (S) and the full (D) collimator-detector response of the 364 keV photons to form a comprehensive compensation method. We evaluated this

  8. Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

    PubMed

    Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano

    2016-09-13

    We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution.

  9. Accuracy of sign interpreting and real-time captioning of science videos for the delivery of instruction to deaf students

    NASA Astrophysics Data System (ADS)

    Sadler, Karen L.

    2009-04-01

    The purpose of this study was to quantitatively examine the impact of third-party support service providers on the quality of science information available to deaf students in regular science classrooms. Three different videotapes that were developed by NASA for high school science classrooms were selected for the study, allowing for different concepts and vocabulary to be examined. The focus was on the accuracy of translation as measured by the number of key science words included in the transcripts (captions) or videos (interpreted). Data were collected via transcripts completed by CART (computer assisted real-time captionists) or through videos of sign language interpreters. All participants were required to listen to and translate these NASA educational videos with no prior experience with this information so as not to influence their delivery. CART personnel using captions were found to be significantly more accurate in the delivery of science words as compared to the sign language interpreters in this study.

  10. Study on the position accuracy of a mechanical alignment system

    NASA Astrophysics Data System (ADS)

    Cai, Yimin

    In this thesis, we investigated the precision level and established the baseline achieved by a mechanical alignment system using datums and reference surfaces. The factors which affect the accuracy of mechanical alignment system were studied and methodology was developed to suppress these factors so as to reach its full potential precision. In order to characterize the mechanical alignment system quantitatively, a new optical position monitoring system by using quadrant detectors has been developed in this thesis, it can monitor multi-dimensional degrees of mechanical workpieces in real time with high precision. We studied the noise factors inside the system and optimized the optical system. Based on the fact that one of the major limiting noise factors is the shifting of the laser beam, a noise cancellation technique has been developed successfully to suppress this noise, the feasibility of an ultra high resolution (<20 A) for displacement monitoring has been demonstrated. Using the optical position monitoring system, repeatability experiment of the mechanical alignment system has been conducted on different kinds of samples including steel, aluminum, glass and plastics with the same size 100mm x 130mm. The alignment accuracy was studied quantitatively rather than qualitatively before. In a controlled environment, the alignment precision can be improved 5 folds by securing the datum without other means of help. The alignment accuracy of an aluminum workpiece having reference surface by milling is about 3 times better than by shearing. Also we have found that sample material can have fairly significant effect on the alignment precision of the system. Contamination trapped between the datum and reference surfaces in mechanical alignment system can cause errors of registration or reduce the level of manufacturing precision. In the thesis, artificial and natural dust particles were used to simulate the real situations and their effects on system precision have been

  11. Cardiovascular and pulmonary dynamics by quantitative imaging

    NASA Technical Reports Server (NTRS)

    Wood, E. H.

    1976-01-01

    The accuracy and range of studies on cardiovascular and pulmonary functions can be greatly facilitated if the motions of the underlying organ systems throughout individual cycles can be directly visualized and readily measured with minimum or preferably no effect on these motions. Achievement of this objective requires development of techniques for quantitative noninvasive or minimally invasive dynamic and stop-action imaging of the organ systems. A review of advances in dynamic quantitative imaging of moving organs reveals that the revolutionary value of cross-sectional and three-dimensional images produced by various types of radiant energy such as X-rays and gamma rays, positrons, electrons, protons, light, and ultrasound for clinical diagnostic and biomedical research applications is just beginning to be realized. The fabrication of a clinically useful cross-section reconstruction device with sensing capabilities for both anatomical structural composition and chemical composition may be possible and awaits future development.

  12. Analysis of the accuracy and robustness of the leap motion controller.

    PubMed

    Weichert, Frank; Bachmann, Daniel; Rudak, Bartholomäus; Fisseler, Denis

    2013-05-14

    The Leap Motion Controller is a new device for hand gesture controlled user interfaces with declared sub-millimeter accuracy. However, up to this point its capabilities in real environments have not been analyzed. Therefore, this paper presents a first study of a Leap Motion Controller. The main focus of attention is on the evaluation of the accuracy and repeatability. For an appropriate evaluation, a novel experimental setup was developed making use of an industrial robot with a reference pen allowing a position accuracy of 0.2 mm. Thereby, a deviation between a desired 3D position and the average measured positions below 0.2 mm has been obtained for static setups and of 1.2 mm for dynamic setups. Using the conclusion of this analysis can improve the development of applications for the Leap Motion controller in the field of Human-Computer Interaction.

  13. Quantitative and Sensitive Detection of Chloramphenicol by Surface-Enhanced Raman Scattering

    PubMed Central

    Ding, Yufeng; Yin, Hongjun; Meng, Qingyun; Zhao, Yongmei; Liu, Luo; Wu, Zhenglong; Xu, Haijun

    2017-01-01

    We used surface-enhanced Raman scattering (SERS) for the quantitative and sensitive detection of chloramphenicol (CAP). Using 30 nm colloidal Au nanoparticles (NPs), a low detection limit for CAP of 10−8 M was obtained. The characteristic Raman peak of CAP centered at 1344 cm−1 was used for the rapid quantitative detection of CAP in three different types of CAP eye drops, and the accuracy of the measurement result was verified by high-performance liquid chromatography (HPLC). The experimental results reveal that the SERS technique based on colloidal Au NPs is accurate and sensitive, and can be used for the rapid detection of various antibiotics. PMID:29261161

  14. Quantitative Peptidomics with Five-plex Reductive Methylation labels

    NASA Astrophysics Data System (ADS)

    Tashima, Alexandre K.; Fricker, Lloyd D.

    2017-12-01

    Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines. Up to five different isotopic forms can be generated, depending on the isotopic forms of formaldehyde and cyanoborohydride reagents, allowing for five-plex quantitation. However, the mass difference between each of these forms is only 1 Da per methyl group incorporated into the peptide, and for many peptides there is substantial overlap from the natural abundance of 13C and other isotopes. In this study, we calculated the contribution from the natural isotopes for 26 native peptides and derived equations to correct the peak intensities. These equations were applied to data from a study using human embryonic kidney HEK293T cells in which five replicates were treated with 100 nM vinblastine for 3 h and compared with five replicates of cells treated with control medium. The correction equations brought the replicates to the expected 1:1 ratios and revealed significant decreases in levels of 21 peptides upon vinblastine treatment. These equations enable accurate quantitation of small changes in peptide levels using the reductive methylation labeling approach. [Figure not available: see fulltext.

  15. Quantitative Peptidomics with Five-plex Reductive Methylation labels

    NASA Astrophysics Data System (ADS)

    Tashima, Alexandre K.; Fricker, Lloyd D.

    2018-05-01

    Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines. Up to five different isotopic forms can be generated, depending on the isotopic forms of formaldehyde and cyanoborohydride reagents, allowing for five-plex quantitation. However, the mass difference between each of these forms is only 1 Da per methyl group incorporated into the peptide, and for many peptides there is substantial overlap from the natural abundance of 13C and other isotopes. In this study, we calculated the contribution from the natural isotopes for 26 native peptides and derived equations to correct the peak intensities. These equations were applied to data from a study using human embryonic kidney HEK293T cells in which five replicates were treated with 100 nM vinblastine for 3 h and compared with five replicates of cells treated with control medium. The correction equations brought the replicates to the expected 1:1 ratios and revealed significant decreases in levels of 21 peptides upon vinblastine treatment. These equations enable accurate quantitation of small changes in peptide levels using the reductive methylation labeling approach. [Figure not available: see fulltext.

  16. Investigation of the Matrix Effect on the Accuracy of Quantitative Analysis of Trace Metals in Liquids Using Laser-Induced Breakdown Spectroscopy with Solid Substrates.

    PubMed

    Xiu, Junshan; Dong, Lili; Qin, Hua; Liu, Yunyan; Yu, Jin

    2016-12-01

    The detection limit of trace metals in liquids has been improved greatly by laser-induced breakdown spectroscopy (LIBS) using solid substrate. A paper substrate and a metallic substrate were used as a solid substrate for the detection of trace metals in aqueous solutions and viscous liquids (lubricating oils) respectively. The matrix effect on quantitative analysis of trace metals in two types of liquids was investigated. For trace metals in aqueous solutions using paper substrate, the calibration curves established for pure solutions and mixed solutions samples presented large variation on both the slope and the intercept for the Cu, Cd, and Cr. The matrix effects among the different elements in mixed solutions were observed. However, good agreement was obtained between the measured and known values in real wastewater. For trace metals in lubricating oils, the matrix effect between the different oils is relatively small and reasonably negligible under the conditions of our experiment. A universal calibration curve can be established for trace metals in different types of oils. The two approaches are verified that it is possible to develop a feasible and sensitive method with accuracy results for rapid detection of trace metals in industrial wastewater and viscous liquids by laser-induced breakdown spectroscopy. © The Author(s) 2016.

  17. Can we predict necrosis intra-operatively? Real-time optical quantitative perfusion imaging in surgery: study protocol for a prospective, observational, in vivo pilot study.

    PubMed

    Jansen, Sanne M; de Bruin, Daniel M; van Berge Henegouwen, Mark I; Strackee, Simon D; Veelo, Denise P; van Leeuwen, Ton G; Gisbertz, Suzanne S

    2017-01-01

    Compromised perfusion as a result of surgical intervention causes a reduction of oxygen and nutrients in tissue and therefore decreased tissue vitality. Quantitative imaging of tissue perfusion during reconstructive surgery, therefore, may reduce the incidence of complications. Non-invasive optical techniques allow real-time tissue imaging, with high resolution and high contrast. The objectives of this study are, first, to assess the feasibility and accuracy of optical coherence tomography (OCT), sidestream darkfield microscopy (SDF), laser speckle contrast imaging (LSCI), and fluorescence imaging (FI) for quantitative perfusion imaging and, second, to identify/search for criteria that enable risk prediction of necrosis during gastric tube and free flap reconstruction. This prospective, multicenter, observational in vivo pilot study will assess tissue perfusion using four optical technologies: OCT, SDF, LSCI, and FI in 40 patients: 20 patients who will undergo gastric tube reconstruction after esophagectomy and 20 patients who will undergo free flap surgery. Intra-operative images of gastric perfusion will be obtained directly after reconstruction at four perfusion areas. Feasibility of perfusion imaging will be analyzed per technique. Quantitative parameters directly related to perfusion will be scored per perfusion area, and differences between biologically good versus reduced perfusion will be tested statistically. Patient outcome will be correlated to images and perfusion parameters. Differences in perfusion parameters before and after a bolus of ephedrine will be tested for significance. This study will identify quantitative perfusion-related parameters for an objective assessment of tissue perfusion during surgery. This will likely allow early risk stratification of necrosis development, which will aid in achieving a reduction of complications in gastric tube reconstruction and free flap transplantation. Clinicaltrials.gov registration number NCT02902549

  18. 42 CFR 61.8 - Benefits: Stipends; dependency allowances; travel allowances; vacation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 1 2014-10-01 2014-10-01 false Benefits: Stipends; dependency allowances; travel...; dependency allowances; travel allowances; vacation. Individuals awarded regular fellowships shall be entitled...) Stipend. (b) Dependency allowances. (c) When authorized in advance, separate allowances for travel. Such...

  19. 42 CFR 61.8 - Benefits: Stipends; dependency allowances; travel allowances; vacation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 1 2011-10-01 2011-10-01 false Benefits: Stipends; dependency allowances; travel...; dependency allowances; travel allowances; vacation. Individuals awarded regular fellowships shall be entitled...) Stipend. (b) Dependency allowances. (c) When authorized in advance, separate allowances for travel. Such...

  20. 42 CFR 61.8 - Benefits: Stipends; dependency allowances; travel allowances; vacation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 1 2010-10-01 2010-10-01 false Benefits: Stipends; dependency allowances; travel...; dependency allowances; travel allowances; vacation. Individuals awarded regular fellowships shall be entitled...) Stipend. (b) Dependency allowances. (c) When authorized in advance, separate allowances for travel. Such...

  1. 42 CFR 61.8 - Benefits: Stipends; dependency allowances; travel allowances; vacation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 1 2012-10-01 2012-10-01 false Benefits: Stipends; dependency allowances; travel...; dependency allowances; travel allowances; vacation. Individuals awarded regular fellowships shall be entitled...) Stipend. (b) Dependency allowances. (c) When authorized in advance, separate allowances for travel. Such...

  2. 42 CFR 61.8 - Benefits: Stipends; dependency allowances; travel allowances; vacation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 1 2013-10-01 2013-10-01 false Benefits: Stipends; dependency allowances; travel...; dependency allowances; travel allowances; vacation. Individuals awarded regular fellowships shall be entitled...) Stipend. (b) Dependency allowances. (c) When authorized in advance, separate allowances for travel. Such...

  3. Digital micromirror device-based common-path quantitative phase imaging.

    PubMed

    Zheng, Cheng; Zhou, Renjie; Kuang, Cuifang; Zhao, Guangyuan; Yaqoob, Zahid; So, Peter T C

    2017-04-01

    We propose a novel common-path quantitative phase imaging (QPI) method based on a digital micromirror device (DMD). The DMD is placed in a plane conjugate to the objective back-aperture plane for the purpose of generating two plane waves that illuminate the sample. A pinhole is used in the detection arm to filter one of the beams after sample to create a reference beam. Additionally, a transmission-type liquid crystal device, placed at the objective back-aperture plane, eliminates the specular reflection noise arising from all the "off" state DMD micromirrors, which is common in all DMD-based illuminations. We have demonstrated high sensitivity QPI, which has a measured spatial and temporal noise of 4.92 nm and 2.16 nm, respectively. Experiments with calibrated polystyrene beads illustrate the desired phase measurement accuracy. In addition, we have measured the dynamic height maps of red blood cell membrane fluctuations, showing the efficacy of the proposed system for live cell imaging. Most importantly, the DMD grants the system convenience in varying the interference fringe period on the camera to easily satisfy the pixel sampling conditions. This feature also alleviates the pinhole alignment complexity. We envision that the proposed DMD-based common-path QPI system will allow for system miniaturization and automation for a broader adaption.

  4. SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.

    PubMed

    Blattmann, Peter; Heusel, Moritz; Aebersold, Ruedi

    2016-01-01

    SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quantification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient processing of the data into a format directly readable by the downstream analysis tools. In addition, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.

  5. Location Accuracy of INS/Gravity-Integrated Navigation System on the Basis of Ocean Experiment and Simulation

    PubMed Central

    Wang, Hubiao; Chai, Hua; Bao, Lifeng; Wang, Yong

    2017-01-01

    An experiment comparing the location accuracy of gravity matching-aided navigation in the ocean and simulation is very important to evaluate the feasibility and the performance of an INS/gravity-integrated navigation system (IGNS) in underwater navigation. Based on a 1′ × 1′ marine gravity anomaly reference map and multi-model adaptive Kalman filtering algorithm, a matching location experiment of IGNS was conducted using data obtained using marine gravimeter. The location accuracy under actual ocean conditions was 2.83 nautical miles (n miles). Several groups of simulated data of marine gravity anomalies were obtained by establishing normally distributed random error N(u,σ2) with varying mean u and noise variance σ2. Thereafter, the matching location of IGNS was simulated. The results show that the changes in u had little effect on the location accuracy. However, an increase in σ2 resulted in a significant decrease in the location accuracy. A comparison between the actual ocean experiment and the simulation along the same route demonstrated the effectiveness of the proposed simulation method and quantitative analysis results. In addition, given the gravimeter (1–2 mGal accuracy) and the reference map (resolution 1′ × 1′; accuracy 3–8 mGal), location accuracy of IGNS was up to reach ~1.0–3.0 n miles in the South China Sea. PMID:29261136

  6. Location Accuracy of INS/Gravity-Integrated Navigation System on the Basis of Ocean Experiment and Simulation.

    PubMed

    Wang, Hubiao; Wu, Lin; Chai, Hua; Bao, Lifeng; Wang, Yong

    2017-12-20

    An experiment comparing the location accuracy of gravity matching-aided navigation in the ocean and simulation is very important to evaluate the feasibility and the performance of an INS/gravity-integrated navigation system (IGNS) in underwater navigation. Based on a 1' × 1' marine gravity anomaly reference map and multi-model adaptive Kalman filtering algorithm, a matching location experiment of IGNS was conducted using data obtained using marine gravimeter. The location accuracy under actual ocean conditions was 2.83 nautical miles (n miles). Several groups of simulated data of marine gravity anomalies were obtained by establishing normally distributed random error N ( u , σ 2 ) with varying mean u and noise variance σ 2 . Thereafter, the matching location of IGNS was simulated. The results show that the changes in u had little effect on the location accuracy. However, an increase in σ 2 resulted in a significant decrease in the location accuracy. A comparison between the actual ocean experiment and the simulation along the same route demonstrated the effectiveness of the proposed simulation method and quantitative analysis results. In addition, given the gravimeter (1-2 mGal accuracy) and the reference map (resolution 1' × 1'; accuracy 3-8 mGal), location accuracy of IGNS was up to reach ~1.0-3.0 n miles in the South China Sea.

  7. Normalised quantitative polymerase chain reaction for diagnosis of tuberculosis-associated uveitis.

    PubMed

    Barik, Manas Ranjan; Rath, Soveeta; Modi, Rohit; Rana, Rajkishori; Reddy, Mamatha M; Basu, Soumyava

    2018-05-01

    Polymerase chain reaction (PCR)-based diagnosis of tuberculosis-associated uveitis (TBU) in TB-endemic countries is challenging due to likelihood of latent mycobacterial infection in both immune and non-immune cells. In this study, we investigated normalised quantitative PCR (nqPCR) in ocular fluids (aqueous/vitreous) for diagnosis of TBU in a TB-endemic population. Mycobacterial copy numbers (mpb64 gene) were normalised to host genome copy numbers (RNAse P RNA component H1 [RPPH1] gene) in TBU (n = 16) and control (n = 13) samples (discovery cohort). The mpb64:RPPH1 ratios (normalised value) from each TBU and control sample were tested against the current reference standard i.e. clinically-diagnosed TBU, to generate Receiver Operating Characteristic (ROC) curves. The optimum cut-off value of mpb64:RPPH1 ratio (0.011) for diagnosing TBU was identified from the highest Youden index. This cut-off value was then tested in a different cohort of TBU and controls (validation cohort, 20 cases and 18 controls), where it yielded specificity, sensitivity and diagnostic accuracy of 94.4%, 85.0%, and 89.4% respectively. The above values for conventional quantitative PCR (≥1 copy of mpb64 per reaction) were 61.1%, 90.0%, and 74.3% respectively. Normalisation markedly improved the specificity and diagnostic accuracy of quantitative PCR for diagnosis of TBU. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. High-throughput quantitative analysis by desorption electrospray ionization mass spectrometry.

    PubMed

    Manicke, Nicholas E; Kistler, Thomas; Ifa, Demian R; Cooks, R Graham; Ouyang, Zheng

    2009-02-01

    A newly developed high-throughput desorption electrospray ionization (DESI) source was characterized in terms of its performance in quantitative analysis. A 96-sample array, containing pharmaceuticals in various matrices, was analyzed in a single run with a total analysis time of 3 min. These solution-phase samples were examined from a hydrophobic PTFE ink printed on glass. The quantitative accuracy, precision, and limit of detection (LOD) were characterized. Chemical background-free samples of propranolol (PRN) with PRN-d(7) as internal standard (IS) and carbamazepine (CBZ) with CBZ-d(10) as IS were examined. So were two other sample sets consisting of PRN/PRN-d(7) at varying concentration in a biological milieu of 10% urine or porcine brain total lipid extract, total lipid concentration 250 ng/microL. The background-free samples, examined in a total analysis time of 1.5 s/sample, showed good quantitative accuracy and precision, with a relative error (RE) and relative standard deviation (RSD) generally less than 3% and 5%, respectively. The samples in urine and the lipid extract required a longer analysis time (2.5 s/sample) and showed RSD values of around 10% for the samples in urine and 4% for the lipid extract samples and RE values of less than 3% for both sets. The LOD for PRN and CBZ when analyzed without chemical background was 10 and 30 fmol, respectively. The LOD of PRN increased to 400 fmol analyzed in 10% urine, and 200 fmol when analyzed in the brain lipid extract.

  9. Bayesian view of single-qubit clocks, and an energy versus accuracy tradeoff

    NASA Astrophysics Data System (ADS)

    Gopalkrishnan, Manoj; Kandula, Varshith; Sriram, Praveen; Deshpande, Abhishek; Muralidharan, Bhaskaran

    2017-09-01

    We bring a Bayesian approach to the analysis of clocks. Using exponential distributions as priors for clocks, we analyze how well one can keep time with a single qubit freely precessing under a magnetic field. We find that, at least with a single qubit, quantum mechanics does not allow exact timekeeping, in contrast to classical mechanics, which does. We find the design of the single-qubit clock that leads to maximum accuracy. Further, we find an energy versus accuracy tradeoff—the energy cost is at least kBT times the improvement in accuracy as measured by the entropy reduction in going from the prior distribution to the posterior distribution. We propose a physical realization of the single-qubit clock using charge transport across a capacitively coupled quantum dot.

  10. Micro-anatomical quantitative optical imaging: toward automated assessment of breast tissues.

    PubMed

    Dobbs, Jessica L; Mueller, Jenna L; Krishnamurthy, Savitri; Shin, Dongsuk; Kuerer, Henry; Yang, Wei; Ramanujam, Nirmala; Richards-Kortum, Rebecca

    2015-08-20

    Pathologists currently diagnose breast lesions through histologic assessment, which requires fixation and tissue preparation. The diagnostic criteria used to classify breast lesions are qualitative and subjective, and inter-observer discordance has been shown to be a significant challenge in the diagnosis of selected breast lesions, particularly for borderline proliferative lesions. Thus, there is an opportunity to develop tools to rapidly visualize and quantitatively interpret breast tissue morphology for a variety of clinical applications. Toward this end, we acquired images of freshly excised breast tissue specimens from a total of 34 patients using confocal fluorescence microscopy and proflavine as a topical stain. We developed computerized algorithms to segment and quantify nuclear and ductal parameters that characterize breast architectural features. A total of 33 parameters were evaluated and used as input to develop a decision tree model to classify benign and malignant breast tissue. Benign features were classified in tissue specimens acquired from 30 patients and malignant features were classified in specimens from 22 patients. The decision tree model that achieved the highest accuracy for distinguishing between benign and malignant breast features used the following parameters: standard deviation of inter-nuclear distance and number of duct lumens. The model achieved 81 % sensitivity and 93 % specificity, corresponding to an area under the curve of 0.93 and an overall accuracy of 90 %. The model classified IDC and DCIS with 92 % and 96 % accuracy, respectively. The cross-validated model achieved 75 % sensitivity and 93 % specificity and an overall accuracy of 88 %. These results suggest that proflavine staining and confocal fluorescence microscopy combined with image analysis strategies to segment morphological features could potentially be used to quantitatively diagnose freshly obtained breast tissue at the point of care without the need for

  11. Error and Uncertainty in the Accuracy Assessment of Land Cover Maps

    NASA Astrophysics Data System (ADS)

    Sarmento, Pedro Alexandre Reis

    Traditionally the accuracy assessment of land cover maps is performed through the comparison of these maps with a reference database, which is intended to represent the "real" land cover, being this comparison reported with the thematic accuracy measures through confusion matrixes. Although, these reference databases are also a representation of reality, containing errors due to the human uncertainty in the assignment of the land cover class that best characterizes a certain area, causing bias in the thematic accuracy measures that are reported to the end users of these maps. The main goal of this dissertation is to develop a methodology that allows the integration of human uncertainty present in reference databases in the accuracy assessment of land cover maps, and analyse the impacts that uncertainty may have in the thematic accuracy measures reported to the end users of land cover maps. The utility of the inclusion of human uncertainty in the accuracy assessment of land cover maps is investigated. Specifically we studied the utility of fuzzy sets theory, more precisely of fuzzy arithmetic, for a better understanding of human uncertainty associated to the elaboration of reference databases, and their impacts in the thematic accuracy measures that are derived from confusion matrixes. For this purpose linguistic values transformed in fuzzy intervals that address the uncertainty in the elaboration of reference databases were used to compute fuzzy confusion matrixes. The proposed methodology is illustrated using a case study in which the accuracy assessment of a land cover map for Continental Portugal derived from Medium Resolution Imaging Spectrometer (MERIS) is made. The obtained results demonstrate that the inclusion of human uncertainty in reference databases provides much more information about the quality of land cover maps, when compared with the traditional approach of accuracy assessment of land cover maps. None

  12. Optical surface pressure measurements: Accuracy and application field evaluation

    NASA Astrophysics Data System (ADS)

    Bukov, A.; Mosharov, V.; Orlov, A.; Pesetsky, V.; Radchenko, V.; Phonov, S.; Matyash, S.; Kuzmin, M.; Sadovskii, N.

    1994-07-01

    Optical pressure measurement (OPM) is a new pressure measurement method rapidly developed in several aerodynamic research centers: TsAGI (Russia), Boeing, NASA, McDonnell Douglas (all USA), and DLR (Germany). Present level of OPM-method provides its practice as standard experimental method of aerodynamic investigations in definite application fields. Applications of OPM-method are determined mainly by its accuracy. The accuracy of OPM-method is determined by the errors of three following groups: (1) errors of the luminescent pressure sensor (LPS) itself, such as uncompensated temperature influence, photo degradation, temperature and pressure hysteresis, variation of the LPS parameters from point to point on the model surface, etc.; (2) errors of the measurement system, such as noise of the photodetector, nonlinearity and nonuniformity of the photodetector, time and temperature offsets, etc.; and (3) methodological errors, owing to displacement and deformation of the model in an airflow, a contamination of the model surface, scattering of the excitation and luminescent light from the model surface and test section walls, etc. OPM-method allows getting total error of measured pressure not less than 1 percent. This accuracy is enough to visualize the pressure field and allows determining total and distributed aerodynamic loads and solving some problems of local aerodynamic investigations at transonic and supersonic velocities. OPM is less effective at low subsonic velocities (M less than 0.4), and for precise measurements, for example, an airfoil optimization. Current limitations of the OPM-method are discussed on an example of the surface pressure measurements and calculations of the integral loads on the wings of canard-aircraft model. The pressure measurement system and data reduction methods used on these tests are also described.

  13. High-accuracy direct aerial platform orientation with tightly coupled GPS/INS system : executive summary.

    DOT National Transportation Integrated Search

    2004-09-01

    Obtaining sensor orientation by direct measurements is : a rapidly emerging mapping technology. Modern GPS : and INS systems allow for the direct determination of : platform position and orientation at an unprecedented : accuracy. In airborne surveyi...

  14. Evaluation of spatial filtering on the accuracy of wheat area estimate

    NASA Technical Reports Server (NTRS)

    Dejesusparada, N. (Principal Investigator); Moreira, M. A.; Chen, S. C.; Delima, A. M.

    1982-01-01

    A 3 x 3 pixel spatial filter for postclassification was used for wheat classification to evaluate the effects of this procedure on the accuracy of area estimation using LANDSAT digital data obtained from a single pass. Quantitative analyses were carried out in five test sites (approx 40 sq km each) and t tests showed that filtering with threshold values significantly decreased errors of commission and omission. In area estimation filtering improved the overestimate of 4.5% to 2.7% and the root-mean-square error decreased from 126.18 ha to 107.02 ha. Extrapolating the same procedure of automatic classification using spatial filtering for postclassification to the whole study area, the accuracy in area estimate was improved from the overestimate of 10.9% to 9.7%. It is concluded that when single pass LANDSAT data is used for crop identification and area estimation the postclassification procedure using a spatial filter provides a more accurate area estimate by reducing classification errors.

  15. Analysis of the Accuracy and Robustness of the Leap Motion Controller

    PubMed Central

    Weichert, Frank; Bachmann, Daniel; Rudak, Bartholomäus; Fisseler, Denis

    2013-01-01

    The Leap Motion Controller is a new device for hand gesture controlled user interfaces with declared sub-millimeter accuracy. However, up to this point its capabilities in real environments have not been analyzed. Therefore, this paper presents a first study of a Leap Motion Controller. The main focus of attention is on the evaluation of the accuracy and repeatability. For an appropriate evaluation, a novel experimental setup was developed making use of an industrial robot with a reference pen allowing a position accuracy of 0.2 mm. Thereby, a deviation between a desired 3D position and the average measured positions below 0.2 mm has been obtained for static setups and of 1.2 mm for dynamic setups. Using the conclusion of this analysis can improve the development of applications for the Leap Motion controller in the field of Human-Computer Interaction. PMID:23673678

  16. Estimated Accuracy of Three Common Trajectory Statistical Methods

    NASA Technical Reports Server (NTRS)

    Kabashnikov, Vitaliy P.; Chaikovsky, Anatoli P.; Kucsera, Tom L.; Metelskaya, Natalia S.

    2011-01-01

    Three well-known trajectory statistical methods (TSMs), namely concentration field (CF), concentration weighted trajectory (CWT), and potential source contribution function (PSCF) methods were tested using known sources and artificially generated data sets to determine the ability of TSMs to reproduce spatial distribution of the sources. In the works by other authors, the accuracy of the trajectory statistical methods was estimated for particular species and at specified receptor locations. We have obtained a more general statistical estimation of the accuracy of source reconstruction and have found optimum conditions to reconstruct source distributions of atmospheric trace substances. Only virtual pollutants of the primary type were considered. In real world experiments, TSMs are intended for application to a priori unknown sources. Therefore, the accuracy of TSMs has to be tested with all possible spatial distributions of sources. An ensemble of geographical distributions of virtual sources was generated. Spearman s rank order correlation coefficient between spatial distributions of the known virtual and the reconstructed sources was taken to be a quantitative measure of the accuracy. Statistical estimates of the mean correlation coefficient and a range of the most probable values of correlation coefficients were obtained. All the TSMs that were considered here showed similar close results. The maximum of the ratio of the mean correlation to the width of the correlation interval containing the most probable correlation values determines the optimum conditions for reconstruction. An optimal geographical domain roughly coincides with the area supplying most of the substance to the receptor. The optimal domain s size is dependent on the substance decay time. Under optimum reconstruction conditions, the mean correlation coefficients can reach 0.70 0.75. The boundaries of the interval with the most probable correlation values are 0.6 0.9 for the decay time of 240 h

  17. Semi-quantitative MALDI-TOF for antimicrobial susceptibility testing in Staphylococcus aureus.

    PubMed

    Maxson, Tucker; Taylor-Howell, Cheryl L; Minogue, Timothy D

    2017-01-01

    Antibiotic resistant bacterial infections are a significant problem in the healthcare setting, in many cases requiring the rapid administration of appropriate and effective antibiotic therapy. Diagnostic assays capable of quickly and accurately determining the pathogen resistance profile are therefore crucial to initiate or modify care. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a standard method for species identification in many clinical microbiology laboratories and is well positioned to be applied towards antimicrobial susceptibility testing. One recently reported approach utilizes semi-quantitative MALDI-TOF MS for growth rate analysis to provide a resistance profile independent of resistance mechanism. This method was previously successfully applied to Gram-negative pathogens and mycobacteria; here, we evaluated this method with the Gram-positive pathogen Staphylococcus aureus. Specifically, we used 35 strains of S. aureus and four antibiotics to optimize and test the assay, resulting in an overall accuracy rate of 95%. Application of the optimized assay also successfully determined susceptibility from mock blood cultures, allowing both species identification and resistance determination for all four antibiotics within 3 hours of blood culture positivity.

  18. Prospects and challenges of quantitative phase imaging in tumor cell biology

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Götte, Martin; Greve, Burkhard; Ketelhut, Steffi

    2016-03-01

    Quantitative phase imaging (QPI) techniques provide high resolution label-free quantitative live cell imaging. Here, prospects and challenges of QPI in tumor cell biology are presented, using the example of digital holographic microscopy (DHM). It is shown that the evaluation of quantitative DHM phase images allows the retrieval of different parameter sets for quantification of cellular motion changes in migration and motility assays that are caused by genetic modifications. Furthermore, we demonstrate simultaneously label-free imaging of cell growth and morphology properties.

  19. Development of one novel multiple-target plasmid for duplex quantitative PCR analysis of roundup ready soybean.

    PubMed

    Zhang, Haibo; Yang, Litao; Guo, Jinchao; Li, Xiang; Jiang, Lingxi; Zhang, Dabing

    2008-07-23

    To enforce the labeling regulations of genetically modified organisms (GMOs), the application of reference molecules as calibrators is becoming essential for practical quantification of GMOs. However, the reported reference molecules with tandem marker multiple targets have been proved not suitable for duplex PCR analysis. In this study, we developed one unique plasmid molecule based on one pMD-18T vector with three exogenous target DNA fragments of Roundup Ready soybean GTS 40-3-2 (RRS), that is, CaMV35S, NOS, and RRS event fragments, plus one fragment of soybean endogenous Lectin gene. This Lectin gene fragment was separated from the three exogenous target DNA fragments of RRS by inserting one 2.6 kb DNA fragment with no relatedness to RRS detection targets in this resultant plasmid. Then, we proved that this design allows the quantification of RRS using the three duplex real-time PCR assays targeting CaMV35S, NOS, and RRS events employing this reference molecule as the calibrator. In these duplex PCR assays, the limits of detection (LOD) and quantification (LOQ) were 10 and 50 copies, respectively. For the quantitative analysis of practical RRS samples, the results of accuracy and precision were similar to those of simplex PCR assays, for instance, the quantitative results were at the 1% level, the mean bias of the simplex and duplex PCR were 4.0% and 4.6%, respectively, and the statistic analysis ( t-test) showed that the quantitative data from duplex and simplex PCR had no significant discrepancy for each soybean sample. Obviously, duplex PCR analysis has the advantages of saving the costs of PCR reaction and reducing the experimental errors in simplex PCR testing. The strategy reported in the present study will be helpful for the development of new reference molecules suitable for duplex PCR quantitative assays of GMOs.

  20. Towards the automatization of the Foucault knife-edge quantitative test

    NASA Astrophysics Data System (ADS)

    Rodríguez, G.; Villa, J.; Martínez, G.; de la Rosa, I.; Ivanov, R.

    2017-08-01

    Given the increasing necessity of simple, economical and reliable methods and instruments for performing quality tests of optical surfaces such as mirrors and lenses, in the recent years we resumed the study of the long forgotten Foucault knife-edge test from the point of view of the physical optics, ultimately achieving a closed mathematical expression that directly relates the knife-edge position along the displacement paraxial axis with the observable irradiance pattern, which later allowed us to propose a quantitative methodology for estimating the wavefront error of an aspherical mirror with precision akin to interferometry. In this work, we present a further improved digital image processing algorithm in which the sigmoidal cost-function for calculating the transient slope-point of each associated intensity-illumination profile is replaced for a simplified version of it, thus making the whole process of estimating the wavefront gradient remarkably more stable and efficient, at the same time, the Fourier based algorithm employed for gradient integration has been replaced as well for a regularized quadratic cost-function that allows a considerably easier introduction of the region of interest (ROI) of the function, which solved by means of a linear gradient conjugate method largely increases the overall accuracy and efficiency of the algorithm. This revised approach of our methodology can be easily implemented and handled by most single-board microcontrollers in the market, hence enabling the implementation of a full-integrated automatized test apparatus, opening a realistic path for even the proposal of a stand-alone optical mirror analyzer prototype.

  1. Photocleavable DNA barcode-antibody conjugates allow sensitive and multiplexed protein analysis in single cells.

    PubMed

    Agasti, Sarit S; Liong, Monty; Peterson, Vanessa M; Lee, Hakho; Weissleder, Ralph

    2012-11-14

    DNA barcoding is an attractive technology, as it allows sensitive and multiplexed target analysis. However, DNA barcoding of cellular proteins remains challenging, primarily because barcode amplification and readout techniques are often incompatible with the cellular microenvironment. Here we describe the development and validation of a photocleavable DNA barcode-antibody conjugate method for rapid, quantitative, and multiplexed detection of proteins in single live cells. Following target binding, this method allows DNA barcodes to be photoreleased in solution, enabling easy isolation, amplification, and readout. As a proof of principle, we demonstrate sensitive and multiplexed detection of protein biomarkers in a variety of cancer cells.

  2. Quantitative measurement of a candidate serum biomarker peptide derived from α2-HS-glycoprotein, and a preliminary trial of multidimensional peptide analysis in females with pregnancy-induced hypertension.

    PubMed

    Hamamura, Kensuke; Yanagida, Mitsuaki; Ishikawa, Hitoshi; Banzai, Michio; Yoshitake, Hiroshi; Nonaka, Daisuke; Tanaka, Kenji; Sakuraba, Mayumi; Miyakuni, Yasuka; Takamori, Kenji; Nojima, Michio; Yoshida, Koyo; Fujiwara, Hiroshi; Takeda, Satoru; Araki, Yoshihiko

    2018-03-01

    Purpose We previously attempted to develop quantitative enzyme-linked immunosorbent assay (ELISA) systems for the PDA039/044/071 peptides, potential serum disease biomarkers (DBMs) of pregnancy-induced hypertension (PIH), primarily identified by a peptidomic approach (BLOTCHIP®-mass spectrometry (MS)). However, our methodology did not extend to PDA071 (cysteinyl α2-HS-glycoprotein 341-367 ), due to difficulty to produce a specific antibody against the peptide. The aim of the present study was to establish an alternative PDA071 quantitation system using liquid chromatography-multiple reaction monitoring (LC-MRM)/MS, to explore the potential utility of PDA071 as a DBM for PIH. Methods We tested heat/acid denaturation methods in efforts to purify serum PDA071 and developed an LC-MRM/MS method allowing for specific quantitation thereof. We measured serum PDA071 concentrations, and these results were validated including by three-dimensional (3D) plotting against PDA039 (kininogen-1 439-456 )/044 (kininogen-1 438-456 ) concentrations, followed by discriminant analysis. Results PDA071 was successfully extracted from serum using a heat denaturation method. Optimum conditions for quantitation via LC-MRM/MS were developed; the assayed serum PDA071 correlated well with the BLOTCHIP® assay values. Although the PDA071 alone did not significantly differ between patients and controls, 3D plotting of PDA039/044/071 peptide concentrations and construction of a Jackknife classification matrix were satisfactory in terms of PIH diagnostic precision. Conclusions Combination analysis using both PDA071 and PDA039/044 concentrations allowed PIH diagnostic accuracy to be attained, and our method will be valuable in future pathophysiological studies of hypertensive disorders of pregnancy.

  3. A new item response theory model to adjust data allowing examinee choice

    PubMed Central

    Costa, Marcelo Azevedo; Braga Oliveira, Rivert Paulo

    2018-01-01

    In a typical questionnaire testing situation, examinees are not allowed to choose which items they answer because of a technical issue in obtaining satisfactory statistical estimates of examinee ability and item difficulty. This paper introduces a new item response theory (IRT) model that incorporates information from a novel representation of questionnaire data using network analysis. Three scenarios in which examinees select a subset of items were simulated. In the first scenario, the assumptions required to apply the standard Rasch model are met, thus establishing a reference for parameter accuracy. The second and third scenarios include five increasing levels of violating those assumptions. The results show substantial improvements over the standard model in item parameter recovery. Furthermore, the accuracy was closer to the reference in almost every evaluated scenario. To the best of our knowledge, this is the first proposal to obtain satisfactory IRT statistical estimates in the last two scenarios. PMID:29389996

  4. RECENT ADVANCES IN QUANTITATIVE NEUROPROTEOMICS

    PubMed Central

    Craft, George E; Chen, Anshu; Nairn, Angus C

    2014-01-01

    The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson’s disease and Alzheimer’s disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to

  5. Recent advances in quantitative neuroproteomics.

    PubMed

    Craft, George E; Chen, Anshu; Nairn, Angus C

    2013-06-15

    The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed

  6. Quantitative proteomics in cardiovascular research: global and targeted strategies

    PubMed Central

    Shen, Xiaomeng; Young, Rebeccah; Canty, John M.; Qu, Jun

    2014-01-01

    Extensive technical advances in the past decade have substantially expanded quantitative proteomics in cardiovascular research. This has great promise for elucidating the mechanisms of cardiovascular diseases (CVD) and the discovery of cardiac biomarkers used for diagnosis and treatment evaluation. Global and targeted proteomics are the two major avenues of quantitative proteomics. While global approaches enable unbiased discovery of altered proteins via relative quantification at the proteome level, targeted techniques provide higher sensitivity and accuracy, and are capable of multiplexed absolute quantification in numerous clinical/biological samples. While promising, technical challenges need to be overcome to enable full utilization of these techniques in cardiovascular medicine. Here we discuss recent advances in quantitative proteomics and summarize applications in cardiovascular research with an emphasis on biomarker discovery and elucidating molecular mechanisms of disease. We propose the integration of global and targeted strategies as a high-throughput pipeline for cardiovascular proteomics. Targeted approaches enable rapid, extensive validation of biomarker candidates discovered by global proteomics. These approaches provide a promising alternative to immunoassays and other low-throughput means currently used for limited validation. PMID:24920501

  7. The Effects of Corrective Feedback on Chinese Learners' Writing Accuracy: A Quantitative Analysis in an EFL Context

    ERIC Educational Resources Information Center

    Wang, Xin

    2017-01-01

    Scholars debate whether corrective feedback contributes to improving L2 learners' grammatical accuracy in writing performance. Some researchers take a stance on the ineffectiveness of corrective feedback based on the impracticality of providing detailed corrective feedback for all L2 learners and detached grammar instruction in language…

  8. Axial Colocalization of Single Molecules with Nanometer Accuracy Using Metal-Induced Energy Transfer.

    PubMed

    Isbaner, Sebastian; Karedla, Narain; Kaminska, Izabela; Ruhlandt, Daja; Raab, Mario; Bohlen, Johann; Chizhik, Alexey; Gregor, Ingo; Tinnefeld, Philip; Enderlein, Jörg; Tsukanov, Roman

    2018-04-11

    Single-molecule localization based super-resolution microscopy has revolutionized optical microscopy and routinely allows for resolving structural details down to a few nanometers. However, there exists a rather large discrepancy between lateral and axial localization accuracy, the latter typically three to five times worse than the former. Here, we use single-molecule metal-induced energy transfer (smMIET) to localize single molecules along the optical axis, and to measure their axial distance with an accuracy of 5 nm. smMIET relies only on fluorescence lifetime measurements and does not require additional complex optical setups.

  9. Accuracy of Kinect's skeleton tracking for upper body rehabilitation applications.

    PubMed

    Mobini, Amir; Behzadipour, Saeed; Saadat Foumani, Mahmoud

    2014-07-01

    Games and their use in rehabilitation have formed a new and rapidly growing area of research. A critical hardware component of rehabilitation programs is the input device that measures the patients' movements. After Microsoft released Kinect, extensive research has been initiated on its applications as an input device for rehabilitation. However, since most of the works in this area rely on a qualitative determination of the joints' movements rather than an accurate quantitative one, detailed analysis of patients' movements is hindered. The aim of this article is to determine the accuracy of the Kinect's joint tracking. To fulfill this task, a model of upper body was fabricated. The displacements of the joint centers were estimated by Kinect at different positions and were then compared with the actual ones from measurement. Moreover, the dependency of Kinect's error on distance and joint type was measured and analyzed. It measures and reports the accuracy of a sensor that can be directly used for monitoring physical therapy exercises. Using this sensor facilitates remote rehabilitation.

  10. Evaluation of chemotherapy response in ovarian cancer treatment using quantitative CT image biomarkers: a preliminary study

    NASA Astrophysics Data System (ADS)

    Qiu, Yuchen; Tan, Maxine; McMeekin, Scott; Thai, Theresa; Moore, Kathleen; Ding, Kai; Liu, Hong; Zheng, Bin

    2015-03-01

    The purpose of this study is to identify and apply quantitative image biomarkers for early prediction of the tumor response to the chemotherapy among the ovarian cancer patients participated in the clinical trials of testing new drugs. In the experiment, we retrospectively selected 30 cases from the patients who participated in Phase I clinical trials of new drug or drug agents for ovarian cancer treatment. Each case is composed of two sets of CT images acquired pre- and post-treatment (4-6 weeks after starting treatment). A computer-aided detection (CAD) scheme was developed to extract and analyze the quantitative image features of the metastatic tumors previously tracked by the radiologists using the standard Response Evaluation Criteria in Solid Tumors (RECIST) guideline. The CAD scheme first segmented 3-D tumor volumes from the background using a hybrid tumor segmentation scheme. Then, for each segmented tumor, CAD computed three quantitative image features including the change of tumor volume, tumor CT number (density) and density variance. The feature changes were calculated between the matched tumors tracked on the CT images acquired pre- and post-treatments. Finally, CAD predicted patient's 6-month progression-free survival (PFS) using a decision-tree based classifier. The performance of the CAD scheme was compared with the RECIST category. The result shows that the CAD scheme achieved a prediction accuracy of 76.7% (23/30 cases) with a Kappa coefficient of 0.493, which is significantly higher than the performance of RECIST prediction with a prediction accuracy and Kappa coefficient of 60% (17/30) and 0.062, respectively. This study demonstrated the feasibility of analyzing quantitative image features to improve the early predicting accuracy of the tumor response to the new testing drugs or therapeutic methods for the ovarian cancer patients.

  11. Influence of the limited detector size on spatial variations of the reconstruction accuracy in holographic tomography

    NASA Astrophysics Data System (ADS)

    Kostencka, Julianna; Kozacki, Tomasz; Hennelly, Bryan; Sheridan, John T.

    2017-06-01

    Holographic tomography (HT) allows noninvasive, quantitative, 3D imaging of transparent microobjects, such as living biological cells and fiber optics elements. The technique is based on acquisition of multiple scattered fields for various sample perspectives using digital holographic microscopy. Then, the captured data is processed with one of the tomographic reconstruction algorithms, which enables 3D reconstruction of refractive index distribution. In our recent works we addressed the issue of spatially variant accuracy of the HT reconstructions, which results from the insufficient model of diffraction that is applied in the widely-used tomographic reconstruction algorithms basing on the Rytov approximation. In the present study, we continue investigating the spatially variant properties of the HT imaging, however, we are now focusing on the limited spatial size of holograms as a source of this problem. Using the Wigner distribution representation and the Ewald sphere approach, we show that the limited size of the holograms results in a decreased quality of tomographic imaging in off-center regions of the HT reconstructions. This is because the finite detector extent becomes a limiting aperture that prohibits acquisition of full information about diffracted fields coming from the out-of-focus structures of a sample. The incompleteness of the data results in an effective truncation of the tomographic transfer function for the out-of-center regions of the tomographic image. In this paper, the described effect is quantitatively characterized for three types of the tomographic systems: the configuration with 1) object rotation, 2) scanning of the illumination direction, 3) the hybrid HT solution combing both previous approaches.

  12. Quantitative Aging Pattern in Mouse Urine Vapor as Measured by Gas-Liquid Chromatography

    NASA Technical Reports Server (NTRS)

    Robinson, Arthur B.; Dirren, Henri; Sheets, Alan; Miquel, Jaime; Lundgren, Paul R.

    1975-01-01

    We have discovered a quantitative aging pattern in mouse urine vapor. The diagnostic power of the pattern has been found to be high. We hope that this pattern will eventually allow quantitative estimates of physiological age and some insight into the biochemistry of aging.

  13. A Spectral Method for Color Quantitation of a Protein Drug Solution.

    PubMed

    Swartz, Trevor E; Yin, Jian; Patapoff, Thomas W; Horst, Travis; Skieresz, Susan M; Leggett, Gordon; Morgan, Charles J; Rahimi, Kimia; Marhoul, Joseph; Kabakoff, Bruce

    2016-01-01

    Color is an important quality attribute for biotherapeutics. In the biotechnology industry, a visual method is most commonly utilized for color characterization of liquid drug protein solutions. The color testing method is used for both batch release and on stability testing for quality control. Using that method, an analyst visually determines the color of the sample by choosing the closest matching European Pharmacopeia reference color solution. The requirement to judge the best match makes it a subjective method. Furthermore, the visual method does not capture data on hue or chroma that would allow for improved product characterization and the ability to detect subtle differences between samples. To overcome these challenges, we describe a quantitative method for color determination that greatly reduces the variability in measuring color and allows for a more precise understanding of color differences. Following color industry standards established by International Commission on Illumination, this method converts a protein solution's visible absorption spectra to L*a*b* color space. Color matching is achieved within the L*a*b* color space, a practice that is already widely used in other industries. The work performed here is to facilitate the adoption and transition for the traditional visual assessment method to a quantitative spectral method. We describe here the algorithm used such that the quantitative spectral method correlates with the currently used visual method. In addition, we provide the L*a*b* values for the European Pharmacopeia reference color solutions required for the quantitative method. We have determined these L*a*b* values by gravimetrically preparing and measuring multiple lots of the reference color solutions. We demonstrate that the visual assessment and the quantitative spectral method are comparable using both low- and high-concentration antibody solutions and solutions with varying turbidity. In the biotechnology industry, a visual

  14. ABRF-PRG07: advanced quantitative proteomics study.

    PubMed

    Falick, Arnold M; Lane, William S; Lilley, Kathryn S; MacCoss, Michael J; Phinney, Brett S; Sherman, Nicholas E; Weintraub, Susan T; Witkowska, H Ewa; Yates, Nathan A

    2011-04-01

    A major challenge for core facilities is determining quantitative protein differences across complex biological samples. Although there are numerous techniques in the literature for relative and absolute protein quantification, the majority is nonroutine and can be challenging to carry out effectively. There are few studies comparing these technologies in terms of their reproducibility, accuracy, and precision, and no studies to date deal with performance across multiple laboratories with varied levels of expertise. Here, we describe an Association of Biomolecular Resource Facilities (ABRF) Proteomics Research Group (PRG) study based on samples composed of a complex protein mixture into which 12 known proteins were added at varying but defined ratios. All of the proteins were present at the same concentration in each of three tubes that were provided. The primary goal of this study was to allow each laboratory to evaluate its capabilities and approaches with regard to: detection and identification of proteins spiked into samples that also contain complex mixtures of background proteins and determination of relative quantities of the spiked proteins. The results returned by 43 participants were compiled by the PRG, which also collected information about the strategies used to assess overall performance and as an aid to development of optimized protocols for the methodologies used. The most accurate results were generally reported by the most experienced laboratories. Among laboratories that used the same technique, values that were closer to the expected ratio were obtained by more experienced groups.

  15. Variance estimates and confidence intervals for the Kappa measure of classification accuracy

    Treesearch

    M. A. Kalkhan; R. M. Reich; R. L. Czaplewski

    1997-01-01

    The Kappa statistic is frequently used to characterize the results of an accuracy assessment used to evaluate land use and land cover classifications obtained by remotely sensed data. This statistic allows comparisons of alternative sampling designs, classification algorithms, photo-interpreters, and so forth. In order to make these comparisons, it is...

  16. Quantitative traits and diversification.

    PubMed

    FitzJohn, Richard G

    2010-12-01

    Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.

  17. High Accuracy Monocular SFM and Scale Correction for Autonomous Driving.

    PubMed

    Song, Shiyu; Chandraker, Manmohan; Guest, Clark C

    2016-04-01

    We present a real-time monocular visual odometry system that achieves high accuracy in real-world autonomous driving applications. First, we demonstrate robust monocular SFM that exploits multithreading to handle driving scenes with large motions and rapidly changing imagery. To correct for scale drift, we use known height of the camera from the ground plane. Our second contribution is a novel data-driven mechanism for cue combination that allows highly accurate ground plane estimation by adapting observation covariances of multiple cues, such as sparse feature matching and dense inter-frame stereo, based on their relative confidences inferred from visual data on a per-frame basis. Finally, we demonstrate extensive benchmark performance and comparisons on the challenging KITTI dataset, achieving accuracy comparable to stereo and exceeding prior monocular systems. Our SFM system is optimized to output pose within 50 ms in the worst case, while average case operation is over 30 fps. Our framework also significantly boosts the accuracy of applications like object localization that rely on the ground plane.

  18. Ultra-fast quantitative imaging using ptychographic iterative engine based digital micro-mirror device

    NASA Astrophysics Data System (ADS)

    Sun, Aihui; Tian, Xiaolin; Kong, Yan; Jiang, Zhilong; Liu, Fei; Xue, Liang; Wang, Shouyu; Liu, Cheng

    2018-01-01

    As a lensfree imaging technique, ptychographic iterative engine (PIE) method can provide both quantitative sample amplitude and phase distributions avoiding aberration. However, it requires field of view (FoV) scanning often relying on mechanical translation, which not only slows down measuring speed, but also introduces mechanical errors decreasing both resolution and accuracy in retrieved information. In order to achieve high-accurate quantitative imaging with fast speed, digital micromirror device (DMD) is adopted in PIE for large FoV scanning controlled by on/off state coding by DMD. Measurements were implemented using biological samples as well as USAF resolution target, proving high resolution in quantitative imaging using the proposed system. Considering its fast and accurate imaging capability, it is believed the DMD based PIE technique provides a potential solution for medical observation and measurements.

  19. Stress-only myocardial perfusion scintigraphy: a prospective study on the accuracy and observer agreement with quantitative coronary angiography as the gold standard.

    PubMed

    Ejlersen, June A; May, Ole; Mortensen, Jesper; Nielsen, Gitte L; Lauridsen, Jeppe F; Allan, Johansen

    2017-11-01

    Patients with normal stress perfusion have an excellent prognosis. Prospective studies on the diagnostic accuracy of stress-only scans with contemporary, independent examinations as gold standards are lacking. A total of 109 patients with typical angina and no previous coronary artery disease underwent a 2-day stress (exercise)/rest, gated, and attenuation-corrected (AC), 99m-technetium-sestamibi perfusion study, followed by invasive coronary angiography. The stress datasets were evaluated twice by four physicians with two different training levels (expert and novice): familiar and unfamiliar with AC. The two experts also made a consensus reading of the integrated stress-rest datasets. The consensus reading and quantitative data from the invasive coronary angiography were applied as reference methods. The sensitivity/specificity were 0.92-1.00/0.73-0.90 (reference: expert consensus reading), 0.93-0.96/0.63-0.82 (reference: ≥1 stenosis>70%), and 0.75-0.88/0.70-0.88 (reference: ≥1 stenosis>50%). The four readers showed a high and fairly equal sensitivity independent of their familiarity with AC. The expert familiar with AC had the highest specificity independent of the reference method. The intraobserver and interobserver agreements on the stress-only readings were good (readers without AC experience) to excellent (readers with AC experience). AC stress-only images yielded a high sensitivity independent of the training level and experience with AC of the nuclear physician, whereas the specificity correlated positively with both. Interobserver and intraobserver agreements tended to be the best for physicians with AC experience.

  20. An automated method for the evaluation of the pointing accuracy of sun-tracking devices

    NASA Astrophysics Data System (ADS)

    Baumgartner, Dietmar J.; Rieder, Harald E.; Pötzi, Werner; Freislich, Heinrich; Strutzmann, Heinz

    2016-04-01

    The accuracy of measurements of solar radiation (direct and diffuse radiation) depends significantly on the accuracy of the operational sun-tracking device. Thus rigid targets for instrument performance and operation are specified for international monitoring networks, such as e.g., the Baseline Surface Radiation Network (BSRN) operating under the auspices of the World Climate Research Program (WCRP). Sun-tracking devices fulfilling these accuracy targets are available from various instrument manufacturers, however none of the commercially available systems comprises a secondary accuracy control system, allowing platform operators to independently validate the pointing accuracy of sun-tracking sensors during operation. Here we present KSO-STREAMS (KSO-SunTRackEr Accuracy Monitoring System), a fully automated, system independent and cost-effective method for evaluating the pointing accuracy of sun-tracking devices. We detail the monitoring system setup, its design and specifications and results from its application to the sun-tracking system operated at the Austrian RADiation network (ARAD) site Kanzelhöhe Observatory (KSO). Results from KSO-STREAMS (for mid-March to mid-June 2015) show that the tracking accuracy of the device operated at KSO lies well within BSRN specifications (i.e. 0.1 degree accuracy). We contrast results during clear-sky and partly cloudy conditions documenting sun-tracking performance at manufacturer specified accuracies for active tracking (0.02 degrees) and highlight accuracies achieved during passive tracking i.e. periods with less than 300 W m-2 direct radiation. Furthermore we detail limitations to tracking surveillance during overcast conditions and periods of partial solar limb coverage by clouds.

  1. A Quantitative Study Identifying Political Strategies Used by Principals of Dual Language Programs

    ERIC Educational Resources Information Center

    Girard, Guadalupe

    2017-01-01

    Purpose. The purpose of this quantitative study was to identify the external and internal political strategies used by principals that allow them to successfully navigate the political environment surrounding dual language programs. Methodology. This quantitative study used descriptive research to collect, analyze, and report data that identified…

  2. Accuracy assessment of linear spectral mixture model due to terrain undulation

    NASA Astrophysics Data System (ADS)

    Wang, Tianxing; Chen, Songlin; Ma, Ya

    2008-12-01

    Mixture spectra are common in remote sensing due to the limitations of spatial resolution and the heterogeneity of land surface. During the past 30 years, a lot of subpixel model have developed to investigate the information within mixture pixels. Linear spectral mixture model (LSMM) is a simper and more general subpixel model. LSMM also known as spectral mixture analysis is a widely used procedure to determine the proportion of endmembers (constituent materials) within a pixel based on the endmembers' spectral characteristics. The unmixing accuracy of LSMM is restricted by variety of factors, but now the research about LSMM is mostly focused on appraisement of nonlinear effect relating to itself and techniques used to select endmembers, unfortunately, the environment conditions of study area which could sway the unmixing-accuracy, such as atmospheric scatting and terrain undulation, are not studied. This paper probes emphatically into the accuracy uncertainty of LSMM resulting from the terrain undulation. ASTER dataset was chosen and the C terrain correction algorithm was applied to it. Based on this, fractional abundances for different cover types were extracted from both pre- and post-C terrain illumination corrected ASTER using LSMM. Simultaneously, the regression analyses and the IKONOS image were introduced to assess the unmixing accuracy. Results showed that terrain undulation could dramatically constrain the application of LSMM in mountain area. Specifically, for vegetation abundances, a improved unmixing accuracy of 17.6% (regression against to NDVI) and 18.6% (regression against to MVI) for R2 was achieved respectively by removing terrain undulation. Anyway, this study indicated in a quantitative way that effective removal or minimization of terrain illumination effects was essential for applying LSMM. This paper could also provide a new instance for LSMM applications in mountainous areas. In addition, the methods employed in this study could be

  3. Patient-specific coronary blood supply territories for quantitative perfusion analysis

    PubMed Central

    Zakkaroff, Constantine; Biglands, John D.; Greenwood, John P.; Plein, Sven; Boyle, Roger D.; Radjenovic, Aleksandra; Magee, Derek R.

    2018-01-01

    Abstract Myocardial perfusion imaging, coupled with quantitative perfusion analysis, provides an important diagnostic tool for the identification of ischaemic heart disease caused by coronary stenoses. The accurate mapping between coronary anatomy and under-perfused areas of the myocardium is important for diagnosis and treatment. However, in the absence of the actual coronary anatomy during the reporting of perfusion images, areas of ischaemia are allocated to a coronary territory based on a population-derived 17-segment (American Heart Association) AHA model of coronary blood supply. This work presents a solution for the fusion of 2D Magnetic Resonance (MR) myocardial perfusion images and 3D MR angiography data with the aim to improve the detection of ischaemic heart disease. The key contribution of this work is a novel method for the mediated spatiotemporal registration of perfusion and angiography data and a novel method for the calculation of patient-specific coronary supply territories. The registration method uses 4D cardiac MR cine series spanning the complete cardiac cycle in order to overcome the under-constrained nature of non-rigid slice-to-volume perfusion-to-angiography registration. This is achieved by separating out the deformable registration problem and solving it through phase-to-phase registration of the cine series. The use of patient-specific blood supply territories in quantitative perfusion analysis (instead of the population-based model of coronary blood supply) has the potential of increasing the accuracy of perfusion analysis. Quantitative perfusion analysis diagnostic accuracy evaluation with patient-specific territories against the AHA model demonstrates the value of the mediated spatiotemporal registration in the context of ischaemic heart disease diagnosis. PMID:29392098

  4. Accuracy assessment of fluoroscopy-transesophageal echocardiography registration

    NASA Astrophysics Data System (ADS)

    Lang, Pencilla; Seslija, Petar; Bainbridge, Daniel; Guiraudon, Gerard M.; Jones, Doug L.; Chu, Michael W.; Holdsworth, David W.; Peters, Terry M.

    2011-03-01

    This study assesses the accuracy of a new transesophageal (TEE) ultrasound (US) fluoroscopy registration technique designed to guide percutaneous aortic valve replacement. In this minimally invasive procedure, a valve is inserted into the aortic annulus via a catheter. Navigation and positioning of the valve is guided primarily by intra-operative fluoroscopy. Poor anatomical visualization of the aortic root region can result in incorrect positioning, leading to heart valve embolization, obstruction of the coronary ostia and acute kidney injury. The use of TEE US images to augment intra-operative fluoroscopy provides significant improvements to image-guidance. Registration is achieved using an image-based TEE probe tracking technique and US calibration. TEE probe tracking is accomplished using a single-perspective pose estimation algorithm. Pose estimation from a single image allows registration to be achieved using only images collected in standard OR workflow. Accuracy of this registration technique is assessed using three models: a point target phantom, a cadaveric porcine heart with implanted fiducials, and in-vivo porcine images. Results demonstrate that registration can be achieved with an RMS error of less than 1.5mm, which is within the clinical accuracy requirements of 5mm. US-fluoroscopy registration based on single-perspective pose estimation demonstrates promise as a method for providing guidance to percutaneous aortic valve replacement procedures. Future work will focus on real-time implementation and a visualization system that can be used in the operating room.

  5. Towards quantitative assessment of calciphylaxis

    NASA Astrophysics Data System (ADS)

    Deserno, Thomas M.; Sárándi, István.; Jose, Abin; Haak, Daniel; Jonas, Stephan; Specht, Paula; Brandenburg, Vincent

    2014-03-01

    Calciphylaxis is a rare disease that has devastating conditions associated with high morbidity and mortality. Calciphylaxis is characterized by systemic medial calcification of the arteries yielding necrotic skin ulcerations. In this paper, we aim at supporting the installation of multi-center registries for calciphylaxis, which includes a photographic documentation of skin necrosis. However, photographs acquired in different centers under different conditions using different equipment and photographers cannot be compared quantitatively. For normalization, we use a simple color pad that is placed into the field of view, segmented from the image, and its color fields are analyzed. In total, 24 colors are printed on that scale. A least-squares approach is used to determine the affine color transform. Furthermore, the card allows scale normalization. We provide a case study for qualitative assessment. In addition, the method is evaluated quantitatively using 10 images of two sets of different captures of the same necrosis. The variability of quantitative measurements based on free hand photography is assessed regarding geometric and color distortions before and after our simple calibration procedure. Using automated image processing, the standard deviation of measurements is significantly reduced. The coefficients of variations yield 5-20% and 2-10% for geometry and color, respectively. Hence, quantitative assessment of calciphylaxis becomes practicable and will impact a better understanding of this rare but fatal disease.

  6. Communicating risk information: the influence of graphical display format on quantitative information perception-Accuracy, comprehension and preferences.

    PubMed

    Price, Melanie; Cameron, Rachel; Butow, Phyllis

    2007-12-01

    Statistical health risk information has proved notoriously confusing and difficult to understand. While past research indicates that presenting risk information in a frequency format is superior to relative risk and probability formats, the optimal characteristics of frequency formats are still unclear. The aim of this study is to determine the features of 1000 person frequency diagrams (pictographs) which result in the greatest speed and accuracy of graphical perception. Participants estimated the difference in chance of survival when taking or not taking Drug A, on a pictograph format, varying by mode (one-graph/two-graph), direction (vertical/horizontal), and shading (shaded/unshaded), and their preferences for the different formats. Their understanding of different components of the 1000 person diagram was assessed. Responses were timed and scored for accuracy. Horizontal pictographs were perceived faster and more accurately than vertical formats. Two-graph pictographs were perceived faster than one-graph formats. Shading reduced response time in two-graph formats, but increased response times in one-graph formats. Shaded and one-graph pictographs were preferred. As shading and one-graph formats were preferred, further clarification as to why shading negatively impacts on response times in the one-graph format is warranted. Horizontal pictographs are optimal.

  7. An adaptive model approach for quantitative wrist rigidity evaluation during deep brain stimulation surgery.

    PubMed

    Assis, Sofia; Costa, Pedro; Rosas, Maria Jose; Vaz, Rui; Silva Cunha, Joao Paulo

    2016-08-01

    Intraoperative evaluation of the efficacy of Deep Brain Stimulation includes evaluation of the effect on rigidity. A subjective semi-quantitative scale is used, dependent on the examiner perception and experience. A system was proposed previously, aiming to tackle this subjectivity, using quantitative data and providing real-time feedback of the computed rigidity reduction, hence supporting the physician decision. This system comprised of a gyroscope-based motion sensor in a textile band, placed in the patients hand, which communicated its measurements to a laptop. The latter computed a signal descriptor from the angular velocity of the hand during wrist flexion in DBS surgery. The first approach relied on using a general rigidity reduction model, regardless of the initial severity of the symptom. Thus, to enhance the performance of the previously presented system, we aimed to develop models for high and low baseline rigidity, according to the examiner assessment before any stimulation. This would allow a more patient-oriented approach. Additionally, usability was improved by having in situ processing in a smartphone, instead of a computer. Such system has shown to be reliable, presenting an accuracy of 82.0% and a mean error of 3.4%. Relatively to previous results, the performance was similar, further supporting the importance of considering the cogwheel rigidity to better infer about the reduction in rigidity. Overall, we present a simple, wearable, mobile system, suitable for intra-operatory conditions during DBS, supporting a physician in decision-making when setting stimulation parameters.

  8. The effect of stimulus strength on the speed and accuracy of a perceptual decision.

    PubMed

    Palmer, John; Huk, Alexander C; Shadlen, Michael N

    2005-05-02

    Both the speed and the accuracy of a perceptual judgment depend on the strength of the sensory stimulation. When stimulus strength is high, accuracy is high and response time is fast; when stimulus strength is low, accuracy is low and response time is slow. Although the psychometric function is well established as a tool for analyzing the relationship between accuracy and stimulus strength, the corresponding chronometric function for the relationship between response time and stimulus strength has not received as much consideration. In this article, we describe a theory of perceptual decision making based on a diffusion model. In it, a decision is based on the additive accumulation of sensory evidence over time to a bound. Combined with simple scaling assumptions, the proportional-rate and power-rate diffusion models predict simple analytic expressions for both the chronometric and psychometric functions. In a series of psychophysical experiments, we show that this theory accounts for response time and accuracy as a function of both stimulus strength and speed-accuracy instructions. In particular, the results demonstrate a close coupling between response time and accuracy. The theory is also shown to subsume the predictions of Piéron's Law, a power function dependence of response time on stimulus strength. The theory's analytic chronometric function allows one to extend theories of accuracy to response time.

  9. PubChem3D: conformer ensemble accuracy

    PubMed Central

    2013-01-01

    Background PubChem is a free and publicly available resource containing substance descriptions and their associated biological activity information. PubChem3D is an extension to PubChem containing computationally-derived three-dimensional (3-D) structures of small molecules. All the tools and services that are a part of PubChem3D rely upon the quality of the 3-D conformer models. Construction of the conformer models currently available in PubChem3D involves a clustering stage to sample the conformational space spanned by the molecule. While this stage allows one to downsize the conformer models to more manageable size, it may result in a loss of the ability to reproduce experimentally determined “bioactive” conformations, for example, found for PDB ligands. This study examines the extent of this accuracy loss and considers its effect on the 3-D similarity analysis of molecules. Results The conformer models consisting of up to 100,000 conformers per compound were generated for 47,123 small molecules whose structures were experimentally determined, and the conformers in each conformer model were clustered to reduce the size of the conformer model to a maximum of 500 conformers per molecule. The accuracy of the conformer models before and after clustering was evaluated using five different measures: root-mean-square distance (RMSD), shape-optimized shape-Tanimoto (STST-opt) and combo-Tanimoto (ComboTST-opt), and color-optimized color-Tanimoto (CTCT-opt) and combo-Tanimoto (ComboTCT-opt). On average, the effect of clustering decreased the conformer model accuracy, increasing the conformer ensemble’s RMSD to the bioactive conformer (by 0.18 ± 0.12 Å), and decreasing the STST-opt, ComboTST-opt, CTCT-opt, and ComboTCT-opt scores (by 0.04 ± 0.03, 0.16 ± 0.09, 0.09 ± 0.05, and 0.15 ± 0.09, respectively). Conclusion This study shows the RMSD accuracy performance of the PubChem3D conformer models is operating as designed. In addition, the effect of PubChem3D

  10. Quantitative differential phase contrast imaging at high resolution with radially asymmetric illumination.

    PubMed

    Lin, Yu-Zi; Huang, Kuang-Yuh; Luo, Yuan

    2018-06-15

    Half-circle illumination-based differential phase contrast (DPC) microscopy has been utilized to recover phase images through a pair of images along multiple axes. Recently, the half-circle based DPC using 12-axis measurements significantly provides a circularly symmetric phase transfer function to improve accuracy for more stable phase recovery. Instead of using half-circle-based DPC, we propose a new scheme of DPC under radially asymmetric illumination to achieve circularly symmetric phase transfer function and enhance the accuracy of phase recovery in a more stable and efficient fashion. We present the design, implementation, and experimental image data demonstrating the ability of our method to obtain quantitative phase images of microspheres, as well as live fibroblast cell samples.

  11. Techniques for 3D tracking of single molecules with nanometer accuracy in living cells

    NASA Astrophysics Data System (ADS)

    Gardini, Lucia; Capitanio, Marco; Pavone, Francesco S.

    2013-06-01

    We describe a microscopy technique that, combining wide-field single molecule microscopy, bifocal imaging and Highly Inclined and Laminated Optical sheet (HILO) microscopy, allows a 3D tracking with nanometer accuracy of single fluorescent molecules in vitro and in living cells.

  12. Predictive accuracy of combined genetic and environmental risk scores.

    PubMed

    Dudbridge, Frank; Pashayan, Nora; Yang, Jian

    2018-02-01

    The substantial heritability of most complex diseases suggests that genetic data could provide useful risk prediction. To date the performance of genetic risk scores has fallen short of the potential implied by heritability, but this can be explained by insufficient sample sizes for estimating highly polygenic models. When risk predictors already exist based on environment or lifestyle, two key questions are to what extent can they be improved by adding genetic information, and what is the ultimate potential of combined genetic and environmental risk scores? Here, we extend previous work on the predictive accuracy of polygenic scores to allow for an environmental score that may be correlated with the polygenic score, for example when the environmental factors mediate the genetic risk. We derive common measures of predictive accuracy and improvement as functions of the training sample size, chip heritabilities of disease and environmental score, and genetic correlation between disease and environmental risk factors. We consider simple addition of the two scores and a weighted sum that accounts for their correlation. Using examples from studies of cardiovascular disease and breast cancer, we show that improvements in discrimination are generally small but reasonable degrees of reclassification could be obtained with current sample sizes. Correlation between genetic and environmental scores has only minor effects on numerical results in realistic scenarios. In the longer term, as the accuracy of polygenic scores improves they will come to dominate the predictive accuracy compared to environmental scores. © 2017 WILEY PERIODICALS, INC.

  13. Predictive accuracy of combined genetic and environmental risk scores

    PubMed Central

    Pashayan, Nora; Yang, Jian

    2017-01-01

    ABSTRACT The substantial heritability of most complex diseases suggests that genetic data could provide useful risk prediction. To date the performance of genetic risk scores has fallen short of the potential implied by heritability, but this can be explained by insufficient sample sizes for estimating highly polygenic models. When risk predictors already exist based on environment or lifestyle, two key questions are to what extent can they be improved by adding genetic information, and what is the ultimate potential of combined genetic and environmental risk scores? Here, we extend previous work on the predictive accuracy of polygenic scores to allow for an environmental score that may be correlated with the polygenic score, for example when the environmental factors mediate the genetic risk. We derive common measures of predictive accuracy and improvement as functions of the training sample size, chip heritabilities of disease and environmental score, and genetic correlation between disease and environmental risk factors. We consider simple addition of the two scores and a weighted sum that accounts for their correlation. Using examples from studies of cardiovascular disease and breast cancer, we show that improvements in discrimination are generally small but reasonable degrees of reclassification could be obtained with current sample sizes. Correlation between genetic and environmental scores has only minor effects on numerical results in realistic scenarios. In the longer term, as the accuracy of polygenic scores improves they will come to dominate the predictive accuracy compared to environmental scores. PMID:29178508

  14. Development of a Postcolumn Infused-Internal Standard Liquid Chromatography Mass Spectrometry Method for Quantitative Metabolomics Studies.

    PubMed

    Liao, Hsiao-Wei; Chen, Guan-Yuan; Wu, Ming-Shiang; Liao, Wei-Chih; Lin, Ching-Hung; Kuo, Ching-Hua

    2017-02-03

    Quantitative metabolomics has become much more important in clinical research in recent years. Individual differences in matrix effects (MEs) and the injection order effect are two major factors that reduce the quantification accuracy in liquid chromatography-electrospray ionization-mass spectrometry-based (LC-ESI-MS) metabolomics studies. This study proposed a postcolumn infused-internal standard (PCI-IS) combined with a matrix normalization factor (MNF) strategy to improve the analytical accuracy of quantitative metabolomics. The PCI-IS combined with the MNF method was applied for a targeted metabolomics study of amino acids (AAs). D8-Phenylalanine was used as the PCI-IS, and it was postcolumn-infused into the ESI interface for calibration purposes. The MNF was used to bridge the AA response in a standard solution with the plasma samples. The MEs caused signal changes that were corrected by dividing the AA signal intensities by the PCI-IS intensities after adjustment with the MNF. After the method validation, we evaluated the method applicability for breast cancer research using 100 plasma samples. The quantification results revealed that the 11 tested AAs exhibit an accuracy between 88.2 and 110.7%. The principal component analysis score plot revealed that the injection order effect can be successfully removed, and most of the within-group variation of the tested AAs decreased after the PCI-IS correction. Finally, targeted metabolomics studies on the AAs showed that tryptophan was expressed more in malignant patients than in the benign group. We anticipate that a similar approach can be applied to other endogenous metabolites to facilitate quantitative metabolomics studies.

  15. Overlay accuracy fundamentals

    NASA Astrophysics Data System (ADS)

    Kandel, Daniel; Levinski, Vladimir; Sapiens, Noam; Cohen, Guy; Amit, Eran; Klein, Dana; Vakshtein, Irina

    2012-03-01

    Currently, the performance of overlay metrology is evaluated mainly based on random error contributions such as precision and TIS variability. With the expected shrinkage of the overlay metrology budget to < 0.5nm, it becomes crucial to include also systematic error contributions which affect the accuracy of the metrology. Here we discuss fundamental aspects of overlay accuracy and a methodology to improve accuracy significantly. We identify overlay mark imperfections and their interaction with the metrology technology, as the main source of overlay inaccuracy. The most important type of mark imperfection is mark asymmetry. Overlay mark asymmetry leads to a geometrical ambiguity in the definition of overlay, which can be ~1nm or less. It is shown theoretically and in simulations that the metrology may enhance the effect of overlay mark asymmetry significantly and lead to metrology inaccuracy ~10nm, much larger than the geometrical ambiguity. The analysis is carried out for two different overlay metrology technologies: Imaging overlay and DBO (1st order diffraction based overlay). It is demonstrated that the sensitivity of DBO to overlay mark asymmetry is larger than the sensitivity of imaging overlay. Finally, we show that a recently developed measurement quality metric serves as a valuable tool for improving overlay metrology accuracy. Simulation results demonstrate that the accuracy of imaging overlay can be improved significantly by recipe setup optimized using the quality metric. We conclude that imaging overlay metrology, complemented by appropriate use of measurement quality metric, results in optimal overlay accuracy.

  16. Systematic feasibility analysis of a quantitative elasticity estimation for breast anatomy using supine/prone patient postures.

    PubMed

    Hasse, Katelyn; Neylon, John; Sheng, Ke; Santhanam, Anand P

    2016-03-01

    Breast elastography is a critical tool for improving the targeted radiotherapy treatment of breast tumors. Current breast radiotherapy imaging protocols only involve prone and supine CT scans. There is a lack of knowledge on the quantitative accuracy with which breast elasticity can be systematically measured using only prone and supine CT datasets. The purpose of this paper is to describe a quantitative elasticity estimation technique for breast anatomy using only these supine/prone patient postures. Using biomechanical, high-resolution breast geometry obtained from CT scans, a systematic assessment was performed in order to determine the feasibility of this methodology for clinically relevant elasticity distributions. A model-guided inverse analysis approach is presented in this paper. A graphics processing unit (GPU)-based linear elastic biomechanical model was employed as a forward model for the inverse analysis with the breast geometry in a prone position. The elasticity estimation was performed using a gradient-based iterative optimization scheme and a fast-simulated annealing (FSA) algorithm. Numerical studies were conducted to systematically analyze the feasibility of elasticity estimation. For simulating gravity-induced breast deformation, the breast geometry was anchored at its base, resembling the chest-wall/breast tissue interface. Ground-truth elasticity distributions were assigned to the model, representing tumor presence within breast tissue. Model geometry resolution was varied to estimate its influence on convergence of the system. A priori information was approximated and utilized to record the effect on time and accuracy of convergence. The role of the FSA process was also recorded. A novel error metric that combined elasticity and displacement error was used to quantify the systematic feasibility study. For the authors' purposes, convergence was set to be obtained when each voxel of tissue was within 1 mm of ground-truth deformation. The authors

  17. Accuracy Assessment in Determining the Location of Corners of Building Structures Using a Combination of Various Measurement Methods

    NASA Astrophysics Data System (ADS)

    Krzyżek, Robert; Przewięźlikowska, Anna

    2017-12-01

    When surveys of corners of building structures are carried out, surveyors frequently use a compilation of two surveying methods. The first one involves the determination of several corners with reference to a geodetic control using classical methods of surveying field details. The second method relates to the remaining corner points of a structure, which are determined in sequence from distance-distance intersection, using control linear values of the wall faces of the building, the so-called tie distances. This paper assesses the accuracy of coordinates of corner points of a building structure, determined using the method of distance-distance intersection, based on the corners which had previously been determined by the conducted surveys tied to a geodetic control. It should be noted, however, that such a method of surveying the corners of building structures from linear measures is based on the details of the first-order accuracy, while the regulations explicitly allow such measurement only for the details of the second- and third-order accuracy. Therefore, a question arises whether this legal provision is unfounded, or whether surveyors are acting not only against the applicable standards but also without due diligence while performing surveys? This study provides answers to the formulated problem. The main purpose of the study was to verify whether the actual method which is used in practice for surveying building structures allows to obtain the required accuracy of coordinates of the points being determined, or whether it should be strictly forbidden. The results of the conducted studies clearly demonstrate that the problem is definitely more complex. Eventually, however, it might be assumed that assessment of the accuracy in determining a location of corners of a building using a combination of two different surveying methods will meet the requirements of the regulation [MIA, 2011), subject to compliance with relevant baseline criteria, which have been

  18. Accuracy assessment of seven global land cover datasets over China

    NASA Astrophysics Data System (ADS)

    Yang, Yongke; Xiao, Pengfeng; Feng, Xuezhi; Li, Haixing

    2017-03-01

    Land cover (LC) is the vital foundation to Earth science. Up to now, several global LC datasets have arisen with efforts of many scientific communities. To provide guidelines for data usage over China, nine LC maps from seven global LC datasets (IGBP DISCover, UMD, GLC, MCD12Q1, GLCNMO, CCI-LC, and GlobeLand30) were evaluated in this study. First, we compared their similarities and discrepancies in both area and spatial patterns, and analysed their inherent relations to data sources and classification schemes and methods. Next, five sets of validation sample units (VSUs) were collected to calculate their accuracy quantitatively. Further, we built a spatial analysis model and depicted their spatial variation in accuracy based on the five sets of VSUs. The results show that, there are evident discrepancies among these LC maps in both area and spatial patterns. For LC maps produced by different institutes, GLC 2000 and CCI-LC 2000 have the highest overall spatial agreement (53.8%). For LC maps produced by same institutes, overall spatial agreement of CCI-LC 2000 and 2010, and MCD12Q1 2001 and 2010 reach up to 99.8% and 73.2%, respectively; while more efforts are still needed if we hope to use these LC maps as time series data for model inputting, since both CCI-LC and MCD12Q1 fail to represent the rapid changing trend of several key LC classes in the early 21st century, in particular urban and built-up, snow and ice, water bodies, and permanent wetlands. With the highest spatial resolution, the overall accuracy of GlobeLand30 2010 is 82.39%. For the other six LC datasets with coarse resolution, CCI-LC 2010/2000 has the highest overall accuracy, and following are MCD12Q1 2010/2001, GLC 2000, GLCNMO 2008, IGBP DISCover, and UMD in turn. Beside that all maps exhibit high accuracy in homogeneous regions; local accuracies in other regions are quite different, particularly in Farming-Pastoral Zone of North China, mountains in Northeast China, and Southeast Hills. Special

  19. Data from quantitative label free proteomics analysis of rat spleen.

    PubMed

    Dudekula, Khadar; Le Bihan, Thierry

    2016-09-01

    The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides). A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.

  20. Towards in vivo focal cortical dysplasia phenotyping using quantitative MRI.

    PubMed

    Adler, Sophie; Lorio, Sara; Jacques, Thomas S; Benova, Barbora; Gunny, Roxana; Cross, J Helen; Baldeweg, Torsten; Carmichael, David W

    2017-01-01

    Focal cortical dysplasias (FCDs) are a range of malformations of cortical development each with specific histopathological features. Conventional radiological assessment of standard structural MRI is useful for the localization of lesions but is unable to accurately predict the histopathological features. Quantitative MRI offers the possibility to probe tissue biophysical properties in vivo and may bridge the gap between radiological assessment and ex-vivo histology. This review will cover histological, genetic and radiological features of FCD following the ILAE classification and will explain how quantitative voxel- and surface-based techniques can characterise these features. We will provide an overview of the quantitative MRI measures available, their link with biophysical properties and finally the potential application of quantitative MRI to the problem of FCD subtyping. Future research linking quantitative MRI to FCD histological properties should improve clinical protocols, allow better characterisation of lesions in vivo and tailored surgical planning to the individual.

  1. Accuracy of magnetic resonance based susceptibility measurements

    NASA Astrophysics Data System (ADS)

    Erdevig, Hannah E.; Russek, Stephen E.; Carnicka, Slavka; Stupic, Karl F.; Keenan, Kathryn E.

    2017-05-01

    Magnetic Resonance Imaging (MRI) is increasingly used to map the magnetic susceptibility of tissue to identify cerebral microbleeds associated with traumatic brain injury and pathological iron deposits associated with neurodegenerative diseases such as Parkinson's and Alzheimer's disease. Accurate measurements of susceptibility are important for determining oxygen and iron content in blood vessels and brain tissue for use in noninvasive clinical diagnosis and treatment assessments. Induced magnetic fields with amplitude on the order of 100 nT, can be detected using MRI phase images. The induced field distributions can then be inverted to obtain quantitative susceptibility maps. The focus of this research was to determine the accuracy of MRI-based susceptibility measurements using simple phantom geometries and to compare the susceptibility measurements with magnetometry measurements where SI-traceable standards are available. The susceptibilities of paramagnetic salt solutions in cylindrical containers were measured as a function of orientation relative to the static MRI field. The observed induced fields as a function of orientation of the cylinder were in good agreement with simple models. The MRI susceptibility measurements were compared with SQUID magnetometry using NIST-traceable standards. MRI can accurately measure relative magnetic susceptibilities while SQUID magnetometry measures absolute magnetic susceptibility. Given the accuracy of moment measurements of tissue mimicking samples, and the need to look at small differences in tissue properties, the use of existing NIST standard reference materials to calibrate MRI reference structures is problematic and better reference materials are required.

  2. Accuracy and eligibility of CBCT to digitize dental plaster casts.

    PubMed

    Becker, Kathrin; Schmücker, Ulf; Schwarz, Frank; Drescher, Dieter

    2018-05-01

    Software-based dental planning requires digital casts and oftentimes cone-beam computed tomography (CBCT) radiography. However, buying a dedicated model digitizing device can be expensive and might not be required. The present study aimed to assess whether digital models derived from CBCT and models digitized using a dedicated optical device are of comparable accuracy. A total of 20 plaster casts were digitized with eight CBCT and five optical model digitizers. Corresponding models were superimposed using six control points and subsequent iterative closest point matching. Median distances were calculated among all registered models. Data were pooled per scanner and model. Boxplots were generated, and the paired t test, a Friedman test, and a post-hoc Nemenyi test were employed for statistical comparison. Results were found significant at p < 0.05. All CBCT devices allowed the digitization of plaster casts, but failed to reach the accuracy of the dedicated model digitizers (p < 0.001). Median distances between CBCT and optically digitized casts were 0.064 + - 0.005 mm. Qualitative differences among the CBCT systems were detected (χ 2  = 78.07, p < 0.001), and one CBCT providing a special plaster cast digitization mode was found superior to the competitors (p < 0.05). CBCT systems failed to reach the accuracy from optical digitizers, but within the limits of the study, accuracy appeared to be sufficient for digital planning and forensic purposes. Most CBCT systems enabled digitization of plaster casts, and accuracy was found sufficient for digital planning and storage purposes.

  3. Accuracy and precision of pseudo-continuous arterial spin labeling perfusion during baseline and hypercapnia: a head-to-head comparison with ¹⁵O H₂O positron emission tomography.

    PubMed

    Heijtel, D F R; Mutsaerts, H J M M; Bakker, E; Schober, P; Stevens, M F; Petersen, E T; van Berckel, B N M; Majoie, C B L M; Booij, J; van Osch, M J P; Vanbavel, E; Boellaard, R; Lammertsma, A A; Nederveen, A J

    2014-05-15

    Measurements of the cerebral blood flow (CBF) and cerebrovascular reactivity (CVR) provide useful information about cerebrovascular condition and regional metabolism. Pseudo-continuous arterial spin labeling (pCASL) is a promising non-invasive MRI technique to quantitatively measure the CBF, whereas additional hypercapnic pCASL measurements are currently showing great promise to quantitatively assess the CVR. However, the introduction of pCASL at a larger scale awaits further evaluation of the exact accuracy and precision compared to the gold standard. (15)O H₂O positron emission tomography (PET) is currently regarded as the most accurate and precise method to quantitatively measure both CBF and CVR, though it is one of the more invasive methods as well. In this study we therefore assessed the accuracy and precision of quantitative pCASL-based CBF and CVR measurements by performing a head-to-head comparison with (15)O H₂O PET, based on quantitative CBF measurements during baseline and hypercapnia. We demonstrate that pCASL CBF imaging is accurate during both baseline and hypercapnia with respect to (15)O H₂O PET with a comparable precision. These results pave the way for quantitative usage of pCASL MRI in both clinical and research settings. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. End-to-end deep neural network for optical inversion in quantitative photoacoustic imaging.

    PubMed

    Cai, Chuangjian; Deng, Kexin; Ma, Cheng; Luo, Jianwen

    2018-06-15

    An end-to-end deep neural network, ResU-net, is developed for quantitative photoacoustic imaging. A residual learning framework is used to facilitate optimization and to gain better accuracy from considerably increased network depth. The contracting and expanding paths enable ResU-net to extract comprehensive context information from multispectral initial pressure images and, subsequently, to infer a quantitative image of chromophore concentration or oxygen saturation (sO 2 ). According to our numerical experiments, the estimations of sO 2 and indocyanine green concentration are accurate and robust against variations in both optical property and object geometry. An extremely short reconstruction time of 22 ms is achieved.

  5. Accuracy Analysis for Finite-Volume Discretization Schemes on Irregular Grids

    NASA Technical Reports Server (NTRS)

    Diskin, Boris; Thomas, James L.

    2010-01-01

    A new computational analysis tool, downscaling test, is introduced and applied for studying the convergence rates of truncation and discretization errors of nite-volume discretization schemes on general irregular (e.g., unstructured) grids. The study shows that the design-order convergence of discretization errors can be achieved even when truncation errors exhibit a lower-order convergence or, in some cases, do not converge at all. The downscaling test is a general, efficient, accurate, and practical tool, enabling straightforward extension of verification and validation to general unstructured grid formulations. It also allows separate analysis of the interior, boundaries, and singularities that could be useful even in structured-grid settings. There are several new findings arising from the use of the downscaling test analysis. It is shown that the discretization accuracy of a common node-centered nite-volume scheme, known to be second-order accurate for inviscid equations on triangular grids, degenerates to first order for mixed grids. Alternative node-centered schemes are presented and demonstrated to provide second and third order accuracies on general mixed grids. The local accuracy deterioration at intersections of tangency and in flow/outflow boundaries is demonstrated using the DS tests tailored to examining the local behavior of the boundary conditions. The discretization-error order reduction within inviscid stagnation regions is demonstrated. The accuracy deterioration is local, affecting mainly the velocity components, but applies to any order scheme.

  6. Digital image analysis: improving accuracy and reproducibility of radiographic measurement.

    PubMed

    Bould, M; Barnard, S; Learmonth, I D; Cunningham, J L; Hardy, J R

    1999-07-01

    To assess the accuracy and reproducibility of a digital image analyser and the human eye, in measuring radiographic dimensions. We experimentally compared radiographic measurement using either an image analyser system or the human eye with digital caliper. The assessment of total hip arthroplasty wear from radiographs relies on both the accuracy of radiographic images and the accuracy of radiographic measurement. Radiographs were taken of a slip gauge (30+/-0.00036 mm) and slip gauge with a femoral stem. The projected dimensions of the radiographic images were calculated by trigonometry. The radiographic dimensions were then measured by blinded observers using both techniques. For a single radiograph, the human eye was accurate to 0.26 mm and reproducible to +/-0.1 mm. In comparison the digital image analyser system was accurate to 0.01 mm with a reproducibility of +/-0.08 mm. In an arthroplasty model, where the dimensions of an object were corrected for magnification by the known dimensions of a femoral head, the human eye was accurate to 0.19 mm, whereas the image analyser system was accurate to 0.04 mm. The digital image analysis system is up to 20 times more accurate than the human eye, and in an arthroplasty model the accuracy of measurement increases four-fold. We believe such image analysis may allow more accurate and reproducible measurement of wear from standard follow-up radiographs.

  7. UK audit of analysis of quantitative parameters from renography data generated using a physical phantom.

    PubMed

    Nijran, Kuldip S; Houston, Alex S; Fleming, John S; Jarritt, Peter H; Heikkinen, Jari O; Skrypniuk, John V

    2014-07-01

    In this second UK audit of quantitative parameters obtained from renography, phantom simulations were used in cases in which the 'true' values could be estimated, allowing the accuracy of the parameters measured to be assessed. A renal physical phantom was used to generate a set of three phantom simulations (six kidney functions) acquired on three different gamma camera systems. A total of nine phantom simulations and three real patient studies were distributed to UK hospitals participating in the audit. Centres were asked to provide results for the following parameters: relative function and time-to-peak (whole kidney and cortical region). As with previous audits, a questionnaire collated information on methodology. Errors were assessed as the root mean square deviation from the true value. Sixty-one centres responded to the audit, with some hospitals providing multiple sets of results. Twenty-one centres provided a complete set of parameter measurements. Relative function and time-to-peak showed a reasonable degree of accuracy and precision in most UK centres. The overall average root mean squared deviation of the results for (i) the time-to-peak measurement for the whole kidney and (ii) the relative function measurement from the true value was 7.7 and 4.5%, respectively. These results showed a measure of consistency in the relative function and time-to-peak that was similar to the results reported in a previous renogram audit by our group. Analysis of audit data suggests a reasonable degree of accuracy in the quantification of renography function using relative function and time-to-peak measurements. However, it is reasonable to conclude that the objectives of the audit could not be fully realized because of the limitations of the mechanical phantom in providing true values for renal parameters.

  8. Digital micromirror device-based common-path quantitative phase imaging

    PubMed Central

    Zheng, Cheng; Zhou, Renjie; Kuang, Cuifang; Zhao, Guangyuan; Yaqoob, Zahid; So, Peter T. C.

    2017-01-01

    We propose a novel common-path quantitative phase imaging (QPI) method based on a digital micromirror device (DMD). The DMD is placed in a plane conjugate to the objective back-aperture plane for the purpose of generating two plane waves that illuminate the sample. A pinhole is used in the detection arm to filter one of the beams after sample to create a reference beam. Additionally, a transmission-type liquid crystal device, placed at the objective back-aperture plane, eliminates the specular reflection noise arising from all the “off” state DMD micromirrors, which is common in all DMD-based illuminations. We have demonstrated high sensitivity QPI, which has a measured spatial and temporal noise of 4.92 nm and 2.16 nm, respectively. Experiments with calibrated polystyrene beads illustrate the desired phase measurement accuracy. In addition, we have measured the dynamic height maps of red blood cell membrane fluctuations, showing the efficacy of the proposed system for live cell imaging. Most importantly, the DMD grants the system convenience in varying the interference fringe period on the camera to easily satisfy the pixel sampling conditions. This feature also alleviates the pinhole alignment complexity. We envision that the proposed DMD-based common-path QPI system will allow for system miniaturization and automation for a broader adaption. PMID:28362789

  9. Quantitative analysis of pork and chicken products by droplet digital PCR.

    PubMed

    Cai, Yicun; Li, Xiang; Lv, Rong; Yang, Jielin; Li, Jian; He, Yuping; Pan, Liangwen

    2014-01-01

    In this project, a highly precise quantitative method based on the digital polymerase chain reaction (dPCR) technique was developed to determine the weight of pork and chicken in meat products. Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of species-specific DNAs in meat products. However, it is limited in amplification efficiency and relies on standard curves based Ct values, detecting and quantifying low copy number target DNA, as in some complex mixture meat products. By using the dPCR method, we find the relationships between the raw meat weight and DNA weight and between the DNA weight and DNA copy number were both close to linear. This enabled us to establish formulae to calculate the raw meat weight based on the DNA copy number. The accuracy and applicability of this method were tested and verified using samples of pork and chicken powder mixed in known proportions. Quantitative analysis indicated that dPCR is highly precise in quantifying pork and chicken in meat products and therefore has the potential to be used in routine analysis by government regulators and quality control departments of commercial food and feed enterprises.

  10. Quantitative analysis of low-density SNP data for parentage assignment and estimation of family contributions to pooled samples.

    PubMed

    Henshall, John M; Dierens, Leanne; Sellars, Melony J

    2014-09-02

    While much attention has focused on the development of high-density single nucleotide polymorphism (SNP) assays, the costs of developing and running low-density assays have fallen dramatically. This makes it feasible to develop and apply SNP assays for agricultural species beyond the major livestock species. Although low-cost low-density assays may not have the accuracy of the high-density assays widely used in human and livestock species, we show that when combined with statistical analysis approaches that use quantitative instead of discrete genotypes, their utility may be improved. The data used in this study are from a 63-SNP marker Sequenom® iPLEX Platinum panel for the Black Tiger shrimp, for which high-density SNP assays are not currently available. For quantitative genotypes that could be estimated, in 5% of cases the most likely genotype for an individual at a SNP had a probability of less than 0.99. Matrix formulations of maximum likelihood equations for parentage assignment were developed for the quantitative genotypes and also for discrete genotypes perturbed by an assumed error term. Assignment rates that were based on maximum likelihood with quantitative genotypes were similar to those based on maximum likelihood with perturbed genotypes but, for more than 50% of cases, the two methods resulted in individuals being assigned to different families. Treating genotypes as quantitative values allows the same analysis framework to be used for pooled samples of DNA from multiple individuals. Resulting correlations between allele frequency estimates from pooled DNA and individual samples were consistently greater than 0.90, and as high as 0.97 for some pools. Estimates of family contributions to the pools based on quantitative genotypes in pooled DNA had a correlation of 0.85 with estimates of contributions from DNA-derived pedigree. Even with low numbers of SNPs of variable quality, parentage testing and family assignment from pooled samples are

  11. Improving accuracy of genomic prediction in Brangus cattle by adding animals with imputed low-density SNP genotypes.

    PubMed

    Lopes, F B; Wu, X-L; Li, H; Xu, J; Perkins, T; Genho, J; Ferretti, R; Tait, R G; Bauck, S; Rosa, G J M

    2018-02-01

    Reliable genomic prediction of breeding values for quantitative traits requires the availability of sufficient number of animals with genotypes and phenotypes in the training set. As of 31 October 2016, there were 3,797 Brangus animals with genotypes and phenotypes. These Brangus animals were genotyped using different commercial SNP chips. Of them, the largest group consisted of 1,535 animals genotyped by the GGP-LDV4 SNP chip. The remaining 2,262 genotypes were imputed to the SNP content of the GGP-LDV4 chip, so that the number of animals available for training the genomic prediction models was more than doubled. The present study showed that the pooling of animals with both original or imputed 40K SNP genotypes substantially increased genomic prediction accuracies on the ten traits. By supplementing imputed genotypes, the relative gains in genomic prediction accuracies on estimated breeding values (EBV) were from 12.60% to 31.27%, and the relative gain in genomic prediction accuracies on de-regressed EBV was slightly small (i.e. 0.87%-18.75%). The present study also compared the performance of five genomic prediction models and two cross-validation methods. The five genomic models predicted EBV and de-regressed EBV of the ten traits similarly well. Of the two cross-validation methods, leave-one-out cross-validation maximized the number of animals at the stage of training for genomic prediction. Genomic prediction accuracy (GPA) on the ten quantitative traits was validated in 1,106 newly genotyped Brangus animals based on the SNP effects estimated in the previous set of 3,797 Brangus animals, and they were slightly lower than GPA in the original data. The present study was the first to leverage currently available genotype and phenotype resources in order to harness genomic prediction in Brangus beef cattle. © 2018 Blackwell Verlag GmbH.

  12. One step screening of retroviral producer clones by real time quantitative PCR.

    PubMed

    Towers, G J; Stockholm, D; Labrousse-Najburg, V; Carlier, F; Danos, O; Pagès, J C

    1999-01-01

    Recombinant retroviruses are obtained from either stably or transiently transfected retrovirus producer cells. In the case of stably producing lines, a large number of clones must be screened in order to select the one with the highest titre. The multi-step selection of high titre producing clones is time consuming and expensive. We have taken advantage of retroviral endogenous reverse transcription to develop a quantitative PCR assay on crude supernatant from producing clones. We used Taqman PCR technology, which, by using fluorescence measurement at each cycle of amplification, allows PCR product quantification. Fluorescence results from specific degradation of a probe oligonucleotide by the Taq polymerase 3'-5' exonuclease activity. Primers and probe sequences were chosen to anneal to the viral strong stop species, which is the first DNA molecule synthesised during reverse transcription. The protocol consists of a single real time PCR, using as template filtered viral supernatant without any other pre-treatment. We show that the primers and probe described allow quantitation of serially diluted plasmid to as few as 15 plasmid molecules. We then test 200 GFP-expressing retroviral-producing clones either by FACS analysis of infected cells or by using the quantitative PCR. We confirm that the Taqman protocol allows the detection of virus in supernatant and selection of high titre clones. Furthermore, we can determine infectious titre by quantitative PCR on genomic DNA from infected cells, using an additional set of primers and probe to albumin to normalise for the genomic copy number. We demonstrate that real time quantitative PCR can be used as a powerful and reliable single step, high throughput screen for high titre retroviral producer clones.

  13. Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures.

    PubMed

    Lim, Issel Anne L; Faria, Andreia V; Li, Xu; Hsu, Johnny T C; Airan, Raag D; Mori, Susumu; van Zijl, Peter C M

    2013-11-15

    The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a "deep gray matter parcellation map" (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established "white matter parcellation map" (WMPM) from the same subject's T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the "Everything Parcellation Map in Eve Space," also known as the "EvePM." It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting "almost perfect" agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray

  14. Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures

    PubMed Central

    Lim, Issel Anne L.; Faria, Andreia V.; Li, Xu; Hsu, Johnny T.C.; Airan, Raag D.; Mori, Susumu; van Zijl, Peter C. M.

    2013-01-01

    The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a “deep gray matter parcellation map” (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established “white matter parcellation map” (WMPM) from the same subject’s T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the “Everything Parcellation Map in Eve Space,” also known as the “EvePM.” It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting “almost perfect” agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron

  15. Quantitative magnetic resonance (MR) neurography for evaluation of peripheral nerves and plexus injuries

    PubMed Central

    Barousse, Rafael; Socolovsky, Mariano; Luna, Antonio

    2017-01-01

    Traumatic conditions of peripheral nerves and plexus have been classically evaluated by morphological imaging techniques and electrophysiological tests. New magnetic resonance imaging (MRI) studies based on 3D fat-suppressed techniques are providing high accuracy for peripheral nerve injury evaluation from a qualitative point of view. However, these techniques do not provide quantitative information. Diffusion weighted imaging (DWI) and diffusion tensor imaging (DTI) are functional MRI techniques that are able to evaluate and quantify the movement of water molecules within different biological structures. These techniques have been successfully applied in other anatomical areas, especially in the assessment of central nervous system, and now are being imported, with promising results for peripheral nerve and plexus evaluation. DWI and DTI allow performing a qualitative and quantitative peripheral nerve analysis, providing valuable pathophysiological information about functional integrity of these structures. In the field of trauma and peripheral nerve or plexus injury, several derived parameters from DWI and DTI studies such as apparent diffusion coefficient (ADC) or fractional anisotropy (FA) among others, can be used as potential biomarkers of neural damage providing information about fiber organization, axonal flow or myelin integrity. A proper knowledge of physical basis of these techniques and their limitations is important for an optimal interpretation of the imaging findings and derived data. In this paper, a comprehensive review of the potential applications of DWI and DTI neurographic studies is performed with a focus on traumatic conditions, including main nerve entrapment syndromes in both peripheral nerves and brachial or lumbar plexus. PMID:28932698

  16. Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gritsenko, Marina A.; Xu, Zhe; Liu, Tao

    Comprehensive, quantitative information on abundances of proteins and their post-translational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labelling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification andmore » quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples, and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.« less

  17. Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS.

    PubMed

    Gritsenko, Marina A; Xu, Zhe; Liu, Tao; Smith, Richard D

    2016-01-01

    Comprehensive, quantitative information on abundances of proteins and their posttranslational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labeling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification and quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.

  18. Quantitative Electron Probe Microanalysis: State of the Art

    NASA Technical Reports Server (NTRS)

    Carpernter, P. K.

    2005-01-01

    Quantitative electron-probe microanalysis (EPMA) has improved due to better instrument design and X-ray correction methods. Design improvement of the electron column and X-ray spectrometer has resulted in measurement precision that exceeds analytical accuracy. Wavelength-dispersive spectrometer (WDS) have layered-dispersive diffraction crystals with improved light-element sensitivity. Newer energy-dispersive spectrometers (EDS) have Si-drift detector elements, thin window designs, and digital processing electronics with X-ray throughput approaching that of WDS Systems. Using these systems, digital X-ray mapping coupled with spectrum imaging is a powerful compositional mapping tool. Improvements in analytical accuracy are due to better X-ray correction algorithms, mass absorption coefficient data sets,and analysis method for complex geometries. ZAF algorithms have ban superceded by Phi(pz) algorithms that better model the depth distribution of primary X-ray production. Complex thin film and particle geometries are treated using Phi(pz) algorithms, end results agree well with Monte Carlo simulations. For geological materials, X-ray absorption dominates the corretions end depends on the accuracy of mass absorption coefficient (MAC) data sets. However, few MACs have been experimentally measured, and the use of fitted coefficients continues due to general success of the analytical technique. A polynomial formulation of the Bence-Albec alpha-factor technique, calibrated using Phi(pz) algorithms, is used to critically evaluate accuracy issues and can be also be used for high 2% relative and is limited by measurement precision for ideal cases, but for many elements the analytical accuracy is unproven. The EPMA technique has improved to the point where it is frequently used instead of the petrogaphic microscope for reconnaissance work. Examples of stagnant research areas are: WDS detector design characterization of calibration standards, and the need for more complete

  19. Allowable SEM noise for unbiased LER measurement

    NASA Astrophysics Data System (ADS)

    Papavieros, George; Constantoudis, Vassilios; Gogolides, Evangelos

    2018-03-01

    Recently, a novel method for the calculation of unbiased Line Edge Roughness based on Power Spectral Density analysis has been proposed. In this paper first an alternative method is discussed and investigated, utilizing the Height-Height Correlation Function (HHCF) of edges. The HHCF-based method enables the unbiased determination of the whole triplet of LER parameters including besides rms the correlation length and roughness exponent. The key of both methods is the sensitivity of PSD and HHCF on noise at high frequencies and short distance respectively. Secondly, we elaborate a testbed of synthesized SEM images with controlled LER and noise to justify the effectiveness of the proposed unbiased methods. Our main objective is to find out the boundaries of the method in respect to noise levels and roughness characteristics, for which the method remains reliable, i.e the maximum amount of noise allowed, for which the output results cope with the controllable known inputs. At the same time, we will also set the extremes of roughness parameters for which the methods hold their accuracy.

  20. Quantitative computed tomography assessment of transfusional iron overload.

    PubMed

    Wood, John C; Mo, Ashley; Gera, Aakansha; Koh, Montre; Coates, Thomas; Gilsanz, Vicente

    2011-06-01

    Quantitative computed tomography (QCT) has been proposed for iron quantification for more than 30 years, however there has been little clinical validation. We compared liver attenuation by QCT with magnetic resonance imaging (MRI)-derived estimates of liver iron concentration (LIC) in 37 patients with transfusional siderosis. MRI and QCT measurements were performed as clinically indicated monitoring of LIC and vertebral bone-density respectively, over a 6-year period. Mean time difference between QCT and MRI studies was 14 d, with 25 studies performed on the same day. For liver attenuation outside the normal range, attenuation values rose linearly with LIC (r(2) = 0·94). However, intersubject variability in intrinsic liver attenuation prevented quantitation of LIC <8 mg/g dry weight of liver, and was the dominant source of measurement uncertainty. Calculated QCT and MRI accuracies were equivalent for LIC values approaching 22 mg/g dry weight, with QCT having superior performance at higher LIC's. Although not suitable for monitoring patients with good iron control, QCT may nonetheless represent a viable technique for liver iron quantitation in patients with moderate to severe iron in regions where MRI resources are limited because of its low cost, availability, and high throughput. © 2011 Blackwell Publishing Ltd.

  1. Climate Change Observation Accuracy: Requirements and Economic Value

    NASA Technical Reports Server (NTRS)

    Wielicki, Bruce; Cooke, Roger; Golub, Alexander; Baize, Rosemary; Mlynczak, Martin; Lukashin, Constantin; Thome, Kurt; Shea, Yolanda; Kopp, Greg; Pilewskie, Peter; hide

    2016-01-01

    This presentation will summarize a new quantitative approach to determining the required accuracy for climate change observations. Using this metric, most current global satellite observations struggle to meet this accuracy level. CLARREO (Climate Absolute Radiance and Refractivity Observatory) is a new satellite mission designed to resolve this challenge is by achieving advances of a factor of 10 for reflected solar spectra and a factor of 3 to 5 for thermal infrared spectra. The CLARREO spectrometers can serve as SI traceable benchmarks for the Global Satellite Intercalibration System (GSICS) and greatly improve the utility of a wide range of LEO and GEO infrared and reflected solar satellite sensors for climate change observations (e.g. CERES, MODIS, VIIIRS, CrIS, IASI, Landsat, etc). A CLARREO Pathfinder mission for flight on the International Space Station is included in the U.S. Presidentâ€"TM"s fiscal year 2016 budget, with launch in 2019 or 2020. Providing more accurate decadal change trends can in turn lead to more rapid narrowing of key climate science uncertainties such as cloud feedback and climate sensitivity. A new study has been carried out to quantify the economic benefits of such an advance and concludes that the economic value is $9 Trillion U.S. dollars. The new value includes the cost of carbon emissions reductions.

  2. 40 CFR 53.53 - Test for flow rate accuracy, regulation, measurement accuracy, and cut-off.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., measurement accuracy, and cut-off. 53.53 Section 53.53 Protection of Environment ENVIRONMENTAL PROTECTION..., measurement accuracy, and cut-off. (a) Overview. This test procedure is designed to evaluate a candidate... measurement accuracy, coefficient of variability measurement accuracy, and the flow rate cut-off function. The...

  3. Accuracy of lung nodule density on HRCT: analysis by PSF-based image simulation.

    PubMed

    Ohno, Ken; Ohkubo, Masaki; Marasinghe, Janaka C; Murao, Kohei; Matsumoto, Toru; Wada, Shinichi

    2012-11-08

    A computed tomography (CT) image simulation technique based on the point spread function (PSF) was applied to analyze the accuracy of CT-based clinical evaluations of lung nodule density. The PSF of the CT system was measured and used to perform the lung nodule image simulation. Then, the simulated image was resampled at intervals equal to the pixel size and the slice interval found in clinical high-resolution CT (HRCT) images. On those images, the nodule density was measured by placing a region of interest (ROI) commonly used for routine clinical practice, and comparing the measured value with the true value (a known density of object function used in the image simulation). It was quantitatively determined that the measured nodule density depended on the nodule diameter and the image reconstruction parameters (kernel and slice thickness). In addition, the measured density fluctuated, depending on the offset between the nodule center and the image voxel center. This fluctuation was reduced by decreasing the slice interval (i.e., with the use of overlapping reconstruction), leading to a stable density evaluation. Our proposed method of PSF-based image simulation accompanied with resampling enables a quantitative analysis of the accuracy of CT-based evaluations of lung nodule density. These results could potentially reveal clinical misreadings in diagnosis, and lead to more accurate and precise density evaluations. They would also be of value for determining the optimum scan and reconstruction parameters, such as image reconstruction kernels and slice thicknesses/intervals.

  4. On the accuracy of the Padé-resummed master equation approach to dissipative quantum dynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chen, Hsing-Ta; Reichman, David R.; Berkelbach, Timothy C.

    2016-04-21

    Well-defined criteria are proposed for assessing the accuracy of quantum master equations whose memory functions are approximated by Padé resummation of the first two moments in the electronic coupling. These criteria partition the parameter space into distinct levels of expected accuracy, ranging from quantitatively accurate regimes to regions of parameter space where the approach is not expected to be applicable. Extensive comparison of Padé-resummed master equations with numerically exact results in the context of the spin–boson model demonstrates that the proposed criteria correctly demarcate the regions of parameter space where the Padé approximation is reliable. The applicability analysis we presentmore » is not confined to the specifics of the Hamiltonian under consideration and should provide guidelines for other classes of resummation techniques.« less

  5. A high accuracy sequential solver for simulation and active control of a longitudinal combustion instability

    NASA Technical Reports Server (NTRS)

    Shyy, W.; Thakur, S.; Udaykumar, H. S.

    1993-01-01

    A high accuracy convection scheme using a sequential solution technique has been developed and applied to simulate the longitudinal combustion instability and its active control. The scheme has been devised in the spirit of the Total Variation Diminishing (TVD) concept with special source term treatment. Due to the substantial heat release effect, a clear delineation of the key elements employed by the scheme, i.e., the adjustable damping factor and the source term treatment has been made. By comparing with the first-order upwind scheme previously utilized, the present results exhibit less damping and are free from spurious oscillations, offering improved quantitative accuracy while confirming the spectral analysis reported earlier. A simple feedback type of active control has been found to be capable of enhancing or attenuating the magnitude of the combustion instability.

  6. Quantitative characterization of gold nanoparticles by size-exclusion and hydrodynamic chromatography, coupled to inductively coupled plasma mass spectrometry and quasi-elastic light scattering.

    PubMed

    Pitkänen, Leena; Montoro Bustos, Antonio R; Murphy, Karen E; Winchester, Michael R; Striegel, André M

    2017-08-18

    The physicochemical characterization of nanoparticles (NPs) is of paramount importance for tailoring and optimizing the properties of these materials as well as for evaluating the environmental fate and impact of the NPs. Characterizing the size and chemical identity of disperse NP sample populations can be accomplished by coupling size-based separation methods to physical and chemical detection methods. Informed decisions regarding the NPs can only be made, however, if the separations themselves are quantitative, i.e., if all or most of the analyte elutes from the column within the course of the experiment. We undertake here the size-exclusion chromatographic characterization of Au NPs spanning a six-fold range in mean size. The main problem which has plagued the size-exclusion chromatography (SEC) analysis of Au NPs, namely lack of quantitation accountability due to generally poor NP recovery from the columns, is overcome by carefully matching eluent formulation with the appropriate stationary phase chemistry, and by the use of on-line inductively coupled plasma mass spectrometry (ICP-MS) detection. Here, for the first time, we demonstrate the quantitative analysis of Au NPs by SEC/ICP-MS, including the analysis of a ternary NP blend. The SEC separations are contrasted to HDC/ICP-MS (HDC: hydrodynamic chromatography) separations employing the same stationary phase chemistry. Additionally, analysis of Au NPs by HDC with on-line quasi-elastic light scattering (QELS) allowed for continuous determination of NP size across the chromatographic profiles, circumventing issues related to the shedding of fines from the SEC columns. The use of chemically homogeneous reference materials with well-defined size range allowed for better assessment of the accuracy and precision of the analyses, and for a more direct interpretation of results, than would be possible employing less rigorously characterized analytes. Published by Elsevier B.V.

  7. Accuracy of Orthomosaic Generated by Different Methods in Example of UAV Platform MUST Q

    NASA Astrophysics Data System (ADS)

    Liba, N.; Berg-Jürgens, J.

    2015-11-01

    Development of photogrammetry has reached a new level due to the use of unmanned aerial vehicles (UAV). In Estonia, the main areas of use of UAVs are monitoring overhead power lines for energy companies and fields in agriculture, and estimating the use of stockpile in mining. The project was carried out by the order of the City of Tartu for future road construction. In this research, automation of UAV platform MUST Q aerial image processing and reduction of time spent on the use of ground control points (GCP) is studied. For that two projects were created with software Pix4D. First one was processed automatically without GCP. Second one did use GCP, but all the processing was done automatically. As the result of the project, two orthomosaics with the pixel size of 5 cm were composed. Projects allowed ensuring accuracy limit of three times of the pixel size. The project that turned out to be the most accurate was the one using ground control points to do the levelling, which remained within the error limit allowed and the accuracy of the orthomosaic was 0.132 m. The project that didn't use ground control points had the accuracy of 1.417 m.

  8. A rapid and quantitative assay for measuring antibody-mediated neutralization of West Nile virus infection

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pierson, Theodore C.; Sanchez, Melissa D.; Puffer, Bridget A.

    2006-03-01

    West Nile virus (WNV) is a neurotropic flavivirus within the Japanese encephalitis antigenic complex that is responsible for causing West Nile encephalitis in humans. The surface of WNV virions is covered by a highly ordered icosahedral array of envelope proteins that is responsible for mediating attachment and fusion with target cells. These envelope proteins are also primary targets for the generation of neutralizing antibodies in vivo. In this study, we describe a novel approach for measuring antibody-mediated neutralization of WNV infection using virus-like particles that measure infection as a function of reporter gene expression. These reporter virus particles (RVPs) aremore » produced by complementation of a sub-genomic replicon with WNV structural proteins provided in trans using conventional DNA expression vectors. The precision and accuracy of this approach stem from an ability to measure the outcome of the interaction between antibody and viral antigens under conditions that satisfy the assumptions of the law of mass action as applied to virus neutralization. In addition to its quantitative strengths, this approach allows the production of WNV RVPs bearing the prM-E proteins of different WNV strains and mutants, offering considerable flexibility for the study of the humoral immune response to WNV in vitro. WNV RVPs are capable of only a single round of infection, can be used under BSL-2 conditions, and offer a rapid and quantitative approach for detecting virus entry and its inhibition by neutralizing antibody.« less

  9. Control of separation and quantitative analysis by GC-FTIR

    NASA Astrophysics Data System (ADS)

    Semmoud, A.; Huvenne, Jean P.; Legrand, P.

    1992-03-01

    Software for 3-D representations of the 'Absorbance-Wavenumber-Retention time' is used to control the quality of the GC separation. Spectral information given by the FTIR detection allows the user to be sure that a chromatographic peak is 'pure.' The analysis of peppermint essential oil is presented as an example. This assurance is absolutely required for quantitative applications. In these conditions, we have worked out a quantitative analysis of caffeine. Correlation coefficients between integrated absorbance measurements and concentration of caffeine are discussed at two steps of the data treatment.

  10. Evaluation of the geomorphometric results and residual values of a robust plane fitting method applied to different DTMs of various scales and accuracy

    NASA Astrophysics Data System (ADS)

    Koma, Zsófia; Székely, Balázs; Dorninger, Peter; Kovács, Gábor

    2013-04-01

    Due to the need for quantitative analysis of various geomorphological landforms, the importance of fast and effective automatic processing of the different kind of digital terrain models (DTMs) is increasing. The robust plane fitting (segmentation) method, developed at the Institute of Photogrammetry and Remote Sensing at Vienna University of Technology, allows the processing of large 3D point clouds (containing millions of points), performs automatic detection of the planar elements of the surface via parameter estimation, and provides a considerable data reduction for the modeled area. Its geoscientific application allows the modeling of different landforms with the fitted planes as planar facets. In our study we aim to analyze the accuracy of the resulting set of fitted planes in terms of accuracy, model reliability and dependence on the input parameters. To this end we used DTMs of different scales and accuracy: (1) artificially generated 3D point cloud model with different magnitudes of error; (2) LiDAR data with 0.1 m error; (3) SRTM (Shuttle Radar Topography Mission) DTM database with 5 m accuracy; (4) DTM data from HRSC (High Resolution Stereo Camera) of the planet Mars with 10 m error. The analysis of the simulated 3D point cloud with normally distributed errors comprised different kinds of statistical tests (for example Chi-square and Kolmogorov-Smirnov tests) applied on the residual values and evaluation of dependence of the residual values on the input parameters. These tests have been repeated on the real data supplemented with the categorization of the segmentation result depending on the input parameters, model reliability and the geomorphological meaning of the fitted planes. The simulation results show that for the artificially generated data with normally distributed errors the null hypothesis can be accepted based on the residual value distribution being also normal, but in case of the test on the real data the residual value distribution is

  11. Fast-tracking determination of homozygous transgenic lines and transgene stacking using a reliable quantitative real-time PCR assay.

    PubMed

    Wang, Xianghong; Jiang, Daiming; Yang, Daichang

    2015-01-01

    The selection of homozygous lines is a crucial step in the characterization of newly generated transgenic plants. This is particularly time- and labor-consuming when transgenic stacking is required. Here, we report a fast and accurate method based on quantitative real-time PCR with a rice gene RBE4 as a reference gene for selection of homozygous lines when using multiple transgenic stacking in rice. Use of this method allowed can be used to determine the stacking of up to three transgenes within four generations. Selection accuracy reached 100 % for a single locus and 92.3 % for two loci. This method confers distinct advantages over current transgenic research methodologies, as it is more accurate, rapid, and reliable. Therefore, this protocol could be used to efficiently select homozygous plants and to expedite time- and labor-consuming processes normally required for multiple transgene stacking. This protocol was standardized for determination of multiple gene stacking in molecular breeding via marker-assisted selection.

  12. Quantitative Appearance Inspection for Film Coated Tablets.

    PubMed

    Yoshino, Hiroyuki; Yamashita, Kazunari; Iwao, Yasunori; Noguchi, Shuji; Itai, Shigeru

    2016-01-01

    The decision criteria for the physical appearance of pharmaceutical products are subjective and qualitative means of evaluation that are based entirely on human interpretation. In this study, we have developed a comprehensive method for the quantitative analysis of the physical appearance of film coated tablets. Three different kinds of film coated tablets with considerable differences in their physical appearances were manufactured as models, and their surface roughness, contact angle, color measurements and physicochemical properties were investigated as potential characteristics for the quantitative analysis of their physical appearance. All of these characteristics were useful for the quantitative evaluation of the physical appearances of the tablets, and could potentially be used to establish decision criteria to assess the quality of tablets. In particular, the analysis of the surface roughness and film coating properties of the tablets by terahertz spectroscopy allowed for an effective evaluation of the tablets' properties. These results indicated the possibility of inspecting the appearance of tablets during the film coating process.

  13. A Quantitative Methodology to Examine the Development of Moral Judgment

    ERIC Educational Resources Information Center

    Buchanan, James P.; Thompson, Spencer K.

    1973-01-01

    Unlike Piaget's clinical procedure, the experiment's methodology allowed substantiation of the ability of children to simultaneously weigh damage and intent information when making a moral judgment. Other advantages of this quantitative methodology are also presented. (Authors)

  14. SDAR 1.0 a New Quantitative Toolkit for Analyze Stratigraphic Data

    NASA Astrophysics Data System (ADS)

    Ortiz, John; Moreno, Carlos; Cardenas, Andres; Jaramillo, Carlos

    2015-04-01

    Since the foundation of stratigraphy geoscientists have recognized that data obtained from stratigraphic columns (SC), two dimensional schemes recording descriptions of both geological and paleontological features (e.g., thickness of rock packages, grain size, fossil and lithological components, and sedimentary structures), are key elements for establishing reliable hypotheses about the distribution in space and time of rock sequences, and ancient sedimentary environmental and paleobiological dynamics. Despite the tremendous advances on the way geoscientists store, plot, and quantitatively analyze sedimentological and paleontological data (e.g., Macrostrat [http://www.macrostrat.org/], Paleobiology Database [http://www.paleodb.org/], respectively), there is still a lack of computational methodologies designed to quantitatively examine data from a highly detailed SCs. Moreover, frequently the stratigraphic information is plotted "manually" using vector graphics editors (e.g., Corel Draw, Illustrator), however, this information although store on a digital format, cannot be used readily for any quantitative analysis. Therefore, any attempt to examine the stratigraphic data in an analytical fashion necessarily takes further steps. Given these issues, we have developed the sofware 'Stratigraphic Data Analysis in R' (SDAR), which stores in a database all sedimentological, stratigraphic, and paleontological information collected from a SC, allowing users to generate high-quality graphic plots (including one or multiple features stored in the database). SDAR also encompasses quantitative analyses helping users to quantify stratigraphic information (e.g. grain size, sorting and rounding, proportion of sand/shale). Finally, given that the SDAR analysis module, has been written in the open-source high-level computer language "R graphics/statistics language" [R Development Core Team, 2014], it is already loaded with many of the crucial features required to accomplish basic and

  15. Improving the accuracy of k-nearest neighbor using local mean based and distance weight

    NASA Astrophysics Data System (ADS)

    Syaliman, K. U.; Nababan, E. B.; Sitompul, O. S.

    2018-03-01

    In k-nearest neighbor (kNN), the determination of classes for new data is normally performed by a simple majority vote system, which may ignore the similarities among data, as well as allowing the occurrence of a double majority class that can lead to misclassification. In this research, we propose an approach to resolve the majority vote issues by calculating the distance weight using a combination of local mean based k-nearest neighbor (LMKNN) and distance weight k-nearest neighbor (DWKNN). The accuracy of results is compared to the accuracy acquired from the original k-NN method using several datasets from the UCI Machine Learning repository, Kaggle and Keel, such as ionosphare, iris, voice genre, lower back pain, and thyroid. In addition, the proposed method is also tested using real data from a public senior high school in city of Tualang, Indonesia. Results shows that the combination of LMKNN and DWKNN was able to increase the classification accuracy of kNN, whereby the average accuracy on test data is 2.45% with the highest increase in accuracy of 3.71% occurring on the lower back pain symptoms dataset. For the real data, the increase in accuracy is obtained as high as 5.16%.

  16. Methods for the computation of detailed geoids and their accuracy

    NASA Technical Reports Server (NTRS)

    Rapp, R. H.; Rummel, R.

    1975-01-01

    Two methods for the computation of geoid undulations using potential coefficients and 1 deg x 1 deg terrestrial anomaly data are examined. It was found that both methods give the same final result but that one method allows a more simplified error analysis. Specific equations were considered for the effect of the mass of the atmosphere and a cap dependent zero-order undulation term was derived. Although a correction to a gravity anomaly for the effect of the atmosphere is only about -0.87 mgal, this correction causes a fairly large undulation correction that was not considered previously. The accuracy of a geoid undulation computed by these techniques was estimated considering anomaly data errors, potential coefficient errors, and truncation (only a finite set of potential coefficients being used) errors. It was found that an optimum cap size of 20 deg should be used. The geoid and its accuracy were computed in the Geos 3 calibration area using the GEM 6 potential coefficients and 1 deg x 1 deg terrestrial anomaly data. The accuracy of the computed geoid is on the order of plus or minus 2 m with respect to an unknown set of best earth parameter constants.

  17. Comparison of qualitative and quantitative evaluation of diffusion-weighted MRI and chemical-shift imaging in the differentiation of benign and malignant vertebral body fractures.

    PubMed

    Geith, Tobias; Schmidt, Gerwin; Biffar, Andreas; Dietrich, Olaf; Dürr, Hans Roland; Reiser, Maximilian; Baur-Melnyk, Andrea

    2012-11-01

    The objective of our study was to compare the diagnostic value of qualitative diffusion-weighted imaging (DWI), quantitative DWI, and chemical-shift imaging in a single prospective cohort of patients with acute osteoporotic and malignant vertebral fractures. The study group was composed of patients with 26 osteoporotic vertebral fractures (18 women, eight men; mean age, 69 years; age range, 31 years 6 months to 86 years 2 months) and 20 malignant vertebral fractures (nine women, 11 men; mean age, 63.4 years; age range, 24 years 8 months to 86 years 4 months). T1-weighted, STIR, and T2-weighted sequences were acquired at 1.5 T. A DW reverse fast imaging with steady-state free precession (PSIF) sequence at different delta values was evaluated qualitatively. A DW echo-planar imaging (EPI) sequence and a DW single-shot turbo spin-echo (TSE) sequence at different b values were evaluated qualitatively and quantitatively using the apparent diffusion coefficient. Opposed-phase sequences were used to assess signal intensity qualitatively. The signal loss between in- and opposed-phase images was determined quantitatively. Two-tailed Fisher exact test, Mann-Whitney test, and receiver operating characteristic analysis were performed. Sensitivities, specificities, and accuracies were determined. Qualitative DW-PSIF imaging (delta = 3 ms) showed the best performance for distinguishing between benign and malignant fractures (sensitivity, 100%; specificity, 88.5%; accuracy, 93.5%). Qualitative DW-EPI (b = 50 s/mm(2) [p = 1.00]; b = 250 s/mm(2) [p = 0.50]) and DW single-shot TSE imaging (b = 100 s/mm(2) [p = 1.00]; b = 250 s/mm(2) [p = 0.18]; b = 400 s/mm(2) [p = 0.18]; b = 600 s/mm(2) [p = 0.39]) did not indicate significant differences between benign and malignant fractures. DW-EPI using a b value of 500 s/mm(2) (p = 0.01) indicated significant differences between benign and malignant vertebral fractures. Quantitative DW-EPI (p = 0.09) and qualitative opposed-phase imaging (p = 0

  18. Investigation of influence of errors of cutting machines with CNC on displacement trajectory accuracy of their actuating devices

    NASA Astrophysics Data System (ADS)

    Fedonin, O. N.; Petreshin, D. I.; Ageenko, A. V.

    2018-03-01

    In the article, the issue of increasing a CNC lathe accuracy by compensating for the static and dynamic errors of the machine is investigated. An algorithm and a diagnostic system for a CNC machine tool are considered, which allows determining the errors of the machine for their compensation. The results of experimental studies on diagnosing and improving the accuracy of a CNC lathe are presented.

  19. Quantitative Secondary Electron Detector (QSED)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nayak, Subu; Joy, David C.

    2013-12-31

    Research is proposed to investigate the feasibility of applying recent advances in semiconductor technology to fabricate direct digital Quantitative Secondary Electron Detectors (QSED) for scanning electron microscopes (SEMs). If successful, commercial versions of the QSED would transform the SEM into a quantitative, metrological system with enhanced capabilities that, in turn, would broaden research horizons across industries. This project will be conducted in collaboration with Dr. David C Joy at the University of Tennessee, who has demonstrated limited (to the 1keV range) digital collection of the energy from backscattered signals in a SEM using a modified silicon drift detector. Several detectormore » configurations will be fabricated and tested for sensitivities, background noise reduction, DC offset elimination, and metrological capabilities (linearity, accuracy, etc.) against a set of commercially important performance criteria to ascertain concept feasibility. Once feasibility is proven, the solid state digital device array and its switching frequency will be scaled-up, in Phase II, to improve temporal resolution. If successful, this work will produce a crucial advancement in electron microscopy with wide-ranging applications. The following are key advantages anticipated from direct digital QSED: 1. High signal-to-noise ratio will improve SEM resolution in nano-scale, which is critical for dimensional metrology in any application. 2. Quantitative measurement will enhance process control and design validation in semiconductors, photo-voltaics, bio-medical devices and catalysts; and will improve accuracy in predicting the reliability and the lifecycle of materials across industries. 3. Video and dynamic-imaging capabilities will advance study in nano-scale phenomena in a variety of industries, including pharmaceutical and semiconductor materials. 4. Lower cost will make high-performing electron microscopes affordable to more researchers. 5. Compact size and

  20. Accuracy of CNV Detection from GWAS Data.

    PubMed

    Zhang, Dandan; Qian, Yudong; Akula, Nirmala; Alliey-Rodriguez, Ney; Tang, Jinsong; Gershon, Elliot S; Liu, Chunyu

    2011-01-13

    Several computer programs are available for detecting copy number variants (CNVs) using genome-wide SNP arrays. We evaluated the performance of four CNV detection software suites--Birdsuite, Partek, HelixTree, and PennCNV-Affy--in the identification of both rare and common CNVs. Each program's performance was assessed in two ways. The first was its recovery rate, i.e., its ability to call 893 CNVs previously identified in eight HapMap samples by paired-end sequencing of whole-genome fosmid clones, and 51,440 CNVs identified by array Comparative Genome Hybridization (aCGH) followed by validation procedures, in 90 HapMap CEU samples. The second evaluation was program performance calling rare and common CNVs in the Bipolar Genome Study (BiGS) data set (1001 bipolar cases and 1033 controls, all of European ancestry) as measured by the Affymetrix SNP 6.0 array. Accuracy in calling rare CNVs was assessed by positive predictive value, based on the proportion of rare CNVs validated by quantitative real-time PCR (qPCR), while accuracy in calling common CNVs was assessed by false positive/false negative rates based on qPCR validation results from a subset of common CNVs. Birdsuite recovered the highest percentages of known HapMap CNVs containing >20 markers in two reference CNV datasets. The recovery rate increased with decreased CNV frequency. In the tested rare CNV data, Birdsuite and Partek had higher positive predictive values than the other software suites. In a test of three common CNVs in the BiGS dataset, Birdsuite's call was 98.8% consistent with qPCR quantification in one CNV region, but the other two regions showed an unacceptable degree of accuracy. We found relatively poor consistency between the two "gold standards," the sequence data of Kidd et al., and aCGH data of Conrad et al. Algorithms for calling CNVs especially common ones need substantial improvement, and a "gold standard" for detection of CNVs remains to be established.

  1. TH-AB-209-09: Quantitative Imaging of Electrical Conductivity by VHF-Induced Thermoacoustics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Patch, S; Hull, D; See, W

    Purpose: To demonstrate that very high frequency (VHF) induced thermoacoustics has the potential to provide quantitative images of electrical conductivity in Siemens/meter, much as shear wave elastography provides tissue stiffness in kPa. Quantitatively imaging a large organ requires exciting thermoacoustic pulses throughout the volume and broadband detection of those pulses because tomographic image reconstruction preserves frequency content. Applying the half-wavelength limit to a 200-micron inclusion inside a 7.5 cm diameter organ requires measurement sensitivity to frequencies ranging from 4 MHz down to 10 kHz, respectively. VHF irradiation provides superior depth penetration over near infrared used in photoacoustics. Additionally, VHF signalmore » production is proportional to electrical conductivity, and prostate cancer is known to suppress electrical conductivity of prostatic fluid. Methods: A dual-transducer system utilizing a P4-1 array connected to a Verasonics V1 system augmented by a lower frequency focused single element transducer was developed. Simultaneous acquisition of VHF-induced thermoacoustic pulses by both transducers enabled comparison of transducer performance. Data from the clinical array generated a stack of 96-images with separation of 0.3 mm, whereas the single element transducer imaged only in a single plane. In-plane resolution and quantitative accuracy were measured at isocenter. Results: The array provided volumetric imaging capability with superior resolution whereas the single element transducer provided superior quantitative accuracy. Combining axial images from both transducers preserved resolution of the P4-1 array and improved image contrast. Neither transducer was sensitive to frequencies below 50 kHz, resulting in a DC offset and low-frequency shading over fields of view exceeding 15 mm. Fresh human prostates were imaged ex vivo and volumetric reconstructions reveal structures rarely seen in diagnostic images. Conclusion

  2. Accuracy of Liver Fat Quantification With Advanced CT, MRI, and Ultrasound Techniques: Prospective Comparison With MR Spectroscopy.

    PubMed

    Kramer, Harald; Pickhardt, Perry J; Kliewer, Mark A; Hernando, Diego; Chen, Guang-Hong; Zagzebski, James A; Reeder, Scott B

    2017-01-01

    The purpose of this study was to prospectively evaluate the accuracy of proton-density fat-fraction, single- and dual-energy CT (SECT and DECT), gray-scale ultrasound (US), and US shear-wave elastography (US-SWE) in the quantification of hepatic steatosis with MR spectroscopy (MRS) as the reference standard. Fifty adults who did not have symptoms (23 men, 27 women; mean age, 57 ± 5 years; body mass index, 27 ± 5) underwent liver imaging with un-enhanced SECT, DECT, gray-scale US, US-SWE, proton-density fat-fraction MRI, and MRS for this prospective trial. MRS voxels for the reference standard were colocalized with all other modalities under investigation. For SECT (120 kVp), attenuation values were recorded. For rapid-switching DECT (80/140 kVp), monochromatic images (70-140 keV) and fat density-derived material decomposition images were reconstructed. For proton-density fat fraction MRI, a quantitative chemical shift-encoded method was used. For US, echogenicity was evaluated on a qualitative 0-3 scale. Quantitative US shear-wave velocities were also recorded. Data were analyzed by linear regression for each technique compared with MRS. There was excellent correlation between MRS and both proton-density fat-fraction MRI (r 2 = 0.992; slope, 0.974; intercept, -0.943) and SECT (r 2 = 0.856; slope, -0.559; intercept, 35.418). DECT fat attenuation had moderate correlation with MRS measurements (r 2 = 0.423; slope, 0.034; intercept, 8.459). There was good correlation between qualitative US echogenicity and MRS measurements with a weighted kappa value of 0.82. US-SWE velocity did not have reliable correlation with MRS measurements (r 2 = 0.004; slope, 0.069; intercept, 6.168). Quantitative MRI proton-density fat fraction and SECT fat attenuation have excellent linear correlation with MRS measurements and can serve as accurate noninvasive biomarkers for quantifying steatosis. Material decomposition with DECT does not improve the accuracy of fat quantification over

  3. Accuracy of Blood Loss Measurement during Cesarean Delivery.

    PubMed

    Doctorvaladan, Sahar V; Jelks, Andrea T; Hsieh, Eric W; Thurer, Robert L; Zakowski, Mark I; Lagrew, David C

    2017-04-01

    Objective  This study aims to compare the accuracy of visual, quantitative gravimetric, and colorimetric methods used to determine blood loss during cesarean delivery procedures employing a hemoglobin extraction assay as the reference standard. Study Design  In 50 patients having cesarean deliveries blood loss determined by assays of hemoglobin content on surgical sponges and in suction canisters was compared with obstetricians' visual estimates, a quantitative gravimetric method, and the blood loss determined by a novel colorimetric system. Agreement between the reference assay and other measures was evaluated by the Bland-Altman method. Results  Compared with the blood loss measured by the reference assay (470 ± 296 mL), the colorimetric system (572 ± 334 mL) was more accurate than either visual estimation (928 ± 261 mL) or gravimetric measurement (822 ± 489 mL). The correlation between the assay method and the colorimetric system was more predictive (standardized coefficient = 0.951, adjusted R 2  = 0.902) than either visual estimation (standardized coefficient = 0.700, adjusted R 2  = 00.479) or the gravimetric determination (standardized coefficient = 0.564, adjusted R 2  = 0.304). Conclusion  During cesarean delivery, measuring blood loss using colorimetric image analysis is superior to visual estimation and a gravimetric method. Implementation of colorimetric analysis may enhance the ability of management protocols to improve clinical outcomes.

  4. Accuracy of Blood Loss Measurement during Cesarean Delivery

    PubMed Central

    Doctorvaladan, Sahar V.; Jelks, Andrea T.; Hsieh, Eric W.; Thurer, Robert L.; Zakowski, Mark I.; Lagrew, David C.

    2017-01-01

    Objective This study aims to compare the accuracy of visual, quantitative gravimetric, and colorimetric methods used to determine blood loss during cesarean delivery procedures employing a hemoglobin extraction assay as the reference standard. Study Design In 50 patients having cesarean deliveries blood loss determined by assays of hemoglobin content on surgical sponges and in suction canisters was compared with obstetricians' visual estimates, a quantitative gravimetric method, and the blood loss determined by a novel colorimetric system. Agreement between the reference assay and other measures was evaluated by the Bland–Altman method. Results Compared with the blood loss measured by the reference assay (470 ± 296 mL), the colorimetric system (572 ± 334 mL) was more accurate than either visual estimation (928 ± 261 mL) or gravimetric measurement (822 ± 489 mL). The correlation between the assay method and the colorimetric system was more predictive (standardized coefficient = 0.951, adjusted R2 = 0.902) than either visual estimation (standardized coefficient = 0.700, adjusted R2 = 00.479) or the gravimetric determination (standardized coefficient = 0.564, adjusted R2 = 0.304). Conclusion During cesarean delivery, measuring blood loss using colorimetric image analysis is superior to visual estimation and a gravimetric method. Implementation of colorimetric analysis may enhance the ability of management protocols to improve clinical outcomes. PMID:28497007

  5. [The accuracy of rapid equilibrium assumption in steady-state enzyme kinetics is the function of equilibrium segment structure and properties].

    PubMed

    Vrzheshch, P V

    2015-01-01

    Quantitative evaluation of the accuracy of the rapid equilibrium assumption in the steady-state enzyme kinetics was obtained for an arbitrary mechanism of an enzyme-catalyzed reaction. This evaluation depends only on the structure and properties of the equilibrium segment, but doesn't depend on the structure and properties of the rest (stationary part) of the kinetic scheme. The smaller the values of the edges leaving equilibrium segment in relation to values of the edges within the equilibrium segment, the higher the accuracy of determination of intermediate concentrations and reaction velocity in a case of the rapid equilibrium assumption.

  6. Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.

    PubMed

    Tu, Chengjian; Li, Jun; Sheng, Quanhu; Zhang, Ming; Qu, Jun

    2014-04-04

    Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.

  7. Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data

    PubMed Central

    2015-01-01

    Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R2 > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery. PMID:24635752

  8. Optical Ptychographic Microscope for Quantitative Bio-Mechanical Imaging

    NASA Astrophysics Data System (ADS)

    Anthony, Nicholas; Cadenazzi, Guido; Nugent, Keith; Abbey, Brian

    The role that mechanical forces play in biological processes such as cell movement and death is becoming of significant interest to further develop our understanding of the inner workings of cells. The most common method used to obtain stress information is photoelasticity which maps a samples birefringence, or its direction dependent refractive indices, using polarized light. However this method only provides qualitative data and for stress information to be useful quantitative data is required. Ptychography is a method for quantitatively determining the phase of a samples complex transmission function. The technique relies upon the collection of multiple overlapping coherent diffraction patterns from laterally displaced points on the sample. The overlap of measurement points provides complementary information that significantly aids in the reconstruction of the complex wavefield exiting the sample and allows for quantitative imaging of weakly interacting specimens. Here we describe recent advances at La Trobe University Melbourne on achieving quantitative birefringence mapping using polarized light ptychography with applications in cell mechanics. Australian Synchrotron, ARC Centre of Excellence for Advanced Molecular Imaging.

  9. Accuracy assessment: The statistical approach to performance evaluation in LACIE. [Great Plains corridor, United States

    NASA Technical Reports Server (NTRS)

    Houston, A. G.; Feiveson, A. H.; Chhikara, R. S.; Hsu, E. M. (Principal Investigator)

    1979-01-01

    A statistical methodology was developed to check the accuracy of the products of the experimental operations throughout crop growth and to determine whether the procedures are adequate to accomplish the desired accuracy and reliability goals. It has allowed the identification and isolation of key problems in wheat area yield estimation, some of which have been corrected and some of which remain to be resolved. The major unresolved problem in accuracy assessment is that of precisely estimating the bias of the LACIE production estimator. Topics covered include: (1) evaluation techniques; (2) variance and bias estimation for the wheat production estimate; (3) the 90/90 evaluation; (4) comparison of the LACIE estimate with reference standards; and (5) first and second order error source investigations.

  10. Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity

    PubMed Central

    Zhu, Jin; Heinecke, Dominic; Mulla, Wahid A.; Bradford, William D.; Rubinstein, Boris; Box, Andrew; Haug, Jeffrey S.; Li, Rong

    2015-01-01

    Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein−based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation. PMID:25823586

  11. Methodology to Define Delivery Accuracy Under Current Day ATC Operations

    NASA Technical Reports Server (NTRS)

    Sharma, Shivanjli; Robinson, John E., III

    2015-01-01

    In order to enable arrival management concepts and solutions in a NextGen environment, ground- based sequencing and scheduling functions have been developed to support metering operations in the National Airspace System. These sequencing and scheduling algorithms as well as tools are designed to aid air traffic controllers in developing an overall arrival strategy. The ground systems being developed will support the management of aircraft to their Scheduled Times of Arrival (STAs) at flow-constrained meter points. This paper presents a methodology for determining the undelayed delivery accuracy for current day air traffic control operations. This new method analyzes the undelayed delivery accuracy at meter points in order to understand changes of desired flow rates as well as enabling definition of metrics that will allow near-future ground automation tools to successfully achieve desired separation at the meter points. This enables aircraft to meet their STAs while performing high precision arrivals. The research presents a possible implementation that would allow delivery performance of current tools to be estimated and delivery accuracy requirements for future tools to be defined, which allows analysis of Estimated Time of Arrival (ETA) accuracy for Time-Based Flow Management (TBFM) and the FAA's Traffic Management Advisor (TMA). TMA is a deployed system that generates scheduled time-of-arrival constraints for en- route air traffic controllers in the US. This new method of automated analysis provides a repeatable evaluation of the delay metrics for current day traffic, new releases of TMA, implementation of different tools, and across different airspace environments. This method utilizes a wide set of data from the Operational TMA-TBFM Repository (OTTR) system, which processes raw data collected by the FAA from operational TMA systems at all ARTCCs in the nation. The OTTR system generates daily reports concerning ATC status, intent and actions. Due to its

  12. Qualis-SIS: automated standard curve generation and quality assessment for multiplexed targeted quantitative proteomic experiments with labeled standards.

    PubMed

    Mohammed, Yassene; Percy, Andrew J; Chambers, Andrew G; Borchers, Christoph H

    2015-02-06

    Multiplexed targeted quantitative proteomics typically utilizes multiple reaction monitoring and allows the optimized quantification of a large number of proteins. One challenge, however, is the large amount of data that needs to be reviewed, analyzed, and interpreted. Different vendors provide software for their instruments, which determine the recorded responses of the heavy and endogenous peptides and perform the response-curve integration. Bringing multiplexed data together and generating standard curves is often an off-line step accomplished, for example, with spreadsheet software. This can be laborious, as it requires determining the concentration levels that meet the required accuracy and precision criteria in an iterative process. We present here a computer program, Qualis-SIS, that generates standard curves from multiplexed MRM experiments and determines analyte concentrations in biological samples. Multiple level-removal algorithms and acceptance criteria for concentration levels are implemented. When used to apply the standard curve to new samples, the software flags each measurement according to its quality. From the user's perspective, the data processing is instantaneous due to the reactivity paradigm used, and the user can download the results of the stepwise calculations for further processing, if necessary. This allows for more consistent data analysis and can dramatically accelerate the downstream data analysis.

  13. Comparative study of quantitative phase imaging techniques for refractometry of optical fibers

    NASA Astrophysics Data System (ADS)

    de Dorlodot, Bertrand; Bélanger, Erik; Bérubé, Jean-Philippe; Vallée, Réal; Marquet, Pierre

    2018-02-01

    The refractive index difference profile of optical fibers is the key design parameter because it determines, among other properties, the insertion losses and propagating modes. Therefore, an accurate refractive index profiling method is of paramount importance to their development and optimization. Quantitative phase imaging (QPI) is one of the available tools to retrieve structural characteristics of optical fibers, including the refractive index difference profile. Having the advantage of being non-destructive, several different QPI methods have been developed over the last decades. Here, we present a comparative study of three different available QPI techniques, namely the transport-of-intensity equation, quadriwave lateral shearing interferometry and digital holographic microscopy. To assess the accuracy and precision of those QPI techniques, quantitative phase images of the core of a well-characterized optical fiber have been retrieved for each of them and a robust image processing procedure has been applied in order to retrieve their refractive index difference profiles. As a result, even if the raw images for all the three QPI methods were suffering from different shortcomings, our robust automated image-processing pipeline successfully corrected these. After this treatment, all three QPI techniques yielded accurate, reliable and mutually consistent refractive index difference profiles in agreement with the accuracy and precision of the refracted near-field benchmark measurement.

  14. Measuring the effect of spray plume angle on the accuracy of droplet size data

    USDA-ARS?s Scientific Manuscript database

    Analysis of droplet size data using laser diffraction allows for quick and easy assessment of droplet size for agricultural spray nozzles and pesticides; however, operation and setup of the instrument and test system can potentially influence the accuracy of the data. One of the factors is the orie...

  15. A Microfluidic Platform for High-Throughput Multiplexed Protein Quantitation

    PubMed Central

    Volpetti, Francesca; Garcia-Cordero, Jose; Maerkl, Sebastian J.

    2015-01-01

    We present a high-throughput microfluidic platform capable of quantitating up to 384 biomarkers in 4 distinct samples by immunoassay. The microfluidic device contains 384 unit cells, which can be individually programmed with pairs of capture and detection antibody. Samples are quantitated in each unit cell by four independent MITOMI detection areas, allowing four samples to be analyzed in parallel for a total of 1,536 assays per device. We show that the device can be pre-assembled and stored for weeks at elevated temperature and we performed proof-of-concept experiments simultaneously quantitating IL-6, IL-1β, TNF-α, PSA, and GFP. Finally, we show that the platform can be used to identify functional antibody combinations by screening 64 antibody combinations requiring up to 384 unique assays per device. PMID:25680117

  16. Meta-Analyses of Diagnostic Accuracy in Imaging Journals: Analysis of Pooling Techniques and Their Effect on Summary Estimates of Diagnostic Accuracy.

    PubMed

    McGrath, Trevor A; McInnes, Matthew D F; Korevaar, Daniël A; Bossuyt, Patrick M M

    2016-10-01

    Purpose To determine whether authors of systematic reviews of diagnostic accuracy studies published in imaging journals used recommended methods for meta-analysis, and to evaluate the effect of traditional methods on summary estimates of sensitivity and specificity. Materials and Methods Medline was searched for published systematic reviews that included meta-analysis of test accuracy data limited to imaging journals published from January 2005 to May 2015. Two reviewers independently extracted study data and classified methods for meta-analysis as traditional (univariate fixed- or random-effects pooling or summary receiver operating characteristic curve) or recommended (bivariate model or hierarchic summary receiver operating characteristic curve). Use of methods was analyzed for variation with time, geographical location, subspecialty, and journal. Results from reviews in which study authors used traditional univariate pooling methods were recalculated with a bivariate model. Results Three hundred reviews met the inclusion criteria, and in 118 (39%) of those, authors used recommended meta-analysis methods. No change in the method used was observed with time (r = 0.54, P = .09); however, there was geographic (χ(2) = 15.7, P = .001), subspecialty (χ(2) = 46.7, P < .001), and journal (χ(2) = 27.6, P < .001) heterogeneity. Fifty-one univariate random-effects meta-analyses were reanalyzed with the bivariate model; the average change in the summary estimate was -1.4% (P < .001) for sensitivity and -2.5% (P < .001) for specificity. The average change in width of the confidence interval was 7.7% (P < .001) for sensitivity and 9.9% (P ≤ .001) for specificity. Conclusion Recommended methods for meta-analysis of diagnostic accuracy in imaging journals are used in a minority of reviews; this has not changed significantly with time. Traditional (univariate) methods allow overestimation of diagnostic accuracy and provide narrower confidence intervals than do recommended

  17. UAV, LiDAR & ground-based surveying from Stackpole Quay: best practice for accuracy of virtual outcrops and structural models

    NASA Astrophysics Data System (ADS)

    Cawood, A.; Bond, C. E.; Howell, J.; Totake, Y.

    2016-12-01

    Virtual outcrops derived from techniques such as LiDAR and SfM (digital photogrammetry) provide a viable and potentially powerful addition or alternative to traditional field studies, given the large amounts of raw data that can be acquired rapidly and safely. The use of these digital representations of outcrops as a source of geological data has increased greatly in the past decade, and as such, the accuracy and precision of these new acquisition methods applied to geological problems has been addressed by a number of authors. Little work has been done, however, on the integration of virtual outcrops into fundamental structural geology workflows and to systematically studying the fidelity of the data derived from them. Here, we use the classic Stackpole Quay syncline outcrop in South Wales to quantitatively evaluate the accuracy of three virtual outcrop models (LiDAR, aerial and terrestrial digital photogrammetry) compared to data collected directly in the field. Using these structural data, we have built 2D and 3D geological models which make predictions of fold geometries. We examine the fidelity of virtual outcrops generated using different acquisition techniques to outcrop geology and how these affect model building and final outcomes. Finally, we utilize newly acquired data to deterministically test model validity. Based upon these results, we find that acquisition of digital imagery by UAS (Unmanned Autonomous Vehicle) yields highly accurate virtual outcrops when compared to terrestrial methods, allowing the construction of robust data-driven predictive models. Careful planning, survey design and choice of suitable acquisition method are, however, of key importance for best results.

  18. Quantitative risk assessment system (QRAS)

    NASA Technical Reports Server (NTRS)

    Tan, Zhibin (Inventor); Mosleh, Ali (Inventor); Weinstock, Robert M (Inventor); Smidts, Carol S (Inventor); Chang, Yung-Hsien (Inventor); Groen, Francisco J (Inventor); Swaminathan, Sankaran (Inventor)

    2001-01-01

    A quantitative risk assessment system (QRAS) builds a risk model of a system for which risk of failure is being assessed, then analyzes the risk of the system corresponding to the risk model. The QRAS performs sensitivity analysis of the risk model by altering fundamental components and quantifications built into the risk model, then re-analyzes the risk of the system using the modifications. More particularly, the risk model is built by building a hierarchy, creating a mission timeline, quantifying failure modes, and building/editing event sequence diagrams. Multiplicities, dependencies, and redundancies of the system are included in the risk model. For analysis runs, a fixed baseline is first constructed and stored. This baseline contains the lowest level scenarios, preserved in event tree structure. The analysis runs, at any level of the hierarchy and below, access this baseline for risk quantitative computation as well as ranking of particular risks. A standalone Tool Box capability exists, allowing the user to store application programs within QRAS.

  19. Clumsiness in fine motor tasks: evidence from the quantitative drawing evaluation of children with Down Syndrome.

    PubMed

    Vimercati, S L; Galli, M; Stella, G; Caiazzo, G; Ancillao, A; Albertini, G

    2015-03-01

    Drawing tests are commonly used for the clinical evaluation of cognitive capabilities in children with learning disabilities. We analysed quantitatively the drawings of children with Down Syndrome (DS) and of healthy, mental age-matched controls to characterise the features of fine motor skills in DS during a drawing task, with particular attention to clumsiness, a well-known feature of DS gross movements. Twenty-three children with DS and 13 controls hand-copied the figures of a circle, a cross and a square on a sheet. An optoelectronic system allowed the acquisition of the three-dimensional track of the drawing. The participants' posture and upper limb movements were analysed as well. Results showed that the participants with DS tended to draw faster but with less accuracy than controls. While clumsiness in gross movements manifests mainly as slow, less efficient movements, it manifests as high velocity and inaccurate movements in fine motor tasks such as drawing. © 2014 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

  20. High-Content Screening for Quantitative Cell Biology.

    PubMed

    Mattiazzi Usaj, Mojca; Styles, Erin B; Verster, Adrian J; Friesen, Helena; Boone, Charles; Andrews, Brenda J

    2016-08-01

    High-content screening (HCS), which combines automated fluorescence microscopy with quantitative image analysis, allows the acquisition of unbiased multiparametric data at the single cell level. This approach has been used to address diverse biological questions and identify a plethora of quantitative phenotypes of varying complexity in numerous different model systems. Here, we describe some recent applications of HCS, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions. We review the steps involved in the design of useful biological assays and automated image analysis, and describe major challenges associated with each. Additionally, we highlight emerging technologies and future challenges, and discuss how the field of HCS might be enhanced in the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Optimization of homonuclear 2D NMR for fast quantitative analysis: application to tropine-nortropine mixtures.

    PubMed

    Giraudeau, Patrick; Guignard, Nadia; Hillion, Emilie; Baguet, Evelyne; Akoka, Serge

    2007-03-12

    Quantitative analysis by (1)H NMR is often hampered by heavily overlapping signals that may occur for complex mixtures, especially those containing similar compounds. Bidimensional homonuclear NMR spectroscopy can overcome this difficulty. A thorough review of acquisition and post-processing parameters was carried out to obtain accurate and precise, quantitative 2D J-resolved and DQF-COSY spectra in a much reduced time, thus limiting the spectrometer instabilities in the course of time. The number of t(1) increments was reduced as much as possible, and standard deviation was improved by optimization of spectral width, number of transients, phase cycling and apodization function. Localized polynomial baseline corrections were applied to the relevant chemical shift areas. Our method was applied to tropine-nortropine mixtures. Quantitative J-resolved spectra were obtained in less than 3 min and quantitative DQF-COSY spectra in 12 min, with an accuracy of 3% for J-spectroscopy and 2% for DQF-COSY, and a standard deviation smaller than 1%.

  2. Evaluation of MRI sequences for quantitative T1 brain mapping

    NASA Astrophysics Data System (ADS)

    Tsialios, P.; Thrippleton, M.; Glatz, A.; Pernet, C.

    2017-11-01

    T1 mapping constitutes a quantitative MRI technique finding significant application in brain imaging. It allows evaluation of contrast uptake, blood perfusion, volume, providing a more specific biomarker of disease progression compared to conventional T1-weighted images. While there are many techniques for T1-mapping there is a wide range of reported T1-values in tissues, raising the issue of protocols reproducibility and standardization. The gold standard for obtaining T1-maps is based on acquiring IR-SE sequence. Widely used alternative sequences are IR-SE-EPI, VFA (DESPOT), DESPOT-HIFI and MP2RAGE that speed up scanning and fitting procedures. A custom MRI phantom was used to assess the reproducibility and accuracy of the different methods. All scans were performed using a 3T Siemens Prisma scanner. The acquired data processed using two different codes. The main difference was observed for VFA (DESPOT) which grossly overestimated T1 relaxation time by 214 ms [126 270] compared to the IR-SE sequence. MP2RAGE and DESPOT-HIFI sequences gave slightly shorter time than IR-SE (~20 to 30ms) and can be considered as alternative and time-efficient methods for acquiring accurate T1 maps of the human brain, while IR-SE-EPI gave identical result, at a cost of a lower image quality.

  3. The Quantitative Relationship Between ISO 15197 Accuracy Criteria and Mean Absolute Relative Difference (MARD) in the Evaluation of Analytical Performance of Self-Monitoring of Blood Glucose (SMBG) Systems.

    PubMed

    Pardo, Scott; Simmons, David A

    2016-09-01

    The relationship between International Organization for Standardization (ISO) accuracy criteria and mean absolute relative difference (MARD), 2 methods for assessing the accuracy of blood glucose meters, is complex. While lower MARD values are generally better than higher MARD values, it is not possible to define a particular MARD value that ensures a blood glucose meter will satisfy the ISO accuracy criteria. The MARD value that ensures passing the ISO accuracy test can be described only as a probabilistic range. In this work, a Bayesian model is presented to represent the relationship between ISO accuracy criteria and MARD. Under the assumptions made in this work, there is nearly a 100% chance of satisfying ISO 15197:2013 accuracy requirements if the MARD value is between 3.25% and 5.25%. © 2016 Diabetes Technology Society.

  4. Quantitative mouse brain phenotyping based on single and multispectral MR protocols

    PubMed Central

    Badea, Alexandra; Gewalt, Sally; Avants, Brian B.; Cook, James J.; Johnson, G. Allan

    2013-01-01

    Sophisticated image analysis methods have been developed for the human brain, but such tools still need to be adapted and optimized for quantitative small animal imaging. We propose a framework for quantitative anatomical phenotyping in mouse models of neurological and psychiatric conditions. The framework encompasses an atlas space, image acquisition protocols, and software tools to register images into this space. We show that a suite of segmentation tools (Avants, Epstein et al., 2008) designed for human neuroimaging can be incorporated into a pipeline for segmenting mouse brain images acquired with multispectral magnetic resonance imaging (MR) protocols. We present a flexible approach for segmenting such hyperimages, optimizing registration, and identifying optimal combinations of image channels for particular structures. Brain imaging with T1, T2* and T2 contrasts yielded accuracy in the range of 83% for hippocampus and caudate putamen (Hc and CPu), but only 54% in white matter tracts, and 44% for the ventricles. The addition of diffusion tensor parameter images improved accuracy for large gray matter structures (by >5%), white matter (10%), and ventricles (15%). The use of Markov random field segmentation further improved overall accuracy in the C57BL/6 strain by 6%; so Dice coefficients for Hc and CPu reached 93%, for white matter 79%, for ventricles 68%, and for substantia nigra 80%. We demonstrate the segmentation pipeline for the widely used C57BL/6 strain, and two test strains (BXD29, APP/TTA). This approach appears promising for characterizing temporal changes in mouse models of human neurological and psychiatric conditions, and may provide anatomical constraints for other preclinical imaging, e.g. fMRI and molecular imaging. This is the first demonstration that multiple MR imaging modalities combined with multivariate segmentation methods lead to significant improvements in anatomical segmentation in the mouse brain. PMID:22836174

  5. An automated method for the evaluation of the pointing accuracy of Sun-tracking devices

    NASA Astrophysics Data System (ADS)

    Baumgartner, Dietmar J.; Pötzi, Werner; Freislich, Heinrich; Strutzmann, Heinz; Veronig, Astrid M.; Rieder, Harald E.

    2017-03-01

    The accuracy of solar radiation measurements, for direct (DIR) and diffuse (DIF) radiation, depends significantly on the precision of the operational Sun-tracking device. Thus, rigid targets for instrument performance and operation have been specified for international monitoring networks, e.g., the Baseline Surface Radiation Network (BSRN) operating under the auspices of the World Climate Research Program (WCRP). Sun-tracking devices that fulfill these accuracy requirements are available from various instrument manufacturers; however, none of the commercially available systems comprise an automatic accuracy control system allowing platform operators to independently validate the pointing accuracy of Sun-tracking sensors during operation. Here we present KSO-STREAMS (KSO-SunTRackEr Accuracy Monitoring System), a fully automated, system-independent, and cost-effective system for evaluating the pointing accuracy of Sun-tracking devices. We detail the monitoring system setup, its design and specifications, and the results from its application to the Sun-tracking system operated at the Kanzelhöhe Observatory (KSO) Austrian radiation monitoring network (ARAD) site. The results from an evaluation campaign from March to June 2015 show that the tracking accuracy of the device operated at KSO lies within BSRN specifications (i.e., 0.1° tracking accuracy) for the vast majority of observations (99.8 %). The evaluation of manufacturer-specified active-tracking accuracies (0.02°), during periods with direct solar radiation exceeding 300 W m-2, shows that these are satisfied in 72.9 % of observations. Tracking accuracies are highest during clear-sky conditions and on days where prevailing clear-sky conditions are interrupted by frontal movement; in these cases, we obtain the complete fulfillment of BSRN requirements and 76.4 % of observations within manufacturer-specified active-tracking accuracies. Limitations to tracking surveillance arise during overcast conditions and

  6. Chemical analysis and quantitation of the tapetum lucidum

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gee, N.A.; Fisher, G.L.; Nash, C.P.

    1975-06-01

    A study was conducted to provide a basis for the evaluation of the biochemical nature of the $sup 226$Ra alterations of the beagle tapetum. Results indicated that zinc and/or melanin determinations in the tapetum nigrum and tapetum lucidum may allow quantitation of tapetum lucidum tissue without the need for physical separation of the tapetal layers. (HLW)

  7. High-density marker imputation accuracy in sixteen French cattle breeds.

    PubMed

    Hozé, Chris; Fouilloux, Marie-Noëlle; Venot, Eric; Guillaume, François; Dassonneville, Romain; Fritz, Sébastien; Ducrocq, Vincent; Phocas, Florence; Boichard, Didier; Croiseau, Pascal

    2013-09-03

    Genotyping with the medium-density Bovine SNP50 BeadChip® (50K) is now standard in cattle. The high-density BovineHD BeadChip®, which contains 777,609 single nucleotide polymorphisms (SNPs), was developed in 2010. Increasing marker density increases the level of linkage disequilibrium between quantitative trait loci (QTL) and SNPs and the accuracy of QTL localization and genomic selection. However, re-genotyping all animals with the high-density chip is not economically feasible. An alternative strategy is to genotype part of the animals with the high-density chip and to impute high-density genotypes for animals already genotyped with the 50K chip. Thus, it is necessary to investigate the error rate when imputing from the 50K to the high-density chip. Five thousand one hundred and fifty three animals from 16 breeds (89 to 788 per breed) were genotyped with the high-density chip. Imputation error rates from the 50K to the high-density chip were computed for each breed with a validation set that included the 20% youngest animals. Marker genotypes were masked for animals in the validation population in order to mimic 50K genotypes. Imputation was carried out using the Beagle 3.3.0 software. Mean allele imputation error rates ranged from 0.31% to 2.41% depending on the breed. In total, 1980 SNPs had high imputation error rates in several breeds, which is probably due to genome assembly errors, and we recommend to discard these in future studies. Differences in imputation accuracy between breeds were related to the high-density-genotyped sample size and to the genetic relationship between reference and validation populations, whereas differences in effective population size and level of linkage disequilibrium showed limited effects. Accordingly, imputation accuracy was higher in breeds with large populations and in dairy breeds than in beef breeds. More than 99% of the alleles were correctly imputed if more than 300 animals were genotyped at high-density. No

  8. Effect of platform, reference material, and quantification model on enumeration of Enterococcus by quantitative PCR methods

    EPA Science Inventory

    Quantitative polymerase chain reaction (qPCR) is increasingly being used for the quantitative detection of fecal indicator bacteria in beach water. QPCR allows for same-day health warnings, and its application is being considered as an optionn for recreational water quality testi...

  9. Quantitative image fusion in infrared radiometry

    NASA Astrophysics Data System (ADS)

    Romm, Iliya; Cukurel, Beni

    2018-05-01

    Towards high-accuracy infrared radiance estimates, measurement practices and processing techniques aimed to achieve quantitative image fusion using a set of multi-exposure images of a static scene are reviewed. The conventional non-uniformity correction technique is extended, as the original is incompatible with quantitative fusion. Recognizing the inherent limitations of even the extended non-uniformity correction, an alternative measurement methodology, which relies on estimates of the detector bias using self-calibration, is developed. Combining data from multi-exposure images, two novel image fusion techniques that ultimately provide high tonal fidelity of a photoquantity are considered: ‘subtract-then-fuse’, which conducts image subtraction in the camera output domain and partially negates the bias frame contribution common to both the dark and scene frames; and ‘fuse-then-subtract’, which reconstructs the bias frame explicitly and conducts image fusion independently for the dark and the scene frames, followed by subtraction in the photoquantity domain. The performances of the different techniques are evaluated for various synthetic and experimental data, identifying the factors contributing to potential degradation of the image quality. The findings reflect the superiority of the ‘fuse-then-subtract’ approach, conducting image fusion via per-pixel nonlinear weighted least squares optimization.

  10. FPGA-Based Fused Smart-Sensor for Tool-Wear Area Quantitative Estimation in CNC Machine Inserts

    PubMed Central

    Trejo-Hernandez, Miguel; Osornio-Rios, Roque Alfredo; de Jesus Romero-Troncoso, Rene; Rodriguez-Donate, Carlos; Dominguez-Gonzalez, Aurelio; Herrera-Ruiz, Gilberto

    2010-01-01

    Manufacturing processes are of great relevance nowadays, when there is a constant claim for better productivity with high quality at low cost. The contribution of this work is the development of a fused smart-sensor, based on FPGA to improve the online quantitative estimation of flank-wear area in CNC machine inserts from the information provided by two primary sensors: the monitoring current output of a servoamplifier, and a 3-axis accelerometer. Results from experimentation show that the fusion of both parameters makes it possible to obtain three times better accuracy when compared with the accuracy obtained from current and vibration signals, individually used. PMID:22319304

  11. FPGA-based fused smart-sensor for tool-wear area quantitative estimation in CNC machine inserts.

    PubMed

    Trejo-Hernandez, Miguel; Osornio-Rios, Roque Alfredo; de Jesus Romero-Troncoso, Rene; Rodriguez-Donate, Carlos; Dominguez-Gonzalez, Aurelio; Herrera-Ruiz, Gilberto

    2010-01-01

    Manufacturing processes are of great relevance nowadays, when there is a constant claim for better productivity with high quality at low cost. The contribution of this work is the development of a fused smart-sensor, based on FPGA to improve the online quantitative estimation of flank-wear area in CNC machine inserts from the information provided by two primary sensors: the monitoring current output of a servoamplifier, and a 3-axis accelerometer. Results from experimentation show that the fusion of both parameters makes it possible to obtain three times better accuracy when compared with the accuracy obtained from current and vibration signals, individually used.

  12. In vitro modelling of familial amyloidotic polyneuropathy allows quantitative detection of transthyretin amyloid fibril-like structures in hepatic derivatives of patient-specific induced pluripotent stem cells.

    PubMed

    Hoepfner, Jeannine; Kleinsorge, Mandy; Papp, Oliver; Alfken, Susanne; Heiringhoff, Robin; Pich, Andreas; Sauer, Vanessa; Zibert, Andree; Göhring, Gudrun; Schmidt, Hartmut; Sgodda, Malte; Cantz, Tobias

    2017-07-26

    The transthyretin protein is thermodynamically destabilised by mutations in the transthyretin gene, promoting the formation of amyloid fibrils in various tissues. Consequently, impaired autonomic organ function is observed in patients suffering from transthyretin-related familial amyloidotic polyneuropathy (FAP). The influence of individual genetic backgrounds on fibril formation as a potential cause of genotype-phenotype variations needs to be investigated in order to ensure efficient patient-specific therapies. We reprogrammed FAP patient fibroblasts to induced pluripotent stem (iPS) cells and differentiated these cells into transthyretin-expressing hepatocyte-like cells (HLCs). HLCs differentiated from FAP iPS cells and healthy control iPS cells secreted the transthyretin protein in similar concentrations. Mass spectrometry revealed the presence of mutant transthyretin protein in FAP HLC supernatants. In comparison to healthy control iPS cells, we demonstrated the formation of transthyretin amyloid fibril-like structures in FAP HLC supernatants using the amyloid-specific dyes Congo red and thioflavin T. These dyes were also applicable for the quantitative determination of in vitro formed transthyretin fibril-like structures. Moreover, we confirmed the inhibition of fibril formation by the TTR kinetic stabiliser diclofenac. Thioflavin T fluorescence intensity measurements even allowed the quantification of amyloid fibril-like structures in 96-well plate formats as a prerequisite for patient-specific drug screening approaches.

  13. Photogrammetric Accuracy and Modeling of Rolling Shutter Cameras

    NASA Astrophysics Data System (ADS)

    Ye, W.; Qiao, G.; Kong, F.; Guo, S.; Ma, X.; Tong, X.; Li, R.

    2016-06-01

    Global climate change is one of the major challenges that all nations are commonly facing. Long-term observations of the Antarctic ice sheet have been playing a critical role in quantitatively estimating and predicting effects resulting from the global changes. The film-based ARGON reconnaissance imagery provides a remarkable data source for studying the Antarctic ice-sheet in 1960s, thus greatly extending the time period of Antarctica surface observations. To deal with the low-quality images and the unavailability of camera poses, a systematic photogrammetric approach is proposed to reconstruct the interior and exterior orientation information for further glacial mapping applications, including ice flow velocity mapping and mass balance estimation. Some noteworthy details while performing geometric modelling using the ARGON images were introduced, including methods and results for handling specific effects of film deformation, damaged or missing fiducial marks and calibration report, automatic fiducial mark detection, control point selection through Antarctic shadow and ice surface terrain analysis, and others. Several sites in East Antarctica were tested. As an example, four images in the Byrd glacier region were used to assess the accuracy of the geometric modelling. A digital elevation model (DEM) and an orthophoto map of Byrd glacier were generated. The accuracy of the ground positions estimated by using independent check points is within one nominal pixel of 140 m of ARGON imagery. Furthermore, a number of significant features, such as ice flow velocity and regional change patterns, will be extracted and analysed.

  14. DNA DAMAGE QUANTITATION BY ALKALINE GEL ELECTROPHORESIS.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    SUTHERLAND,B.M.; BENNETT,P.V.; SUTHERLAND, J.C.

    2004-03-24

    Physical and chemical agents in the environment, those used in clinical applications, or encountered during recreational exposures to sunlight, induce damages in DNA. Understanding the biological impact of these agents requires quantitation of the levels of such damages in laboratory test systems as well as in field or clinical samples. Alkaline gel electrophoresis provides a sensitive (down to {approx} a few lesions/5Mb), rapid method of direct quantitation of a wide variety of DNA damages in nanogram quantities of non-radioactive DNAs from laboratory, field, or clinical specimens, including higher plants and animals. This method stems from velocity sedimentation studies of DNAmore » populations, and from the simple methods of agarose gel electrophoresis. Our laboratories have developed quantitative agarose gel methods, analytical descriptions of DNA migration during electrophoresis on agarose gels (1-6), and electronic imaging for accurate determinations of DNA mass (7-9). Although all these components improve sensitivity and throughput of large numbers of samples (7,8,10), a simple version using only standard molecular biology equipment allows routine analysis of DNA damages at moderate frequencies. We present here a description of the methods, as well as a brief description of the underlying principles, required for a simplified approach to quantitation of DNA damages by alkaline gel electrophoresis.« less

  15. Improved quantitative analysis of spectra using a new method of obtaining derivative spectra based on a singular perturbation technique.

    PubMed

    Li, Zhigang; Wang, Qiaoyun; Lv, Jiangtao; Ma, Zhenhe; Yang, Linjuan

    2015-06-01

    Spectroscopy is often applied when a rapid quantitative analysis is required, but one challenge is the translation of raw spectra into a final analysis. Derivative spectra are often used as a preliminary preprocessing step to resolve overlapping signals, enhance signal properties, and suppress unwanted spectral features that arise due to non-ideal instrument and sample properties. In this study, to improve quantitative analysis of near-infrared spectra, derivatives of noisy raw spectral data need to be estimated with high accuracy. A new spectral estimator based on singular perturbation technique, called the singular perturbation spectra estimator (SPSE), is presented, and the stability analysis of the estimator is given. Theoretical analysis and simulation experimental results confirm that the derivatives can be estimated with high accuracy using this estimator. Furthermore, the effectiveness of the estimator for processing noisy infrared spectra is evaluated using the analysis of beer spectra. The derivative spectra of the beer and the marzipan are used to build the calibration model using partial least squares (PLS) modeling. The results show that the PLS based on the new estimator can achieve better performance compared with the Savitzky-Golay algorithm and can serve as an alternative choice for quantitative analytical applications.

  16. Condenser: a statistical aggregation tool for multi-sample quantitative proteomic data from Matrix Science Mascot Distiller™.

    PubMed

    Knudsen, Anders Dahl; Bennike, Tue; Kjeldal, Henrik; Birkelund, Svend; Otzen, Daniel Erik; Stensballe, Allan

    2014-05-30

    We describe Condenser, a freely available, comprehensive open-source tool for merging multidimensional quantitative proteomics data from the Matrix Science Mascot Distiller Quantitation Toolbox into a common format ready for subsequent bioinformatic analysis. A number of different relative quantitation technologies, such as metabolic (15)N and amino acid stable isotope incorporation, label-free and chemical-label quantitation are supported. The program features multiple options for curative filtering of the quantified peptides, allowing the user to choose data quality thresholds appropriate for the current dataset, and ensure the quality of the calculated relative protein abundances. Condenser also features optional global normalization, peptide outlier removal, multiple testing and calculation of t-test statistics for highlighting and evaluating proteins with significantly altered relative protein abundances. Condenser provides an attractive addition to the gold-standard quantitative workflow of Mascot Distiller, allowing easy handling of larger multi-dimensional experiments. Source code, binaries, test data set and documentation are available at http://condenser.googlecode.com/. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Design and preliminary accuracy studies of an MRI-guided transrectal prostate intervention system.

    PubMed

    Krieger, Axel; Csoma, Csaba; Iordachital, Iulian I; Guion, Peter; Singh, Anurag K; Fichtinger, Gabor; Whitcomb, Louis L

    2007-01-01

    This paper reports a novel system for magnetic resonance imaging (MRI) guided transrectal prostate interventions, such as needle biopsy, fiducial marker placement, and therapy delivery. The system utilizes a hybrid tracking method, comprised of passive fiducial tracking for initial registration and subsequent incremental motion measurement along the degrees of freedom using fiber-optical encoders and mechanical scales. Targeting accuracy of the system is evaluated in prostate phantom experiments. Achieved targeting accuracy and procedure times were found to compare favorably with existing systems using passive and active tracking methods. Moreover, the portable design of the system using only standard MRI image sequences and minimal custom scanner interfacing allows the system to be easily used on different MRI scanners.

  18. Effect of radiance-to-reflectance transformation and atmosphere removal on maximum likelihood classification accuracy of high-dimensional remote sensing data

    NASA Technical Reports Server (NTRS)

    Hoffbeck, Joseph P.; Landgrebe, David A.

    1994-01-01

    Many analysis algorithms for high-dimensional remote sensing data require that the remotely sensed radiance spectra be transformed to approximate reflectance to allow comparison with a library of laboratory reflectance spectra. In maximum likelihood classification, however, the remotely sensed spectra are compared to training samples, thus a transformation to reflectance may or may not be helpful. The effect of several radiance-to-reflectance transformations on maximum likelihood classification accuracy is investigated in this paper. We show that the empirical line approach, LOWTRAN7, flat-field correction, single spectrum method, and internal average reflectance are all non-singular affine transformations, and that non-singular affine transformations have no effect on discriminant analysis feature extraction and maximum likelihood classification accuracy. (An affine transformation is a linear transformation with an optional offset.) Since the Atmosphere Removal Program (ATREM) and the log residue method are not affine transformations, experiments with Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data were conducted to determine the effect of these transformations on maximum likelihood classification accuracy. The average classification accuracy of the data transformed by ATREM and the log residue method was slightly less than the accuracy of the original radiance data. Since the radiance-to-reflectance transformations allow direct comparison of remotely sensed spectra with laboratory reflectance spectra, they can be quite useful in labeling the training samples required by maximum likelihood classification, but these transformations have only a slight effect or no effect at all on discriminant analysis and maximum likelihood classification accuracy.

  19. Diagnostic value of (99m)Tc-3PRGD2 scintimammography for differentiation of malignant from benign breast lesions: Comparison of visual and semi-quantitative analysis.

    PubMed

    Chen, Qianqian; Xie, Qian; Zhao, Min; Chen, Bin; Gao, Shi; Zhang, Haishan; Xing, Hua; Ma, Qingjie

    2015-01-01

    To compare the diagnostic value of visual and semi-quantitative analysis of technetium-99m-poly-ethylene glycol, 4-arginine-glycine-aspartic acid ((99m)Tc-3PRGD2) scintimammography (SMG) for better differentiation of benign from malignant breast masses, and also investigate the incremental role of semi-quantitative index of SMG. A total of 72 patients with breast lesions were included in the study. Technetium-99m-3PRGD2 SMG was performed with single photon emission computed tomography (SPET) at 60 min after intravenous injection of 749 ± 86MBq of the radiotracer. Images were evaluated by visual interpretation and semi-quantitative indices of tumor to non-tumor (T/N) ratios, which were compared with pathology results. Receiver operating characteristics (ROC) curve analyses were performed to determine the optimal visual grade, to calculate cut-off values of semi-quantitative indices, and to compare visual and semi-quantitative diagnostic values. Among the 72 patients, 89 lesions were confirmed by histopathology after fine needle aspiration biopsy or surgery, 48 malignant and 41 benign lesions. The mean T/N ratio of (99m)Tc-3PRGD2 SMG in malignant lesions was significantly higher than that in benign lesions (P<0.05). When grade 2 of the disease was used as cut-off value for the detection of primary breast cancer, the sensitivity, specificity and accuracy were 81.3%, 70.7%, and 76.4%, respectively. When a T/N ratio of 2.01 was used as cut-off value, the sensitivity, specificity and accuracy were 79.2%, 75.6%, and 77.5%, respectively. According to ROC analysis, the area under the curve for semi-quantitative analysis was higher than that for visual analysis, but the statistical difference was not significant (P=0.372). Compared with visual analysis or semi-quantitative analysis alone, the sensitivity, specificity and accuracy of visual analysis combined with semi-quantitative analysis in diagnosing primary breast cancer were higher, being: 87.5%, 82.9%, and 85

  20. Identification and Quantitation of Malonic Acid Biomarkers of In-Born Error Metabolism by Targeted Metabolomics

    NASA Astrophysics Data System (ADS)

    Ambati, Chandra Shekar R.; Yuan, Furong; Abu-Elheiga, Lutfi A.; Zhang, Yiqing; Shetty, Vivekananda

    2017-05-01

    Malonic acid (MA), methylmalonic acid (MMA), and ethylmalonic acid (EMA) metabolites are implicated in various non-cancer disorders that are associated with inborn-error metabolism. In this study, we have slightly modified the published 3-nitrophenylhydrazine (3NPH) derivatization method and applied it to derivatize MA, MMA, and EMA to their hydrazone derivatives, which were amenable for liquid chromatography- mass spectrometry (LC-MS) quantitation. 3NPH was used to derivatize MA, MMA, and EMA, and multiple reaction monitoring (MRM) transitions of the corresponding derivatives were determined by product-ion experiments. Data normalization and absolute quantitation were achieved by using 3NPH derivatized isotopic labeled compounds 13C2-MA, MMA-D3, and EMA-D3. The detection limits were found to be at nanomolar concentrations and a good linearity was achieved from nanomolar to millimolar concentrations. As a proof of concept study, we have investigated the levels of malonic acids in mouse plasma with malonyl-CoA decarboxylase deficiency (MCD-D), and we have successfully applied 3NPH method to identify and quantitate all three malonic acids in wild type (WT) and MCD-D plasma with high accuracy. The results of this method were compared with that of underivatized malonic acid standards experiments that were performed using hydrophilic interaction liquid chromatography (HILIC)-MRM. Compared with HILIC method, 3NPH derivatization strategy was found to be very efficient to identify these molecules as it greatly improved the sensitivity, quantitation accuracy, as well as peak shape and resolution. Furthermore, there was no matrix effect in LC-MS analysis and the derivatized metabolites were found to be very stable for longer time.

  1. Quantitative 3D investigation of Neuronal network in mouse spinal cord model

    NASA Astrophysics Data System (ADS)

    Bukreeva, I.; Campi, G.; Fratini, M.; Spanò, R.; Bucci, D.; Battaglia, G.; Giove, F.; Bravin, A.; Uccelli, A.; Venturi, C.; Mastrogiacomo, M.; Cedola, A.

    2017-01-01

    The investigation of the neuronal network in mouse spinal cord models represents the basis for the research on neurodegenerative diseases. In this framework, the quantitative analysis of the single elements in different districts is a crucial task. However, conventional 3D imaging techniques do not have enough spatial resolution and contrast to allow for a quantitative investigation of the neuronal network. Exploiting the high coherence and the high flux of synchrotron sources, X-ray Phase-Contrast multiscale-Tomography allows for the 3D investigation of the neuronal microanatomy without any aggressive sample preparation or sectioning. We investigated healthy-mouse neuronal architecture by imaging the 3D distribution of the neuronal-network with a spatial resolution of 640 nm. The high quality of the obtained images enables a quantitative study of the neuronal structure on a subject-by-subject basis. We developed and applied a spatial statistical analysis on the motor neurons to obtain quantitative information on their 3D arrangement in the healthy-mice spinal cord. Then, we compared the obtained results with a mouse model of multiple sclerosis. Our approach paves the way to the creation of a “database” for the characterization of the neuronal network main features for a comparative investigation of neurodegenerative diseases and therapies.

  2. Demons deformable registration for CBCT-guided procedures in the head and neck: convergence and accuracy.

    PubMed

    Nithiananthan, S; Brock, K K; Daly, M J; Chan, H; Irish, J C; Siewerdsen, J H

    2009-10-01

    The accuracy and convergence behavior of a variant of the Demons deformable registration algorithm were investigated for use in cone-beam CT (CBCT)-guided procedures of the head and neck. Online use of deformable registration for guidance of therapeutic procedures such as image-guided surgery or radiation therapy places trade-offs on accuracy and computational expense. This work describes a convergence criterion for Demons registration developed to balance these demands; the accuracy of a multiscale Demons implementation using this convergence criterion is quantified in CBCT images of the head and neck. Using an open-source "symmetric" Demons registration algorithm, a convergence criterion based on the change in the deformation field between iterations was developed to advance among multiple levels of a multiscale image pyramid in a manner that optimized accuracy and computation time. The convergence criterion was optimized in cadaver studies involving CBCT images acquired using a surgical C-arm prototype modified for 3D intraoperative imaging. CBCT-to-CBCT registration was performed and accuracy was quantified in terms of the normalized cross-correlation (NCC) and target registration error (TRE). The accuracy and robustness of the algorithm were then tested in clinical CBCT images of ten patients undergoing radiation therapy of the head and neck. The cadaver model allowed optimization of the convergence factor and initial measurements of registration accuracy: Demons registration exhibited TRE=(0.8+/-0.3) mm and NCC =0.99 in the cadaveric head compared to TRE=(2.6+/-1.0) mm and NCC=0.93 with rigid registration. Similarly for the patient data, Demons registration gave mean TRE=(1.6+/-0.9) mm compared to rigid registration TRE=(3.6+/-1.9) mm, suggesting registration accuracy at or near the voxel size of the patient images (1 x 1 x 2 mm3). The multiscale implementation based on optimal convergence criteria completed registration in 52 s for the cadaveric head and in

  3. Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells.

    PubMed

    Park, Han Sang; Rinehart, Matthew T; Walzer, Katelyn A; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-01-01

    Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection

  4. Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells

    PubMed Central

    Park, Han Sang; Rinehart, Matthew T.; Walzer, Katelyn A.; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-01-01

    Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection

  5. Predicting the Accuracy of Protein–Ligand Docking on Homology Models

    PubMed Central

    BORDOGNA, ANNALISA; PANDINI, ALESSANDRO; BONATI, LAURA

    2011-01-01

    Ligand–protein docking is increasingly used in Drug Discovery. The initial limitations imposed by a reduced availability of target protein structures have been overcome by the use of theoretical models, especially those derived by homology modeling techniques. While this greatly extended the use of docking simulations, it also introduced the need for general and robust criteria to estimate the reliability of docking results given the model quality. To this end, a large-scale experiment was performed on a diverse set including experimental structures and homology models for a group of representative ligand–protein complexes. A wide spectrum of model quality was sampled using templates at different evolutionary distances and different strategies for target–template alignment and modeling. The obtained models were scored by a selection of the most used model quality indices. The binding geometries were generated using AutoDock, one of the most common docking programs. An important result of this study is that indeed quantitative and robust correlations exist between the accuracy of docking results and the model quality, especially in the binding site. Moreover, state-of-the-art indices for model quality assessment are already an effective tool for an a priori prediction of the accuracy of docking experiments in the context of groups of proteins with conserved structural characteristics. PMID:20607693

  6. Required experimental accuracy to select between supersymmetrical models

    NASA Astrophysics Data System (ADS)

    Grellscheid, David

    2004-03-01

    We will present a method to decide a priori whether various supersymmetrical scenarios can be distinguished based on sparticle mass data alone. For each model, a scan over all free SUSY breaking parameters reveals the extent of that model's physically allowed region of sparticle-mass-space. Based on the geometrical configuration of these regions in mass-space, it is possible to obtain an estimate of the required accuracy of future sparticle mass measurements to distinguish between the models. We will illustrate this algorithm with an example. This talk is based on work done in collaboration with B C Allanach (LAPTH, Annecy) and F Quevedo (DAMTP, Cambridge).

  7. Dynamic Modeling Accuracy Dependence on Errors in Sensor Measurements, Mass Properties, and Aircraft Geometry

    NASA Technical Reports Server (NTRS)

    Grauer, Jared A.; Morelli, Eugene A.

    2013-01-01

    A nonlinear simulation of the NASA Generic Transport Model was used to investigate the effects of errors in sensor measurements, mass properties, and aircraft geometry on the accuracy of dynamic models identified from flight data. Measurements from a typical system identification maneuver were systematically and progressively deteriorated and then used to estimate stability and control derivatives within a Monte Carlo analysis. Based on the results, recommendations were provided for maximum allowable errors in sensor measurements, mass properties, and aircraft geometry to achieve desired levels of dynamic modeling accuracy. Results using other flight conditions, parameter estimation methods, and a full-scale F-16 nonlinear aircraft simulation were compared with these recommendations.

  8. Evaluation of a rapid quantitative determination method of PSA concentration with gold immunochromatographic strips.

    PubMed

    Wu, Cheng-Ching; Lin, Hung-Yu; Wang, Chao-Ping; Lu, Li-Fen; Yu, Teng-Hung; Hung, Wei-Chin; Houng, Jer-Yiing; Chung, Fu-Mei; Lee, Yau-Jiunn; Hu, Jin-Jia

    2015-11-03

    Prostate cancer remains the most common cancer in men. Qualitative or semi-quantitative immunochromatographic measurements of prostate specific antigen (PSA) have been shown to be simple, noninvasive and feasible. The aim of this study was to evaluate an optimized gold immunochromatographic strip device for the detection of PSA, in which the results can be analysed using a Chromogenic Rapid Test Reader to quantitatively assess the test results. This reader measures the reflectance of the signal line via a charge-coupled device camera. For quantitative analysis, PSA concentration was computed via a calibration equation. Capillary blood samples from 305 men were evaluated, and two independent observers interpreted the test results after 12 min. Blood samples were also collected and tested with a conventional quantitative assay. Sensitivity, specificity, positive and negative predictive values, and accuracy of the PSA rapid quantitative test system were 100, 96.6, 89.5, 100, and 97.4 %, respectively. Reproducibility of the test was 99.2, and interobserver variation was 8 % with a false positive rate of 3.4 %. The correlation coefficient between the ordinary quantitative assay and the rapid quantitative test was 0.960. The PSA rapid quantitative test system provided results quickly and was easy to use, so that tests using this system can be easily performed at outpatient clinics or elsewhere. This system may also be useful for initial cancer screening and for point-of-care testing, because results can be obtained within 12 min and at a cost lower than that of conventional quantitative assays.

  9. Quantitation by Portable Gas Chromatography: Mass Spectrometry of VOCs Associated with Vapor Intrusion

    PubMed Central

    Fair, Justin D.; Bailey, William F.; Felty, Robert A.; Gifford, Amy E.; Shultes, Benjamin; Volles, Leslie H.

    2010-01-01

    Development of a robust reliable technique that permits for the rapid quantitation of volatile organic chemicals is an important first step to remediation associated with vapor intrusion. This paper describes the development of an analytical method that allows for the rapid and precise identification and quantitation of halogenated and nonhalogenated contaminants commonly found within the ppbv level at sites where vapor intrusion is a concern. PMID:20885969

  10. Promote quantitative ischemia imaging via myocardial perfusion CT iterative reconstruction with tensor total generalized variation regularization

    NASA Astrophysics Data System (ADS)

    Gu, Chengwei; Zeng, Dong; Lin, Jiahui; Li, Sui; He, Ji; Zhang, Hao; Bian, Zhaoying; Niu, Shanzhou; Zhang, Zhang; Huang, Jing; Chen, Bo; Zhao, Dazhe; Chen, Wufan; Ma, Jianhua

    2018-06-01

    Myocardial perfusion computed tomography (MPCT) imaging is commonly used to detect myocardial ischemia quantitatively. A limitation in MPCT is that an additional radiation dose is required compared to unenhanced CT due to its repeated dynamic data acquisition. Meanwhile, noise and streak artifacts in low-dose cases are the main factors that degrade the accuracy of quantifying myocardial ischemia and hamper the diagnostic utility of the filtered backprojection reconstructed MPCT images. Moreover, it is noted that the MPCT images are composed of a series of 2/3D images, which can be naturally regarded as a 3/4-order tensor, and the MPCT images are globally correlated along time and are sparse across space. To obtain higher fidelity ischemia from low-dose MPCT acquisitions quantitatively, we propose a robust statistical iterative MPCT image reconstruction algorithm by incorporating tensor total generalized variation (TTGV) regularization into a penalized weighted least-squares framework. Specifically, the TTGV regularization fuses the spatial correlation of the myocardial structure and the temporal continuation of the contrast agent intake during the perfusion. Then, an efficient iterative strategy is developed for the objective function optimization. Comprehensive evaluations have been conducted on a digital XCAT phantom and a preclinical porcine dataset regarding the accuracy of the reconstructed MPCT images, the quantitative differentiation of ischemia and the algorithm’s robustness and efficiency.

  11. Validation of a new UNIX-based quantitative coronary angiographic system for the measurement of coronary artery lesions.

    PubMed

    Bell, M R; Britson, P J; Chu, A; Holmes, D R; Bresnahan, J F; Schwartz, R S

    1997-01-01

    We describe a method of validation of computerized quantitative coronary arteriography and report the results of a new UNIX-based quantitative coronary arteriography software program developed for rapid on-line (digital) and off-line (digital or cinefilm) analysis. The UNIX operating system is widely available in computer systems using very fast processors and has excellent graphics capabilities. The system is potentially compatible with any cardiac digital x-ray system for on-line analysis and has been designed to incorporate an integrated database, have on-line and immediate recall capabilities, and provide digital access to all data. The accuracy (mean signed differences of the observed minus the true dimensions) and precision (pooled standard deviations of the measurements) of the program were determined x-ray vessel phantoms. Intra- and interobserver variabilities were assessed from in vivo studies during routine clinical coronary arteriography. Precision from the x-ray phantom studies (6-In. field of view) for digital images was 0.066 mm and for digitized cine images was 0.060 mm. Accuracy was 0.076 mm (overestimation) for digital images compared to 0.008 mm for digitized cine images. Diagnostic coronary catheters were also used for calibration; accuracy.varied according to size of catheter and whether or not they were filled with iodinated contrast. Intra- and interobserver variabilities were excellent and indicated that coronary lesion measurements were relatively user-independent. Thus, this easy to use and very fast UNIX based program appears to be robust with optimal accuracy and precision for clinical and research applications.

  12. Determination of subthalamic nucleus location by quantitative analysis of despiked background neural activity from microelectrode recordings obtained during deep brain stimulation surgery.

    PubMed

    Danish, Shabbar F; Baltuch, Gordon H; Jaggi, Jurg L; Wong, Stephen

    2008-04-01

    Microelectrode recording during deep brain stimulation surgery is a useful adjunct for subthalamic nucleus (STN) localization. We hypothesize that information in the nonspike background activity can help identify STN boundaries. We present results from a novel quantitative analysis that accomplishes this goal. Thirteen consecutive microelectrode recordings were retrospectively analyzed. Spikes were removed from the recordings with an automated algorithm. The remaining "despiked" signals were converted via root mean square amplitude and curve length calculations into "feature profile" time series. Subthalamic nucleus boundaries determined by inspection, based on sustained deviations from baseline for each feature profile, were compared against those determined intraoperatively by the clinical neurophysiologist. Feature profile activity within STN exhibited a sustained rise in 10 of 13 tracks (77%). The sensitivity of STN entry was 60% and 90% for curve length and root mean square amplitude, respectively, when agreement within 0.5 mm of the neurophysiologist's prediction was used. Sensitivities were 70% and 100% for 1 mm accuracy. Exit point sensitivities were 80% and 90% for both features within 0.5 mm and 1.0 mm, respectively. Reproducible activity patterns in deep brain stimulation microelectrode recordings can allow accurate identification of STN boundaries. Quantitative analyses of this type may provide useful adjunctive information for electrode placement in deep brain stimulation surgery.

  13. Continuous Glucose Monitoring and Trend Accuracy

    PubMed Central

    Gottlieb, Rebecca; Le Compte, Aaron; Chase, J. Geoffrey

    2014-01-01

    Continuous glucose monitoring (CGM) devices are being increasingly used to monitor glycemia in people with diabetes. One advantage with CGM is the ability to monitor the trend of sensor glucose (SG) over time. However, there are few metrics available for assessing the trend accuracy of CGM devices. The aim of this study was to develop an easy to interpret tool for assessing trend accuracy of CGM data. SG data from CGM were compared to hourly blood glucose (BG) measurements and trend accuracy was quantified using the dot product. Trend accuracy results are displayed on the Trend Compass, which depicts trend accuracy as a function of BG. A trend performance table and Trend Index (TI) metric are also proposed. The Trend Compass was tested using simulated CGM data with varying levels of error and variability, as well as real clinical CGM data. The results show that the Trend Compass is an effective tool for differentiating good trend accuracy from poor trend accuracy, independent of glycemic variability. Furthermore, the real clinical data show that the Trend Compass assesses trend accuracy independent of point bias error. Finally, the importance of assessing trend accuracy as a function of BG level is highlighted in a case example of low and falling BG data, with corresponding rising SG data. This study developed a simple to use tool for quantifying trend accuracy. The resulting trend accuracy is easily interpreted on the Trend Compass plot, and if required, performance table and TI metric. PMID:24876437

  14. Trait Perception Accuracy and Acquaintance Within Groups: Tracking Accuracy Development.

    PubMed

    Brown, Jill A; Bernieri, Frank

    2017-05-01

    Previous work on trait perception has evaluated accuracy at discrete stages of relationships (e.g., strangers, best friends). A relatively limited body of literature has investigated changes in accuracy as acquaintance within a dyad or group increases. Small groups of initially unacquainted individuals spent more than 30 hr participating in a wide range of activities designed to represent common interpersonal contexts (e.g., eating, traveling). We calculated how accurately each participant judged others in their group on the big five traits across three distinct points within the acquaintance process: zero acquaintance, after a getting-to-know-you conversation, and after 10 weeks of interaction and activity. Judgments of all five traits exhibited accuracy above chance levels after 10 weeks. An examination of the trait rating stability revealed that much of the revision in judgments occurred not over the course of the 10-week relationship as suspected, but between zero acquaintance and the getting-to-know-you conversation.

  15. Quantitation of tumor uptake with molecular breast imaging.

    PubMed

    Bache, Steven T; Kappadath, S Cheenu

    2017-09-01

    We developed scatter and attenuation-correction techniques for quantifying images obtained with Molecular Breast Imaging (MBI) systems. To investigate scatter correction, energy spectra of a 99m Tc point source were acquired with 0-7-cm-thick acrylic to simulate scatter between the detector heads. System-specific scatter correction factor, k, was calculated as a function of thickness using a dual energy window technique. To investigate attenuation correction, a 7-cm-thick rectangular phantom containing 99m Tc-water simulating breast tissue and fillable spheres simulating tumors was imaged. Six spheres 10-27 mm in diameter were imaged with sphere-to-background ratios (SBRs) of 3.5, 2.6, and 1.7 and located at depths of 0.5, 1.5, and 2.5 cm from the center of the water bath for 54 unique tumor scenarios (3 SBRs × 6 sphere sizes × 3 depths). Phantom images were also acquired in-air under scatter- and attenuation-free conditions, which provided ground truth counts. To estimate true counts, T, from each tumor, the geometric mean (GM) of the counts within a prescribed region of interest (ROI) from the two projection images was calculated as T=C1C2eμtF, where C are counts within the square ROI circumscribing each sphere on detectors 1 and 2, μ is the linear attenuation coefficient of water, t is detector separation, and the factor F accounts for background activity. Four unique F definitions-standard GM, background-subtraction GM, MIRD Primer 16 GM, and a novel "volumetric GM"-were investigated. Error in T was calculated as the percentage difference with respect to in-air. Quantitative accuracy using the different GM definitions was calculated as a function of SBR, depth, and sphere size. Sensitivity of quantitative accuracy to ROI size was investigated. We developed an MBI simulation to investigate the robustness of our corrections for various ellipsoidal tumor shapes and detector separations. Scatter correction factor k varied slightly (0.80-0.95) over a compressed

  16. A Novel Method for Relative Quantitation of N-Glycans by Isotopic Labeling Using 18O-Water

    PubMed Central

    Tao, Shujuan; Orlando, Ron

    2014-01-01

    Quantitation is an essential aspect of comprehensive glycomics study. Here, a novel isotopic-labeling method is described for N-glycan quantitation using 18O-water. The incorporation of the 18O-labeling into the reducing end of N-glycans is simply and efficiently achieved during peptide-N4-(N-acetyl-β-glucosaminyl) asparagine amidase F release. This process provides a 2-Da mass difference compared with the N-glycans released in 16O-water. A mathematical calculation method was also developed to determine the 18O/16O ratios from isotopic peaks. Application of this method to several standard glycoprotein mixtures and human serum demonstrated that this method can facilitate the relative quantitation of N-glycans over a linear dynamic range of two orders, with high accuracy and reproducibility. PMID:25365792

  17. Accuracy Enhancement of Raman Spectroscopy Using Complementary Laser-Induced Breakdown Spectroscopy (LIBS) with Geologically Mixed Samples.

    PubMed

    Choi, Soojin; Kim, Dongyoung; Yang, Junho; Yoh, Jack J

    2017-04-01

    Quantitative Raman analysis was carried out with geologically mixed samples that have various matrices. In order to compensate the matrix effect in Raman shift, laser-induced breakdown spectroscopy (LIBS) analysis was performed. Raman spectroscopy revealed the geological materials contained in the mixed samples. However, the analysis of a mixture containing different matrices was inaccurate due to the weak signal of the Raman shift, interference, and the strong matrix effect. On the other hand, the LIBS quantitative analysis of atomic carbon and calcium in mixed samples showed high accuracy. In the case of the calcite and gypsum mixture, the coefficient of determination of atomic carbon using LIBS was 0.99, while the signal using Raman was less than 0.9. Therefore, the geological composition of the mixed samples is first obtained using Raman and the LIBS-based quantitative analysis is then applied to the Raman outcome in order to construct highly accurate univariate calibration curves. The study also focuses on a method to overcome matrix effects through the two complementary spectroscopic techniques of Raman spectroscopy and LIBS.

  18. Innovative Technique for High-Accuracy Remote Monitoring of Surface Water

    NASA Astrophysics Data System (ADS)

    Gisler, A.; Barton-Grimley, R. A.; Thayer, J. P.; Crowley, G.

    2016-12-01

    Lidar (light detection and ranging) provides absolute depth and topographic mapping capability compared to other remote sensing methods, which is useful for mapping rapidly changing environments such as riverine systems and agricultural waterways. Effectiveness of current lidar bathymetric systems is limited by the difficulty in unambiguously identifying backscattered lidar signals from the water surface versus the bottom, limiting their depth resolution to 0.3-0.5 m. Additionally these are large, bulky systems that are constrained to expensive aircraft-mounted platforms and use waveform-processing techniques requiring substantial computation time. These restrictions are prohibitive for many potential users. A novel lidar device has been developed that allows for non-contact measurements of water depth down to 1 cm with an accuracy and precision of < 1 cm by exploiting the polarization properties of the light-surface interaction. This system can transition seamlessly from ranging over land to shallow to deep water allowing for shoreline charting, measuring water volume, mapping bottom topology, and identifying submerged objects. The scalability of the technique opens up the ability for handheld or UAS-mounted lidar bathymetric systems, which provides for potential applications currently unavailable to the community. The high laser pulse repetition rate allows for very fine horizontal resolution while the photon-counting technique permits real-time depth measurement and object detection. The enhanced measurement capability, portability, scalability, and relatively low-cost creates the opportunity to perform frequent high-accuracy monitoring and measuring of aquatic environments which is crucial for monitoring water resources on fast timescales. Results from recent campaigns measuring water depth in flowing creeks and murky ponds will be presented which demonstrate that the method is not limited by rough water surfaces and can map underwater topology through

  19. SU-E-J-219: Quantitative Evaluation of Motion Effects On Accuracy of Image-Guided Radiotherapy with Fiducial Markers Using CT Imaging

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ali, I; Oyewale, S; Ahmad, S

    2014-06-01

    Purpose: To investigate quantitatively patient motion effects on the localization accuracy of image-guided radiation with fiducial markers using axial CT (ACT), helical CT (HCT) and cone-beam CT (CBCT) using modeling and experimental phantom studies. Methods: Markers with different lengths (2.5 mm, 5 mm, 10 mm, and 20 mm) were inserted in a mobile thorax phantom which was imaged using ACT, HCT and CBCT. The phantom moved with sinusoidal motion with amplitudes ranging 0–20 mm and a frequency of 15 cycles-per-minute. Three parameters that include: apparent marker lengths, center position and distance between the centers of the markers were measured inmore » the different CT images of the mobile phantom. A motion mathematical model was derived to predict the variations in the previous three parameters and their dependence on the motion in the different imaging modalities. Results: In CBCT, the measured marker lengths increased linearly with increase in motion amplitude. For example, the apparent length of the 10 mm marker was about 20 mm when phantom moved with amplitude of 5 mm. Although the markers have elongated, the center position and the distance between markers remained at the same position for different motion amplitudes in CBCT. These parameters were not affected by motion frequency and phase in CBCT. In HCT and ACT, the measured marker length, center and distance between markers varied irregularly with motion parameters. The apparent lengths of the markers varied with inverse of the phantom velocity which depends on motion frequency and phase. Similarly the center position and distance between markers varied inversely with phantom speed. Conclusion: Motion may lead to variations in maker length, center position and distance between markers using CT imaging. These effects should be considered in patient setup using image-guided radiation therapy based on fiducial markers matching using 2D-radiographs or volumetric CT imaging.« less

  20. Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity.

    PubMed

    Zhu, Jin; Heinecke, Dominic; Mulla, Wahid A; Bradford, William D; Rubinstein, Boris; Box, Andrew; Haug, Jeffrey S; Li, Rong

    2015-03-30

    Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein-based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation. Copyright © 2015 Zhu et al.

  1. Label-free cell-cycle analysis by high-throughput quantitative phase time-stretch imaging flow cytometry

    NASA Astrophysics Data System (ADS)

    Mok, Aaron T. Y.; Lee, Kelvin C. M.; Wong, Kenneth K. Y.; Tsia, Kevin K.

    2018-02-01

    Biophysical properties of cells could complement and correlate biochemical markers to characterize a multitude of cellular states. Changes in cell size, dry mass and subcellular morphology, for instance, are relevant to cell-cycle progression which is prevalently evaluated by DNA-targeted fluorescence measurements. Quantitative-phase microscopy (QPM) is among the effective biophysical phenotyping tools that can quantify cell sizes and sub-cellular dry mass density distribution of single cells at high spatial resolution. However, limited camera frame rate and thus imaging throughput makes QPM incompatible with high-throughput flow cytometry - a gold standard in multiparametric cell-based assay. Here we present a high-throughput approach for label-free analysis of cell cycle based on quantitative-phase time-stretch imaging flow cytometry at a throughput of > 10,000 cells/s. Our time-stretch QPM system enables sub-cellular resolution even at high speed, allowing us to extract a multitude (at least 24) of single-cell biophysical phenotypes (from both amplitude and phase images). Those phenotypes can be combined to track cell-cycle progression based on a t-distributed stochastic neighbor embedding (t-SNE) algorithm. Using multivariate analysis of variance (MANOVA) discriminant analysis, cell-cycle phases can also be predicted label-free with high accuracy at >90% in G1 and G2 phase, and >80% in S phase. We anticipate that high throughput label-free cell cycle characterization could open new approaches for large-scale single-cell analysis, bringing new mechanistic insights into complex biological processes including diseases pathogenesis.

  2. The Social Accuracy Model of Interpersonal Perception: Assessing Individual Differences in Perceptive and Expressive Accuracy

    ERIC Educational Resources Information Center

    Biesanz, Jeremy C.

    2010-01-01

    The social accuracy model of interpersonal perception (SAM) is a componential model that estimates perceiver and target effects of different components of accuracy across traits simultaneously. For instance, Jane may be generally accurate in her perceptions of others and thus high in "perceptive accuracy"--the extent to which a particular…

  3. Children's Age-Related Speed--Accuracy Strategies in Intercepting Moving Targets in Two Dimensions

    ERIC Educational Resources Information Center

    Rothenberg-Cunningham, Alek; Newell, Karl M.

    2013-01-01

    Purpose: This study investigated the age-related speed--accuracy strategies of children, adolescents, and adults in performing a rapid striking task that allowed the self-selection of the interception position in a virtual, two-dimensional environment. Method: The moving target had curvilinear trajectories that were determined by combinations of…

  4. Speed-Accuracy Response Models: Scoring Rules Based on Response Time and Accuracy

    ERIC Educational Resources Information Center

    Maris, Gunter; van der Maas, Han

    2012-01-01

    Starting from an explicit scoring rule for time limit tasks incorporating both response time and accuracy, and a definite trade-off between speed and accuracy, a response model is derived. Since the scoring rule is interpreted as a sufficient statistic, the model belongs to the exponential family. The various marginal and conditional distributions…

  5. Accuracy of neuro-navigated cranial screw placement using optical surface imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Jakubovic, Raphael; Gupta, Shuarya; Guha, Daipayan; Mainprize, Todd; Yang, Victor X. D.

    2017-02-01

    Cranial neurosurgical procedures are especially delicate considering that the surgeon must localize the subsurface anatomy with limited exposure and without the ability to see beyond the surface of the surgical field. Surgical accuracy is imperative as even minor surgical errors can cause major neurological deficits. Traditionally surgical precision was highly dependent on surgical skill. However, the introduction of intraoperative surgical navigation has shifted the paradigm to become the current standard of care for cranial neurosurgery. Intra-operative image guided navigation systems are currently used to allow the surgeon to visualize the three-dimensional subsurface anatomy using pre-acquired computed tomography (CT) or magnetic resonance (MR) images. The patient anatomy is fused to the pre-acquired images using various registration techniques and surgical tools are typically localized using optical tracking methods. Although these techniques positively impact complication rates, surgical accuracy is limited by the accuracy of the navigation system and as such quantification of surgical error is required. While many different measures of registration accuracy have been presented true navigation accuracy can only be quantified post-operatively by comparing a ground truth landmark to the intra-operative visualization. In this study we quantified the accuracy of cranial neurosurgical procedures using a novel optical surface imaging navigation system to visualize the three-dimensional anatomy of the surface anatomy. A tracked probe was placed on the screws of cranial fixation plates during surgery and the reported position of the centre of the screw was compared to the co-ordinates of the post-operative CT or MR images, thus quantifying cranial neurosurgical error.

  6. Isomer-Specific Hydrogen Bonding as a Design Principle for Bidirectionally Quantitative and Redshifted Hemithioindigo Photoswitches.

    PubMed

    Zweig, Joshua E; Newhouse, Timothy R

    2017-08-16

    A new class of bidirectionally quantitative photoswitches based on the hemithioindigo (HTI) scaffold is reported. Incorporation of a pyrrole hydrogen-bond donor leads to a bathochromic shift allowing for quantitative bidirectional isomerization. Additionally, extending conjugation from the electron-rich pyrrole results in quantitative visible-light photoswitches, as well as photoswitches that isomerize with red and near-infrared light. The presence of the hydrogen bond leading to the observed redshift is supported by computational and spectroscopic evidence.

  7. Quantitative determination of dimethicone in commercial tablets and capsules by Fourier transform infrared spectroscopy and antifoaming activity test.

    PubMed

    Torrado, G; García-Arieta, A; de los Ríos, F; Menéndez, J C; Torrado, S

    1999-03-01

    Fourier transform infrared (FTIR) spectroscopy and antifoaming activity test have been employed for the quantitative analysis of dimethicone. Linearity, accuracy and precision are presented for both methods. These methods have been also used to compare different dimethicone-containing proprietary medicines. FTIR spectroscopy has shown to be adequate for quantitation of dimethicone in commercial tablets and capsules in order to comply with USP requirements. The antifoaming activity test is able to detect incompatibilities between dimethicone and other constituents. The presence of certain enzymes in some medicinal products increases the defoaming properties of these formulations.

  8. Weight Multispectral Reconstruction Strategy for Enhanced Reconstruction Accuracy and Stability With Cerenkov Luminescence Tomography.

    PubMed

    Hongbo Guo; Xiaowei He; Muhan Liu; Zeyu Zhang; Zhenhua Hu; Jie Tian

    2017-06-01

    Cerenkov luminescence tomography (CLT) provides a novel technique for 3-D noninvasive detection of radiopharmaceuticals in living subjects. However, because of the severe scattering of Cerenkov light, the reconstruction accuracy and stability of CLT is still unsatisfied. In this paper, a modified weight multispectral CLT (wmCLT) reconstruction strategy was developed which split the Cerenkov radiation spectrum into several sub-spectral bands and weighted the sub-spectral results to obtain the final result. To better evaluate the property of the wmCLT reconstruction strategy in terms of accuracy, stability and practicability, several numerical simulation experiments and in vivo experiments were conducted and the results obtained were compared with the traditional multispectral CLT (mCLT) and hybrid-spectral CLT (hCLT) reconstruction strategies. The numerical simulation results indicated that wmCLT strategy significantly improved the accuracy of Cerenkov source localization and intensity quantitation and exhibited good stability in suppressing noise in numerical simulation experiments. And the comparison of the results achieved from different in vivo experiments further indicated significant improvement of the wmCLT strategy in terms of the shape recovery of the bladder and the spatial resolution of imaging xenograft tumors. Overall the strategy reported here will facilitate the development of nuclear and optical molecular tomography in theoretical study.

  9. Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection.

    PubMed

    Johansson, Magnus; Zhang, Jingji; Ehrenberg, Måns

    2012-01-03

    Rapid and accurate translation of the genetic code into protein is fundamental to life. Yet due to lack of a suitable assay, little is known about the accuracy-determining parameters and their correlation with translational speed. Here, we develop such an assay, based on Mg(2+) concentration changes, to determine maximal accuracy limits for a complete set of single-mismatch codon-anticodon interactions. We found a simple, linear trade-off between efficiency of cognate codon reading and accuracy of tRNA selection. The maximal accuracy was highest for the second codon position and lowest for the third. The results rationalize the existence of proofreading in code reading and have implications for the understanding of tRNA modifications, as well as of translation error-modulating ribosomal mutations and antibiotics. Finally, the results bridge the gap between in vivo and in vitro translation and allow us to calibrate our test tube conditions to represent the environment inside the living cell.

  10. Congruent climate-related genecological responses from molecular markers and quantitative traits for western white pine (Pinus monticola)

    Treesearch

    Bryce A. Richardson; Gerald E. Rehfeldt; Mee-Sook Kim

    2009-01-01

    Analyses of molecular and quantitative genetic data demonstrate the existence of congruent climate-related patterns in western white pine (Pinus monticola). Two independent studies allowed comparisons of amplified fragment length polymorphism (AFLP) markers with quantitative variation in adaptive traits. Principal component analyses...

  11. A thioacidolysis method tailored for higher‐throughput quantitative analysis of lignin monomers

    PubMed Central

    Foster, Cliff; Happs, Renee M.; Doeppke, Crissa; Meunier, Kristoffer; Gehan, Jackson; Yue, Fengxia; Lu, Fachuang; Davis, Mark F.

    2016-01-01

    Abstract Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β‐O‐4 linkages. Current thioacidolysis methods are low‐throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non‐chlorinated organic solvent and is tailored for higher‐throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1–2 mg of biomass per assay and has been quantified using fast‐GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, including standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day‐to‐day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. The method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses. PMID:27534715

  12. A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.

    Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

  13. A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

    DOE PAGES

    Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.; ...

    2016-09-14

    Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

  14. Quantitative 3D high resolution transmission ultrasound tomography: creating clinically relevant images (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wiskin, James; Klock, John; Iuanow, Elaine; Borup, Dave T.; Terry, Robin; Malik, Bilal H.; Lenox, Mark

    2017-03-01

    There has been a great deal of research into ultrasound tomography for breast imaging over the past 35 years. Few successful attempts have been made to reconstruct high-resolution images using transmission ultrasound. To this end, advances have been made in 2D and 3D algorithms that utilize either time of arrival or full wave data to reconstruct images with high spatial and contrast resolution suitable for clinical interpretation. The highest resolution and quantitative accuracy result from inverse scattering applied to full wave data in 3D. However, this has been prohibitively computationally expensive, meaning that full inverse scattering ultrasound tomography has not been considered clinically viable. Here we show the results of applying a nonlinear inverse scattering algorithm to 3D data in a clinically useful time frame. This method yields Quantitative Transmission (QT) ultrasound images with high spatial and contrast resolution. We reconstruct sound speeds for various 2D and 3D phantoms and verify these values with independent measurements. The data are fully 3D as is the reconstruction algorithm, with no 2D approximations. We show that 2D reconstruction algorithms can introduce artifacts into the QT breast image which are avoided by using a full 3D algorithm and data. We show high resolution gross and microscopic anatomic correlations comparing cadaveric breast QT images with MRI to establish imaging capability and accuracy. Finally, we show reconstructions of data from volunteers, as well as an objective visual grading analysis to confirm clinical imaging capability and accuracy.

  15. Static headspace gas chromatographic method for quantitative determination of residual solvents in pharmaceutical drug substances according to european pharmacopoeia requirements.

    PubMed

    Otero, Raquel; Carrera, Guillem; Dulsat, Joan Francesc; Fábregas, José Luís; Claramunt, Juan

    2004-11-19

    A static headspace (HS) gas chromatographic method for quantitative determination of residual solvents in a drug substance has been developed according to European Pharmacopoeia general procedure. A water-dimethylformamide mixture is proposed as sample solvent to obtain good sensitivity and recovery. The standard addition technique with internal standard quantitation was used for ethanol, tetrahydrofuran and toluene determination. Validation was performed within the requirements of ICH validation guidelines Q2A and Q2B. Selectivity was tested for 36 solvents, and system suitability requirements described in the European Pharmacopoeia were checked. Limits of detection and quantitation, precision, linearity, accuracy, intermediate precision and robustness were determined, and excellent results were obtained.

  16. Semi-quantitative analysis of salivary gland scintigraphy in Sjögren's syndrome diagnosis: a first-line tool.

    PubMed

    Angusti, Tiziana; Pilati, Emanuela; Parente, Antonella; Carignola, Renato; Manfredi, Matteo; Cauda, Simona; Pizzigati, Elena; Dubreuil, Julien; Giammarile, Francesco; Podio, Valerio; Skanjeti, Andrea

    2017-09-01

    The aim of this study was the assessment of semi-quantified salivary gland dynamic scintigraphy (SGdS) parameters independently and in an integrated way in order to predict primary Sjögren's syndrome (pSS). Forty-six consecutive patients (41 females; age 61 ± 11 years) with sicca syndrome were studied by SGdS after injection of 200 MBq of pertechnetate. In sixteen patients, pSS was diagnosed, according to American-European Consensus Group criteria (AECGc). Semi-quantitative parameters (uptake (UP) and excretion fraction (EF)) were obtained for each gland. ROC curves were used to determine the best cut-off value. The area under the curve (AUC) was used to estimate the accuracy of each semi-quantitative analysis. To assess the correlation between scintigraphic results and disease severity, semi-quantitative parameters were plotted versus Sjögren's syndrome disease activity index (ESSDAI). A nomogram was built to perform an integrated evaluation of all the scintigraphic semi-quantitative data. Both UP and EF of salivary glands were significantly lower in pSS patients compared to those in non-pSS (p < 0.001). ROC curve showed significantly large AUC for both the parameters (p < 0.05). Parotid UP and submandibular EF, assessed by univariated and multivariate logistic regression, showed a significant and independent correlation with pSS diagnosis (p value <0.05). No correlation was found between SGdS semi-quantitative parameters and ESSDAI. The proposed nomogram accuracy was 87%. SGdS is an accurate and reproducible tool for the diagnosis of pSS. ESSDAI was not shown to be correlated with SGdS data. SGdS should be the first-line imaging technique in patients with suspected pSS.

  17. Accuracy assessment of minimum control points for UAV photography and georeferencing

    NASA Astrophysics Data System (ADS)

    Skarlatos, D.; Procopiou, E.; Stavrou, G.; Gregoriou, M.

    2013-08-01

    In recent years, Autonomous Unmanned Aerial Vehicles (AUAV) became popular among researchers across disciplines because they combine many advantages. One major application is monitoring and mapping. Their ability to fly beyond eye sight autonomously, collecting data over large areas whenever, wherever, makes them excellent platform for monitoring hazardous areas or disasters. In both cases rapid mapping is needed while human access isn't always a given. Indeed, current automatic processing of aerial photos using photogrammetry and computer vision algorithms allows for rapid orthophomap production and Digital Surface Model (DSM) generation, as tools for monitoring and damage assessment. In such cases, control point measurement using GPS is either impossible, or time consuming or costly. This work investigates accuracies that can be attained using few or none control points over areas of one square kilometer, in two test sites; a typical block and a corridor survey. On board GPS data logged during AUAV's flight are being used for direct georeferencing, while ground check points are being used for evaluation. In addition various control point layouts are being tested using bundle adjustment for accuracy evaluation. Results indicate that it is possible to use on board single frequency GPS for direct georeferencing in cases of disaster management or areas without easy access, or even over featureless areas. Due to large numbers of tie points in the bundle adjustment, horizontal accuracy can be fulfilled with a rather small number of control points, but vertical accuracy may not.

  18. UAV-LiDAR accuracy and comparison to Structure from Motion photogrammetry

    NASA Astrophysics Data System (ADS)

    Kucharczyk, M.; Hugenholtz, C.; Zou, X.; Nesbit, P. R.; Barchyn, T.

    2016-12-01

    We compare the spatial accuracy of a UAV-LiDAR system with Structure from Motion (SfM) photogrammetry. UAV-based LiDAR remote sensing potentially offers advantages over SfM photogrammetry in vegetated terrain, particularly with respect to canopy penetration and related measurements of ground surface elevation and vegetation height; however, little quantitative evidence has been presented to date. To address this, we performed a case study at a field site in Alberta, Canada with six different land cover types: short grass, tall grass, short shrubs, tall shrubs, deciduous trees, and coniferous trees. Both UAV datasets were acquired on the same day. The SfM dataset was derived from images acquired by a senseFly eBee fixed-wing UAV equipped with a 16.1 megapixel RGB camera. The UAV-LiDAR system is a proprietary design that consists of a single-rotor helicopter (2-m rotor diameter) equipped with a Riegl VUX-1UAV laser scanner, KVH 1750 inertial measurement unit, and dual NovAtel GNSS receivers. We measured vegetation height from at least 30 samples in each land cover type and acquired check point measurements to determine horizontal and vertical accuracy. Vegetation height was measured manually for grasses and shrubs with a level staff, and with a total station for trees. Coordinates of horizontal and vertical check points were surveyed with real-time kinematic (RTK) GNSS. We followed standard methods for computing horizontal and vertical accuracies based on the 2015 guidelines from the American Society of Photogrammetry and Remote Sensing. Results will be presented at the AGU Fall Meeting.

  19. [True color accuracy in digital forensic photography].

    PubMed

    Ramsthaler, Frank; Birngruber, Christoph G; Kröll, Ann-Katrin; Kettner, Mattias; Verhoff, Marcel A

    2016-01-01

    Forensic photographs not only need to be unaltered and authentic and capture context-relevant images, along with certain minimum requirements for image sharpness and information density, but color accuracy also plays an important role, for instance, in the assessment of injuries or taphonomic stages, or in the identification and evaluation of traces from photos. The perception of color not only varies subjectively from person to person, but as a discrete property of an image, color in digital photos is also to a considerable extent influenced by technical factors such as lighting, acquisition settings, camera, and output medium (print, monitor). For these reasons, consistent color accuracy has so far been limited in digital photography. Because images usually contain a wealth of color information, especially for complex or composite colors or shades of color, and the wavelength-dependent sensitivity to factors such as light and shadow may vary between cameras, the usefulness of issuing general recommendations for camera capture settings is limited. Our results indicate that true image colors can best and most realistically be captured with the SpyderCheckr technical calibration tool for digital cameras tested in this study. Apart from aspects such as the simplicity and quickness of the calibration procedure, a further advantage of the tool is that the results are independent of the camera used and can also be used for the color management of output devices such as monitors and printers. The SpyderCheckr color-code patches allow true colors to be captured more realistically than with a manual white balance tool or an automatic flash. We therefore recommend that the use of a color management tool should be considered for the acquisition of all images that demand high true color accuracy (in particular in the setting of injury documentation).

  20. Pediatric Surgeon-Directed Wound Classification Improves Accuracy

    PubMed Central

    Zens, Tiffany J.; Rusy, Deborah A.; Gosain, Ankush

    2015-01-01

    Background Surgical wound classification (SWC) communicates the degree of contamination in the surgical field and is used to stratify risk of surgical site infection and compare outcomes amongst centers. We hypothesized that changing from nurse-directed to surgeon-directed SWC during a structured operative debrief we will improve accuracy of documentation. Methods An IRB-approved retrospective chart review was performed. Two time periods were defined: initially, SWC was determined and recorded by the circulating nurse (Pre-Debrief 6/2012-5/2013) and allowing six months for adoption and education, we implemented a structured operative debriefing including surgeon-directed SWC (Post-Debrief 1/2014-8/2014). Accuracy of SWC was determined for four commonly performed Pediatric General Surgery operations: inguinal hernia repair (clean), gastrostomy +/− Nissen fundoplication (clean-contaminated), appendectomy without perforation (contaminated), and appendectomy with perforation (dirty). Results 183 cases Pre-Debrief and 142 cases Post-Debrief met inclusion criteria. No differences between time periods were noted in regards to patient demographics, ASA class, or case mix. Accuracy of wound classification improved Post-Debrief (42% vs. 58.5%, p=0.003). Pre-Debrief, 26.8% of cases were overestimated or underestimated by more than one wound class, vs. 3.5% of cases Post-Debrief (p<0.001). Interestingly, the majority of Post-Debrief contaminated cases were incorrectly classified as clean-contaminated. Conclusions Implementation of a structured operative debrief including surgeon-directed SWC improves the percentage of correctly classified wounds and decreases the degree of inaccuracy in incorrectly classified cases. However, following implementation of the debriefing, we still observed a 41.5% rate of incorrect documentation, most notably in contaminated cases, indicating further education and process improvement is needed. PMID:27020829