Sample records for accurate quantitative snp-typing

  1. Toward Accurate and Quantitative Comparative Metagenomics.

    Nayfach, Stephen; Pollard, Katherine S


    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  2. SNP typing on the NanoChip electronic microarray

    Børsting, Claus; Sanchez Sanchez, Juan Jose; Morling, Niels


    We describe a single nucleotide polymorphism (SNP) typing protocol developed for the NanoChip electronic microarray. The NanoChip array consists of 100 electrodes covered by a thin hydrogel layer containing streptavidin. An electric currency can be applied to one, several, or all electrodes at the...... the bound DNA. Base stacking between the short reporter and the longer stabilizer oligo stabilizes the binding of a matching reporter, whereas the binding of a reporter carrying a mismatch in the SNP position will be relatively weak. Thermal stringency is applied to the NanoChip array according to a...

  3. A sensitive issue: Pyrosequencing as a valuable forensic SNP typing platform

    Harrison, C.; Musgrave-Brown, E.; Bender, K.;


    Analysing minute amounts of DNA is a routine challenge in forensics in part due to the poor sensitivity of an instrument and its inability to detect results from forensic samples. In this study, the sensitivity of the Pyrosequencing method is investigated using varying concentrations of DNA and...... Pyrosequencing as a valuable forensic SNP typing platform...

  4. Designer cantilevers for even more accurate quantitative measurements of biological systems with multifrequency AFM

    Contera, S.


    Multifrequency excitation/monitoring of cantilevers has made it possible both to achieve fast, relatively simple, nanometre-resolution quantitative mapping of mechanical of biological systems in solution using atomic force microscopy (AFM), and single molecule resolution detection by nanomechanical biosensors. A recent paper by Penedo et al [2015 Nanotechnology 26 485706] has made a significant contribution by developing simple methods to improve the signal to noise ratio in liquid environments, by selectively enhancing cantilever modes, which will lead to even more accurate quantitative measurements.

  5. A correlative imaging based methodology for accurate quantitative assessment of bone formation in additive manufactured implants.

    Geng, Hua; Todd, Naomi M; Devlin-Mullin, Aine; Poologasundarampillai, Gowsihan; Kim, Taek Bo; Madi, Kamel; Cartmell, Sarah; Mitchell, Christopher A; Jones, Julian R; Lee, Peter D


    A correlative imaging methodology was developed to accurately quantify bone formation in the complex lattice structure of additive manufactured implants. Micro computed tomography (μCT) and histomorphometry were combined, integrating the best features from both, while demonstrating the limitations of each imaging modality. This semi-automatic methodology registered each modality using a coarse graining technique to speed the registration of 2D histology sections to high resolution 3D μCT datasets. Once registered, histomorphometric qualitative and quantitative bone descriptors were directly correlated to 3D quantitative bone descriptors, such as bone ingrowth and bone contact. The correlative imaging allowed the significant volumetric shrinkage of histology sections to be quantified for the first time (~15 %). This technique demonstrated the importance of location of the histological section, demonstrating that up to a 30 % offset can be introduced. The results were used to quantitatively demonstrate the effectiveness of 3D printed titanium lattice implants. PMID:27153828

  6. Should scatter be corrected in both transmission and emission data for accurate quantitation in cardiac SPET?

    Ideally, reliable quantitation in single-photon emission tomography (SPET) requires both emission and transmission data to be scatter free. Although scatter in emission data has been extensively studied, it is not well known how scatter in transmission data affects relative and absolute quantitation in reconstructed images. We studied SPET quantitative accuracy for different amounts of scatter in emission and transmission data using a Utah phantom and a cardiac Data Spectrum phantom including different attenuating media. Acquisitions over 180 were considered and three projection sets were derived: 20% images and Jaszczak and triple-energy-window scatter-corrected projections. Transmission data were acquired using gadolinium-153 line sources in a 90-110 keV window using a narrow or wide scanning window. The transmission scans were performed either simultaneously with the emission acquisition or 24 h later. Transmission maps were reconstructed using filtered backprojection and μ values were linearly scaled from 100 to 140 keV. Attenuation-corrected images were reconstructed using a conjugate gradient minimal residual algorithm. The μ value underestimation varied between 4% with a narrow transmission window in soft tissue and 22% with a wide window in a material simulating bone. Scatter in the emission and transmission data had little effect on the uniformity of activity distribution in the left ventricle wall and in a uniformly hot compartment of the Utah phantom. Correcting the transmission data for scatter had no impact on contrast between a hot and a cold region or on signal-to-noise ratio (SNR) in regions with uniform activity distribution, while correcting the emission data for scatter improved contrast and reduced SNR. For absolute quantitation, the most accurate results (bias <4% in both phantoms) were obtained when reducing scatter in both emission and transmission data. In conclusion, trying to obtain the same amount of scatter in emission and transmission

  7. Should scatter be corrected in both transmission and emission data for accurate quantitation in cardiac SPET?

    Fakhri, G.E. [Harvard Medical School, Boston, MA (United States). Dept. of Radiology; U494 INSERM, CHU Pitie-Salpetriere, Paris (France); Buvat, I.; Todd-Pokropek, A.; Benali, H. [U494 INSERM, CHU Pitie-Salpetriere, Paris (France); Almeida, P. [Servico de Medicina Nuclear, Hospital Garcia de Orta, Almada (Portugal); Bendriem, B. [CTI, Inc., Knoxville, TN (United States)


    Ideally, reliable quantitation in single-photon emission tomography (SPET) requires both emission and transmission data to be scatter free. Although scatter in emission data has been extensively studied, it is not well known how scatter in transmission data affects relative and absolute quantitation in reconstructed images. We studied SPET quantitative accuracy for different amounts of scatter in emission and transmission data using a Utah phantom and a cardiac Data Spectrum phantom including different attenuating media. Acquisitions over 180 were considered and three projection sets were derived: 20% images and Jaszczak and triple-energy-window scatter-corrected projections. Transmission data were acquired using gadolinium-153 line sources in a 90-110 keV window using a narrow or wide scanning window. The transmission scans were performed either simultaneously with the emission acquisition or 24 h later. Transmission maps were reconstructed using filtered backprojection and {mu} values were linearly scaled from 100 to 140 keV. Attenuation-corrected images were reconstructed using a conjugate gradient minimal residual algorithm. The {mu} value underestimation varied between 4% with a narrow transmission window in soft tissue and 22% with a wide window in a material simulating bone. Scatter in the emission and transmission data had little effect on the uniformity of activity distribution in the left ventricle wall and in a uniformly hot compartment of the Utah phantom. Correcting the transmission data for scatter had no impact on contrast between a hot and a cold region or on signal-to-noise ratio (SNR) in regions with uniform activity distribution, while correcting the emission data for scatter improved contrast and reduced SNR. For absolute quantitation, the most accurate results (bias <4% in both phantoms) were obtained when reducing scatter in both emission and transmission data. In conclusion, trying to obtain the same amount of scatter in emission and

  8. Accurate and quantitative polarization-sensitive OCT by unbiased birefringence estimator with noise-stochastic correction

    Kasaragod, Deepa; Sugiyama, Satoshi; Ikuno, Yasushi; Alonso-Caneiro, David; Yamanari, Masahiro; Fukuda, Shinichi; Oshika, Tetsuro; Hong, Young-Joo; Li, En; Makita, Shuichi; Miura, Masahiro; Yasuno, Yoshiaki


    Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that contrasts the polarization properties of tissues. It has been applied to ophthalmology, cardiology, etc. Proper quantitative imaging is required for a widespread clinical utility. However, the conventional method of averaging to improve the signal to noise ratio (SNR) and the contrast of the phase retardation (or birefringence) images introduce a noise bias offset from the true value. This bias reduces the effectiveness of birefringence contrast for a quantitative study. Although coherent averaging of Jones matrix tomography has been widely utilized and has improved the image quality, the fundamental limitation of nonlinear dependency of phase retardation and birefringence to the SNR was not overcome. So the birefringence obtained by PS-OCT was still not accurate for a quantitative imaging. The nonlinear effect of SNR to phase retardation and birefringence measurement was previously formulated in detail for a Jones matrix OCT (JM-OCT) [1]. Based on this, we had developed a maximum a-posteriori (MAP) estimator and quantitative birefringence imaging was demonstrated [2]. However, this first version of estimator had a theoretical shortcoming. It did not take into account the stochastic nature of SNR of OCT signal. In this paper, we present an improved version of the MAP estimator which takes into account the stochastic property of SNR. This estimator uses a probability distribution function (PDF) of true local retardation, which is proportional to birefringence, under a specific set of measurements of the birefringence and SNR. The PDF was pre-computed by a Monte-Carlo (MC) simulation based on the mathematical model of JM-OCT before the measurement. A comparison between this new MAP estimator, our previous MAP estimator [2], and the standard mean estimator is presented. The comparisons are performed both by numerical simulation and in vivo measurements of anterior and

  9. Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples

    Børsting, Claus; Mogensen, Helle Smidt; Morling, Niels


    case investigation and only partial profiles (0-6 STRs) were obtained. Eleven of the samples could not be quantified with the Quantifiler™ Human DNA Quantification kit because of partial or complete inhibition of the PCR. For eight of these samples, SNP typing was only possible when the buffer and DNA......Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR...... amplification of tandem repeats. These artifacts may be avoided by typing bi-allelic markers instead of STRs. In this work, the SNPforID multiplex assay was used to type LtDNA. A sensitized SNP typing protocol was introduced, that increased signal strengths without increasing noise and without affecting the...

  10. Multiobjective optimization in quantitative structure-activity relationships: deriving accurate and interpretable QSARs.

    Nicolotti, Orazio; Gillet, Valerie J; Fleming, Peter J; Green, Darren V S


    Deriving quantitative structure-activity relationship (QSAR) models that are accurate, reliable, and easily interpretable is a difficult task. In this study, two new methods have been developed that aim to find useful QSAR models that represent an appropriate balance between model accuracy and complexity. Both methods are based on genetic programming (GP). The first method, referred to as genetic QSAR (or GPQSAR), uses a penalty function to control model complexity. GPQSAR is designed to derive a single linear model that represents an appropriate balance between the variance and the number of descriptors selected for the model. The second method, referred to as multiobjective genetic QSAR (MoQSAR), is based on multiobjective GP and represents a new way of thinking of QSAR. Specifically, QSAR is considered as a multiobjective optimization problem that comprises a number of competitive objectives. Typical objectives include model fitting, the total number of terms, and the occurrence of nonlinear terms. MoQSAR results in a family of equivalent QSAR models where each QSAR represents a different tradeoff in the objectives. A practical consideration often overlooked in QSAR studies is the need for the model to promote an understanding of the biochemical response under investigation. To accomplish this, chemically intuitive descriptors are needed but do not always give rise to statistically robust models. This problem is addressed by the addition of a further objective, called chemical desirability, that aims to reward models that consist of descriptors that are easily interpretable by chemists. GPQSAR and MoQSAR have been tested on various data sets including the Selwood data set and two different solubility data sets. The study demonstrates that the MoQSAR method is able to find models that are at least as good as models derived using standard statistical approaches and also yields models that allow a medicinal chemist to trade statistical robustness for chemical

  11. Quantitative evaluation of gas entrainment by numerical simulation with accurate physics model

    In the design study on a large-scale sodium-cooled fast reactor (JSFR), the reactor vessel is compactified to reduce the construction costs and enhance the economical competitiveness. However, such a reactor vessel induces higher coolant flows in the vessel and causes several thermal-hydraulics issues, e.g. gas entrainment (GE) phenomenon. The GE in the JSFR may occur at the cover gas-coolant interface in the vessel by a strong vortex at the interface. This type of GE has been studied experimentally, numerically and theoretically. Therefore, the onset condition of the GE can be evaluated conservatively. However, to clarify the negative influences of the GE on the JSFR, not only the onset condition of the GE but also the entrained gas (bubble) flow rate has to be evaluated. As long as we know, studies on the entrained gas flow rates are quite limited in both experimental and numerical fields. In this study, the authors performs numerical simulations to investigate the entrained gas amount in a hollow vortex experiment (a cylindrical vessel experiment). To simulate interfacial deformations accurately, a high-precision numerical simulation algorithm for gas-liquid two-phase flows is employed. In the first place, fine cells are applied to the region near the center of the vortex to reproduce the steep radial gradient of the circumferential velocity in this region. Then, the entrained gas flow rates are evaluated in the simulation results and are compared to the experimental data. As a result, the numerical simulation gives somewhat larger entrained gas flow rate than the experiment. However, both the numerical simulation and experiment show the entrained gas flow rates which are proportional to the outlet water velocity. In conclusion, it is confirmed that the developed numerical simulation algorithm can be applied to the quantitative evaluation of the GE. (authors)

  12. Accurate single-shot quantitative phase imaging of biological specimens with telecentric digital holographic microscopy

    Doblas Expósito, Ana Isabel; Sánchez Ortiga, Emilio; Saavedra Tortosa, Genaro; Martínez Corral, Manuel; García Sucerquia, Jorge Iván


    The advantages of using a telecentric imaging system in digital holographic microscopy (DHM) to study biological specimens are highlighted. To this end, the performances of nontelecentric DHM and telecentric DHM are evaluated from the quantitative phase imaging (QPI) point of view. The evaluated stability of the microscope allows single-shot QPI in DHM by using telecentric imaging systems. Quantitative phase maps of a section of the head of the drosophila melanogaster fly and of red blood cel...

  13. There's plenty of gloom at the bottom: the many challenges of accurate quantitation in size-based oligomeric separations.

    Striegel, André M


    There is a variety of small-molecule species (e.g., tackifiers, plasticizers, oligosaccharides) the size-based characterization of which is of considerable scientific and industrial importance. Likewise, quantitation of the amount of oligomers in a polymer sample is crucial for the import and export of substances into the USA and European Union (EU). While the characterization of ultra-high molar mass macromolecules by size-based separation techniques is generally considered a challenge, it is this author's contention that a greater challenge is encountered when trying to perform, for quantitation purposes, separations in and of the oligomeric region. The latter thesis is expounded herein, by detailing the various obstacles encountered en route to accurate, quantitative oligomeric separations by entropically dominated techniques such as size-exclusion chromatography, hydrodynamic chromatography, and asymmetric flow field-flow fractionation, as well as by methods which are, principally, enthalpically driven such as liquid adsorption and temperature gradient interaction chromatography. These obstacles include, among others, the diminished sensitivity of static light scattering (SLS) detection at low molar masses, the non-constancy of the response of SLS and of commonly employed concentration-sensitive detectors across the oligomeric region, and the loss of oligomers through the accumulation wall membrane in asymmetric flow field-flow fractionation. The battle is not lost, however, because, with some care and given a sufficient supply of sample, the quantitation of both individual oligomeric species and of the total oligomeric region is often possible. PMID:23887277

  14. Autosomal SNP typing of forensic samples with the GenPlex(TM) HID System: Results of a collaborative study

    Tomas, C.; Axler-DiPerte, G.; Budimlija, Z.M.;


    Europe and 5 in the US) in order to test the robustness and reliability of the GenPlex(TM) HID System on forensic samples. Three samples with partly degraded DNA and 10 samples with low amounts of DNA were analyzed in duplicates using various amounts of DNA. In order to compare the performance of the Gen......The GenPlex(TM) HID System (Applied Biosystems - AB) offers typing of 48 of the 52 SNPforID SNPs and amelogenin. Previous studies have shown a high reproducibility of the GenPlex(TM) HID System using 250-500 pg DNA of good quality. An international exercise was performed by 14 laboratories (9 in......Plex(TM) HID System with the most commonly used STR kits, 500 pg of partly degraded DNA from three samples was typed by the laboratories using one or more STR kits. The median SNP typing success rate was 92.3% with 500 pg of partly degraded DNA. Three of the fourteen laboratories counted for more than two...

  15. High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children

    Holt, Kathryn E


    Abstract Background Salmonella Typhi (S. Typhi) causes typhoid fever, which remains an important public health issue in many developing countries. Kathmandu, the capital of Nepal, is an area of high incidence and the pediatric population appears to be at high risk of exposure and infection. Methods We recently defined the population structure of S. Typhi, using new sequencing technologies to identify nearly 2,000 single nucleotide polymorphisms (SNPs) that can be used as unequivocal phylogenetic markers. Here we have used the GoldenGate (Illumina) platform to simultaneously type 1,500 of these SNPs in 62 S. Typhi isolates causing severe typhoid in children admitted to Patan Hospital in Kathmandu. Results Eight distinct S. Typhi haplotypes were identified during the 20-month study period, with 68% of isolates belonging to a subclone of the previously defined H58 S. Typhi. This subclone was closely associated with resistance to nalidixic acid, with all isolates from this group demonstrating a resistant phenotype and harbouring the same resistance-associated SNP in GyrA (Phe83). A secondary clone, comprising 19% of isolates, was observed only during the second half of the study. Conclusions Our data demonstrate the utility of SNP typing for monitoring bacterial populations over a defined period in a single endemic setting. We provide evidence for genotype introduction and define a nalidixic acid resistant subclone of S. Typhi, which appears to be the dominant cause of severe pediatric typhoid in Kathmandu during the study period.

  16. A method for accurate detection of genomic microdeletions using real-time quantitative PCR

    Bassett Anne S


    Full Text Available Abstract Background Quantitative Polymerase Chain Reaction (qPCR is a well-established method for quantifying levels of gene expression, but has not been routinely applied to the detection of constitutional copy number alterations of human genomic DNA. Microdeletions or microduplications of the human genome are associated with a variety of genetic disorders. Although, clinical laboratories routinely use fluorescence in situ hybridization (FISH to identify such cryptic genomic alterations, there remains a significant number of individuals in which constitutional genomic imbalance is suspected, based on clinical parameters, but cannot be readily detected using current cytogenetic techniques. Results In this study, a novel application for real-time qPCR is presented that can be used to reproducibly detect chromosomal microdeletions and microduplications. This approach was applied to DNA from a series of patient samples and controls to validate genomic copy number alteration at cytoband 22q11. The study group comprised 12 patients with clinical symptoms of chromosome 22q11 deletion syndrome (22q11DS, 1 patient trisomic for 22q11 and 4 normal controls. 6 of the patients (group 1 had known hemizygous deletions, as detected by standard diagnostic FISH, whilst the remaining 6 patients (group 2 were classified as 22q11DS negative using the clinical FISH assay. Screening of the patients and controls with a set of 10 real time qPCR primers, spanning the 22q11.2-deleted region and flanking sequence, confirmed the FISH assay results for all patients with 100% concordance. Moreover, this qPCR enabled a refinement of the region of deletion at 22q11. Analysis of DNA from chromosome 22 trisomic sample demonstrated genomic duplication within 22q11. Conclusion In this paper we present a qPCR approach for the detection of chromosomal microdeletions and microduplications. The strategic use of in silico modelling for qPCR primer design to avoid regions of repetitive

  17. Development and evaluation of a liquid chromatography-mass spectrometry method for rapid, accurate quantitation of malondialdehyde in human plasma.

    Sobsey, Constance A; Han, Jun; Lin, Karen; Swardfager, Walter; Levitt, Anthony; Borchers, Christoph H


    Malondialdhyde (MDA) is a commonly used marker of lipid peroxidation in oxidative stress. To provide a sensitive analytical method that is compatible with high throughput, we developed a multiple reaction monitoring-mass spectrometry (MRM-MS) approach using 3-nitrophenylhydrazine chemical derivatization, isotope-labeling, and liquid chromatography (LC) with electrospray ionization (ESI)-tandem mass spectrometry assay to accurately quantify MDA in human plasma. A stable isotope-labeled internal standard was used to compensate for ESI matrix effects. The assay is linear (R(2)=0.9999) over a 20,000-fold concentration range with a lower limit of quantitation of 30fmol (on-column). Intra- and inter-run coefficients of variation (CVs) were 36h at 5°C. Standards spiked into plasma had recoveries of 92-98%. When compared to a common LC-UV method, the LC-MS method found near-identical MDA concentrations. A pilot project to quantify MDA in patient plasma samples (n=26) in a study of major depressive disorder with winter-type seasonal pattern (MDD-s) confirmed known associations between MDA concentrations and obesity (p<0.02). The LC-MS method provides high sensitivity and high reproducibility for quantifying MDA in human plasma. The simple sample preparation and rapid analysis time (5x faster than LC-UV) offers high throughput for large-scale clinical applications. PMID:27437618

  18. A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using quantitative nuclear magnetic resonance.

    Goldoni, Luca; Beringhelli, Tiziana; Rocchia, Walter; Realini, Natalia; Piomelli, Daniele


    Absolute analyte quantification by nuclear magnetic resonance (NMR) spectroscopy is rarely pursued in metabolomics, even though this would allow researchers to compare results obtained using different techniques. Here we report on a new protocol that permits, after pH-controlled serum protein removal, the sensitive quantification (limit of detection [LOD] = 5-25 μM) of hydrophilic nutrients and metabolites in the extracellular medium of cells in cultures. The method does not require the use of databases and uses PULCON (pulse length-based concentration determination) quantitative NMR to obtain results that are significantly more accurate and reproducible than those obtained by CPMG (Carr-Purcell-Meiboom-Gill) sequence or post-processing filtering approaches. Three practical applications of the method highlight its flexibility under different cell culture conditions. We identified and quantified (i) metabolic differences between genetically engineered human cell lines, (ii) alterations in cellular metabolism induced by differentiation of mouse myoblasts into myotubes, and (iii) metabolic changes caused by activation of neurotransmitter receptors in mouse myoblasts. Thus, the new protocol offers an easily implementable, efficient, and versatile tool for the investigation of cellular metabolism and signal transduction. PMID:26898303

  19. Automated and quantitative headspace in-tube extraction for the accurate determination of highly volatile compounds from wines and beers.

    Zapata, Julián; Mateo-Vivaracho, Laura; Lopez, Ricardo; Ferreira, Vicente


    An automatic headspace in-tube extraction (ITEX) method for the accurate determination of acetaldehyde, ethyl acetate, diacetyl and other volatile compounds from wine and beer has been developed and validated. Method accuracy is based on the nearly quantitative transference of volatile compounds from the sample to the ITEX trap. For achieving that goal most methodological aspects and parameters have been carefully examined. The vial and sample sizes and the trapping materials were found to be critical due to the pernicious saturation effects of ethanol. Small 2 mL vials containing very small amounts of sample (20 μL of 1:10 diluted sample) and a trap filled with 22 mg of Bond Elut ENV resins could guarantee a complete trapping of sample vapors. The complete extraction requires 100 × 0.5 mL pumping strokes at 60 °C and takes 24 min. Analytes are further desorbed at 240 °C into the GC injector under a 1:5 split ratio. The proportion of analytes finally transferred to the trap ranged from 85 to 99%. The validation of the method showed satisfactory figures of merit. Determination coefficients were better than 0.995 in all cases and good repeatability was also obtained (better than 7% in all cases). Reproducibility was better than 8.3% except for acetaldehyde (13.1%). Detection limits were below the odor detection thresholds of these target compounds in wine and beer and well below the normal ranges of occurrence. Recoveries were not significantly different to 100%, except in the case of acetaldehyde. In such a case it could be determined that the method is not able to break some of the adducts that this compound forms with sulfites. However, such problem was avoided after incubating the sample with glyoxal. The method can constitute a general and reliable alternative for the analysis of very volatile compounds in other difficult matrixes. PMID:22340891

  20. Optimization of Specimen-Handling Procedures for Accurate Quantitation of Levels of Human Immunodeficiency Virus RNA in Plasma by Reverse Transcriptase PCR

    Dickover, Ruth E.; Herman, Steven A.; Saddiq, Khaliq; Wafer, Deborah; Dillon, Maryanne; Bryson, Yvonne J.


    Human immunodeficiency virus type 1 (HIV-1) RNA levels in plasma are currently widely used clinically for prognostication and in monitoring antiretroviral therapy. Accurate and reproducible results are critical for patient management. To determine the effects of specimen collection and handling procedures on quantitative measurement of HIV-1 RNA, we compared anticoagulants and sample processing times. Whole blood was collected from 20 HIV-1-infected patients in EDTA, acid citrate dextrose (AC...

  1. Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data

    Alves-Ferreira Marcio; Grossi-de-Sa Maria; Brilhante Osmundo; Nardeli Sarah M; Artico Sinara


    Abstract Background Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on i...

  2. Wavelet prism decomposition analysis applied to CARS spectroscopy: a tool for accurate and quantitative extraction of resonant vibrational responses.

    Kan, Yelena; Lensu, Lasse; Hehl, Gregor; Volkmer, Andreas; Vartiainen, Erik M


    We propose an approach, based on wavelet prism decomposition analysis, for correcting experimental artefacts in a coherent anti-Stokes Raman scattering (CARS) spectrum. This method allows estimating and eliminating a slowly varying modulation error function in the measured normalized CARS spectrum and yields a corrected CARS line-shape. The main advantage of the approach is that the spectral phase and amplitude corrections are avoided in the retrieved Raman line-shape spectrum, thus significantly simplifying the quantitative reconstruction of the sample's Raman response from a normalized CARS spectrum in the presence of experimental artefacts. Moreover, the approach obviates the need for assumptions about the modulation error distribution and the chemical composition of the specimens under study. The method is quantitatively validated on normalized CARS spectra recorded for equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose. PMID:27410113

  3. Is SPECT or CT Based Attenuation Correction More Quantitatively Accurate for Dedicated Breast SPECT Acquired with Non-Traditional Trajectories?

    Perez, Kristy L.; Mann, Steve D.; Pachon, Jan H.; Madhav, Priti; Tornai, Martin P.


    Attenuation correction is necessary for SPECT quantification. There are a variety of methods to create attenuation maps. For dedicated breast SPECT imaging, it is unclear if either SPECT- or CT-based attenuation map would provide the most accurate quantification and whether or not segmenting the different tissue types will have an effect on the qunatification. For these experiments, 99mTc diluted in methanol and water was filled into geometric and anthropomorphic breast phantoms and was image...

  4. Self-aliquoting microarray plates for accurate quantitative matrix-assisted laser desorption/ionization mass spectrometry.

    Pabst, Martin; Fagerer, Stephan R; Köhling, Rudolf; Küster, Simon K; Steinhoff, Robert; Badertscher, Martin; Wahl, Fabian; Dittrich, Petra S; Jefimovs, Konstantins; Zenobi, Renato


    Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a fast analysis tool employed for the detection of a broad range of analytes. However, MALDI-MS has a reputation of not being suitable for quantitative analysis. Inhomogeneous analyte/matrix co-crystallization, spot-to-spot inhomogeneity, as well as a typically low number of replicates are the main contributing factors. Here, we present a novel MALDI sample target for quantitative MALDI-MS applications, which addresses the limitations mentioned above. The platform is based on the recently developed microarray for mass spectrometry (MAMS) technology and contains parallel lanes of hydrophilic reservoirs. Samples are not pipetted manually but deposited by dragging one or several sample droplets with a metal sliding device along these lanes. Sample is rapidly and automatically aliquoted into the sample spots due to the interplay of hydrophilic/hydrophobic interactions. With a few microliters of sample, it is possible to aliquot up to 40 replicates within seconds, each aliquot containing just 10 nL. The analyte droplet dries immediately and homogeneously, and consumption of the whole spot during MALDI-MS analysis is typically accomplished within few seconds. We evaluated these sample targets with respect to their suitability for use with different samples and matrices. Furthermore, we tested their application for generating calibration curves of standard peptides with α-cyano-4-hdydroxycinnamic acid as a matrix. For angiotensin II and [Glu(1)]-fibrinopeptide B we achieved coefficients of determination (r(2)) greater than 0.99 without the use of internal standards. PMID:24003910

  5. Application of an Effective Statistical Technique for an Accurate and Powerful Mining of Quantitative Trait Loci for Rice Aroma Trait.

    Farahnaz Sadat Golestan Hashemi

    Full Text Available When a phenotype of interest is associated with an external/internal covariate, covariate inclusion in quantitative trait loci (QTL analyses can diminish residual variation and subsequently enhance the ability of QTL detection. In the in vitro synthesis of 2-acetyl-1-pyrroline (2AP, the main fragrance compound in rice, the thermal processing during the Maillard-type reaction between proline and carbohydrate reduction produces a roasted, popcorn-like aroma. Hence, for the first time, we included the proline amino acid, an important precursor of 2AP, as a covariate in our QTL mapping analyses to precisely explore the genetic factors affecting natural variation for rice scent. Consequently, two QTLs were traced on chromosomes 4 and 8. They explained from 20% to 49% of the total aroma phenotypic variance. Additionally, by saturating the interval harboring the major QTL using gene-based primers, a putative allele of fgr (major genetic determinant of fragrance was mapped in the QTL on the 8th chromosome in the interval RM223-SCU015RM (1.63 cM. These loci supported previous studies of different accessions. Such QTLs can be widely used by breeders in crop improvement programs and for further fine mapping. Moreover, no previous studies and findings were found on simultaneous assessment of the relationship among 2AP, proline and fragrance QTLs. Therefore, our findings can help further our understanding of the metabolomic and genetic basis of 2AP biosynthesis in aromatic rice.

  6. Selection of accurate reference genes in mouse trophoblast stem cells for reverse transcription-quantitative polymerase chain reaction.

    Motomura, Kaori; Inoue, Kimiko; Ogura, Atsuo


    Mouse trophoblast stem cells (TSCs) form colonies of different sizes and morphologies, which might reflect their degrees of differentiation. Therefore, each colony type can have a characteristic gene expression profile; however, the expression levels of internal reference genes may also change, causing fluctuations in their estimated gene expression levels. In this study, we validated seven housekeeping genes by using a geometric averaging method and identified Gapdh as the most stable gene across different colony types. Indeed, when Gapdh was used as the reference, expression levels of Elf5, a TSC marker gene, stringently classified TSC colonies into two groups: a high expression groups consisting of type 1 and 2 colonies, and a lower expression group consisting of type 3 and 4 colonies. This clustering was consistent with our putative classification of undifferentiated/differentiated colonies based on their time-dependent colony transitions. By contrast, use of an unstable reference gene (Rn18s) allowed no such clear classification. Cdx2, another TSC marker, did not show any significant colony type-specific expression pattern irrespective of the reference gene. Selection of stable reference genes for quantitative gene expression analysis might be critical, especially when cell lines consisting of heterogeneous cell populations are used. PMID:26853688

  7. Accurate quantitative 13C NMR spectroscopy: repeatability over time of site-specific 13C isotope ratio determination.

    Caytan, Elsa; Botosoa, Eliot P; Silvestre, Virginie; Robins, Richard J; Akoka, Serge; Remaud, Gérald S


    The stability over time (repeatability) for the determination of site-specific 13C/12C ratios at natural abundance by quantitative 13C NMR spectroscopy has been tested on three probes: enriched bilabeled [1,2-13C2]ethanol; ethanol at natural abundance; and vanillin at natural abundance. It is shown in all three cases that the standard deviation for a series of measurements taken every 2-3 months over periods between 9 and 13 months is equal to or smaller than the standard deviation calculated from 5-10 replicate measurements made on a single sample. The precision which can be achieved using the present analytical 13C NMR protocol is higher than the prerequisite value of 1-2 per thousand for the determination of site-specific 13C/12C ratios at natural abundance (13C-SNIF-NMR). Hence, this technique permits the discrimination of very small variations in 13C/12C ratios between carbon positions, as found in biogenic natural products. This observed stability over time in 13C NMR spectroscopy indicates that further improvements in precision will depend primarily on improved signal-to-noise ratio. PMID:17900175

  8. Validation of Reference Genes for Accurate Normalization of Gene Expression in Lilium davidii var. unicolor for Real Time Quantitative PCR.

    XueYan Li

    Full Text Available Lilium is an important commercial market flower bulb. qRT-PCR is an extremely important technique to track gene expression levels. The requirement of suitable reference genes for normalization has become increasingly significant and exigent. The expression of internal control genes in living organisms varies considerably under different experimental conditions. For economically important Lilium, only a limited number of reference genes applied in qRT-PCR have been reported to date. In this study, the expression stability of 12 candidate genes including α-TUB, β-TUB, ACT, eIF, GAPDH, UBQ, UBC, 18S, 60S, AP4, FP, and RH2, in a diverse set of 29 samples representing different developmental processes, three stress treatments (cold, heat, and salt and different organs, has been evaluated. For different organs, the combination of ACT, GAPDH, and UBQ is appropriate whereas ACT together with AP4, or ACT along with GAPDH is suitable for normalization of leaves and scales at different developmental stages, respectively. In leaves, scales and roots under stress treatments, FP, ACT and AP4, respectively showed the most stable expression. This study provides a guide for the selection of a reference gene under different experimental conditions, and will benefit future research on more accurate gene expression studies in a wide variety of Lilium genotypes.

  9. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin.

    Johnston, Ryne C; Zhou, Jing; Smith, Jeremy C; Parks, Jerry M


    Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co-ligand binding equilibrium constants (Kon/off), pKas, and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co(III), Co(II), and Co(I) species, respectively, and the second model features saturation of each vacant axial coordination site on Co(II) and Co(I) species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co-axial ligand binding, leading to substantial errors in predicted pKas and

  10. Tandem Mass Spectrometry Measurement of the Collision Products of Carbamate Anions Derived from CO2 Capture Sorbents: Paving the Way for Accurate Quantitation

    Jackson, Phil; Fisher, Keith J.; Attalla, Moetaz Ibrahim


    The reaction between CO2 and aqueous amines to produce a charged carbamate product plays a crucial role in post-combustion capture chemistry when primary and secondary amines are used. In this paper, we report the low energy negative-ion CID results for several anionic carbamates derived from primary and secondary amines commonly used as post-combustion capture solvents. The study was performed using the modern equivalent of a triple quadrupole instrument equipped with a T-wave collision cell. Deuterium labeling of 2-aminoethanol (1,1,2,2,-d4-2-aminoethanol) and computations at the M06-2X/6-311++G(d,p) level were used to confirm the identity of the fragmentation products for 2-hydroxyethylcarbamate (derived from 2-aminoethanol), in particular the ions CN-, NCO- and facile neutral losses of CO2 and water; there is precedent for the latter in condensed phase isocyanate chemistry. The fragmentations of 2-hydroxyethylcarbamate were generalized for carbamate anions derived from other capture amines, including ethylenediamine, diethanolamine, and piperazine. We also report unequivocal evidence for the existence of carbamate anions derived from sterically hindered amines ( Tris(2-hydroxymethyl)aminomethane and 2-methyl-2-aminopropanol). For the suite of carbamates investigated, diagnostic losses include the decarboxylation product (-CO2, 44 mass units), loss of 46 mass units and the fragments NCO- ( m/z 42) and CN- ( m/z 26). We also report low energy CID results for the dicarbamate dianion (-O2CNHC2H4NHCO{2/-}) commonly encountered in CO2 capture solution utilizing ethylenediamine. Finally, we demonstrate a promising ion chromatography-MS based procedure for the separation and quantitation of aqueous anionic carbamates, which is based on the reported CID findings. The availability of accurate quantitation methods for ionic CO2 capture products could lead to dynamic operational tuning of CO2 capture-plants and, thus, cost-savings via real-time manipulation of solvent

  11. Mitochondrial DNA as a non-invasive biomarker: Accurate quantification using real time quantitative PCR without co-amplification of pseudogenes and dilution bias

    Malik, Afshan N., E-mail: [King' s College London, Diabetes Research Group, Division of Diabetes and Nutritional Sciences, School of Medicine (United Kingdom); Shahni, Rojeen; Rodriguez-de-Ledesma, Ana; Laftah, Abas; Cunningham, Phil [King' s College London, Diabetes Research Group, Division of Diabetes and Nutritional Sciences, School of Medicine (United Kingdom)


    Highlights: {yields} Mitochondrial dysfunction is central to many diseases of oxidative stress. {yields} 95% of the mitochondrial genome is duplicated in the nuclear genome. {yields} Dilution of untreated genomic DNA leads to dilution bias. {yields} Unique primers and template pretreatment are needed to accurately measure mitochondrial DNA content. -- Abstract: Circulating mitochondrial DNA (MtDNA) is a potential non-invasive biomarker of cellular mitochondrial dysfunction, the latter known to be central to a wide range of human diseases. Changes in MtDNA are usually determined by quantification of MtDNA relative to nuclear DNA (Mt/N) using real time quantitative PCR. We propose that the methodology for measuring Mt/N needs to be improved and we have identified that current methods have at least one of the following three problems: (1) As much of the mitochondrial genome is duplicated in the nuclear genome, many commonly used MtDNA primers co-amplify homologous pseudogenes found in the nuclear genome; (2) use of regions from genes such as {beta}-actin and 18S rRNA which are repetitive and/or highly variable for qPCR of the nuclear genome leads to errors; and (3) the size difference of mitochondrial and nuclear genomes cause a 'dilution bias' when template DNA is diluted. We describe a PCR-based method using unique regions in the human mitochondrial genome not duplicated in the nuclear genome; unique single copy region in the nuclear genome and template treatment to remove dilution bias, to accurately quantify MtDNA from human samples.

  12. Accurate and easy-to-use assessment of contiguous DNA methylation sites based on proportion competitive quantitative-PCR and lateral flow nucleic acid biosensor.

    Xu, Wentao; Cheng, Nan; Huang, Kunlun; Lin, Yuehe; Wang, Chenguang; Xu, Yuancong; Zhu, Longjiao; Du, Dan; Luo, Yunbo


    Many types of diagnostic technologies have been reported for DNA methylation, but they require a standard curve for quantification or only show moderate accuracy. Moreover, most technologies have difficulty providing information on the level of methylation at specific contiguous multi-sites, not to mention easy-to-use detection to eliminate labor-intensive procedures. We have addressed these limitations and report here a cascade strategy that combines proportion competitive quantitative PCR (PCQ-PCR) and lateral flow nucleic acid biosensor (LFNAB), resulting in accurate and easy-to-use assessment. The P16 gene with specific multi-methylated sites, a well-studied tumor suppressor gene, was used as the target DNA sequence model. First, PCQ-PCR provided amplification products with an accurate proportion of multi-methylated sites following the principle of proportionality, and double-labeled duplex DNA was synthesized. Then, a LFNAB strategy was further employed for amplified signal detection via immune affinity recognition, and the exact level of site-specific methylation could be determined by the relative intensity of the test line and internal reference line. This combination resulted in all recoveries being greater than 94%, which are pretty satisfactory recoveries in DNA methylation assessment. Moreover, the developed cascades show significantly high usability as a simple, sensitive, and low-cost tool. Therefore, as a universal platform for sensing systems for the detection of contiguous multi-sites of DNA methylation without external standards and expensive instrumentation, this PCQ-PCR-LFNAB cascade method shows great promise for the point-of-care diagnosis of cancer risk and therapeutics. PMID:26914373

  13. Mitochondrial DNA as a non-invasive biomarker: Accurate quantification using real time quantitative PCR without co-amplification of pseudogenes and dilution bias

    Highlights: → Mitochondrial dysfunction is central to many diseases of oxidative stress. → 95% of the mitochondrial genome is duplicated in the nuclear genome. → Dilution of untreated genomic DNA leads to dilution bias. → Unique primers and template pretreatment are needed to accurately measure mitochondrial DNA content. -- Abstract: Circulating mitochondrial DNA (MtDNA) is a potential non-invasive biomarker of cellular mitochondrial dysfunction, the latter known to be central to a wide range of human diseases. Changes in MtDNA are usually determined by quantification of MtDNA relative to nuclear DNA (Mt/N) using real time quantitative PCR. We propose that the methodology for measuring Mt/N needs to be improved and we have identified that current methods have at least one of the following three problems: (1) As much of the mitochondrial genome is duplicated in the nuclear genome, many commonly used MtDNA primers co-amplify homologous pseudogenes found in the nuclear genome; (2) use of regions from genes such as β-actin and 18S rRNA which are repetitive and/or highly variable for qPCR of the nuclear genome leads to errors; and (3) the size difference of mitochondrial and nuclear genomes cause a 'dilution bias' when template DNA is diluted. We describe a PCR-based method using unique regions in the human mitochondrial genome not duplicated in the nuclear genome; unique single copy region in the nuclear genome and template treatment to remove dilution bias, to accurately quantify MtDNA from human samples.

  14. Evaluation of the iPLEX(®) Sample ID Plus Panel designed for the Sequenom MassARRAY(®) system. A SNP typing assay developed for human identification and sample tracking based on the SNPforID panel

    Johansen, P; Andersen, J D; Børsting, Claus; Morling, N


    Sequenom launched the first commercial SNP typing kit for human identification, named the iPLEX(®) Sample ID Plus Panel. The kit amplifies 47 of the 52 SNPs in the SNPforID panel, amelogenin and two Y-chromosome SNPs in one multiplex PCR. The SNPs were analyzed by single base extension (SBE) and Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). In this study, we evaluated the accuracy and sensitivity of the iPLEX(®) Sample ID Plus Panel by comparing ...

  15. Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data

    Alves-Ferreira Marcio


    Full Text Available Abstract Background Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR. Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes. Results By the use of two distinct algorithms, implemented by geNorm and NormFinder, we have assessed the gene expression of nine candidate reference genes in cotton: GhACT4, GhEF1α5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhβTUB3 and GhUBQ14. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of GhPP2A1 and GhUBQ14 genes were the most stable across all samples and also when distinct plants organs are examined. GhACT4 and GhUBQ14 present more stable expression during flower development, GhACT4 and GhFBX6 in the floral verticils and GhMZA and GhPTB during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development. Conclusion We have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references

  16. Quantitative Assessment of Protein Structural Models by Comparison of H/D Exchange MS Data with Exchange Behavior Accurately Predicted by DXCOREX

    Liu, Tong; Pantazatos, Dennis; Li, Sheng; Hamuro, Yoshitomo; Hilser, Vincent J.; Woods, Virgil L.


    Peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) data are often used to qualitatively support models for protein structure. We have developed and validated a method (DXCOREX) by which exchange data can be used to quantitatively assess the accuracy of three-dimensional (3-D) models of protein structure. The method utilizes the COREX algorithm to predict a protein's amide hydrogen exchange rates by reference to a hypothesized structure, and these values are used to generate a virtual data set (deuteron incorporation per peptide) that can be quantitatively compared with the deuteration level of the peptide probes measured by hydrogen exchange experimentation. The accuracy of DXCOREX was established in studies performed with 13 proteins for which both high-resolution structures and experimental data were available. The DXCOREX-calculated and experimental data for each protein was highly correlated. We then employed correlation analysis of DXCOREX-calculated versus DXMS experimental data to assess the accuracy of a recently proposed structural model for the catalytic domain of a Ca2+-independent phospholipase A2. The model's calculated exchange behavior was highly correlated with the experimental exchange results available for the protein, supporting the accuracy of the proposed model. This method of analysis will substantially increase the precision with which experimental hydrogen exchange data can help decipher challenging questions regarding protein structure and dynamics.

  17. Influence of storage time on DNA of Chlamydia trachomatis, Ureaplasma urealyticum, and Neisseria gonorrhoeae for accurate detection by quantitative real-time polymerase chain reaction.

    Lu, Y; Rong, C Z; Zhao, J Y; Lao, X J; Xie, L; Li, S; Qin, X


    The shipment and storage conditions of clinical samples pose a major challenge to the detection accuracy of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Ureaplasma urealyticum (UU) when using quantitative real-time polymerase chain reaction (qRT-PCR). The aim of the present study was to explore the influence of storage time at 4°C on the DNA of these pathogens and its effect on their detection by qRT-PCR. CT, NG, and UU positive genital swabs from 70 patients were collected, and DNA of all samples were extracted and divided into eight aliquots. One aliquot was immediately analyzed with qRT-PCR to assess the initial pathogen load, whereas the remaining samples were stored at 4°C and analyzed after 1, 2, 3, 7, 14, 21, and 28 days. No significant differences in CT, NG, and UU DNA loads were observed between baseline (day 0) and the subsequent time points (days 1, 2, 3, 7, 14, 21, and 28) in any of the 70 samples. Although a slight increase in DNA levels was observed at day 28 compared to day 0, paired sample t-test results revealed no significant differences between the mean DNA levels at different time points following storage at 4°C (all P>0.05). Overall, the CT, UU, and NG DNA loads from all genital swab samples were stable at 4°C over a 28-day period. PMID:27580005

  18. Validation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in strawberry fruits using different cultivars and osmotic stresses.

    Galli, Vanessa; Borowski, Joyce Moura; Perin, Ellen Cristina; Messias, Rafael da Silva; Labonde, Julia; Pereira, Ivan dos Santos; Silva, Sérgio Delmar Dos Anjos; Rombaldi, Cesar Valmor


    The increasing demand of strawberry (Fragaria×ananassa Duch) fruits is associated mainly with their sensorial characteristics and the content of antioxidant compounds. Nevertheless, the strawberry production has been hampered due to its sensitivity to abiotic stresses. Therefore, to understand the molecular mechanisms highlighting stress response is of great importance to enable genetic engineering approaches aiming to improve strawberry tolerance. However, the study of expression of genes in strawberry requires the use of suitable reference genes. In the present study, seven traditional and novel candidate reference genes were evaluated for transcript normalization in fruits of ten strawberry cultivars and two abiotic stresses, using RefFinder, which integrates the four major currently available software programs: geNorm, NormFinder, BestKeeper and the comparative delta-Ct method. The results indicate that the expression stability is dependent on the experimental conditions. The candidate reference gene DBP (DNA binding protein) was considered the most suitable to normalize expression data in samples of strawberry cultivars and under drought stress condition, and the candidate reference gene HISTH4 (histone H4) was the most stable under osmotic stresses and salt stress. The traditional genes GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and 18S (18S ribosomal RNA) were considered the most unstable genes in all conditions. The expression of phenylalanine ammonia lyase (PAL) and 9-cis epoxycarotenoid dioxygenase (NCED1) genes were used to further confirm the validated candidate reference genes, showing that the use of an inappropriate reference gene may induce erroneous results. This study is the first survey on the stability of reference genes in strawberry cultivars and osmotic stresses and provides guidelines to obtain more accurate RT-qPCR results for future breeding efforts. PMID:25445290

  19. Evaluation of the iPLEX(®) Sample ID Plus Panel designed for the Sequenom MassARRAY(®) system. A SNP typing assay developed for human identification and sample tracking based on the SNPforID panel

    Johansen, P; Andersen, J D; Børsting, Claus;


    Sequenom launched the first commercial SNP typing kit for human identification, named the iPLEX(®) Sample ID Plus Panel. The kit amplifies 47 of the 52 SNPs in the SNPforID panel, amelogenin and two Y-chromosome SNPs in one multiplex PCR. The SNPs were analyzed by single base extension (SBE) and...... SNPforID assay. The average call rate for duplicate typing of any one SNPs in the panel was 90.0% when the mass spectra were analyzed automatically with the MassARRAY(®) TYPER 4.0 genotyping software in real time. Two reproducible inconsistencies were observed (error rate: 0.05%) at two different SNP...... loci. In addition, four inconsistencies were observed once. The optimal amount of template DNA in the PCR was ≥10ng. There was a relatively high risk of allele and locus drop-outs when ≤1ng template DNA was used. We developed an R script with a stringent set of "forensic analysis parameters" based on...

  20. The effect of multiple primer-template mismatches on quantitative PCR accuracy and development of a multi-primer set assay for accurate quantification of pcrA gene sequence variants.

    Ledeker, Brett M; De Long, Susan K


    Quantitative PCR (qPCR) is a critical tool for quantifying the abundance of specific organisms and the level or expression of target genes in medically and environmentally relevant systems. However, often the power of this tool has been limited because primer-template mismatches, due to sequence variations of targeted genes, can lead to inaccuracies in measured gene quantities, detection failures, and spurious conclusions. Currently available primer design guidelines for qPCR were developed for pure culture applications, and available primer design strategies for mixed cultures were developed for detection rather than accurate quantification. Furthermore, past studies examining the impact of mismatches have focused only on single mismatches while instances of multiple mismatches are common. There are currently no appropriate solutions to overcome the challenges posed by sequence variations. Here, we report results that provide a comprehensive, quantitative understanding of the impact of multiple primer-template mismatches on qPCR accuracy and demonstrate a multi-primer set approach to accurately quantify a model gene pcrA (encoding perchlorate reductase) that has substantial sequence variation. Results showed that for multiple mismatches (up to 3 mismatches) in primer regions where mismatches were previously considered tolerable (middle and 5' end), quantification accuracies could be as low as ~0.1%. Furthermore, tests were run using a published pcrA primer set with mixtures of genomic DNA from strains known to harbor the target gene, and for some mixtures quantification accuracy was as low as ~0.8% or was non-detect. To overcome these limitations, a multiple primer set assay including minimal degeneracies was developed for pcrA genes. This assay resulted in nearly 100% accurate detection for all mixed microbial communities tested. The multi-primer set approach demonstrated herein can be broadly applied to other genes with known sequences. PMID:23806694

  1. A rapid and accurate method for the quantitative estimation of natural polysaccharides and their fractions using high performance size exclusion chromatography coupled with multi-angle laser light scattering and refractive index detector.

    Cheong, Kit-Leong; Wu, Ding-Tao; Zhao, Jing; Li, Shao-Ping


    In this study, a rapid and accurate method for quantitative analysis of natural polysaccharides and their different fractions was developed. Firstly, high performance size exclusion chromatography (HPSEC) was utilized to separate natural polysaccharides. And then the molecular masses of their fractions were determined by multi-angle laser light scattering (MALLS). Finally, quantification of polysaccharides or their fractions was performed based on their response to refractive index detector (RID) and their universal refractive index increment (dn/dc). Accuracy of the developed method for the quantification of individual and mixed polysaccharide standards, including konjac glucomannan, CM-arabinan, xyloglucan, larch arabinogalactan, oat β-glucan, dextran (410, 270, and 25 kDa), mixed xyloglucan and CM-arabinan, and mixed dextran 270 K and CM-arabinan was determined, and their average recoveries were between 90.6% and 98.3%. The limits of detection (LOD) and quantification (LOQ) were ranging from 10.68 to 20.25 μg/mL, and 42.70 to 68.85 μg/mL, respectively. Comparing to the conventional phenol sulfuric acid assay and HPSEC coupled with evaporative light scattering detection (HPSEC-ELSD) analysis, the developed HPSEC-MALLS-RID method based on universal dn/dc for the quantification of polysaccharides and their fractions is much more simple, rapid, and accurate with no need of individual polysaccharide standard, as well as free of calibration curve. The developed method was also successfully utilized for quantitative analysis of polysaccharides and their different fractions from three medicinal plants of Panax genus, Panax ginseng, Panax notoginseng and Panax quinquefolius. The results suggested that the HPSEC-MALLS-RID method based on universal dn/dc could be used as a routine technique for the quantification of polysaccharides and their fractions in natural resources. PMID:25990349

  2. Development of a multiplex SNP typing assay for Yersinia pestis Orientalis strains based on Luminex technology%基于Luminex悬浮芯片的鼠疫耶尔森菌SNP分型方法研究

    朱鹏; 张青雯; 祁芝珍; 崔玉军; 肖潇; 杨瑞馥; 谭周进; 宋亚军


    目的 利用Luminex悬浮芯片技术,基于单核苷酸多态性(single nucleotide polymorphism,SNP)建立我国鼠疫耶尔森菌东方型菌株(以下简称东方型鼠疫菌)的基因分型方法,为进一步研究东方型鼠疫菌多态性并分析其系统发育关系奠定基础.方法 利用多重PCR,同时扩增东方型鼠疫菌中18个具有分型意义的SNP位点,扩增产物进行多重等位基因特异性引物延伸(allele specific primer extension,ASPE)反应以及Luminex悬浮芯片技术分析,随后利用MasterPlex GT V2.3软件计算平均荧光强度(median fluorescence intensity,MFI)比值,判断各SNP位点的碱基状态;并对SNP分型方法 的重现性进行评价.结果 Luminex多重SNP技术能够快速、高通量地检测出各SNP位点的MFI值,从而在8 h内一次性成功确定东方型鼠疫菌中18个SNP的碱基状态;36株东方型鼠疫菌基于18个SNP可以分为7个基因型.结论 本文建立的Luminex多重SNP检测方法 作为一种高通量检测SNP的技术平台,为后期的东方型鼠疫菌SNP分型及系统发育分析奠定了基础.%Objective To develop a Luminex-based single nucleotide polymorphism ( SNP ) typing assay for the Chinese Yersinia pestis orientalis strains. Method 18 oriental strains specific SNPs were selected and amplified simultaneously by a multiplex PCR assay. The amplicons were subjected to allele specific primer extension ( ASPE ) and Luminex analysis. MasterPlex GT V2. 3 software was used to calculate the median fluorescence intensity ( MFI ) ratios and call SNPs. Assays were repeated to evaluate their reproducibility. Results This assay yielded unambiguous SNP calls for all the 18 targeted SNPs simultaneously with reasonable reproducibility in 8 hours. Thirty-six Y. pestis Orientalis strains were grouped into 7 genotypes based on the SNP profiles. Conclusion The Luminex-assay presented here provides a reliable platform to screen the SNP of Y. pestis Orientalis strains in a high

  3. 粮谷中8种痕量真菌毒素的定量分析方法%Accurate Quantitative Analysis Method for 8 Kinds of Mycotoxins in Cereal

    曹娅; 孙利; 王明林; 冯峰; 储晓刚


    建立了大米、小麦和大豆中黄曲霉毒素B1、黄曲霉毒素B2、黄曲霉毒素G1、黄曲霉毒素G2、伏马毒素B1、伏马毒素B2、柄曲霉素和异烟棒曲霉素C8种真菌毒素的高效液相色谱-串联质谱(HPLC-MS/MS)分析方法.样品加入正己烷去除油脂,用60%乙腈振荡液液分配提取,取乙腈水层过滤膜后分析.在电喷雾电离(ESI)正离子模式下采用多反应监测(MRM)进行测定.定量方法采用同位素内标稀释法,8种真菌毒素在各自浓度范围内线性关系良好,线性系数均不低于0.997 0.空白样品的加标回收率为77%~123%,相对标准偏差(RSD)为0.6%~13.3%.该方法操作简单、灵敏度高,可用于粮谷中真菌毒素的检测.%A high performance liquid chromatography - tandem mass spectrometric( HPLC - MS/MS) method was developed for the determination of 8 kinds of mycotoxins (aflatoxin Bl, aflatoxin B2, af-latoxin Gl, aflatoxin G2, fumonisin Bl, fumonisin B2, sterigmatocystin and roquefortine C) in ce real. The sample was diluted with hexane to remove the oil, then extracted with 60% acetonitrile. The acetonitrile layer was made up to constant volume and passed through the filter before tested. The detection was performed in the electrospray ion positive mode and multiple reaction monitoring (MRM) mode, and the quantitation of target compounds was carried out by the isotope dilution assays. The results indicated that the 8 compounds showed good linear relationships in certain concentration ranges, with correlation coefficients not less than than 0.997 0. The average recoveries ranged from 77% to 123%, with relative standard deviations of 0. 6% - 13. 3% . The method was proved to be rapid and sensitive, and could be used for the detection of mycotoxins in cereal.

  4. Accurate Finite Difference Algorithms

    Goodrich, John W.


    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  5. Quantitative microfocal radiography accurately detects joint changes in rheumatoid arthritis.

    Buckland-Wright, J C; Carmichael, I.; Walker, S R


    Microfocal radiography, producing x5 magnified images of the wrist and hands with a high spacial resolution (25 microns) in the film, permitted direct measurement of erosion area and joint space width in patients with rheumatoid arthritis. The magnitude of errors relating to direct measurement, repositioning the wrist and hand on successive x ray visits, repeated identification of erosions and their area calculation were assessed. The coefficients of variation for length and area measurements...

  6. Quantitatively accurate calculations of conductance and thermopower of molecular junctions

    Markussen, Troels; Jin, Chengjun; Thygesen, Kristian Sommer


    Thermopower measurements of molecular junctions have recently gained interest as a characterization technique that supplements the more traditional conductance measurements. Here we investigate the electronic conductance and thermopower of benzenediamine (BDA) and benzenedicarbonitrile (BDCN) con...

  7. Quantitative film radiography

    We have developed a system of quantitative radiography in order to produce quantitative images displaying homogeneity of parts. The materials that we characterize are synthetic composites and may contain important subtle density variations not discernible by examining a raw film x-radiograph. In order to quantitatively interpret film radiographs, it is necessary to digitize, interpret, and display the images. Our integrated system of quantitative radiography displays accurate, high-resolution pseudo-color images in units of density. We characterize approximately 10,000 parts per year in hundreds of different configurations and compositions with this system. This report discusses: the method; film processor monitoring and control; verifying film and processor performance; and correction of scatter effects

  8. Quantitative EPR A Practitioners Guide

    Eaton, Gareth R; Barr, David P; Weber, Ralph T


    This is the first comprehensive yet practical guide for people who perform quantitative EPR measurements. No existing book provides this level of practical guidance to ensure the successful use of EPR. There is a growing need in both industrial and academic research to provide meaningful and accurate quantitative EPR results. This text discusses the various sample, instrument and software related aspects required for EPR quantitation. Specific topics include: choosing a reference standard, resonator considerations (Q, B1, Bm), power saturation characteristics, sample positioning, and finally, putting all the factors together to obtain an accurate spin concentration of a sample.

  9. Towards accurate emergency response behavior

    Nuclear reactor operator emergency response behavior has persisted as a training problem through lack of information. The industry needs an accurate definition of operator behavior in adverse stress conditions, and training methods which will produce the desired behavior. Newly assembled information from fifty years of research into human behavior in both high and low stress provides a more accurate definition of appropriate operator response, and supports training methods which will produce the needed control room behavior. The research indicates that operator response in emergencies is divided into two modes, conditioned behavior and knowledge based behavior. Methods which assure accurate conditioned behavior, and provide for the recovery of knowledge based behavior, are described in detail

  10. Accurate determination of antenna directivity

    Dich, Mikael


    The derivation of a formula for accurate estimation of the total radiated power from a transmitting antenna for which the radiated power density is known in a finite number of points on the far-field sphere is presented. The main application of the formula is determination of directivity from power...

  11. Quantitative FDG in depression

    Full text: Studies of regional cerebral glucose metabolism (rCMRGlu) using positron emission tomography (PET) in patients with affective disorders have consistently demonstrated reduced metabolism in the frontal regions. Different quantitative and semi-quantitative rCMRGlu regions of interest (ROI) comparisons, e.g. absolute metabolic rates, ratios of dorsolateral prefrontal cortex (DLPFC) to ipsilateral hemisphere cortex, have been reported. These studies suffered from the use of a standard brain atlas to define ROls, whereas in this case study, the individual''s magnetic resonance imaging (MRI) scan was registered with the PET scan to enable accurate neuroanatomical ROI definition for the subject. The patient is a 36-year-old female with a six-week history of major depression (HAM-D = 34, MMSE = 28). A quantitative FDG PET study and an MRI scan were performed. Six MRI-guided ROls (DLPFC, PFC, whole hemisphere) were defined. The average rCMRGlu in the DLPFC (left = 28.8 + 5.8 mol/100g/min; right = 25.6 7.0 mol/100g/min) were slightly reduced compared to the ipsilateral hemispherical rate (left = 30.4 6.8 mol/100g/min; right = 29.5 7.2 mol/100g/min). The ratios of DLPFC to ipsilateral hemispheric rate were close to unity (left = 0.95 0.29; right 0.87 0.32). The right to left DLPFC ratio did not show any significant asymmetry (0.91 0.30). These results do not correlate with earlier published results reporting decreased left DLPFC rates compared to right DLPFC, although our results will need to be replicated with a group of depressed patients. Registration of PET and MRI studies is necessary in ROI-based quantitative FDG PET studies to allow for the normal anatomical variation among individuals, and thus is essential for accurate comparison of rCMRGlu between individuals

  12. Accurate Modeling of Advanced Reflectarrays

    Zhou, Min

    of the incident field, the choice of basis functions, and the technique to calculate the far-field. Based on accurate reference measurements of two offset reflectarrays carried out at the DTU-ESA Spherical NearField Antenna Test Facility, it was concluded that the three latter factors are particularly important...... to the conventional phase-only optimization technique (POT), the geometrical parameters of the array elements are directly optimized to fulfill the far-field requirements, thus maintaining a direct relation between optimization goals and optimization variables. As a result, better designs can be obtained compared...... using the GDOT to demonstrate its capabilities. To verify the accuracy of the GDOT, two offset contoured beam reflectarrays that radiate a high-gain beam on a European coverage have been designed and manufactured, and subsequently measured at the DTU-ESA Spherical Near-Field Antenna Test Facility...

  13. Accurate ab initio spin densities

    Boguslawski, Katharina; Legeza, Örs; Reiher, Markus


    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys. 2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CA...

  14. Accurate thickness measurement of graphene

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.


    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  15. A More Accurate Fourier Transform

    Courtney, Elya


    Fourier transform methods are used to analyze functions and data sets to provide frequencies, amplitudes, and phases of underlying oscillatory components. Fast Fourier transform (FFT) methods offer speed advantages over evaluation of explicit integrals (EI) that define Fourier transforms. This paper compares frequency, amplitude, and phase accuracy of the two methods for well resolved peaks over a wide array of data sets including cosine series with and without random noise and a variety of physical data sets, including atmospheric $\\mathrm{CO_2}$ concentrations, tides, temperatures, sound waveforms, and atomic spectra. The FFT uses MIT's FFTW3 library. The EI method uses the rectangle method to compute the areas under the curve via complex math. Results support the hypothesis that EI methods are more accurate than FFT methods. Errors range from 5 to 10 times higher when determining peak frequency by FFT, 1.4 to 60 times higher for peak amplitude, and 6 to 10 times higher for phase under a peak. The ability t...

  16. Current Status and Advances in Quantitative Proteomic Mass Spectrometry

    Valerie C. Wasinger; Zeng, Ming; Yau, Yunki


    The accurate quantitation of proteins and peptides in complex biological systems is one of the most challenging areas of proteomics. Mass spectrometry-based approaches have forged significant in-roads allowing accurate and sensitive quantitation and the ability to multiplex vastly complex samples through the application of robust bioinformatic tools. These relative and absolute quantitative measures using label-free, tags, or stable isotope labelling have their own strengths and limitations. ...

  17. Fast, accurate standardless XRF analysis with IQ+

    Full text: Due to both chemical and physical effects, the most accurate XRF data are derived from calibrations set up using in-type standards, necessitating some prior knowledge of the samples being analysed. Whilst this is often the case for routine samples, particularly in production control, for completely unknown samples the identification and availability of in-type standards can be problematic. Under these circumstances standardless analysis can offer a viable solution. Successful analysis of completely unknown samples requires a complete chemical overview of the speciemen together with the flexibility of a fundamental parameters (FP) algorithm to handle wide-ranging compositions. Although FP algorithms are improving all the time, most still require set-up samples to define the spectrometer response to a particular element. Whilst such materials may be referred to as standards, the emphasis in this kind of analysis is that only a single calibration point is required per element and that the standard chosen does not have to be in-type. The high sensitivities of modern XRF spectrometers, together with recent developments in detector counting electronics that possess a large dynamic range and high-speed data processing capacity bring significant advances to fast, standardless analysis. Illustrated with a tantalite-columbite heavy-mineral concentrate grading use-case, this paper will present the philosophy behind the semi-quantitative IQ+ software and the required hardware. This combination can give a rapid scan-based overview and quantification of the sample in less than two minutes, together with the ability to define channels for specific elements of interest where higher accuracy and lower levels of quantification are required. The accuracy, precision and limitations of standardless analysis will be assessed using certified reference materials of widely differing chemical and physical composition. Copyright (2002) Australian X-ray Analytical Association Inc

  18. 38 CFR 4.46 - Accurate measurement.


    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  19. Quantitative Analysis in Multimodality Molecular Imaging

    PET offers the possibility of truly quantitative (physiological) measurements of tracer concentration in vivo. However, there are several issues limiting both visual qualitative interpretation and quantitative analysis capabilities of reconstructed PET images that must be considered in order to fully realize this potential. The major challenges to quantitative PET can be categorized in 5 classes: (i) factors related to imaging system performance and data acquisition protocols (instrumentation and measurement factors), (ii) those related to the physics of photon interaction with biologic tissues (physical factors), (iii) image reconstruction (reconstruction factors), (iv) factors related to patient motion and other physiological issues (physiological factors), and (v) Methodological factors: issues related to difficulties in developing accurate tracer kinetic models, especially at the voxel level. This paper reflects the tremendous increase in interest in quantitative molecular imaging using PET as both clinical and research imaging modality in the past decade. It offers an overview of the entire range of quantitative PET imaging from basic principles to various steps required for obtaining quantitatively accurate data from dedicated standalone PET and combined PET/CT and PET/MR systems including data collection methods and algorithms used to correct for physical degrading factors as well as image processing and analysis techniques and their clinical and research applications. Impact of physical degrading factors including attenuation of photons and contribution from photons scattered in the patient and partial volume effect on the diagnostic quality and quantitative accuracy of PET data will be discussed. Considerable advances have been made and much worthwhile research focused on the development of quantitative imaging protocols incorporating accurate data correction techniques and sophisticated image reconstruction algorithms. The fundamental concepts of

  20. Accurate measurement of streamwise vortices using dual-plane PIV

    Waldman, Rye M.; Breuer, Kenneth S. [Brown University, School of Engineering, Providence, RI (United States)


    Low Reynolds number aerodynamic experiments with flapping animals (such as bats and small birds) are of particular interest due to their application to micro air vehicles which operate in a similar parameter space. Previous PIV wake measurements described the structures left by bats and birds and provided insight into the time history of their aerodynamic force generation; however, these studies have faced difficulty drawing quantitative conclusions based on said measurements. The highly three-dimensional and unsteady nature of the flows associated with flapping flight are major challenges for accurate measurements. The challenge of animal flight measurements is finding small flow features in a large field of view at high speed with limited laser energy and camera resolution. Cross-stream measurement is further complicated by the predominately out-of-plane flow that requires thick laser sheets and short inter-frame times, which increase noise and measurement uncertainty. Choosing appropriate experimental parameters requires compromise between the spatial and temporal resolution and the dynamic range of the measurement. To explore these challenges, we do a case study on the wake of a fixed wing. The fixed model simplifies the experiment and allows direct measurements of the aerodynamic forces via load cell. We present a detailed analysis of the wake measurements, discuss the criteria for making accurate measurements, and present a solution for making quantitative aerodynamic load measurements behind free-flyers. (orig.)

  1. Quantitative Analysis of Radar Returns from Insects

    Riley, J. R.


    When a number of flying insects is low enough to permit their resolution as individual radar targets, quantitative estimates of their aerial density are developed. Accurate measurements of heading distribution using a rotating polarization radar to enhance the wingbeat frequency method of identification are presented.

  2. Christhin: Quantitative Analysis of Thin Layer Chromatography

    Barchiesi, Maximiliano; Renaudo, Carlos; Rossi, Pablo; Pramparo, María de Carmen; Nepote, Valeria; Grosso, Nelson Ruben; Gayol, María Fernanda


    Manual for Christhin 0.1.36 Christhin (Chromatography Riser Thin) is software developed for the quantitative analysis of data obtained from thin-layer chromatographic techniques (TLC). Once installed on your computer, the program is very easy to use, and provides data quickly and accurately. This manual describes the program, and reading should be enough to use it properly.

  3. Intracranial Calcifications and Hemorrhages: Characterization with Quantitative Susceptibility Mapping

    Chen, Weiwei; Zhu, Wenzhen; Kovanlikaya, IIhami; Kovanlikaya, Arzu; Liu, Tian; Wang, Shuai; Salustri, Carlo; Wang, Yi


    Quantitative susceptibility mapping demonstrates the negative susceptibility of calcification and the positive susceptibility of hemorrhage and is superior to phase imaging in the specific detection of intracranial calcifications and accurate detection of intracranial hemorrhages.

  4. Automated Selected Reaction Monitoring Software for Accurate Label-Free Protein Quantification

    Teleman, Johan; Karlsson, Christofer; Waldemarson, Sofia; Hansson, Karin; James, Peter; Malmström, Johan; Levander, Fredrik


    Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently...

  5. Laboratory Building for Accurate Determination of Plutonium


    <正>The accurate determination of plutonium is one of the most important assay techniques of nuclear fuel, also the key of the chemical measurement transfer and the base of the nuclear material balance. An

  6. Quantitative lithofacies palaeogeography

    Zeng-Zhao; Feng; Xiu-Juan; Zheng; Zhi-Dong; Bao; Zhen-Kui; Jin; Sheng-He; Wu; You-Bin; He; Yong-Min; Peng; Yu-Qing; Yang; Jia-Qiang; Zhang; Yong-Sheng; Zhang


    Quantitative lithofacies palaeogeography is an important discipline of palaeogeography.It is developed on the foundation of traditional lithofacies palaeogeography and palaeogeography,the core of which is the quantitative lithofacies palaeogeographic map.Quantity means that in the palaeogeographic map,the division and identification of each palaeogeographic unit are supported by quantitative data and quantitative fundamental maps.Our lithofacies palaeogeographic maps are quantitative or mainly quantitative.A great number of quantitative lithofacies palaeogeographic maps have been published,and articles and monographs of quantitative lithofacies palaeogeography have been published successively,thus the quantitative lithofacies palaeogeography was formed and established.It is an important development in lithofacies palaeogeography.In composing quantitative lithofacies palaeogeographic maps,the key measure is the single factor analysis and multifactor comprehensive mapping method—methodology of quantitative lithofacies palaeogeography.In this paper,the authors utilize two case studies,one from the Early Ordovician of South China and the other from the Early Ordovician of Ordos,North China,to explain how to use this methodology to compose the quantitative lithofacies palaeogeographic maps,and to discuss the palaeogeographic units in these maps.Finally,three characteristics,i.e.,quantification,multiple orders and multiple types,of quantitative lithofacies palaeogeographic maps are conclusively discussed.

  7. Quantitative investment analysis

    DeFusco, Richard


    In the "Second Edition" of "Quantitative Investment Analysis," financial experts Richard DeFusco, Dennis McLeavey, Jerald Pinto, and David Runkle outline the tools and techniques needed to understand and apply quantitative methods to today's investment process.

  8. Computationally efficient and quantitatively accurate multiscale simulation of solid-solution strengthening by ab initio calculation

    Ma, D.; Friák, Martin; von Pezold, J.; Raabe, D.; Neugebauer, J.


    Roč. 85, FEB (2015), s. 53-66. ISSN 1359-6454 Institutional support: RVO:68081723 Keywords : Solid-solution strengthening * DFT * Peierls–Nabarro model * Ab initio * Al alloy s Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.465, year: 2014

  9. Invariant Image Watermarking Using Accurate Zernike Moments

    Ismail A. Ismail


    Full Text Available problem statement: Digital image watermarking is the most popular method for image authentication, copyright protection and content description. Zernike moments are the most widely used moments in image processing and pattern recognition. The magnitudes of Zernike moments are rotation invariant so they can be used just as a watermark signal or be further modified to carry embedded data. The computed Zernike moments in Cartesian coordinate are not accurate due to geometrical and numerical error. Approach: In this study, we employed a robust image-watermarking algorithm using accurate Zernike moments. These moments are computed in polar coordinate, where both approximation and geometric errors are removed. Accurate Zernike moments are used in image watermarking and proved to be robust against different kind of geometric attacks. The performance of the proposed algorithm is evaluated using standard images. Results: Experimental results show that, accurate Zernike moments achieve higher degree of robustness than those approximated ones against rotation, scaling, flipping, shearing and affine transformation. Conclusion: By computing accurate Zernike moments, the embedded bits watermark can be extracted at low error rate.

  10. Accurate strand-specific quantification of viral RNA.

    Nicole E Plaskon

    Full Text Available The presence of full-length complements of viral genomic RNA is a hallmark of RNA virus replication within an infected cell. As such, methods for detecting and measuring specific strands of viral RNA in infected cells and tissues are important in the study of RNA viruses. Strand-specific quantitative real-time PCR (ssqPCR assays are increasingly being used for this purpose, but the accuracy of these assays depends on the assumption that the amount of cDNA measured during the quantitative PCR (qPCR step accurately reflects amounts of a specific viral RNA strand present in the RT reaction. To specifically test this assumption, we developed multiple ssqPCR assays for the positive-strand RNA virus o'nyong-nyong (ONNV that were based upon the most prevalent ssqPCR assay design types in the literature. We then compared various parameters of the ONNV-specific assays. We found that an assay employing standard unmodified virus-specific primers failed to discern the difference between cDNAs generated from virus specific primers and those generated through false priming. Further, we were unable to accurately measure levels of ONNV (- strand RNA with this assay when higher levels of cDNA generated from the (+ strand were present. Taken together, these results suggest that assays of this type do not accurately quantify levels of the anti-genomic strand present during RNA virus infectious cycles. However, an assay permitting the use of a tag-specific primer was able to distinguish cDNAs transcribed from ONNV (- strand RNA from other cDNAs present, thus allowing accurate quantification of the anti-genomic strand. We also report the sensitivities of two different detection strategies and chemistries, SYBR(R Green and DNA hydrolysis probes, used with our tagged ONNV-specific ssqPCR assays. Finally, we describe development, design and validation of ssqPCR assays for chikungunya virus (CHIKV, the recent cause of large outbreaks of disease in the Indian Ocean

  11. Using an Educational Electronic Documentation System to Help Nursing Students Accurately Identify Nursing Diagnoses

    Pobocik, Tamara J.


    The use of technology and electronic medical records in healthcare has exponentially increased. This quantitative research project used a pretest/posttest design, and reviewed how an educational electronic documentation system helped nursing students to identify the accurate related to statement of the nursing diagnosis for the patient in the case…

  12. Accurate object tracking system by integrating texture and depth cues

    Chen, Ju-Chin; Lin, Yu-Hang


    A robust object tracking system that is invariant to object appearance variations and background clutter is proposed. Multiple instance learning with a boosting algorithm is applied to select discriminant texture information between the object and background data. Additionally, depth information, which is important to distinguish the object from a complicated background, is integrated. We propose two depth-based models that can compensate texture information to cope with both appearance variants and background clutter. Moreover, in order to reduce the risk of drifting problem increased for the textureless depth templates, an update mechanism is proposed to select more precise tracking results to avoid incorrect model updates. In the experiments, the robustness of the proposed system is evaluated and quantitative results are provided for performance analysis. Experimental results show that the proposed system can provide the best success rate and has more accurate tracking results than other well-known algorithms.

  13. Accurate atomic data for industrial plasma applications

    Griesmann, U.; Bridges, J.M.; Roberts, J.R.; Wiese, W.L.; Fuhr, J.R. [National Inst. of Standards and Technology, Gaithersburg, MD (United States)


    Reliable branching fraction, transition probability and transition wavelength data for radiative dipole transitions of atoms and ions in plasma are important in many industrial applications. Optical plasma diagnostics and modeling of the radiation transport in electrical discharge plasmas (e.g. in electrical lighting) depend on accurate basic atomic data. NIST has an ongoing experimental research program to provide accurate atomic data for radiative transitions. The new NIST UV-vis-IR high resolution Fourier transform spectrometer has become an excellent tool for accurate and efficient measurements of numerous transition wavelengths and branching fractions in a wide wavelength range. Recently, the authors have also begun to employ photon counting techniques for very accurate measurements of branching fractions of weaker spectral lines with the intent to improve the overall accuracy for experimental branching fractions to better than 5%. They have now completed their studies of transition probabilities of Ne I and Ne II. The results agree well with recent calculations and for the first time provide reliable transition probabilities for many weak intercombination lines.

  14. More accurate picture of human body organs

    Computerized tomography and nucler magnetic resonance tomography (NMRT) are revolutionary contributions to radiodiagnosis because they allow to obtain a more accurate image of human body organs. The principles are described of both methods. Attention is mainly devoted to NMRT which has clinically only been used for three years. It does not burden the organism with ionizing radiation. (Ha)

  15. Quantitative biometric phenotype analysis in mouse lenses

    Reilly, Matthew A.; Andley, Usha P.


    The disrupted morphology of lenses in mouse models for cataracts precludes accurate in vitro assessment of lens growth by weight. To overcome this limitation, we developed morphometric methods to assess defects in eye lens growth and shape in mice expressing the αA-crystallin R49C (αA-R49C) mutation. Our morphometric methods determine quantitative shape and dry weight of the whole lens from histological sections of the lens. This method was then used to quantitatively compare the biometric gr...

  16. Accurate 3D quantification of the bronchial parameters in MDCT

    Saragaglia, A.; Fetita, C.; Preteux, F.; Brillet, P. Y.; Grenier, P. A.


    The assessment of bronchial reactivity and wall remodeling in asthma plays a crucial role in better understanding such a disease and evaluating therapeutic responses. Today, multi-detector computed tomography (MDCT) makes it possible to perform an accurate estimation of bronchial parameters (lumen and wall areas) by allowing a quantitative analysis in a cross-section plane orthogonal to the bronchus axis. This paper provides the tools for such an analysis by developing a 3D investigation method which relies on 3D reconstruction of bronchial lumen and central axis computation. Cross-section images at bronchial locations interactively selected along the central axis are generated at appropriate spatial resolution. An automated approach is then developed for accurately segmenting the inner and outer bronchi contours on the cross-section images. It combines mathematical morphology operators, such as "connection cost", and energy-controlled propagation in order to overcome the difficulties raised by vessel adjacencies and wall irregularities. The segmentation accuracy was validated with respect to a 3D mathematically-modeled phantom of a pair bronchus-vessel which mimics the characteristics of real data in terms of gray-level distribution, caliber and orientation. When applying the developed quantification approach to such a model with calibers ranging from 3 to 10 mm diameter, the lumen area relative errors varied from 3.7% to 0.15%, while the bronchus area was estimated with a relative error less than 5.1%.

  17. Feedback about more accurate versus less accurate trials: differential effects on self-confidence and activation.

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi


    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected byfeedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On day 1, participants performed a golf putting task under one of two conditions: one group received feedback on the most accurate trials, whereas another group received feedback on the least accurate trials. On day 2, participants completed an anxiety questionnaire and performed a retention test. Shin conductance level, as a measure of arousal, was determined. The results indicated that feedback about more accurate trials resulted in more effective learning as well as increased self-confidence. Also, activation was a predictor of performance. PMID:22808705

  18. Accurate guitar tuning by cochlear implant musicians.

    Thomas Lu

    Full Text Available Modern cochlear implant (CI users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task.

  19. Accurate guitar tuning by cochlear implant musicians.

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang


    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task. PMID:24651081

  20. How Accurate is inv(A)*b?

    Druinsky, Alex


    Several widely-used textbooks lead the reader to believe that solving a linear system of equations Ax = b by multiplying the vector b by a computed inverse inv(A) is inaccurate. Virtually all other textbooks on numerical analysis and numerical linear algebra advise against using computed inverses without stating whether this is accurate or not. In fact, under reasonable assumptions on how the inverse is computed, x = inv(A)*b is as accurate as the solution computed by the best backward-stable solvers. This fact is not new, but obviously obscure. We review the literature on the accuracy of this computation and present a self-contained numerical analysis of it.

  1. Quantitative analysis chemistry

    This book is about quantitative analysis chemistry. It is divided into ten chapters, which deal with the basic conception of material with the meaning of analysis chemistry and SI units, chemical equilibrium, basic preparation for quantitative analysis, introduction of volumetric analysis, acid-base titration of outline and experiment examples, chelate titration, oxidation-reduction titration with introduction, titration curve, and diazotization titration, precipitation titration, electrometric titration and quantitative analysis.

  2. Quantitative dispersion microscopy

    Fu, Dan; Choi, Wonshik; Sung, Yongjin; Yaqoob, Zahid; Dasari, Ramachandra R.; Feld, Michael


    Refractive index dispersion is an intrinsic optical property and a useful source of contrast in biological imaging studies. In this report, we present the first dispersion phase imaging of living eukaryotic cells. We have developed quantitative dispersion microscopy based on the principle of quantitative phase microscopy. The dual-wavelength quantitative phase microscope makes phase measurements at 310 nm and 400 nm wavelengths to quantify dispersion (refractive index increment ratio) of live...

  3. Accurate, reproducible measurement of blood pressure.

    Campbell, N. R.; Chockalingam, A; Fodor, J. G.; McKay, D. W.


    The diagnosis of mild hypertension and the treatment of hypertension require accurate measurement of blood pressure. Blood pressure readings are altered by various factors that influence the patient, the techniques used and the accuracy of the sphygmomanometer. The variability of readings can be reduced if informed patients prepare in advance by emptying their bladder and bowel, by avoiding over-the-counter vasoactive drugs the day of measurement and by avoiding exposure to cold, caffeine con...

  4. Accurate Finite Difference Methods for Option Pricing

    Persson, Jonas


    Stock options are priced numerically using space- and time-adaptive finite difference methods. European options on one and several underlying assets are considered. These are priced with adaptive numerical algorithms including a second order method and a more accurate method. For American options we use the adaptive technique to price options on one stock with and without stochastic volatility. In all these methods emphasis is put on the control of errors to fulfill predefined tolerance level...

  5. Towards accurate modeling of moving contact lines

    Holmgren, Hanna


    The present thesis treats the numerical simulation of immiscible incompressible two-phase flows with moving contact lines. The conventional Navier–Stokes equations combined with a no-slip boundary condition leads to a non-integrable stress singularity at the contact line. The singularity in the model can be avoided by allowing the contact line to slip. Implementing slip conditions in an accurate way is not straight-forward and different regularization techniques exist where ad-hoc procedures ...

  6. Accurate variational forms for multiskyrmion configurations

    Jackson, A.D.; Weiss, C.; Wirzba, A.; Lande, A.


    Simple variational forms are suggested for the fields of a single skyrmion on a hypersphere, S/sub 3/(L), and of a face-centered cubic array of skyrmions in flat space, R/sub 3/. The resulting energies are accurate at the level of 0.2%. These approximate field configurations provide a useful alternative to brute-force solutions of the corresponding Euler equations.

  7. Efficient Accurate Context-Sensitive Anomaly Detection


    For program behavior-based anomaly detection, the only way to ensure accurate monitoring is to construct an efficient and precise program behavior model. A new program behavior-based anomaly detection model,called combined pushdown automaton (CPDA) model was proposed, which is based on static binary executable analysis. The CPDA model incorporates the optimized call stack walk and code instrumentation technique to gain complete context information. Thereby the proposed method can detect more attacks, while retaining good performance.

  8. Accurate phase-shift velocimetry in rock

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.


    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  9. Illumination coherence engineering and quantitative phase imaging

    Rodrigo Martín-Romo, José Augusto; Alieva, Tatiana Krasheninnikova


    Partially coherent illumination provides significant advantages such as speckle-free imaging and enhanced optical sectioning in optical microscopy. The knowledge of the spatial and temporal coherence is crucial to obtain accurate quantitative phase imaging (QPI) of specimens such as live cells, micrometer-sized particles, etc. In this Letter, we propose a novel technique for illumination coherence engineering. It is based on a DMD projector providing fast switchable both multi-wavelength and ...

  10. Quantitative atomic spectroscopy for primary thermometry

    Truong, Gar-Wing; May, Eric F.; Stace, Thomas M.; Luiten, Andre N.


    Quantitative spectroscopy has been used to measure accurately the Doppler-broadening of atomic transitions in $^{85}$Rb vapor. By using a conventional platinum resistance thermometer and the Doppler thermometry technique, we were able to determine $k_B$ with a relative uncertainty of $4.1\\times 10^{-4}$, and with a deviation of $2.7\\times 10^{-4}$ from the expected value. Our experiment, using an effusive vapour, departs significantly from other Doppler-broadened thermometry (DBT) techniques,...

  11. High Frequency QRS ECG Accurately Detects Cardiomyopathy

    Schlegel, Todd T.; Arenare, Brian; Poulin, Gregory; Moser, Daniel R.; Delgado, Reynolds


    High frequency (HF, 150-250 Hz) analysis over the entire QRS interval of the ECG is more sensitive than conventional ECG for detecting myocardial ischemia. However, the accuracy of HF QRS ECG for detecting cardiomyopathy is unknown. We obtained simultaneous resting conventional and HF QRS 12-lead ECGs in 66 patients with cardiomyopathy (EF = 23.2 plus or minus 6.l%, mean plus or minus SD) and in 66 age- and gender-matched healthy controls using PC-based ECG software recently developed at NASA. The single most accurate ECG parameter for detecting cardiomyopathy was an HF QRS morphological score that takes into consideration the total number and severity of reduced amplitude zones (RAZs) present plus the clustering of RAZs together in contiguous leads. This RAZ score had an area under the receiver operator curve (ROC) of 0.91, and was 88% sensitive, 82% specific and 85% accurate for identifying cardiomyopathy at optimum score cut-off of 140 points. Although conventional ECG parameters such as the QRS and QTc intervals were also significantly longer in patients than controls (P less than 0.001, BBBs excluded), these conventional parameters were less accurate (area under the ROC = 0.77 and 0.77, respectively) than HF QRS morphological parameters for identifying underlying cardiomyopathy. The total amplitude of the HF QRS complexes, as measured by summed root mean square voltages (RMSVs), also differed between patients and controls (33.8 plus or minus 11.5 vs. 41.5 plus or minus 13.6 mV, respectively, P less than 0.003), but this parameter was even less accurate in distinguishing the two groups (area under ROC = 0.67) than the HF QRS morphologic and conventional ECG parameters. Diagnostic accuracy was optimal (86%) when the RAZ score from the HF QRS ECG and the QTc interval from the conventional ECG were used simultaneously with cut-offs of greater than or equal to 40 points and greater than or equal to 445 ms, respectively. In conclusion 12-lead HF QRS ECG employing

  12. Accurate diagnosis is essential for amebiasis


    @@ Amebiasis is one of the three most common causes of death from parasitic disease, and Entamoeba histolytica is the most widely distributed parasites in the world. Particularly, Entamoeba histolytica infection in the developing countries is a significant health problem in amebiasis-endemic areas with a significant impact on infant mortality[1]. In recent years a world wide increase in the number of patients with amebiasis has refocused attention on this important infection. On the other hand, improving the quality of parasitological methods and widespread use of accurate tecniques have improved our knowledge about the disease.

  13. Investigations on Accurate Analysis of Microstrip Reflectarrays

    Zhou, Min; Sørensen, S. B.; Kim, Oleksiy S.;


    An investigation on accurate analysis of microstrip reflectarrays is presented. Sources of error in reflectarray analysis are examined and solutions to these issues are proposed. The focus is on two sources of error, namely the determination of the equivalent currents to calculate the radiation...... pattern, and the inaccurate mutual coupling between array elements due to the lack of periodicity. To serve as reference, two offset reflectarray antennas have been designed, manufactured and measured at the DTUESA Spherical Near-Field Antenna Test Facility. Comparisons of simulated and measured data are...

  14. Niche Genetic Algorithm with Accurate Optimization Performance

    LIU Jian-hua; YAN De-kun


    Based on crowding mechanism, a novel niche genetic algorithm was proposed which can record evolutionary direction dynamically during evolution. After evolution, the solutions's precision can be greatly improved by means of the local searching along the recorded direction. Simulation shows that this algorithm can not only keep population diversity but also find accurate solutions. Although using this method has to take more time compared with the standard GA, it is really worth applying to some cases that have to meet a demand for high solution precision.

  15. How accurately can we calculate thermal systems?

    The objective was to determine how accurately simple reactor lattice integral parameters can be determined, considering user input, differences in the methods, source data and the data processing procedures and assumptions. Three simple square lattice test cases with different fuel to moderator ratios were defined. The effect of the thermal scattering models were shown to be important and much bigger than the spread in the results. Nevertheless, differences of up to 0.4% in the K-eff calculated by continuous energy Monte Carlo codes were observed even when the same source data were used. (author)

  16. Accurate determination of characteristic relative permeability curves

    Krause, Michael H.; Benson, Sally M.


    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  17. Accurate radiative transfer calculations for layered media.

    Selden, Adrian C


    Simple yet accurate results for radiative transfer in layered media with discontinuous refractive index are obtained by the method of K-integrals. These are certain weighted integrals applied to the angular intensity distribution at the refracting boundaries. The radiative intensity is expressed as the sum of the asymptotic angular intensity distribution valid in the depth of the scattering medium and a transient term valid near the boundary. Integrated boundary equations are obtained, yielding simple linear equations for the intensity coefficients, enabling the angular emission intensity and the diffuse reflectance (albedo) and transmittance of the scattering layer to be calculated without solving the radiative transfer equation directly. Examples are given of half-space, slab, interface, and double-layer calculations, and extensions to multilayer systems are indicated. The K-integral method is orders of magnitude more accurate than diffusion theory and can be applied to layered scattering media with a wide range of scattering albedos, with potential applications to biomedical and ocean optics. PMID:27409700

  18. Accurate basis set truncation for wavefunction embedding

    Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.


    Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.

  19. Accurate pose estimation for forensic identification

    Merckx, Gert; Hermans, Jeroen; Vandermeulen, Dirk


    In forensic authentication, one aims to identify the perpetrator among a series of suspects or distractors. A fundamental problem in any recognition system that aims for identification of subjects in a natural scene is the lack of constrains on viewing and imaging conditions. In forensic applications, identification proves even more challenging, since most surveillance footage is of abysmal quality. In this context, robust methods for pose estimation are paramount. In this paper we will therefore present a new pose estimation strategy for very low quality footage. Our approach uses 3D-2D registration of a textured 3D face model with the surveillance image to obtain accurate far field pose alignment. Starting from an inaccurate initial estimate, the technique uses novel similarity measures based on the monogenic signal to guide a pose optimization process. We will illustrate the descriptive strength of the introduced similarity measures by using them directly as a recognition metric. Through validation, using both real and synthetic surveillance footage, our pose estimation method is shown to be accurate, and robust to lighting changes and image degradation.

  20. Accurate shear measurement with faint sources

    Zhang, Jun; Foucaud, Sebastien [Center for Astronomy and Astrophysics, Department of Physics and Astronomy, Shanghai Jiao Tong University, 955 Jianchuan road, Shanghai, 200240 (China); Luo, Wentao, E-mail:, E-mail:, E-mail: [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Nandan Road 80, Shanghai, 200030 (China)


    For cosmic shear to become an accurate cosmological probe, systematic errors in the shear measurement method must be unambiguously identified and corrected for. Previous work of this series has demonstrated that cosmic shears can be measured accurately in Fourier space in the presence of background noise and finite pixel size, without assumptions on the morphologies of galaxy and PSF. The remaining major source of error is source Poisson noise, due to the finiteness of source photon number. This problem is particularly important for faint galaxies in space-based weak lensing measurements, and for ground-based images of short exposure times. In this work, we propose a simple and rigorous way of removing the shear bias from the source Poisson noise. Our noise treatment can be generalized for images made of multiple exposures through MultiDrizzle. This is demonstrated with the SDSS and COSMOS/ACS data. With a large ensemble of mock galaxy images of unrestricted morphologies, we show that our shear measurement method can achieve sub-percent level accuracy even for images of signal-to-noise ratio less than 5 in general, making it the most promising technique for cosmic shear measurement in the ongoing and upcoming large scale galaxy surveys.

  1. Accurate, fully-automated NMR spectral profiling for metabolomics.

    Siamak Ravanbakhsh

    Full Text Available Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile"-i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person's metabolic profile. Given a 1D 1H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid, BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF, defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error, in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively-with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of

  2. Accurate valence band width of diamond

    An accurate width is determined for the valence band of diamond by imaging photoelectron momentum distributions for a variety of initial- and final-state energies. The experimental result of 23.0±0.2 eV2 agrees well with first-principles quasiparticle calculations (23.0 and 22.88 eV) and significantly exceeds the local-density-functional width, 21.5±0.2 eV2. This difference quantifies effects of creating an excited hole state (with associated many-body effects) in a band measurement vs studying ground-state properties treated by local-density-functional calculations. copyright 1997 The American Physical Society

  3. Accurate Telescope Mount Positioning with MEMS Accelerometers

    Mészáros, László; Pál, András; Csépány, Gergely


    This paper describes the advantages and challenges of applying microelectromechanical accelerometer systems (MEMS accelerometers) in order to attain precise, accurate and stateless positioning of telescope mounts. This provides a completely independent method from other forms of electronic, optical, mechanical or magnetic feedback or real-time astrometry. Our goal is to reach the sub-arcminute range which is well smaller than the field-of-view of conventional imaging telescope systems. Here we present how this sub-arcminute accuracy can be achieved with very cheap MEMS sensors and we also detail how our procedures can be extended in order to attain even finer measurements. In addition, our paper discusses how can a complete system design be implemented in order to be a part of a telescope control system.

  4. Accurate estimation of indoor travel times

    Prentow, Thor Siiger; Blunck, Henrik; Stisen, Allan;


    the InTraTime method for accurately estimating indoor travel times via mining of historical and real-time indoor position traces. The method learns during operation both travel routes, travel times and their respective likelihood---both for routes traveled as well as for sub-routes thereof. InTraTime...... allows to specify temporal and other query parameters, such as time-of-day, day-of-week or the identity of the traveling individual. As input the method is designed to take generic position traces and is thus interoperable with a variety of indoor positioning systems. The method's advantages include...... a minimal-effort setup and self-improving operations due to unsupervised learning---as it is able to adapt implicitly to factors influencing indoor travel times such as elevators, rotating doors or changes in building layout. We evaluate and compare the proposed InTraTime method to indoor adaptions...

  5. Accurate sky background modelling for ESO facilities

    Full text: Ground-based measurements like e.g. high resolution spectroscopy are heavily influenced by several physical processes. Amongst others, line absorption/ emission, air glow by OH molecules, and scattering of photons within the earth's atmosphere make observations in particular from facilities like the future European extremely large telescope a challenge. Additionally, emission from unresolved extrasolar objects, the zodiacal light, the moon and even thermal emission from the telescope and the instrument contribute significantly to the broad band background over a wide wavelength range. In our talk we review these influences and give an overview on how they can be accurately modeled for increasing the overall precision of spectroscopic and imaging measurements. (author)

  6. Accurate Weather Forecasting for Radio Astronomy

    Maddalena, Ronald J.


    The NRAO Green Bank Telescope routinely observes at wavelengths from 3 mm to 1 m. As with all mm-wave telescopes, observing conditions depend upon the variable atmospheric water content. The site provides over 100 days/yr when opacities are low enough for good observing at 3 mm, but winds on the open-air structure reduce the time suitable for 3-mm observing where pointing is critical. Thus, to maximum productivity the observing wavelength needs to match weather conditions. For 6 years the telescope has used a dynamic scheduling system (recently upgraded; that requires accurate multi-day forecasts for winds and opacities. Since opacity forecasts are not provided by the National Weather Services (NWS), I have developed an automated system that takes available forecasts, derives forecasted opacities, and deploys the results on the web in user-friendly graphical overviews ( rmaddale/Weather). The system relies on the "North American Mesoscale" models, which are updated by the NWS every 6 hrs, have a 12 km horizontal resolution, 1 hr temporal resolution, run to 84 hrs, and have 60 vertical layers that extend to 20 km. Each forecast consists of a time series of ground conditions, cloud coverage, etc, and, most importantly, temperature, pressure, humidity as a function of height. I use the Liebe's MWP model (Radio Science, 20, 1069, 1985) to determine the absorption in each layer for each hour for 30 observing wavelengths. Radiative transfer provides, for each hour and wavelength, the total opacity and the radio brightness of the atmosphere, which contributes substantially at some wavelengths to Tsys and the observational noise. Comparisons of measured and forecasted Tsys at 22.2 and 44 GHz imply that the forecasted opacities are good to about 0.01 Nepers, which is sufficient for forecasting and accurate calibration. Reliability is high out to 2 days and degrades slowly for longer-range forecasts.

  7. On Quantitative Rorschach Scales.

    Haggard, Ernest A.


    Two types of quantitative Rorschach scales are discussed: first, those based on the response categories of content, location, and the determinants, and second, global scales based on the subject's responses to all ten stimulus cards. (Author/JKS)

  8. Accurate FRET Measurements within Single Diffusing Biomolecules Using Alternating-Laser Excitation

    Lee, Nam Ki; Kapanidis, Achillefs N.; Wang, You; Michalet, Xavier; Mukhopadhyay, Jayanta; Ebright, Richard H.; Weiss, Shimon


    Fluorescence resonance energy transfer (FRET) between a donor (D) and an acceptor (A) at the single-molecule level currently provides qualitative information about distance, and quantitative information about kinetics of distance changes. Here, we used the sorting ability of confocal microscopy equipped with alternating-laser excitation (ALEX) to measure accurate FRET efficiencies and distances from single molecules, using corrections that account for cross-talk terms that contaminate the FRE...

  9. Quantitative phase spectroscopy

    Rinehart, Matthew; Zhu, Yizheng; Wax, Adam


    Quantitative phase spectroscopy is presented as a novel method of measuring the wavelength-dependent refractive index of microscopic volumes. Light from a broadband source is filtered to an ~5 nm bandwidth and rapidly tuned across the visible spectrum in 1 nm increments by an acousto-optic tunable filter (AOTF). Quantitative phase images of semitransparent samples are recovered at each wavelength using off-axis interferometry and are processed to recover relative and absolute dispersion measu...

  10. Application of quantitative proteomics expression analysis using stable isotope labeling

    Quantitative protein expression profiling is a crucial part of proteomics and requires technique that are able to efficiently provide accurate, high-throughput and reproducible differential expression values for proteins in two or more biological samples. At present, stable isotope labeling is probably considered as one of the most accurate ways to relatively quantify protein expression levels and additionally stable isotope labeling may be directly combined to LC MS/MS approaches. In summary, this technique has its advantages in quantitative proteomics. The application and the latest progresses about this technique are discussed. (authors)

  11. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi


    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  12. Mass Spectrometry-Based Label-Free Quantitative Proteomics

    Chun-Ming Huang; Smith, Jeffrey W.; Wenhong Zhu


    In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general c...

  13. Rapid quantitative phase imaging for partially coherent light microscopy

    Rodrigo Martín-Romo, José Augusto; Alieva, Tatiana Krasheninnikova


    Partially coherent light provides promising advantages for imaging applications. In contrast to its completely coherent counterpart, it prevents image degradation due to speckle noise and decreases cross-talk among the imaged objects. These facts make attractive the partially coherent illumination for accurate quantitative imaging in microscopy. In this work, we present a non-interferometric technique and system for quantitative phase imaging with simultaneous determination of the spatial coh...

  14. Accurate measurement of streamwise vortices in low speed aerodynamic flows

    Waldman, Rye M.; Kudo, Jun; Breuer, Kenneth S.


    Low Reynolds number experiments with flapping animals (such as bats and small birds) are of current interest in understanding biological flight mechanics, and due to their application to Micro Air Vehicles (MAVs) which operate in a similar parameter space. Previous PIV wake measurements have described the structures left by bats and birds, and provided insight to the time history of their aerodynamic force generation; however, these studies have faced difficulty drawing quantitative conclusions due to significant experimental challenges associated with the highly three-dimensional and unsteady nature of the flows, and the low wake velocities associated with lifting bodies that only weigh a few grams. This requires the high-speed resolution of small flow features in a large field of view using limited laser energy and finite camera resolution. Cross-stream measurements are further complicated by the high out-of-plane flow which requires thick laser sheets and short interframe times. To quantify and address these challenges we present data from a model study on the wake behind a fixed wing at conditions comparable to those found in biological flight. We present a detailed analysis of the PIV wake measurements, discuss the criteria necessary for accurate measurements, and present a new dual-plane PIV configuration to resolve these issues.

  15. The place of highly accurate methods by RNAA in metrology

    With the introduction of physical metrological concepts to chemical analysis which require that the result should be accompanied by uncertainty statement written down in terms of Sl units, several researchers started to consider lD-MS as the only method fulfilling this requirement. However, recent publications revealed that in certain cases also some expert laboratories using lD-MS and analyzing the same material, produced results for which their uncertainty statements did not overlap, what theoretically should not have taken place. This shows that no monopoly is good in science and it would be desirable to widen the set of methods acknowledged as primary in inorganic trace analysis. Moreover, lD-MS cannot be used for monoisotopic elements. The need for searching for other methods having similar metrological quality as the lD-MS seems obvious. In this paper, our long-time experience on devising highly accurate ('definitive') methods by RNAA for the determination of selected trace elements in biological materials is reviewed. The general idea of definitive methods based on combination of neutron activation with the highly selective and quantitative isolation of the indicator radionuclide by column chromatography followed by gamma spectrometric measurement is reminded and illustrated by examples of the performance of such methods when determining Cd, Co, Mo, etc. lt is demonstrated that such methods are able to provide very reliable results with very low levels of uncertainty traceable to Sl units

  16. Accurate quantification of cells recovered by bronchoalveolar lavage.

    Saltini, C; Hance, A J; Ferrans, V J; Basset, F; Bitterman, P B; Crystal, R G


    Quantification of the differential cell count and total number of cells recovered from the lower respiratory tract by bronchoalveolar lavage is a valuable technique for evaluating the alveolitis of patients with inflammatory disorders of the lower respiratory tract. The most commonly used technique for the evaluation of cells recovered by lavage has been to concentrate cells by centrifugation and then to determine total cell number using a hemocytometer and differential cell count from a Wright-Glemsa-stained cytocentrifuge preparation. However, we have noted that the percentage of small cells present in the original cell suspension recovered by lavage is greater than the percentage of lymphocytes identified on cytocentrifuge preparations. Therefore, we developed procedures for determining differential cell counts on lavage cells collected on Millipore filters and stained with hematoxylin-eosin (filter preparations) and compared the results of differential cell counts performed on filter preparations with those obtained using cytocentrifuge preparations. When cells recovered by lavage were collected on filter preparations, accurate differential cell counts were obtained, as confirmed by performing differential cell counts on cell mixtures of known composition, and by comparing differential cell counts obtained using filter preparations stained with hematoxylin-eosin with those obtained using filter preparations stained with a peroxidase cytochemical stain. The morphology of cells displayed on filter preparations was excellent, and interobserver variability in quantitating cell types recovered by lavage was less than 3%.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6385789

  17. Accurate Measurement of the Relative Abundance of Different DNA Species in Complex DNA Mixtures

    Jeong, Sangkyun; Yu, Hyunjoo; Pfeifer, Karl


    A molecular tool that can compare the abundances of different DNA sequences is necessary for comparing intergenic or interspecific gene expression. We devised and verified such a tool using a quantitative competitive polymerase chain reaction approach. For this approach, we adapted a competitor array, an artificially made plasmid DNA in which all the competitor templates for the target DNAs are arranged with a defined ratio, and melting analysis for allele quantitation for accurate quantitation of the fractional ratios of competitively amplified DNAs. Assays on two sets of DNA mixtures with explicitly known compositional structures of the test sequences were performed. The resultant average relative errors of 0.059 and 0.021 emphasize the highly accurate nature of this method. Furthermore, the method's capability of obtaining biological data is demonstrated by the fact that it can illustrate the tissue-specific quantitative expression signatures of the three housekeeping genes G6pdx, Ubc, and Rps27 by using the forms of the relative abundances of their transcripts, and the differential preferences of Igf2 enhancers for each of the multiple Igf2 promoters for the transcription. PMID:22334570

  18. Intravital spectral imaging as a tool for accurate measurement of vascularization in mice

    Tsatsanis Christos


    Full Text Available Abstract Background Quantitative determination of the development of new blood vessels is crucial for our understanding of the progression of several diseases, including cancer. However, in most cases a high throughput technique that is simple, accurate, user-independent and cost-effective for small animal imaging is not available. Methods In this work we present a simple approach based on spectral imaging to increase the contrast between vessels and surrounding tissue, enabling accurate determination of the blood vessel area. This approach is put to test with a 4T1 breast cancer murine in vivo model and validated with histological and microvessel density analysis. Results We found that one can accurately measure the vascularization area by using excitation/emission filter pairs which enhance the surrounding tissue's autofluorescence, significantly increasing the contrast between surrounding tissue and blood vessels. Additionally, we found excellent correlation between this technique and histological and microvessel density analysis. Conclusions Making use of spectral imaging techniques we have shown that it is possible to accurately determine blood vessel volume intra-vitally. We believe that due to the low cost, accuracy, user-independence and simplicity of this technique, it will be of great value in those cases where in vivo quantitative information is necessary.

  19. Accurate simulation of optical properties in dyes.

    Jacquemin, Denis; Perpète, Eric A; Ciofini, Ilaria; Adamo, Carlo


    Since Antiquity, humans have produced and commercialized dyes. To this day, extraction of natural dyes often requires lengthy and costly procedures. In the 19th century, global markets and new industrial products drove a significant effort to synthesize artificial dyes, characterized by low production costs, huge quantities, and new optical properties (colors). Dyes that encompass classes of molecules absorbing in the UV-visible part of the electromagnetic spectrum now have a wider range of applications, including coloring (textiles, food, paintings), energy production (photovoltaic cells, OLEDs), or pharmaceuticals (diagnostics, drugs). Parallel to the growth in dye applications, researchers have increased their efforts to design and synthesize new dyes to customize absorption and emission properties. In particular, dyes containing one or more metallic centers allow for the construction of fairly sophisticated systems capable of selectively reacting to light of a given wavelength and behaving as molecular devices (photochemical molecular devices, PMDs).Theoretical tools able to predict and interpret the excited-state properties of organic and inorganic dyes allow for an efficient screening of photochemical centers. In this Account, we report recent developments defining a quantitative ab initio protocol (based on time-dependent density functional theory) for modeling dye spectral properties. In particular, we discuss the importance of several parameters, such as the methods used for electronic structure calculations, solvent effects, and statistical treatments. In addition, we illustrate the performance of such simulation tools through case studies. We also comment on current weak points of these methods and ways to improve them. PMID:19113946

  20. Accurate fission data for nuclear safety

    Solders, A; Jokinen, A; Kolhinen, V S; Lantz, M; Mattera, A; Penttila, H; Pomp, S; Rakopoulos, V; Rinta-Antila, S


    The Accurate fission data for nuclear safety (AlFONS) project aims at high precision measurements of fission yields, using the renewed IGISOL mass separator facility in combination with a new high current light ion cyclotron at the University of Jyvaskyla. The 30 MeV proton beam will be used to create fast and thermal neutron spectra for the study of neutron induced fission yields. Thanks to a series of mass separating elements, culminating with the JYFLTRAP Penning trap, it is possible to achieve a mass resolving power in the order of a few hundred thousands. In this paper we present the experimental setup and the design of a neutron converter target for IGISOL. The goal is to have a flexible design. For studies of exotic nuclei far from stability a high neutron flux (10^12 neutrons/s) at energies 1 - 30 MeV is desired while for reactor applications neutron spectra that resembles those of thermal and fast nuclear reactors are preferred. It is also desirable to be able to produce (semi-)monoenergetic neutrons...

  1. Fast and Provably Accurate Bilateral Filtering.

    Chaudhury, Kunal N; Dabhade, Swapnil D


    The bilateral filter is a non-linear filter that uses a range filter along with a spatial filter to perform edge-preserving smoothing of images. A direct computation of the bilateral filter requires O(S) operations per pixel, where S is the size of the support of the spatial filter. In this paper, we present a fast and provably accurate algorithm for approximating the bilateral filter when the range kernel is Gaussian. In particular, for box and Gaussian spatial filters, the proposed algorithm can cut down the complexity to O(1) per pixel for any arbitrary S . The algorithm has a simple implementation involving N+1 spatial filterings, where N is the approximation order. We give a detailed analysis of the filtering accuracy that can be achieved by the proposed approximation in relation to the target bilateral filter. This allows us to estimate the order N required to obtain a given accuracy. We also present comprehensive numerical results to demonstrate that the proposed algorithm is competitive with the state-of-the-art methods in terms of speed and accuracy. PMID:27093722

  2. Accurate adiabatic correction in the hydrogen molecule

    Pachucki, Krzysztof, E-mail: [Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw (Poland); Komasa, Jacek, E-mail: [Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań (Poland)


    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10{sup −12} at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H{sub 2}, HD, HT, D{sub 2}, DT, and T{sub 2} has been determined. For the ground state of H{sub 2} the estimated precision is 3 × 10{sup −7} cm{sup −1}, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  3. Quantitative analysis of endogenous compounds.

    Thakare, Rhishikesh; Chhonker, Yashpal S; Gautam, Nagsen; Alamoudi, Jawaher Abdullah; Alnouti, Yazen


    Accurate quantitative analysis of endogenous analytes is essential for several clinical and non-clinical applications. LC-MS/MS is the technique of choice for quantitative analyses. Absolute quantification by LC/MS requires preparing standard curves in the same matrix as the study samples so that the matrix effect and the extraction efficiency for analytes are the same in both the standard and study samples. However, by definition, analyte-free biological matrices do not exist for endogenous compounds. To address the lack of blank matrices for the quantification of endogenous compounds by LC-MS/MS, four approaches are used including the standard addition, the background subtraction, the surrogate matrix, and the surrogate analyte methods. This review article presents an overview these approaches, cite and summarize their applications, and compare their advantages and disadvantages. In addition, we discuss in details, validation requirements and compatibility with FDA guidelines to ensure method reliability in quantifying endogenous compounds. The standard addition, background subtraction, and the surrogate analyte approaches allow the use of the same matrix for the calibration curve as the one to be analyzed in the test samples. However, in the surrogate matrix approach, various matrices such as artificial, stripped, and neat matrices are used as surrogate matrices for the actual matrix of study samples. For the surrogate analyte approach, it is required to demonstrate similarity in matrix effect and recovery between surrogate and authentic endogenous analytes. Similarly, for the surrogate matrix approach, it is required to demonstrate similar matrix effect and extraction recovery in both the surrogate and original matrices. All these methods represent indirect approaches to quantify endogenous compounds and regardless of what approach is followed, it has to be shown that none of the validation criteria have been compromised due to the indirect analyses. PMID

  4. Accurate paleointensities - the multi-method approach

    de Groot, Lennart


    The accuracy of models describing rapid changes in the geomagnetic field over the past millennia critically depends on the availability of reliable paleointensity estimates. Over the past decade methods to derive paleointensities from lavas (the only recorder of the geomagnetic field that is available all over the globe and through geologic times) have seen significant improvements and various alternative techniques were proposed. The 'classical' Thellier-style approach was optimized and selection criteria were defined in the 'Standard Paleointensity Definitions' (Paterson et al, 2014). The Multispecimen approach was validated and the importance of additional tests and criteria to assess Multispecimen results must be emphasized. Recently, a non-heating, relative paleointensity technique was proposed -the pseudo-Thellier protocol- which shows great potential in both accuracy and efficiency, but currently lacks a solid theoretical underpinning. Here I present work using all three of the aforementioned paleointensity methods on suites of young lavas taken from the volcanic islands of Hawaii, La Palma, Gran Canaria, Tenerife, and Terceira. Many of the sampled cooling units are <100 years old, the actual field strength at the time of cooling is therefore reasonably well known. Rather intuitively, flows that produce coherent results from two or more different paleointensity methods yield the most accurate estimates of the paleofield. Furthermore, the results for some flows pass the selection criteria for one method, but fail in other techniques. Scrutinizing and combing all acceptable results yielded reliable paleointensity estimates for 60-70% of all sampled cooling units - an exceptionally high success rate. This 'multi-method paleointensity approach' therefore has high potential to provide the much-needed paleointensities to improve geomagnetic field models for the Holocene.

  5. Towards Accurate Application Characterization for Exascale (APEX)

    Hammond, Simon David [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)


    Sandia National Laboratories has been engaged in hardware and software codesign activities for a number of years, indeed, it might be argued that prototyping of clusters as far back as the CPLANT machines and many large capability resources including ASCI Red and RedStorm were examples of codesigned solutions. As the research supporting our codesign activities has moved closer to investigating on-node runtime behavior a nature hunger has grown for detailed analysis of both hardware and algorithm performance from the perspective of low-level operations. The Application Characterization for Exascale (APEX) LDRD was a project concieved of addressing some of these concerns. Primarily the research was to intended to focus on generating accurate and reproducible low-level performance metrics using tools that could scale to production-class code bases. Along side this research was an advocacy and analysis role associated with evaluating tools for production use, working with leading industry vendors to develop and refine solutions required by our code teams and to directly engage with production code developers to form a context for the application analysis and a bridge to the research community within Sandia. On each of these accounts significant progress has been made, particularly, as this report will cover, in the low-level analysis of operations for important classes of algorithms. This report summarizes the development of a collection of tools under the APEX research program and leaves to other SAND and L2 milestone reports the description of codesign progress with Sandia’s production users/developers.

  6. Accurate hydrocarbon estimates attained with radioactive isotope

    To make accurate economic evaluations of new discoveries, an oil company needs to know how much gas and oil a reservoir contains. The porous rocks of these reservoirs are not completely filled with gas or oil, but contain a mixture of gas, oil and water. It is extremely important to know what volume percentage of this water--called connate water--is contained in the reservoir rock. The percentage of connate water can be calculated from electrical resistivity measurements made downhole. The accuracy of this method can be improved if a pure sample of connate water can be analyzed or if the chemistry of the water can be determined by conventional logging methods. Because of the similarity of the mud filtrate--the water in a water-based drilling fluid--and the connate water, this is not always possible. If the oil company cannot distinguish between connate water and mud filtrate, its oil-in-place calculations could be incorrect by ten percent or more. It is clear that unless an oil company can be sure that a sample of connate water is pure, or at the very least knows exactly how much mud filtrate it contains, its assessment of the reservoir's water content--and consequently its oil or gas content--will be distorted. The oil companies have opted for the Repeat Formation Tester (RFT) method. Label the drilling fluid with small doses of tritium--a radioactive isotope of hydrogen--and it will be easy to detect and quantify in the sample

  7. Towards a more accurate concept of fuels

    Full text: The introduction of LEU in Atucha and the approval of CARA show an advancement of the Argentine power stations fuels, which stimulate and show a direction to follow. In the first case, the use of enriched U fuel relax an important restriction related to neutronic economy; that means that it is possible to design less penalized fuels using more Zry. The second case allows a decrease in the lineal power of the rods, enabling a better performance of the fuel in normal and also in accident conditions. In this work we wish to emphasize this last point, trying to find a design in which the surface power of the rod is diminished. Hence, in accident conditions owing to lack of coolant, the cladding tube will not reach temperatures that will produce oxidation, with the corresponding H2 formation and with plasticity enough to form blisters, which will obstruct the reflooding and hydration that will produce fragility and rupture of the cladding tube, with the corresponding radioactive material dispersion. This work is oriented to find rods designs with quasi rectangular geometry to lower the surface power of the rods, in order to obtain a lower central temperature of the rod. Thus, critical temperatures will not be reached in case of lack of coolant. This design is becoming a reality after PPFAE's efforts in search of cladding tubes fabrication with different circumferential values, rectangular in particular. This geometry, with an appropriate pellet design, can minimize the pellet-cladding interaction and, through the accurate width election, non rectified pellets could be used. This means an important economy in pellets production, as well as an advance in the fabrication of fuels in gloves box and hot cells in the future. The sequence to determine critical geometrical parameters is described and some rod dispositions are explored

  8. Accurate orbit propagation with planetary close encounters

    Baù, Giulio; Milani Comparetti, Andrea; Guerra, Francesca


    We tackle the problem of accurately propagating the motion of those small bodies that undergo close approaches with a planet. The literature is lacking on this topic and the reliability of the numerical results is not sufficiently discussed. The high-frequency components of the perturbation generated by a close encounter makes the propagation particularly challenging both from the point of view of the dynamical stability of the formulation and the numerical stability of the integrator. In our approach a fixed step-size and order multistep integrator is combined with a regularized formulation of the perturbed two-body problem. When the propagated object enters the region of influence of a celestial body, the latter becomes the new primary body of attraction. Moreover, the formulation and the step-size will also be changed if necessary. We present: 1) the restarter procedure applied to the multistep integrator whenever the primary body is changed; 2) new analytical formulae for setting the step-size (given the order of the multistep, formulation and initial osculating orbit) in order to control the accumulation of the local truncation error and guarantee the numerical stability during the propagation; 3) a new definition of the region of influence in the phase space. We test the propagator with some real asteroids subject to the gravitational attraction of the planets, the Yarkovsky and relativistic perturbations. Our goal is to show that the proposed approach improves the performance of both the propagator implemented in the OrbFit software package (which is currently used by the NEODyS service) and of the propagator represented by a variable step-size and order multistep method combined with Cowell's formulation (i.e. direct integration of position and velocity in either the physical or a fictitious time).

  9. Uncertainty Quantification for Quantitative Imaging Holdup Measurements

    Bevill, Aaron M [ORNL; Bledsoe, Keith C [ORNL


    In nuclear fuel cycle safeguards, special nuclear material "held up" in pipes, ducts, and glove boxes causes significant uncertainty in material-unaccounted-for estimates. Quantitative imaging is a proposed non-destructive assay technique with potential to estimate the holdup mass more accurately and reliably than current techniques. However, uncertainty analysis for quantitative imaging remains a significant challenge. In this work we demonstrate an analysis approach for data acquired with a fast-neutron coded aperture imager. The work includes a calibrated forward model of the imager. Cross-validation indicates that the forward model predicts the imager data typically within 23%; further improvements are forthcoming. A new algorithm based on the chi-squared goodness-of-fit metric then uses the forward model to calculate a holdup confidence interval. The new algorithm removes geometry approximations that previous methods require, making it a more reliable uncertainty estimator.

  10. Quantitative bone gallium scintigraphy in osteomyelitis

    Gallium imaging offers many practical advantages over indium-111-labeled leukocyte imaging, and calculating quantitative ratios in addition to performing the routine bone-gallium images allows accurate and easy evaluation of patients with suspected osteomyelitis. To add objectivity and improve the accuracy and confidence in diagnosis of osteomyelitis, quantitative comparison of abnormalities seen on bone scans and gallium scans was performed. One hundred and ten adult patients with 126 sites of suspected osteomyelitis were evaluated and categorized by gallium-to-bone ratios, gallium-to-background ratios, and spatial incongruency of gallium and bone activity. Combined evaluation using these criteria gave a 70% sensitivity and 93% specificity for the diagnosis of osteomyelitis. (orig.)

  11. A quantitative description for efficient financial markets

    Immonen, Eero


    In this article we develop a control system model for describing efficient financial markets. We define the efficiency of a financial market in quantitative terms by robust asymptotic price-value equality in this model. By invoking the Internal Model Principle of robust output regulation theory we then show that under No Bubble Conditions, in the proposed model, the market is efficient if and only if the following conditions hold true: (1) the traders, as a group, can identify any mispricing in asset value (even if no one single trader can do it accurately), and (2) the traders, as a group, incorporate an internal model of the value process (again, even if no one single trader knows it). This main result of the article, which deliberately avoids the requirement for investor rationality, demonstrates, in quantitative terms, that the more transparent the markets are, the more efficient they are. An extensive example is provided to illustrate the theoretical development.

  12. Simple Mathematical Models Do Not Accurately Predict Early SIV Dynamics

    Cecilia Noecker


    Full Text Available Upon infection of a new host, human immunodeficiency virus (HIV replicates in the mucosal tissues and is generally undetectable in circulation for 1–2 weeks post-infection. Several interventions against HIV including vaccines and antiretroviral prophylaxis target virus replication at this earliest stage of infection. Mathematical models have been used to understand how HIV spreads from mucosal tissues systemically and what impact vaccination and/or antiretroviral prophylaxis has on viral eradication. Because predictions of such models have been rarely compared to experimental data, it remains unclear which processes included in these models are critical for predicting early HIV dynamics. Here we modified the “standard” mathematical model of HIV infection to include two populations of infected cells: cells that are actively producing the virus and cells that are transitioning into virus production mode. We evaluated the effects of several poorly known parameters on infection outcomes in this model and compared model predictions to experimental data on infection of non-human primates with variable doses of simian immunodifficiency virus (SIV. First, we found that the mode of virus production by infected cells (budding vs. bursting has a minimal impact on the early virus dynamics for a wide range of model parameters, as long as the parameters are constrained to provide the observed rate of SIV load increase in the blood of infected animals. Interestingly and in contrast with previous results, we found that the bursting mode of virus production generally results in a higher probability of viral extinction than the budding mode of virus production. Second, this mathematical model was not able to accurately describe the change in experimentally determined probability of host infection with increasing viral doses. Third and finally, the model was also unable to accurately explain the decline in the time to virus detection with increasing viral

  13. Quantitative Compositional Reasoning

    Chatterjee, K.; Alfaro, de L.; Faella, M.; Henzinger, T.A.; Majumdar, R.; Stoelinga, M.I.A.


    We present a compositional theory of system verifica tion, where specifications assign real-numbered costs to systems. These costs can express a wide variety of quantitative system properties, such as resource consumption, price or a measure of how well a system satisfies its specification. The theo

  14. Critical Quantitative Inquiry in Context

    Stage, Frances K.; Wells, Ryan S.


    This chapter briefly traces the development of the concept of critical quantitative inquiry, provides an expanded conceptualization of the tasks of critical quantitative research, offers theoretical explanation and justification for critical research using quantitative methods, and previews the work of quantitative criticalists presented in this…




    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 DNA 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.

  16. Quantitative Phase Retrieval in Transmission Electron Microscopy

    McLeod, Robert Alexander

    Phase retrieval in the transmission electron microscope offers the unique potential to collect quantitative data regarding the electric and magnetic properties of materials at the nanoscale. Substantial progress in the field of quantitative phase imaging was made by improvements to the technique of off-axis electron holography. In this thesis, several breakthroughs have been achieved that improve the quantitative analysis of phase retrieval. An accurate means of measuring the electron wavefront coherence in two-dimensions was developed and pratical applications demonstrated. The detector modulation-transfer function (MTF) was assessed by slanted-edge, noise, and the novel holographic techniques. It was shown the traditional slanted-edge technique underestimates the MTF. In addition, progress was made in dark and gain reference normalization of images, and it was shown that incomplete read-out is a concern for slow-scan CCD detectors. Last, the phase error due to electron shot noise was reduced by the technique of summation of hologram series. The phase error, which limits the finest electric and magnetic phenomena which can be investigated, was reduced by over 900 % with no loss of spatial resolution. Quantitative agreement between the experimental root-mean-square phase error and the analytical prediction of phase error was achieved.

  17. Quantitative analysis of methylation of genomic loci in early-stage rectal cancer predicts distant recurrence.

    Maat, M.F. de; Velde, C.J. van de; Werff, M.P. van der; Putter, H.; Umetani, N.; Klein-Kranenbarg, E.M.; Turner, R.R.; Krieken, J.H.J.M. van; Bilchik, A.; Tollenaar, R.A.; Hoon, D.S.


    PURPOSE: There are no accurate prognostic biomarkers specific for rectal cancer. Epigenetic aberrations, in the form of DNA methylation, accumulate early during rectal tumor formation. In a preliminary study, we investigated absolute quantitative methylation changes associated with tumor progression

  18. Impact of reconstruction parameters on quantitative I-131 SPECT

    van Gils, C. A. J.; Beijst, C.; van Rooij, R.; de Jong, H. W. A. M.


    Radioiodine therapy using I-131 is widely used for treatment of thyroid disease or neuroendocrine tumors. Monitoring treatment by accurate dosimetry requires quantitative imaging. The high energy photons however render quantitative SPECT reconstruction challenging, potentially requiring accurate correction for scatter and collimator effects. The goal of this work is to assess the effectiveness of various correction methods on these effects using phantom studies. A SPECT/CT acquisition of the NEMA IEC body phantom was performed. Images were reconstructed using the following parameters: (1) without scatter correction, (2) with triple energy window (TEW) scatter correction and (3) with Monte Carlo-based scatter correction. For modelling the collimator-detector response (CDR), both (a) geometric Gaussian CDRs as well as (b) Monte Carlo simulated CDRs were compared. Quantitative accuracy, contrast to noise ratios and recovery coefficients were calculated, as well as the background variability and the residual count error in the lung insert. The Monte Carlo scatter corrected reconstruction method was shown to be intrinsically quantitative, requiring no experimentally acquired calibration factor. It resulted in a more accurate quantification of the background compartment activity density compared with TEW or no scatter correction. The quantification error relative to a dose calibrator derived measurement was found to be  <1%,‑26% and 33%, respectively. The adverse effects of partial volume were significantly smaller with the Monte Carlo simulated CDR correction compared with geometric Gaussian or no CDR modelling. Scatter correction showed a small effect on quantification of small volumes. When using a weighting factor, TEW correction was comparable to Monte Carlo reconstruction in all measured parameters, although this approach is clinically impractical since this factor may be patient dependent. Monte Carlo based scatter correction including accurately simulated

  19. SPECT-OPT multimodal imaging enables accurate evaluation of radiotracers for β-cell mass assessments.

    Eter, Wael A; Parween, Saba; Joosten, Lieke; Frielink, Cathelijne; Eriksson, Maria; Brom, Maarten; Ahlgren, Ulf; Gotthardt, Martin


    Single Photon Emission Computed Tomography (SPECT) has become a promising experimental approach to monitor changes in β-cell mass (BCM) during diabetes progression. SPECT imaging of pancreatic islets is most commonly cross-validated by stereological analysis of histological pancreatic sections after insulin staining. Typically, stereological methods do not accurately determine the total β-cell volume, which is inconvenient when correlating total pancreatic tracer uptake with BCM. Alternative methods are therefore warranted to cross-validate β-cell imaging using radiotracers. In this study, we introduce multimodal SPECT - optical projection tomography (OPT) imaging as an accurate approach to cross-validate radionuclide-based imaging of β-cells. Uptake of a promising radiotracer for β-cell imaging by SPECT, (111)In-exendin-3, was measured by ex vivo-SPECT and cross evaluated by 3D quantitative OPT imaging as well as with histology within healthy and alloxan-treated Brown Norway rat pancreata. SPECT signal was in excellent linear correlation with OPT data as compared to histology. While histological determination of islet spatial distribution was challenging, SPECT and OPT revealed similar distribution patterns of (111)In-exendin-3 and insulin positive β-cell volumes between different pancreatic lobes, both visually and quantitatively. We propose ex vivo SPECT-OPT multimodal imaging as a highly accurate strategy for validating the performance of β-cell radiotracers. PMID:27080529

  20. Accurate phase measurements for thick spherical objects using optical quadrature microscopy

    Warger, William C., II; DiMarzio, Charles A.


    In vitro fertilization (IVF) procedures have resulted in the birth of over three million babies since 1978. Yet the live birth rate in the United States was only 34% in 2005, with 32% of the successful pregnancies resulting in multiple births. These multiple pregnancies were directly attributed to the transfer of multiple embryos to increase the probability that a single, healthy embryo was included. Current viability markers used for IVF, such as the cell number, symmetry, size, and fragmentation, are analyzed qualitatively with differential interference contrast (DIC) microscopy. However, this method is not ideal for quantitative measures beyond the 8-cell stage of development because the cells overlap and obstruct the view within and below the cluster of cells. We have developed the phase-subtraction cell-counting method that uses the combination of DIC and optical quadrature microscopy (OQM) to count the number of cells accurately in live mouse embryos beyond the 8-cell stage. We have also created a preliminary analysis to measure the cell symmetry, size, and fragmentation quantitatively by analyzing the relative dry mass from the OQM image in conjunction with the phase-subtraction count. In this paper, we will discuss the characterization of OQM with respect to measuring the phase accurately for spherical samples that are much larger than the depth of field. Once fully characterized and verified with human embryos, this methodology could provide the means for a more accurate method to score embryo viability.

  1. Energy & Climate: Getting Quantitative

    Wolfson, Richard


    A noted environmentalist claims that buying an SUV instead of a regular car is energetically equivalent to leaving your refrigerator door open for seven years. A fossil-fuel apologist argues that solar energy is a pie-in-the-sky dream promulgated by na"ive environmentalists, because there's nowhere near enough solar energy to meet humankind's energy demand. A group advocating shutdown of the Vermont Yankee nuclear plant claims that 70% of its electrical energy is lost in transmission lines. Around the world, thousands agitate for climate action, under the numerical banner ``350.'' Neither the environmentalist, the fossil-fuel apologist, the antinuclear activists, nor most of those marching under the ``350'' banner can back up their assertions with quantitative arguments. Yet questions about energy and its environmental impacts almost always require quantitative answers. Physics can help! This poster gives some cogent examples, based on the newly published 2^nd edition of the author's textbook Energy, Environment, and Climate.

  2. Quantitative shadowgraphy made easy

    This paper is dedicated to the learning of the shadowgraphy technique at graduate and undergraduate levels. It presents an experiment that allows measurement of the refractive index of butane with the help of an affordable quantitative shadowgraphy bench. The paper is constituted of two distinctive parts. The first presents the theory and data processing involved in shadowgraphy, introducing the concept of Abel inversion and modern data computer processing for graduate students. The second focuses on the experimental set-up and results; here, a qualitative interpretation of shadowgrams suitable for undergraduate students is given, as well as a quantitative explanation using a butane gas jet. The refractive index of butane measured with our simple experimental set-up is in close agreement with values available in the literature. (paper)

  3. Quantitative lacrimal scintigraphy

    Quantitative radioisotope dacryoscintigraphy was performed using a gamma camera fitted with a computer system. ROI selection with corresponding time/activity curves allowed the calculation of some parameters such as appearance time and mean transit time in every segment of the lacrimal ducts. The numerical values give some exact clues concerning the knowledge of lacrimal physiology as well as the follow-up of dacryo- and rhino-pathology. (author)

  4. Quantitative analysis of myocardial tissue with digital autofluorescence microscopy

    Thomas Jensen


    Full Text Available Background: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including staining may benefit. Methods: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm are presented. Results: It is shown that the autofluorescence intensity of unstained microsections at two different wavelengths is a suitable starting point for automated digital analysis of myocytes, fibrous tissue, lipofuscin, and the extracellular compartment. The output of the method is absolute quantitation along with accurate outlines of above-mentioned components. The digital quantitations are verified by comparison to point grid quantitations performed on the microsections after Van Gieson staining. Conclusion: The presented method is amply described as a prestain multicomponent quantitation and outlining tool for histological sections of cardiac tissue. The main perspective is the opportunity for combination with digital analysis of stained microsections, for which the method may provide an accurate digital framework.

  5. Foucault test: a quantitative evaluation method.

    Rodríguez, Gustavo; Villa, Jesús; Ivanov, Rumen; González, Efrén; Martínez, Geminiano


    Reliable and accurate testing methods are essential to guiding the polishing process during the figuring of optical telescope mirrors. With the natural advancement of technology, the procedures and instruments used to carry out this delicate task have consistently increased in sensitivity, but also in complexity and cost. Fortunately, throughout history, the Foucault knife-edge test has shown the potential to measure transverse aberrations in the order of the wavelength, mainly when described in terms of physical theory, which allows a quantitative interpretation of its characteristic shadowmaps. Our previous publication on this topic derived a closed mathematical formulation that directly relates the knife-edge position with the observed irradiance pattern. The present work addresses the quite unexplored problem of the wavefront's gradient estimation from experimental captures of the test, which is achieved by means of an optimization algorithm featuring a proposed ad hoc cost function. The partial derivatives thereby calculated are then integrated by means of a Fourier-based algorithm to retrieve the mirror's actual surface profile. To date and to the best of our knowledge, this is the very first time that a complete mathematical-grounded treatment of this optical phenomenon is presented, complemented by an image-processing algorithm which allows a quantitative calculation of the corresponding slope at any given point of the mirror's surface, so that it becomes possible to accurately estimate the aberrations present in the analyzed concave device just through its associated foucaultgrams. PMID:27505659

  6. Qualitative and Quantitative Analysis of the Market – A Factor for Competitive Advantage of Enterprises

    Karolina Ilieska


    The goal of the market analyses is to define accurately the needs, motives and the behavior of the customers so that it can determine the product requests and services if there are any, as well as their quantity. The qualitative methods for data collecting give out an inaccurate vision for the structure and the significance of the information referring to the motives and habits of the purchase.Quantitative methods research the appearances from the quantitative point of view. The quantitative ...

  7. Mining tandem mass spectral data to develop a more accurate mass error model for peptide identification.

    Fu, Yan; Gao, Wen; He, Simin; Sun, Ruixiang; Zhou, Hu; Zeng, Rong


    The assumption on the mass error distribution of fragment ions plays a crucial role in peptide identification by tandem mass spectra. Previous mass error models are the simplistic uniform or normal distribution with empirically set parameter values. In this paper, we propose a more accurate mass error model, namely conditional normal model, and an iterative parameter learning algorithm. The new model is based on two important observations on the mass error distribution, i.e. the linearity between the mean of mass error and the ion mass, and the log-log linearity between the standard deviation of mass error and the peak intensity. To our knowledge, the latter quantitative relationship has never been reported before. Experimental results demonstrate the effectiveness of our approach in accurately quantifying the mass error distribution and the ability of the new model to improve the accuracy of peptide identification. PMID:17990507

  8. Quantitative Computed Tomography

    Balda, Michael


    Computed Tomography (CT) is a wide-spread medical imaging modality. Traditional CT yields information on a patient's anatomy in form of slice images or volume data. Hounsfield Units (HU) are used to quantify the imaged tissue properties. Due to the polychromatic nature of X-rays in CT, the HU values for a specific tissue depend on its density and composition but also on CT system parameters and settings and the surrounding materials. The main objective of Quantitative CT (QCT) is measuring ch...

  9. F# for quantitative finance

    Astborg, Johan


    To develop your confidence in F#, this tutorial will first introduce you to simpler tasks such as curve fitting. You will then advance to more complex tasks such as implementing algorithms for trading semi-automation in a practical scenario-based format.If you are a data analyst or a practitioner in quantitative finance, economics, or mathematics and wish to learn how to use F# as a functional programming language, this book is for you. You should have a basic conceptual understanding of financial concepts and models. Elementary knowledge of the .NET framework would also be helpful.

  10. Quantitative rainbow schlieren deflectometry

    Greenberg, Paul S.; Klimek, Robert B.; Buchele, Donald R.


    In the rainbow schlieren apparatus, a continuously graded rainbow filter is placed in the back focal plane of the decollimating lens. Refractive-index gradients in the test section thus appear as gradations in hue rather than irradiance. A simple system is described wherein a conventional color CCD array and video digitizer are used to quantify accurately the color attributes of the resulting image, and hence the associated ray deflections. The present system provides a sensitivity comparable with that of conventional interferometry, while being simpler to implement and less sensitive to mechanical misalignment.

  11. Accurate core-electron binding energy shifts from density functional theory

    Current review covers description of density functional methods of calculation of accurate core-electron binding energy (CEBE) of second and third row atoms; applications of calculated CEBEs and CEBE shifts (ΔCEBEs) in elucidation of topics such as: hydrogen-bonding, peptide bond, polymers, DNA bases, Hammett substituent (σ) constants, inductive and resonance effects, quantitative structure activity relationship (QSAR), and solid state effect (WD). This review limits itself to works of mainly Chong and his coworkers for the period post-2002. It is not a fully comprehensive account of the current state of the art.

  12. Accurate core-electron binding energy shifts from density functional theory

    Takahata, Yuji, E-mail: taka@iqm.unicamp.b [Amazonas State University, School of Engineering, Av. Darcy Vargas, 1200, Parque 10 - CEP 69065-020, Manaus, Amazonas (Brazil); Department of Chemistry, University of Campinas-UNICAMP, Campinas 13084-862, Sao Paulo (Brazil); Marques, Alberto Dos Santos [Amazonas State University, School of Engineering, Av. Darcy Vargas, 1200, Parque 10 - CEP 69065-020, Manaus, Amazonas (Brazil)


    Current review covers description of density functional methods of calculation of accurate core-electron binding energy (CEBE) of second and third row atoms; applications of calculated CEBEs and CEBE shifts (DELTACEBEs) in elucidation of topics such as: hydrogen-bonding, peptide bond, polymers, DNA bases, Hammett substituent (sigma) constants, inductive and resonance effects, quantitative structure activity relationship (QSAR), and solid state effect (WD). This review limits itself to works of mainly Chong and his coworkers for the period post-2002. It is not a fully comprehensive account of the current state of the art.

  13. An efficient and accurate 3D displacements tracking strategy for digital volume correlation

    Pan, Bing


    Owing to its inherent computational complexity, practical implementation of digital volume correlation (DVC) for internal displacement and strain mapping faces important challenges in improving its computational efficiency. In this work, an efficient and accurate 3D displacement tracking strategy is proposed for fast DVC calculation. The efficiency advantage is achieved by using three improvements. First, to eliminate the need of updating Hessian matrix in each iteration, an efficient 3D inverse compositional Gauss-Newton (3D IC-GN) algorithm is introduced to replace existing forward additive algorithms for accurate sub-voxel displacement registration. Second, to ensure the 3D IC-GN algorithm that converges accurately and rapidly and avoid time-consuming integer-voxel displacement searching, a generalized reliability-guided displacement tracking strategy is designed to transfer accurate and complete initial guess of deformation for each calculation point from its computed neighbors. Third, to avoid the repeated computation of sub-voxel intensity interpolation coefficients, an interpolation coefficient lookup table is established for tricubic interpolation. The computational complexity of the proposed fast DVC and the existing typical DVC algorithms are first analyzed quantitatively according to necessary arithmetic operations. Then, numerical tests are performed to verify the performance of the fast DVC algorithm in terms of measurement accuracy and computational efficiency. The experimental results indicate that, compared with the existing DVC algorithm, the presented fast DVC algorithm produces similar precision and slightly higher accuracy at a substantially reduced computational cost. © 2014 Elsevier Ltd.

  14. Quantitative imaging with a mobile phone microscope.

    Arunan Skandarajah

    Full Text Available Use of optical imaging for medical and scientific applications requires accurate quantification of features such as object size, color, and brightness. High pixel density cameras available on modern mobile phones have made photography simple and convenient for consumer applications; however, the camera hardware and software that enables this simplicity can present a barrier to accurate quantification of image data. This issue is exacerbated by automated settings, proprietary image processing algorithms, rapid phone evolution, and the diversity of manufacturers. If mobile phone cameras are to live up to their potential to increase access to healthcare in low-resource settings, limitations of mobile phone-based imaging must be fully understood and addressed with procedures that minimize their effects on image quantification. Here we focus on microscopic optical imaging using a custom mobile phone microscope that is compatible with phones from multiple manufacturers. We demonstrate that quantitative microscopy with micron-scale spatial resolution can be carried out with multiple phones and that image linearity, distortion, and color can be corrected as needed. Using all versions of the iPhone and a selection of Android phones released between 2007 and 2012, we show that phones with greater than 5 MP are capable of nearly diffraction-limited resolution over a broad range of magnifications, including those relevant for single cell imaging. We find that automatic focus, exposure, and color gain standard on mobile phones can degrade image resolution and reduce accuracy of color capture if uncorrected, and we devise procedures to avoid these barriers to quantitative imaging. By accommodating the differences between mobile phone cameras and the scientific cameras, mobile phone microscopes can be reliably used to increase access to quantitative imaging for a variety of medical and scientific applications.

  15. Quantitative and qualitative coronary arteriography. 1

    The clinical objectives of arteriography are to obtain information that contributes to an understanding of the mechanisms of the clinical syndrome, provides prognostic information, facilitates therapeutic decisions, and guides invasive therapy. Quantitative and improved qualitative assessments of arterial disease provide us with a common descriptive language which has the potential to accomplish these objectives more effectively and thus to improve clinical outcome. In certain situations, this potential has been demonstrated. Clinical investigation using quantitative techniques has definitely contributed to our understanding of disease mechanisms and of atherosclerosis progression/regression. Routine quantitation of clinical images should permit more accurate and repeatable estimates of disease severity and promises to provide useful estimates of coronary flow reserve. But routine clinical QCA awaits more cost- and time-efficient methods and clear proof of a clinical advantage. Careful inspection of highly magnified, high-resolution arteriographic images reveals morphologic features related to the pathophysiology of the clinical syndrome and to the likelihood of future progression or regression of obstruction. Features that have been found useful include thrombus in its various forms, ulceration and irregularity, eccentricity, flexing and dissection. The description of such high-resolution features should be included among, rather than excluded from, the goals of image processing, since they contribute substantially to the understanding and treatment of the clinical syndrome. (author). 81 refs.; 8 figs.; 1 tab

  16. Some exercises in quantitative NMR imaging

    The articles represented in this thesis result from a series of investigations that evaluate the potential of NMR imaging as a quantitative research tool. In the first article the possible use of proton spin-lattice relaxation time T1 in tissue characterization, tumor recognition and monitoring tissue response to radiotherapy is explored. The next article addresses the question whether water proton spin-lattice relaxation curves of biological tissues are adequately described by a single time constant T1, and analyzes the implications of multi-exponentiality for quantitative NMR imaging. In the third article the use of NMR imaging as a quantitative research tool is discussed on the basis of phantom experiments. The fourth article describes a method which enables unambiguous retrieval of sign information in a set of magnetic resonance images of the inversion recovery type. The next article shows how this method can be adapted to allow accurate calculation of T1 pictures on a pixel-by-pixel basis. The sixth article, finally, describes a simulation procedure which enables a straightforward determination of NMR imaging pulse sequence parameters for optimal tissue contrast. (orig.)

  17. Accurate Jones Matrix of the Practical Faraday Rotator

    王林斗; 祝昇翔; 李玉峰; 邢文烈; 魏景芝


    The Jones matrix of practical Faraday rotators is often used in the engineering calculation of non-reciprocal optical field. Nevertheless, only the approximate Jones matrix of practical Faraday rotators has been presented by now. Based on the theory of polarized light, this paper presents the accurate Jones matrix of practical Faraday rotators. In addition, an experiment has been carried out to verify the validity of the accurate Jones matrix. This matrix accurately describes the optical characteristics of practical Faraday rotators, including rotation, loss and depolarization of the polarized light. The accurate Jones matrix can be used to obtain the accurate results for the practical Faraday rotator to transform the polarized light, which paves the way for the accurate analysis and calculation of practical Faraday rotators in relevant engineering applications.

  18. Conjugate whole-body scanning system for quantitative measurement of organ distribution in vivo

    The determination of accurate, quantitative, biokinetic distribution of an internally dispersed radionuclide in humans is important in making realistic radiation absorbed dose estimates, studying biochemical transformations in health and disease, and developing clinical procedures indicative of abnormal functions. In order to collect these data, a whole-body imaging system is required which provides both adequate spatial resolution and some means of absolute quantitation. Based on these considerations, a new whole-body scanning system has been designed and constructed that employs the conjugate counting technique. The conjugate whole-body scanning system provides an efficient and accurate means of collecting absolute quantitative organ distribution data of radioactivity in vivo

  19. Quantifying Methane Fluxes Simply and Accurately: The Tracer Dilution Method

    Rella, Christopher; Crosson, Eric; Green, Roger; Hater, Gary; Dayton, Dave; Lafleur, Rick; Merrill, Ray; Tan, Sze; Thoma, Eben


    Methane is an important atmospheric constituent with a wide variety of sources, both natural and anthropogenic, including wetlands and other water bodies, permafrost, farms, landfills, and areas with significant petrochemical exploration, drilling, transport, or processing, or refining occurs. Despite its importance to the carbon cycle, its significant impact as a greenhouse gas, and its ubiquity in modern life as a source of energy, its sources and sinks in marine and terrestrial ecosystems are only poorly understood. This is largely because high quality, quantitative measurements of methane fluxes in these different environments have not been available, due both to the lack of robust field-deployable instrumentation as well as to the fact that most significant sources of methane extend over large areas (from 10's to 1,000,000's of square meters) and are heterogeneous emitters - i.e., the methane is not emitted evenly over the area in question. Quantifying the total methane emissions from such sources becomes a tremendous challenge, compounded by the fact that atmospheric transport from emission point to detection point can be highly variable. In this presentation we describe a robust, accurate, and easy-to-deploy technique called the tracer dilution method, in which a known gas (such as acetylene, nitrous oxide, or sulfur hexafluoride) is released in the same vicinity of the methane emissions. Measurements of methane and the tracer gas are then made downwind of the release point, in the so-called far-field, where the area of methane emissions cannot be distinguished from a point source (i.e., the two gas plumes are well-mixed). In this regime, the methane emissions are given by the ratio of the two measured concentrations, multiplied by the known tracer emission rate. The challenges associated with atmospheric variability and heterogeneous methane emissions are handled automatically by the transport and dispersion of the tracer. We present detailed methane flux

  20. Biomimetic Approach for Accurate, Real-Time Aerodynamic Coefficients Project

    National Aeronautics and Space Administration — Aerodynamic and structural reliability and efficiency depends critically on the ability to accurately assess the aerodynamic loads and moments for each lifting...

  1. Multiplex PCR with minisequencing as an effective high-throughput SNP typing method for formalin-fixed tissue

    Gilbert, Marcus T P; Sanchez, Juan J; Haselkorn, Tamara;


    Extensive collections of formalin-fixed paraffin-embedded (FFPE) tissues exist that could be exploited for genetic analyses in order to provide important insights into the genetic basis of disease or host/pathogen cointeractions. We report here an evaluation of a 44 SNP multiplex genotyping method...... information using simple, single reactions and minute amounts of archival tissue/DNA. In the light of this evidence, we suggest that the systematic screening of FFPE collections may in the future provide valuable insights into the past. Udgivelsesdato: 2007-Jul...

  2. Peopling of the North Circumpolar Region – Insights from Y Chromosome STR and SNP Typing of Greenlanders

    Olofsson, Jill Katharina; Pereira, Vania; Børsting, Claus;


    17 Y-chromosomal short tandem repeats (Y-STRs). Approximately 40% of the analyzed Greenlandic Y chromosomes were of European origin (I-M170, R1a-M513 and R1b-M343). Y chromosomes of European origin were mainly found in individuals from the west and south coasts of Greenland, which is in agreement...... origin in the northeastern parts of North America and could be descendants of the Dorset culture. This in turn points to the possibility that the current Inuit population in Greenland is comprised of individuals of both Thule and Dorset descent....

  3. Accurate Quantification of Lipid Species by Electrospray Ionization Mass Spectrometry — Meets a Key Challenge in Lipidomics

    Kui Yang


    Full Text Available Electrospray ionization mass spectrometry (ESI-MS has become one of the most popular and powerful technologies to identify and quantify individual lipid species in lipidomics. Meanwhile, quantitative analysis of lipid species by ESI-MS has also become a major obstacle to meet the challenges of lipidomics. Herein, we discuss the principles, advantages, and possible limitations of different mass spectrometry-based methodologies for lipid quantification, as well as a few practical issues important for accurate quantification of individual lipid species. Accordingly, accurate quantification of individual lipid species, one of the key challenges in lipidomics, can be practically met.

  4. Multidetector row computed tomography may accurately estimate plaque vulnerability. Does MDCT accurately estimate plaque vulnerability? (Pro)

    Over the past decade, multidetector row computed tomography (MDCT) has become the most reliable and established of the noninvasive examination techniques for detecting coronary heart disease. Now MDCT is chasing intravascular ultrasound (IVUS) in terms of spatial resolution. Among the components of vulnerable plaque, MDCT may detect lipid-rich plaque, the lipid pool, and calcified spots using computed tomography number. Plaque components are detected by MDCT with high accuracy compared with IVUS and angioscopy when assessing vulnerable plaque. The TWINS study and TOGETHAR trial demonstrated that angioscopic loss of yellow color occurred independently of volumetric plaque change by statin therapy. These 2 studies showed that plaque stabilization and regression reflect independent processes mediated by different mechanisms and time course. Noncalcified plaque and/or low-density plaque was found to be the strongest predictor of cardiac events, regardless of lesion severity, and act as a potential marker of plaque vulnerability. MDCT may be an effective tool for early triage of patients with chest pain who have a normal electrocardiogram (ECG) and cardiac enzymes in the emergency department. MDCT has the potential ability to analyze coronary plaque quantitatively and qualitatively if some problems are resolved. MDCT may become an essential tool for detecting and preventing coronary artery disease in the future. (author)

  5. Multidetector row computed tomography may accurately estimate plaque vulnerability: does MDCT accurately estimate plaque vulnerability? (Pro).

    Komatsu, Sei; Imai, Atsuko; Kodama, Kazuhisa


    Over the past decade, multidetector row computed tomography (MDCT) has become the most reliable and established of the noninvasive examination techniques for detecting coronary heart disease. Now MDCT is chasing intravascular ultrasound (IVUS) in terms of spatial resolution. Among the components of vulnerable plaque, MDCT may detect lipid-rich plaque, the lipid pool, and calcified spots using computed tomography number. Plaque components are detected by MDCT with high accuracy compared with IVUS and angioscopy when assessing vulnerable plaque. The TWINS study and TOGETHAR trial demonstrated that angioscopic loss of yellow color occurred independently of volumetric plaque change by statin therapy. These 2 studies showed that plaque stabilization and regression reflect independent processes mediated by different mechanisms and time course. Noncalcified plaque and/or low-density plaque was found to be the strongest predictor of cardiac events, regardless of lesion severity, and act as a potential marker of plaque vulnerability. MDCT may be an effective tool for early triage of patients with chest pain who have a normal ECG and cardiac enzymes in the emergency department. MDCT has the potential ability to analyze coronary plaque quantitatively and qualitatively if some problems are resolved. MDCT may become an essential tool for detecting and preventing coronary artery disease in the future. PMID:21532180

  6. Quantitative velocity modulation spectroscopy

    Hodges, James N.; McCall, Benjamin J.


    Velocity Modulation Spectroscopy (VMS) is arguably the most important development in the 20th century for spectroscopic study of molecular ions. For decades, interpretation of VMS lineshapes has presented challenges due to the intrinsic covariance of fit parameters including velocity modulation amplitude, linewidth, and intensity. This limitation has stifled the growth of this technique into the quantitative realm. In this work, we show that subtle changes in the lineshape can be used to help address this complexity. This allows for determination of the linewidth, intensity relative to other transitions, velocity modulation amplitude, and electric field strength in the positive column of a glow discharge. Additionally, we explain the large homogeneous component of the linewidth that has been previously described. Using this component, the ion mobility can be determined.

  7. Quantitative metamaterial property extraction

    Schurig, David


    We examine an extraction model for metamaterials, not previously reported, that gives precise, quantitative and causal representation of S parameter data over a broad frequency range, up to frequencies where the free space wavelength is only a modest factor larger than the unit cell dimension. The model is comprised of superposed, slab shaped response regions of finite thickness, one for each observed resonance. The resonance dispersion is Lorentzian and thus strictly causal. This new model is compared with previous models for correctness likelihood, including an appropriate Occam's factor for each fit parameter. We find that this new model is by far the most likely to be correct in a Bayesian analysis of model fits to S parameter simulation data for several classic metamaterial unit cells.

  8. Quantitative Hyperspectral Reflectance Imaging

    Ted A.G. Steemers


    Full Text Available Hyperspectral imaging is a non-destructive optical analysis technique that can for instance be used to obtain information from cultural heritage objects unavailable with conventional colour or multi-spectral photography. This technique can be used to distinguish and recognize materials, to enhance the visibility of faint or obscured features, to detect signs of degradation and study the effect of environmental conditions on the object. We describe the basic concept, working principles, construction and performance of a laboratory instrument specifically developed for the analysis of historical documents. The instrument measures calibrated spectral reflectance images at 70 wavelengths ranging from 365 to 1100 nm (near-ultraviolet, visible and near-infrared. By using a wavelength tunable narrow-bandwidth light-source, the light energy used to illuminate the measured object is minimal, so that any light-induced degradation can be excluded. Basic analysis of the hyperspectral data includes a qualitative comparison of the spectral images and the extraction of quantitative data such as mean spectral reflectance curves and statistical information from user-defined regions-of-interest. More sophisticated mathematical feature extraction and classification techniques can be used to map areas on the document, where different types of ink had been applied or where one ink shows various degrees of degradation. The developed quantitative hyperspectral imager is currently in use by the Nationaal Archief (National Archives of The Netherlands to study degradation effects of artificial samples and original documents, exposed in their permanent exhibition area or stored in their deposit rooms.

  9. Electronic imaging systems for quantitative electrophoresis of DNA

    Gel electrophoresis is one of the most powerful and widely used methods for the separation of DNA. During the last decade, instruments have been developed that accurately quantitate in digital form the distribution of materials in a gel or on a blot prepared from a gel. In this paper, I review the various physical properties that can be used to quantitate the distribution of DNA on gels or blots and the instrumentation that has been developed to perform these tasks. The emphasis here is on DNA, but much of what is said also applies to RNA, proteins and other molecules. 36 refs

  10. Accurate formulas for the penalty caused by interferometric crosstalk

    Rasmussen, Christian Jørgen; Liu, Fenghai; Jeppesen, Palle


    New simple formulas for the penalty caused by interferometric crosstalk in PIN receiver systems and optically preamplified receiver systems are presented. They are more accurate than existing formulas.......New simple formulas for the penalty caused by interferometric crosstalk in PIN receiver systems and optically preamplified receiver systems are presented. They are more accurate than existing formulas....

  11. A new, accurate predictive model for incident hypertension

    Völzke, Henry; Fung, Glenn; Ittermann, Till; Yu, Shipeng; Baumeister, Sebastian E; Dörr, Marcus; Lieb, Wolfgang; Völker, Uwe; Linneberg, Allan; Jørgensen, Torben; Felix, Stephan B; Rettig, Rainer; Rao, Bharat; Kroemer, Heyo K


    Data mining represents an alternative approach to identify new predictors of multifactorial diseases. This work aimed at building an accurate predictive model for incident hypertension using data mining procedures.......Data mining represents an alternative approach to identify new predictors of multifactorial diseases. This work aimed at building an accurate predictive model for incident hypertension using data mining procedures....

  12. 78 FR 34604 - Submitting Complete and Accurate Information


    ... COMMISSION 10 CFR Part 50 Submitting Complete and Accurate Information AGENCY: Nuclear Regulatory Commission... accurate information as would a licensee or an applicant for a license.'' DATES: Submit comments by August... may submit comments by any of the following methods (unless this document describes a different...

  13. The accurate assessment of small-angle X-ray scattering data

    A set of quantitative techniques is suggested for assessing SAXS data quality. These are applied in the form of a script, SAXStats, to a test set of 27 proteins, showing that these techniques are more sensitive than manual assessment of data quality. Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality

  14. Identification and validation of reference genes for accurate normalization of real-time quantitative PCR data in kiwifruit.

    Ferradás, Yolanda; Rey, Laura; Martínez, Óscar; Rey, Manuel; González, M Victoria


    Identification and validation of reference genes are required for the normalization of qPCR data. We studied the expression stability produced by eight primer pairs amplifying four common genes used as references for normalization. Samples representing different tissues, organs and developmental stages in kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) were used. A total of 117 kiwifruit samples were divided into five sample sets (mature leaves, axillary buds, stigmatic arms, fruit flesh and seeds). All samples were also analysed as a single set. The expression stability of the candidate primer pairs was tested using three algorithms (geNorm, NormFinder and BestKeeper). The minimum number of reference genes necessary for normalization was also determined. A unique primer pair was selected for amplifying the 18S rRNA gene. The primer pair selected for amplifying the ACTIN gene was different depending on the sample set. 18S 2 and ACT 2 were the candidate primer pairs selected for normalization in the three sample sets (mature leaves, fruit flesh and stigmatic arms). 18S 2 and ACT 3 were the primer pairs selected for normalization in axillary buds. No primer pair could be selected for use as the reference for the seed sample set. The analysis of all samples in a single set did not produce the selection of any stably expressing primer pair. Considering data previously reported in the literature, we validated the selected primer pairs amplifying the FLOWERING LOCUS T gene for use in the normalization of gene expression in kiwifruit. PMID:26897117

  15. Automated and Accurate Detection of Soma Location and Surface Morphology in Large-Scale 3D Neuron Images

    Cheng Yan; Anan Li; Bin Zhang,; Wenxiang Ding; Qingming Luo; Hui Gong


    Automated and accurate localization and morphometry of somas in 3D neuron images is essential for quantitative studies of neural networks in the brain. However, previous methods are limited in obtaining the location and surface morphology of somas with variable size and uneven staining in large-scale 3D neuron images. In this work, we proposed a method for automated soma locating in large-scale 3D neuron images that contain relatively sparse soma distributions. This method involves three step...

  16. Programmable Quantitative DNA Nanothermometers.

    Gareau, David; Desrosiers, Arnaud; Vallée-Bélisle, Alexis


    Developing molecules, switches, probes or nanomaterials that are able to respond to specific temperature changes should prove of utility for several applications in nanotechnology. Here, we describe bioinspired strategies to design DNA thermoswitches with programmable linear response ranges that can provide either a precise ultrasensitive response over a desired, small temperature interval (±0.05 °C) or an extended linear response over a wide temperature range (e.g., from 25 to 90 °C). Using structural modifications or inexpensive DNA stabilizers, we show that we can tune the transition midpoints of DNA thermometers from 30 to 85 °C. Using multimeric switch architectures, we are able to create ultrasensitive thermometers that display large quantitative fluorescence gains within small temperature variation (e.g., > 700% over 10 °C). Using a combination of thermoswitches of different stabilities or a mix of stabilizers of various strengths, we can create extended thermometers that respond linearly up to 50 °C in temperature range. Here, we demonstrate the reversibility, robustness, and efficiency of these programmable DNA thermometers by monitoring temperature change inside individual wells during polymerase chain reactions. We discuss the potential applications of these programmable DNA thermoswitches in various nanotechnology fields including cell imaging, nanofluidics, nanomedecine, nanoelectronics, nanomaterial, and synthetic biology. PMID:27058370

  17. Quantitative Electron Nanodiffraction.

    Spence, John [Arizona State University


    This Final report summarizes progress under this award for the final reporting period 2002 - 2013 in our development of quantitive electron nanodiffraction to materials problems, especially devoted to atomistic processes in semiconductors and electronic oxides such as the new artificial oxide multilayers, where our microdiffraction is complemented with energy-loss spectroscopy (ELNES) and aberration-corrected STEM imaging (9). The method has also been used to map out the chemical bonds in the important GaN semiconductor (1) used for solid state lighting, and to understand the effects of stacking sequence variations and interfaces in digital oxide superlattices (8). Other projects include the development of a laser-beam Zernike phase plate for cryo-electron microscopy (5) (based on the Kapitza-Dirac effect), work on reconstruction of molecular images using the scattering from many identical molecules lying in random orientations (4), a review article on space-group determination for the International Tables on Crystallography (10), the observation of energy-loss spectra with millivolt energy resolution and sub-nanometer spatial resolution from individual point defects in an alkali halide, a review article for the Centenary of X-ray Diffration (17) and the development of a new method of electron-beam lithography (12). We briefly summarize here the work on GaN, on oxide superlattice ELNES, and on lithography by STEM.

  18. Quantitive DNA Fiber Mapping

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.


    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  19. Quantitative thermal diffusivity measurements of composites

    Heath, D. M.; Winfree, W. P.; Heyman, J. S.; Miller, W. E.; Welch, C. S.


    A remote radiometric technique for making quantitative thermal diffusivity measurements is described. The technique was designed to make assessments of the structural integrity of large composite parts, such as wings, and can be performed at field sites. In the measurement technique, a CO2 laser beam is scanned using two orthogonal servo-controlled deflecting mirrors. An infrared imager, whose scanning mirrors oscillate in the vertical and the horizontal directions, is used as the detector. The analysis technique used to extract the diffusivity from these images is based on a thin infinite plate assumption, which requires waiting a given period of time for the temperature to equilibrate throughout the thickness of the sample. The technique is shown to be accurate to within two percent for values of the order of those for composite diffusivities, and to be insensitive to convection losses.

  20. Accurately bearing measurement in non-cooperative passive location system

    The system of non-cooperative passive location based on array is proposed. In the system, target is detected by beamforming and Doppler matched filtering; and bearing is measured by a long-base-ling interferometer which is composed of long distance sub-arrays. For the interferometer with long-base-line, the bearing is measured accurately but ambiguously. To realize unambiguous accurately bearing measurement, beam width and multiple constraint adoptive beamforming technique is used to resolve azimuth ambiguous. Theory and simulation result shows this method is effective to realize accurately bearing measurement in no-cooperate passive location system. (authors)

  1. Accurate calculation of diffraction-limited encircled and ensquared energy.

    Andersen, Torben B


    Mathematical properties of the encircled and ensquared energy functions for the diffraction-limited point-spread function (PSF) are presented. These include power series and a set of linear differential equations that facilitate the accurate calculation of these functions. Asymptotic expressions are derived that provide very accurate estimates for the relative amount of energy in the diffraction PSF that fall outside a square or rectangular large detector. Tables with accurate values of the encircled and ensquared energy functions are also presented. PMID:26368873

  2. Dual interference channel quantitative phase microscopy of live cell dynamics

    Shaked, Natan T.; Rinehart, Matthew T.; Wax, Adam


    We introduce and experimentally demonstrate a new fast and accurate method for quantitative imaging of the dynamics of live biological cells. Using a dual-channel interferometric setup, two phase-shifted interferograms of nearly-transparent biological samples are acquired in a single digital camera exposure, and digitally processed into the phase profile of the sample. Since two interferograms of the same sample are acquired simultaneously, most of the common phase noise is eliminated, enabli...

  3. A simplified and accurate detection of the genetically modified wheat MON71800 with one calibrator plasmid.

    Kim, Jae-Hwan; Park, Saet-Byul; Roh, Hyo-Jeong; Park, Sunghoon; Shin, Min-Ki; Moon, Gui Im; Hong, Jin-Hwan; Kim, Hae-Yeong


    With the increasing number of genetically modified (GM) events, unauthorized GMO releases into the food market have increased dramatically, and many countries have developed detection tools for them. This study described the qualitative and quantitative detection methods of unauthorized the GM wheat MON71800 with a reference plasmid (pGEM-M71800). The wheat acetyl-CoA carboxylase (acc) gene was used as the endogenous gene. The plasmid pGEM-M71800, which contains both the acc gene and the event-specific target MON71800, was constructed as a positive control for the qualitative and quantitative analyses. The limit of detection in the qualitative PCR assay was approximately 10 copies. In the quantitative PCR assay, the standard deviation and relative standard deviation repeatability values ranged from 0.06 to 0.25 and from 0.23% to 1.12%, respectively. This study supplies a powerful and very simple but accurate detection strategy for unauthorized GM wheat MON71800 that utilizes a single calibrator plasmid. PMID:25624198

  4. Quantitative Literacy: Geosciences and Beyond

    Richardson, R. M.; McCallum, W. G.


    Quantitative literacy seems like such a natural for the geosciences, right? The field has gone from its origin as a largely descriptive discipline to one where it is hard to imagine failing to bring a full range of mathematical tools to the solution of geological problems. Although there are many definitions of quantitative literacy, we have proposed one that is analogous to the UNESCO definition of conventional literacy: "A quantitatively literate person is one who, with understanding, can both read and represent quantitative information arising in his or her everyday life." Central to this definition is the concept that a curriculum for quantitative literacy must go beyond the basic ability to "read and write" mathematics and develop conceptual understanding. It is also critical that a curriculum for quantitative literacy be engaged with a context, be it everyday life, humanities, geoscience or other sciences, business, engineering, or technology. Thus, our definition works both within and outside the sciences. What role do geoscience faculty have in helping students become quantitatively literate? Is it our role, or that of the mathematicians? How does quantitative literacy vary between different scientific and engineering fields? Or between science and nonscience fields? We will argue that successful quantitative literacy curricula must be an across-the-curriculum responsibility. We will share examples of how quantitative literacy can be developed within a geoscience curriculum, beginning with introductory classes for nonmajors (using the Mauna Loa CO2 data set) through graduate courses in inverse theory (using singular value decomposition). We will highlight six approaches to across-the curriculum efforts from national models: collaboration between mathematics and other faculty; gateway testing; intensive instructional support; workshops for nonmathematics faculty; quantitative reasoning requirement; and individual initiative by nonmathematics faculty.

  5. Accurate wall thickness measurement using autointerference of circumferential Lamb wave

    In this paper, a method of accurately measuring the pipe wall thickness by using noncontact air-coupled ultrasonic transducer (NAUT) was presented. In this method, accurate measurement of angular wave number (AWN) is a key technique because the AWN is changes minutely with the wall thickness. An autointerference of the circumferential (C-) Lamb wave was used for accurate measurements of the AWN. Principle of the method was first explained. Modified method for measuring the wall thickness near a butt weld line was also proposed and its accuracy was evaluated within 6 μm error. It was also shown in the paper that wall thickness measurement was accurately carried out beyond the difference among the sensors by calibrating the frequency response of the sensors. (author)

  6. Accurate backgrounds to Higgs production at the LHC

    Kauer, N


    Corrections of 10-30% for backgrounds to the H --> WW --> l^+l^-\\sla{p}_T search in vector boson and gluon fusion at the LHC are reviewed to make the case for precise and accurate theoretical background predictions.



    In this paper, a second order linear differential equation is considered, and an accurate estimate method of characteristic exponent for it is presented. Finally, we give some examples to verify the feasibility of our result.

  8. Highly Accurate Sensor for High-Purity Oxygen Determination Project

    National Aeronautics and Space Administration — In this STTR effort, Los Gatos Research (LGR) and the University of Wisconsin (UW) propose to develop a highly-accurate sensor for high-purity oxygen determination....

  9. Quantitative Luminescence Imaging System

    The goal of the MEASUREMENT OF CHEMILUMINESCENCE project is to develop and deliver a suite of imaging radiometric instruments for measuring spatial distributions of chemiluminescence. Envisioned deliverables include instruments working at the microscopic, macroscopic, and life-sized scales. Both laboratory and field portable instruments are envisioned. The project also includes development of phantoms as enclosures for the diazoluminomelanin (DALM) chemiluminescent chemistry. A suite of either phantoms in a variety of typical poses, or phantoms that could be adjusted to a variety of poses, is envisioned. These are to include small mammals (rats), mid-sized mammals (monkeys), and human body parts. A complete human phantom that can be posed is a long-term goal of the development. Taken together, the chemistry and instrumentation provide a means for imaging rf dosimetry based on chemiluminescence induced by the heat resulting from rf energy absorption. The first delivered instrument, the Quantitative Luminescence Imaging System (QLIS), resulted in a patent, and an R ampersand D Magazine 1991 R ampersand D 100 award, recognizing it as one of the 100 most significant technological developments of 1991. The current status of the project is that three systems have been delivered, several related studies have been conducted, two preliminary human hand phantoms have been delivered, system upgrades have been implemented, and calibrations have been maintained. Current development includes sensitivity improvements to the microscope-based system; extension of the large-scale (potentially life-sized targets) system to field portable applications; extension of the 2-D large-scale system to 3-D measurement; imminent delivery of a more refined human hand phantom and a rat phantom; rf, thermal and imaging subsystem integration; and continued calibration and upgrade support

  10. Quantitative computed tomography

    Adams, Judith E. [Royal Infirmary and University, Manchester (United Kingdom)], E-mail:


    Quantitative computed tomography (QCT) was introduced in the mid 1970s. The technique is most commonly applied to 2D slices in the lumbar spine to measure trabecular bone mineral density (BMD; mg/cm{sup 3}). Although not as widely utilized as dual-energy X-ray absortiometry (DXA) QCT has some advantages when studying the skeleton (separate measures of cortical and trabecular BMD; measurement of volumetric, as opposed to 'areal' DXA-BMDa, so not size dependent; geometric and structural parameters obtained which contribute to bone strength). A limitation is that the World Health Organisation (WHO) definition of osteoporosis in terms of bone densitometry (T score -2.5 or below using DXA) is not applicable. QCT can be performed on conventional body CT scanners, or at peripheral sites (radius, tibia) using smaller, less expensive dedicated peripheral CT scanners (pQCT). Although the ionising radiation dose of spinal QCT is higher than for DXA, the dose compares favorably with those of other radiographic procedures (spinal radiographs) performed in patients suspected of having osteoporosis. The radiation dose from peripheral QCT scanners is negligible. Technical developments in CT (spiral multi-detector CT; improved spatial resolution) allow rapid acquisition of 3D volume images which enable QCT to be applied to the clinically important site of the proximal femur, more sophisticated analysis of cortical and trabecular bone, the imaging of trabecular structure and the application of finite element analysis (FEA). Such research studies contribute importantly to the understanding of bone growth and development, the effect of disease and treatment on the skeleton and the biomechanics of bone strength and fracture.

  11. Quantitative micro-CT

    Prevrhal, Sven


    Micro-CT for bone structural analysis has progressed from an in-vitro laboratory technique to devices for in-vivo assessment of small animals and the peripheral human skeleton. Currently, topological parameters of bone architecture are the primary goals of analysis. Additional measurement of the density or degree of mineralization (DMB) of trabecular and cortical bone at the microscopic level is desirable to study effects of disease and treatment progress. This information is not commonly extracted because of the challenges of accurate measurement and calibration at the tissue level. To assess the accuracy of micro-CT DMB measurements in a realistic but controlled situation, we prepared bone-mimicking watery solutions at concentrations of 100 to 600 mg/cm3 K2PO4H and scanned them with micro-CT, both in glass vials and microcapillary tubes with inner diameters of 50, 100 and 150 μm to simulate trabecular thickness. Values of the linear attenuation coefficients μ in the reconstructed image are commonly affected by beam hardening effects for larger samples and by partial volume effects for small volumes. We implemented an iterative reconstruction technique to reduce beam hardening. Partial voluming was sought to be reduced by excluding voxels near the tube wall. With these two measures, improvement on the constancy of the reconstructed voxel values and linearity with solution concentration could be observed to over 90% accuracy. However, since the expected change in real bone is small more measurements are needed to confirm that micro-CT can indeed be adapted to assess bone mineralization at the tissue level.

  12. Quantitative linguistics within Czech contexts

    Králík, Jan

    Berlin : Mouton de Gruyter, 2007 - (Grzybek, P.; Köhler, R.), s. 343-351 ISBN 978-3-11-019354-1. - (Quantitative Linguistics 62) R&D Projects: GA AV ČR 1ET101120413 Institutional research plan: CEZ:AV0Z90610521 Keywords : quantitative linguistics Subject RIV: AI - Linguistics

  13. Quantitative Nuclear Medicine. Chapter 17

    Planar imaging is still used in clinical practice although tomographic imaging (single photon emission computed tomography (SPECT) and positron emission tomography (PET)) is becoming more established. In this chapter, quantitative methods for both imaging techniques are presented. Planar imaging is limited to single photon. For both SPECT and PET, the focus is on the quantitative methods that can be applied to reconstructed images

  14. Mastering R for quantitative finance

    Berlinger, Edina; Badics, Milán; Banai, Ádám; Daróczi, Gergely; Dömötör, Barbara; Gabler, Gergely; Havran, Dániel; Juhász, Péter; Margitai, István; Márkus, Balázs; Medvegyev, Péter; Molnár, Julia; Szucs, Balázs Árpád; Tuza, Ágnes; Vadász, Tamás; Váradi, Kata; Vidovics-Dancs, Ágnes


    This book is intended for those who want to learn how to use R's capabilities to build models in quantitative finance at a more advanced level. If you wish to perfectly take up the rhythm of the chapters, you need to be at an intermediate level in quantitative finance and you also need to have a reasonable knowledge of R.

  15. Quantitative methods for indirect CT lymphography

    In this investigation, we applied quantitative CT methods to characterize contrast enhanced lymph nodes opacified using iodinated contrast media for indirect CT lymphography. Iodinated nanoparticles were injected into the buccal submucosa and SQ into the metatarsus and metacarpus of four normal swine (1.0-4.0 ml/site, 76 mg I/ml). Attenuation (HU), volume (cm(3)), iodine concentration (mg I/cm(3)), total iodine uptake (mg I), contrast-to-noise ratio (CNR), and percent injected dose (%ID) were estimated in opacified inguinal, cervical and parotid/mandibular lymph nodes using manual image segmentation techniques on 24 hour post-contrast CT images. Lymph node volumes estimated by multiple slice ROI analysis were compared with estimates obtained by post-excisional weight measurements. HU and iodine concentration increased 5-20 foldin opacified nodes (p < 0.01) and CNR increased more than four-fold (p < 0.001), %ID ranged between 3.5 and 11.9% and did not appear dose related. ROI estimated lymph node volumes approximated volumes calculated from weight measurements. (R-2 = 0.94, p < 0.0001). We conclude that interstitially injected iodinated nanoparticles increase attenuationand conspicuity of targeted nodes on CT images. Quantitative methods could play an important clinical role in more accurate metastasis detection

  16. Quantitative diagnosis of skeletons with demineralizing osteopathy

    The quantitative diagnosis of bone diseases must be assessed according to the accuracy of the applied method, the expense in apparatus, personnel and financial resources and the comparability of results. Nuclide absorptiometry and in the future perhaps computed tomography represent the most accurate methods for determining the mineral content of bones. Their application is the clinics' prerogative because of the costs. Morphometry provides quantiative information, in particular in course control, and enables an objective judgement of visual pictures. It requires little expenditure and should be combined with microradioscopy. Direct comparability of the findings of different working groups is most easy in morphometry; it depends on the equipment in computerized tomography and is still hardly possible in nuclide absorptiometry. For fundamental physical reason, it will hardly be possible to produce a low-cost, fast and easy-to-handle instrument for the determination of the mineral salt concentration in bones. Instead, there is rather a trend towards more expensive equipment, e.g. CT instruments; the universal use of these instruments, however, will help to promote quantitative diagnoses. (orig.)

  17. Quantitative Species Measurements In Microgravity Combustion Flames

    Chen, Shin-Juh; Pilgrim, Jeffrey S.; Silver, Joel A.; Piltch, Nancy D.


    The capability of models and theories to accurately predict and describe the behavior of low gravity flames can only be verified by quantitative measurements. Although video imaging, simple temperature measurements, and velocimetry methods have provided useful information in many cases, there is still a need for quantitative species measurements. Over the past decade, we have been developing high sensitivity optical absorption techniques to permit in situ, non-intrusive, absolute concentration measurements for both major and minor flames species using diode lasers. This work has helped to establish wavelength modulation spectroscopy (WMS) as an important method for species detection within the restrictions of microgravity-based measurements. More recently, in collaboration with Prof. Dahm at the University of Michigan, a new methodology combining computed flame libraries with a single experimental measurement has allowed us to determine the concentration profiles for all species in a flame. This method, termed ITAC (Iterative Temperature with Assumed Chemistry) was demonstrated for a simple laminar nonpremixed methane-air flame at both 1-g and at 0-g in a vortex ring flame. In this paper, we report additional normal and microgravity experiments which further confirm the usefulness of this approach. We also present the development of a new type of laser. This is an external cavity diode laser (ECDL) which has the unique capability of high frequency modulation as well as a very wide tuning range. This will permit the detection of multiple species with one laser while using WMS detection.

  18. Quantitative tomographic measurements of opaque multiphase flows



    An electrical-impedance tomography (EIT) system has been developed for quantitative measurements of radial phase distribution profiles in two-phase and three-phase vertical column flows. The EIT system is described along with the computer algorithm used for reconstructing phase volume fraction profiles. EIT measurements were validated by comparison with a gamma-densitometry tomography (GDT) system. The EIT system was used to accurately measure average solid volume fractions up to 0.05 in solid-liquid flows, and radial gas volume fraction profiles in gas-liquid flows with gas volume fractions up to 0.15. In both flows, average phase volume fractions and radial volume fraction profiles from GDT and EIT were in good agreement. A minor modification to the formula used to relate conductivity data to phase volume fractions was found to improve agreement between the methods. GDT and EIT were then applied together to simultaneously measure the solid, liquid, and gas radial distributions within several vertical three-phase flows. For average solid volume fractions up to 0.30, the gas distribution for each gas flow rate was approximately independent of the amount of solids in the column. Measurements made with this EIT system demonstrate that EIT may be used successfully for noninvasive, quantitative measurements of dispersed multiphase flows.

  19. A Quantitative Assessment Approach to COTS Component Security

    Jinfu Chen


    Full Text Available The vulnerability of software components hinders the development of component technology. An effective assessment approach to component security level can promote the development of component technology. Thus, the current paper proposes a quantitative assessment approach to COTS (commercial-off-the-shelf component security. The steps of interface fault injection and the assessment framework are given based on the internal factors of the tested component. The quantitative assessment algorithm and formula of component security level are also presented. The experiment results show that the approach not only can detect component security vulnerabilities effectively but also quantitatively assess the component security level. The score of component security can be accurately calculated, which represents the security level of the tested component.

  20. Quantitative shadowgraphy and proton radiography for large intensity modulations

    Kasim, Muhammad Firmansyah; Ratan, Naren; Sadler, James; Chen, Nicholas; Savert, Alexander; Trines, Raoul; Bingham, Robert; Burrows, Philip N; Kaluza, Malte C; Norreys, Peter


    Shadowgraphy is a technique widely used to diagnose objects or systems in various fields in physics and engineering. In shadowgraphy, an optical beam is deflected by the object and then the intensity modulation is captured on a screen placed some distance away. However, retrieving quantitative information from the shadowgrams themselves is a challenging task because of the non-linear nature of the process. Here, a novel method to retrieve quantitative information from shadowgrams, based on computational geometry, is presented for the first time. This process can be applied to proton radiography for electric and magnetic field diagnosis in high-energy-density plasmas and has been benchmarked using a toroidal magnetic field as the object, among others. It is shown that the method can accurately retrieve quantitative parameters with error bars less than 10%, even when caustics are present. The method is also shown to be robust enough to process real experimental results with simple pre- and post-processing techn...

  1. Reconstructing absorption and scattering distributions in quantitative photoacoustic tomography

    Quantitative photoacoustic tomography is a novel hybrid imaging technique aiming at estimating optical parameters inside tissues. The method combines (functional) optical information and accurate anatomical information obtained using ultrasound techniques. The optical inverse problem of quantitative photoacoustic tomography is to estimate the optical parameters within tissue when absorbed optical energy density is given. In this paper we consider reconstruction of absorption and scattering distributions in quantitative photoacoustic tomography. The radiative transport equation and diffusion approximation are used as light transport models and solutions in different size domains are investigated. The simulations show that scaling of the data, for example by using logarithmic data, can be expected to significantly improve the convergence of the minimization algorithm. Furthermore, both the radiative transport equation and diffusion approximation can give good estimates for absorption. However, depending on the optical properties and the size of the domain, the diffusion approximation may not produce as good estimates for scattering as the radiative transport equation. (paper)

  2. Mass Spectrometry-Based Label-Free Quantitative Proteomics

    Wenhong Zhu


    Full Text Available In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptide peak areas or peak heights. The second is based on the spectral counting of identified proteins. In this paper, we will discuss the technologies of these label-free quantitative methods, statistics, available computational software, and their applications in complex proteomics studies.

  3. Quantitative boron detection by neutron transmission method

    //Quantitative boron detection is mainly performed by chemical methods like colorimetric titration. High neutron absorption cross section of natural boron makes attractive its detection by absorption measurements. This work is an extension of earlier investigations where neutron radiography technique was used for boron detection. In the present investigation, the neutron absorption rate of boron containing solutions is the way to measure quantitatively the boron content of the solutions. The investigation was carried out in Istanbul TRIGA Mark-II reactor. In the end of the experiments, it was observed that even |ppw| grade boron in aqueous solution can be easily detected. The use of this method is certainly very useful for boron utilizing industries like glass and steel industries.The major disadvantage of the method is the obligation to use always aqueous solutions to be able to detect homogeneously the boron content. Then, steel or glass samples have to be put first in an appropriate solution form. The irradiation of steel samples can give the distribution of boron by the help of a imaging and this suggested method will give its quantitative measurement. The superiority of this method are its quick response time and its accuracy. To test this accuracy, a supposed unknown , solution of boric acid is irradiated and then calculated by the help of the calibration curve. The measured value of boric acid was 0.89 mg and the calculated value was found to be 0.98 mg which gives an accuracy of 10 %. It was also seen that the method is more accurate for low concentration. (authors)

  4. Accurately measuring dynamic coefficient of friction in ultraform finishing

    Briggs, Dennis; Echaves, Samantha; Pidgeon, Brendan; Travis, Nathan; Ellis, Jonathan D.


    UltraForm Finishing (UFF) is a deterministic sub-aperture computer numerically controlled grinding and polishing platform designed by OptiPro Systems. UFF is used to grind and polish a variety of optics from simple spherical to fully freeform, and numerous materials from glasses to optical ceramics. The UFF system consists of an abrasive belt around a compliant wheel that rotates and contacts the part to remove material. This work aims to accurately measure the dynamic coefficient of friction (μ), how it changes as a function of belt wear, and how this ultimately affects material removal rates. The coefficient of friction has been examined in terms of contact mechanics and Preston's equation to determine accurate material removal rates. By accurately predicting changes in μ, polishing iterations can be more accurately predicted, reducing the total number of iterations required to meet specifications. We have established an experimental apparatus that can accurately measure μ by measuring triaxial forces during translating loading conditions or while manufacturing the removal spots used to calculate material removal rates. Using this system, we will demonstrate μ measurements for UFF belts during different states of their lifecycle and assess the material removal function from spot diagrams as a function of wear. Ultimately, we will use this system for qualifying belt-wheel-material combinations to develop a spot-morphing model to better predict instantaneous material removal functions.

  5. Understanding quantitative research: part 1.

    Hoe, Juanita; Hoare, Zoë

    This article, which is the first in a two-part series, provides an introduction to understanding quantitative research, basic statistics and terminology used in research articles. Critical appraisal of research articles is essential to ensure that nurses remain up to date with evidence-based practice to provide consistent and high-quality nursing care. This article focuses on developing critical appraisal skills and understanding the use and implications of different quantitative approaches to research. Part two of this article will focus on explaining common statistical terms and the presentation of statistical data in quantitative research. PMID:23346707

  6. Accurate level set method for simulations of liquid atomization☆

    Changxiao Shao; Kun Luo; Jianshan Yang; Song Chen; Jianren Fan


    Computational fluid dynamics is an efficient numerical approach for spray atomization study, but it is chal enging to accurately capture the gas–liquid interface. In this work, an accurate conservative level set method is intro-duced to accurately track the gas–liquid interfaces in liquid atomization. To validate the capability of this method, binary drop collision and drop impacting on liquid film are investigated. The results are in good agreement with experiment observations. In addition, primary atomization (swirling sheet atomization) is studied using this method. To the swirling sheet atomization, it is found that Rayleigh–Taylor instability in the azimuthal direction causes the primary breakup of liquid sheet and complex vortex structures are clustered around the rim of the liq-uid sheet. The effects of central gas velocity and liquid–gas density ratio on atomization are also investigated. This work lays a solid foundation for further studying the mechanism of spray atomization.

  7. Simple and accurate analytical calculation of shortest path lengths

    Melnik, Sergey


    We present an analytical approach to calculating the distribution of shortest paths lengths (also called intervertex distances, or geodesic paths) between nodes in unweighted undirected networks. We obtain very accurate results for synthetic random networks with specified degree distribution (the so-called configuration model networks). Our method allows us to accurately predict the distribution of shortest path lengths on real-world networks using their degree distribution, or joint degree-degree distribution. Compared to some other methods, our approach is simpler and yields more accurate results. In order to obtain the analytical results, we use the analogy between an infection reaching a node in $n$ discrete time steps (i.e., as in the susceptible-infected epidemic model) and that node being at a distance $n$ from the source of the infection.

  8. Accurate and Simple Calibration of DLP Projector Systems

    Wilm, Jakob; Olesen, Oline Vinter; Larsen, Rasmus


    Much work has been devoted to the calibration of optical cameras, and accurate and simple methods are now available which require only a small number of calibration targets. The problem of obtaining these parameters for light projectors has not been studied as extensively and most current methods...... require a camera and involve feature extraction from a known projected pattern. In this work we present a novel calibration technique for DLP Projector systems based on phase shifting profilometry projection onto a printed calibration target. In contrast to most current methods, the one presented here...... does not rely on an initial camera calibration, and so does not carry over the error into projector calibration. A radial interpolation scheme is used to convert features coordinates into projector space, thereby allowing for a very accurate procedure. This allows for highly accurate determination of...

  9. Accurate nuclear radii and binding energies from a chiral interaction

    Ekstrom, A; Wendt, K A; Hagen, G; Papenbrock, T; Carlsson, B D; Forssen, C; Hjorth-Jensen, M; Navratil, P; Nazarewicz, W


    The accurate reproduction of nuclear radii and binding energies is a long-standing challenge in nuclear theory. To address this problem two-nucleon and three-nucleon forces from chiral effective field theory are optimized simultaneously to low-energy nucleon-nucleon scattering data, as well as binding energies and radii of few-nucleon systems and selected isotopes of carbon and oxygen. Coupled-cluster calculations based on this interaction, named NNLOsat, yield accurate binding energies and radii of nuclei up to 40Ca, and are consistent with the empirical saturation point of symmetric nuclear matter. In addition, the low-lying collective 3- states in 16O and 40Ca are described accurately, while spectra for selected p- and sd-shell nuclei are in reasonable agreement with experiment.

  10. Evaluating Multiplexed Quantitative Phosphopeptide Analysis on a Hybrid Quadrupole Mass Filter/Linear Ion Trap/Orbitrap Mass Spectrometer

    Erickson, Brian K.; Jedrychowski, Mark P.; McAlister, Graeme C.; Everley, Robert A.; Kunz, Ryan; Gygi, Steven P.


    As a driver for many biological processes, phosphorylation remains an area of intense research interest. Advances in multiplexed quantitation utilizing isobaric tags (e.g., TMT and iTRAQ) have the potential to create a new paradigm in quantitative proteomics. New instrumentation and software are propelling these multiplexed workflows forward, which results in more accurate, sensitive, and reproducible quantitation across tens of thousands of phosphopeptides. This study assesses the performanc...

  11. Accurate upwind-monotone (nonoscillatory) methods for conservation laws

    Huynh, Hung T.


    The well known MUSCL scheme of Van Leer is constructed using a piecewise linear approximation. The MUSCL scheme is second order accurate at the smooth part of the solution except at extrema where the accuracy degenerates to first order due to the monotonicity constraint. To construct accurate schemes which are free from oscillations, the author introduces the concept of upwind monotonicity. Several classes of schemes, which are upwind monotone and of uniform second or third order accuracy are then presented. Results for advection with constant speed are shown. It is also shown that the new scheme compares favorably with state of the art methods.

  12. Equivalent method for accurate solution to linear interval equations

    王冲; 邱志平


    Based on linear interval equations, an accurate interval finite element method for solving structural static problems with uncertain parameters in terms of optimization is discussed. On the premise of ensuring the consistency of solution sets, the original interval equations are equivalently transformed into some deterministic inequations. On this basis, calculating the structural displacement response with interval parameters is predigested to a number of deterministic linear optimization problems. The results are proved to be accurate to the interval governing equations. Finally, a numerical example is given to demonstrate the feasibility and efficiency of the proposed method.

  13. Accurate determination of the 235U isotope abundance by gamma spectrometry

    The purpose of this manual is to serve as guide in applications of the Certified Reference Material EC-NRM-171/NBS-SRM-969 for accurate U-235 isotope abundance measurements on bulk uranium samples by means of gamma spectrometry. The manual provides a thorough description of this non-destructive assay technique. Crucial measurement parameters affecting the accuracy of the gamma-spectrometric U-235 isotope abundance determination are discussed in detail and, whereever possible, evaluated quantitatively. The correction terms and tolerance limits given refer both to physical and chemical properties of the samples under assay and to relevant parameters of typical measurement systems such as counting geometry, signal processing, data evaluation and calibration. (orig.)

  14. High accurate thickness gauge system of zirconium and Zircaloy-2 layers for zirconium liner cladding tubes

    In boiling water reactors, zirconium(Zr)-Zircaloy cladding tubes have been put into practice for lengthening a life cycle of the cladding tube. The cladding tube is a duplex tube with an inner layer of pure Zr bonded to Zircaloy-2 layer metallurgically. The assurance of the inner and outer layer thickness is essential for a reliability of the cladding tube. A new thickness gauge system in the manufacturing process has been developed to measure the thickness of each layer over an entire tube length instead of the conventional microscopic viewing method. This system uses an eddy current method and an ultrasonic method. In this paper, the quantitative analysis of undesirable factors in eddy current method and the signal processing method for accurate measurement are described. The outline of fully automated thickness gauge system is also reported

  15. Chemically Accurate Simulation of a Polyatomic Molecule-Metal Surface Reaction.

    Nattino, Francesco; Migliorini, Davide; Kroes, Geert-Jan; Dombrowski, Eric; High, Eric A; Killelea, Daniel R; Utz, Arthur L


    Although important to heterogeneous catalysis, the ability to accurately model reactions of polyatomic molecules with metal surfaces has not kept pace with developments in gas phase dynamics. Partnering the specific reaction parameter (SRP) approach to density functional theory with ab initio molecular dynamics (AIMD) extends our ability to model reactions with metals with quantitative accuracy from only the lightest reactant, H2, to essentially all molecules. This is demonstrated with AIMD calculations on CHD3 + Ni(111) in which the SRP functional is fitted to supersonic beam experiments, and validated by showing that AIMD with the resulting functional reproduces initial-state selected sticking measurements with chemical accuracy (4.2 kJ/mol ≈ 1 kcal/mol). The need for only semilocal exchange makes our scheme computationally tractable for dissociation on transition metals. PMID:27284787

  16. Accurate Non-adiabatic Quantum Dynamics from Pseudospectral Sampling of Time-dependent Gaussian Basis Sets

    Heaps, Charles W


    Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required. In this paper, we employ pseudospectral sampling of time-dependent Gaussian basis functions for the simulation of non-adiabatic dynamics. Unlike other methods, the pseudospectral Gaussian molecular dynamics tests the Schr\\"{o}dinger equation with $N$ Dirac delta functions located at the centers of the Gaussian functions reducing the scaling of potential energy evaluations from $\\mathcal{O}(N^2)$ to $\\mathcal{O}(N)$. By projecting the Gaussian basis onto discrete points in space, the method is capable of efficiently and quantitatively describing nonadiabatic population transfer and intra-surface quantum coherence. We investigate three model systems; the photodissociation of three coupled Morse oscillators, the bound state dynamics of two coupled Morse oscillators, and a two-d...

  17. Accurate formula for dissipative interaction in frequency modulation atomic force microscopy

    Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM

  18. Chemically Accurate Simulation of a Polyatomic Molecule-Metal Surface Reaction


    Although important to heterogeneous catalysis, the ability to accurately model reactions of polyatomic molecules with metal surfaces has not kept pace with developments in gas phase dynamics. Partnering the specific reaction parameter (SRP) approach to density functional theory with ab initio molecular dynamics (AIMD) extends our ability to model reactions with metals with quantitative accuracy from only the lightest reactant, H2, to essentially all molecules. This is demonstrated with AIMD calculations on CHD3 + Ni(111) in which the SRP functional is fitted to supersonic beam experiments, and validated by showing that AIMD with the resulting functional reproduces initial-state selected sticking measurements with chemical accuracy (4.2 kJ/mol ≈ 1 kcal/mol). The need for only semilocal exchange makes our scheme computationally tractable for dissociation on transition metals. PMID:27284787

  19. Accurate formula for dissipative interaction in frequency modulation atomic force microscopy

    Suzuki, Kazuhiro; Matsushige, Kazumi; Yamada, Hirofumi [Department of Electronic Science and Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510 (Japan); Kobayashi, Kei [Department of Electronic Science and Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510 (Japan); The Hakubi Center for Advanced Research, Kyoto University, Katsura, Nishikyo, Kyoto 615-8520 (Japan); Labuda, Aleksander [Department of Physics, McGill University, Montreal H3A 2T8 (Canada)


    Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.

  20. Accurate formula for dissipative interaction in frequency modulation atomic force microscopy

    Suzuki, Kazuhiro; Kobayashi, Kei; Labuda, Aleksander; Matsushige, Kazumi; Yamada, Hirofumi


    Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.

  1. Quantitative methods in accounting research

    Marek Gruszczynski


    Quantitative methods are in frequent use in modern accounting research. The evidence may be found e.g. in the journals like “Journal of Accounting Research”, “European Accounting Review”, “Review of Quantitative Finance and Accounting” or in the Accounting Research Network in SSRN base. Paper presents a brief survey of research areas and statistical-econometric approaches in accounting research. Particular reference goes to research on corporate disclosure. Methodological component of the pap...

  2. Plant biology through quantitative proteomics

    Bygdell, Joakim


    Over the last decade the field of mass spectrometry based proteomics has advanced from qualitative, analyses leading to publications revolving around lists of identified proteins and peptides, to addressing more biologically relevant issues requiring measurement of the abundance of identified proteins and hence quantitive mass spectrometry. The work described in this thesis addresses problems with quantitive proteomics in plant sciences, particularly complications caused by the complexity...

  3. 09432 Report -- Quantitative Software Design

    Kreissig, Astrid; Poernomo, Iman; Reussner, Ralf


    Between 20.10.09 and 23.10.09, the Dagstuhl Seminar 09432, Quantitative Software Design, was held at the International Conference and Research Center (IBFI), Schloss Dagstuhl. Quantitative software design is a field of research that is not yet firmly established. A number of challenging open research issues are only recently being addressed by the academic research community (see below). The topic is also gaining increasing emphasis in industrial research, as any progress...

  4. QIN. Promise and pitfalls of quantitative imaging in oncology clinical trials

    Kurland, Brenda F; Gerstner, Elizabeth R.; Mountz, James M; Schwartz, Lawrence H.; Ryan, Christopher W.; Graham, Michael M.; Buatti, John M.; Fennessy, Fiona M.; Eikman, Edward A.; Kumar, Virendra; Forster, Kenneth M.; Wahl, Richard L.; Lieberman, Frank S.


    Quantitative imaging using CT, MRI, and PET modalities will play an increasingly important role in the design of oncology trials addressing molecularly targeted, personalized therapies. The advent of molecularly targeted therapies, exemplified by antiangiogenic drugs, creates new complexities in the assessment of response. The Quantitative Imaging Network (QIN) addresses the need for imaging modalities which can accurately and reproducibly measure not just change in tumor size, but changes in...

  5. Assessing size of pituitary adenomas: a comparison of qualitative and quantitative methods on MR

    Davies, Benjamin M; Carr, Elizabeth; Soh, Calvin; Gnanalingham, Kanna K.


    Background A variety of methods are used for estimating pituitary tumour size in clinical practice and in research. Quantitative methods, such as maximum tumour dimension, and qualitative methods, such as Hardy and Knosp grades, are well established but do not give an accurate assessment of the tumour volume. We therefore sought to compare existing measures of pituitary tumours with more quantitative methods of tumour volume estimation. Method Magnetic resonance imaging was reviewed for 99 co...

  6. A Simple, Quantitative Method Using Alginate Gel to Determine Rat Colonic Tumor Volume In Vivo

    Amy A. Irving; Young, Lindsay B; Pleiman, Jennifer K; Konrath, Michael J; Marzella, Blake; Nonte, Michael; Cacciatore, Justin; Ford, Madeline R; Clipson, Linda; Amos-Landgraf, James M.; Dove, William F.


    Many studies of the response of colonic tumors to therapeutics use tumor multiplicity as the endpoint to determine the effectiveness of the agent. These studies can be greatly enhanced by accurate measurements of tumor volume. Here we present a quantitative method to easily and accurately determine colonic tumor volume. This approach uses a biocompatible alginate to create a negative mold of a tumor-bearing colon; this mold is then used to make positive casts of dental stone that replicate th...

  7. Accurate Period Approximation for Any Simple Pendulum Amplitude

    XUE De-Sheng; ZHOU Zhao; GAO Mei-Zhen


    Accurate approximate analytical formulae of the pendulum period composed of a few elementary functions for any amplitude are constructed.Based on an approximation of the elliptic integral,two new logarithmic formulae for large amplitude close to 180° are obtained.Considering the trigonometric function modulation results from the dependence of relative error on the amplitude,we realize accurate approximation period expressions for any amplitude between 0 and 180°.A relative error less than 0.02% is achieved for any amplitude.This kind of modulation is also effective for other large-amplitude logarithmic approximation expressions.%Accurate approximate analytical formulae of the pendulum period composed of a few elementary functions for any amplitude are constructed. Based on an approximation of the elliptic integral, two new logarithmic formulae for large amplitude close to 180° are obtained. Considering the trigonometric function modulation results from the dependence of relative error on the amplitude, we realize accurate approximation period expressions for any amplitude between 0 and 180°. A relative error less than 0.02% is achieved for any amplitude. This kind of modulation is also effective for other large-amplitude logarithmic approximation expressions.

  8. Is a Writing Sample Necessary for "Accurate Placement"?

    Sullivan, Patrick; Nielsen, David


    The scholarship about assessment for placement is extensive and notoriously ambiguous. Foremost among the questions that continue to be unresolved in this scholarship is this one: Is a writing sample necessary for "accurate placement"? Using a robust data sample of student assessment essays and ACCUPLACER test scores, we put this question to the…

  9. Accurately Detecting Students' Lies regarding Relational Aggression by Correctional Instructions

    Dickhauser, Oliver; Reinhard, Marc-Andre; Marksteiner, Tamara


    This study investigates the effect of correctional instructions when detecting lies about relational aggression. Based on models from the field of social psychology, we predict that correctional instruction will lead to a less pronounced lie bias and to more accurate lie detection. Seventy-five teachers received videotapes of students' true denial…

  10. Fast and Accurate Residential Fire Detection Using Wireless Sensor Networks

    Bahrepour, Majid; Meratnia, Nirvana; Havinga, Paul J.M.


    Prompt and accurate residential fire detection is important for on-time fire extinguishing and consequently reducing damages and life losses. To detect fire sensors are needed to measure the environmental parameters and algorithms are required to decide about occurrence of fire. Recently, wireless s

  11. Second-order accurate nonoscillatory schemes for scalar conservation laws

    Huynh, Hung T.


    Explicit finite difference schemes for the computation of weak solutions of nonlinear scalar conservation laws is presented and analyzed. These schemes are uniformly second-order accurate and nonoscillatory in the sense that the number of extrema of the discrete solution is not increasing in time.

  12. Is Expressive Language Disorder an Accurate Diagnostic Category?

    Leonard, Laurence B.


    Purpose: To propose that the diagnostic category of "expressive language disorder" as distinct from a disorder of both expressive and receptive language might not be accurate. Method: Evidence that casts doubt on a pure form of this disorder is reviewed from several sources, including the literature on genetic findings, theories of language…

  13. Accurate momentum transfer cross section for the attractive Yukawa potential

    Khrapak, S. A., E-mail: [Forschungsgruppe Komplexe Plasmen, Deutsches Zentrum für Luft- und Raumfahrt, Oberpfaffenhofen (Germany)


    Accurate expression for the momentum transfer cross section for the attractive Yukawa potential is proposed. This simple analytic expression agrees with the numerical results better than to within ±2% in the regime relevant for ion-particle collisions in complex (dusty) plasmas.

  14. Accurate momentum transfer cross section for the attractive Yukawa potential

    Khrapak, Sergey


    Accurate expression for the momentum transfer cross section for the attractive Yukawa potential is proposed. This simple analytic expression agrees with the numerical results better than to within 2% in the regime relevant for ion-particle collisions in complex (dusty) plasmas.

  15. Accurate momentum transfer cross section for the attractive Yukawa potential

    Khrapak, S. A.


    Accurate expression for the momentum transfer cross section for the attractive Yukawa potential is proposed. This simple analytic expression agrees with the numerical results better than to within $\\pm 2\\%$ in the regime relevant for ion-particle collisions in complex (dusty) plasmas.

  16. Accurate segmentation of dense nanoparticles by partially discrete electron tomography

    Roelandts, T., E-mail: [IBBT-Vision Lab University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Batenburg, K.J. [IBBT-Vision Lab University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Centrum Wiskunde and Informatica, Science Park 123, 1098 XG Amsterdam (Netherlands); Biermans, E. [EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Kuebel, C. [Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Bals, S. [EMAT, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Sijbers, J. [IBBT-Vision Lab University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium)


    Accurate segmentation of nanoparticles within various matrix materials is a difficult problem in electron tomography. Due to artifacts related to image series acquisition and reconstruction, global thresholding of reconstructions computed by established algorithms, such as weighted backprojection or SIRT, may result in unreliable and subjective segmentations. In this paper, we introduce the Partially Discrete Algebraic Reconstruction Technique (PDART) for computing accurate segmentations of dense nanoparticles of constant composition. The particles are segmented directly by the reconstruction algorithm, while the surrounding regions are reconstructed using continuously varying gray levels. As no properties are assumed for the other compositions of the sample, the technique can be applied to any sample where dense nanoparticles must be segmented, regardless of the surrounding compositions. For both experimental and simulated data, it is shown that PDART yields significantly more accurate segmentations than those obtained by optimal global thresholding of the SIRT reconstruction. -- Highlights: Black-Right-Pointing-Pointer We present a novel reconstruction method for partially discrete electron tomography. Black-Right-Pointing-Pointer It accurately segments dense nanoparticles directly during reconstruction. Black-Right-Pointing-Pointer The gray level to use for the nanoparticles is determined objectively. Black-Right-Pointing-Pointer The method expands the set of samples for which discrete tomography can be applied.

  17. Efficient and accurate sound propagation using adaptive rectangular decomposition.

    Raghuvanshi, Nikunj; Narain, Rahul; Lin, Ming C


    Accurate sound rendering can add significant realism to complement visual display in interactive applications, as well as facilitate acoustic predictions for many engineering applications, like accurate acoustic analysis for architectural design. Numerical simulation can provide this realism most naturally by modeling the underlying physics of wave propagation. However, wave simulation has traditionally posed a tough computational challenge. In this paper, we present a technique which relies on an adaptive rectangular decomposition of 3D scenes to enable efficient and accurate simulation of sound propagation in complex virtual environments. It exploits the known analytical solution of the Wave Equation in rectangular domains, and utilizes an efficient implementation of the Discrete Cosine Transform on Graphics Processors (GPU) to achieve at least a 100-fold performance gain compared to a standard Finite-Difference Time-Domain (FDTD) implementation with comparable accuracy, while also being 10-fold more memory efficient. Consequently, we are able to perform accurate numerical acoustic simulation on large, complex scenes in the kilohertz range. To the best of our knowledge, it was not previously possible to perform such simulations on a desktop computer. Our work thus enables acoustic analysis on large scenes and auditory display for complex virtual environments on commodity hardware. PMID:19590105

  18. On the importance of having accurate data for astrophysical modelling

    Lique, Francois


    The Herschel telescope and the ALMA and NOEMA interferometers have opened new windows of observation for wavelengths ranging from far infrared to sub-millimeter with spatial and spectral resolutions previously unmatched. To make the most of these observations, an accurate knowledge of the physical and chemical processes occurring in the interstellar and circumstellar media is essential.In this presentation, I will discuss what are the current needs of astrophysics in terms of molecular data and I will show that accurate molecular data are crucial for the proper determination of the physical conditions in molecular clouds.First, I will focus on collisional excitation studies that are needed for molecular lines modelling beyond the Local Thermodynamic Equilibrium (LTE) approach. In particular, I will show how new collisional data for the HCN and HNC isomers, two tracers of star forming conditions, have allowed solving the problem of their respective abundance in cold molecular clouds. I will also present the last collisional data that have been computed in order to analyse new highly resolved observations provided by the ALMA interferometer.Then, I will present the calculation of accurate rate constants for the F+H2 → HF+H and Cl+H2 ↔ HCl+H reactions, which have allowed a more accurate determination of the physical conditions in diffuse molecular clouds. I will also present the recent work on the ortho-para-H2 conversion due to hydrogen exchange that allow more accurate determination of the ortho-to-para-H2 ratio in the universe and that imply a significant revision of the cooling mechanism in astrophysical media.

  19. Very accurate determination of trace amounts of selenium in biological materials by Radiochemical Neutron Activation Analysis

    Selenium is both a toxic and an essential trace element for humans and animals. The purpose of this work was to elaborate a very accurate (definitive) method for the determination of selenium traces in different types of biological materials. The method is based on a combination of neutron activation and quantitative and very selective radiochemical separation of selenium by ion-exchange and extraction chromatography, followed by gamma-spectrometric measurement of 75Se. Three amines: 2,3-diaminonaphtalene, 3,3'-diaminobenzidine and 4-nitro-phenyldiamine supported on Bio Beads SM-2 or Amberlite XAD-4 were chosen to batch experiments. Using 3,3'-diaminobenzidine tracer experiments were carried out with the unirradiated biological samples. They have proved that the whole radiochemical separation procedure is quantitative. Gamma-ray spectrum of the selenium fraction practically did not show any other activities except background peaks. The obtained results demonstrate good agreement of results obtained by our new '' definitive '' method for the determination of selenium with the certified values

  20. Accurate non-adiabatic quantum dynamics from pseudospectral sampling of time-dependent Gaussian basis sets

    Heaps, Charles W.; Mazziotti, David A.


    Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required. In this paper, we employ pseudospectral sampling of time-dependent Gaussian basis functions for the simulation of non-adiabatic dynamics. Unlike other methods, the pseudospectral Gaussian molecular dynamics tests the Schrödinger equation with N Dirac delta functions located at the centers of the Gaussian functions reducing the scaling of potential energy evaluations from O ( N 2 ) to O ( N ) . By projecting the Gaussian basis onto discrete points in space, the method is capable of efficiently and quantitatively describing the nonadiabatic population transfer and intra-surface quantum coherence. We investigate three model systems: the photodissociation of three coupled Morse oscillators, the bound state dynamics of two coupled Morse oscillators, and a two-dimensional model for collinear triatomic vibrational dynamics. In all cases, the pseudospectral Gaussian method is in quantitative agreement with numerically exact calculations. The results are promising for nonadiabatic molecular dynamics in molecular systems where strongly correlated ground or excited states require expensive electronic structure calculations.

  1. Isodesmic reaction for accurate theoretical pKa calculations of amino acids and peptides.

    Sastre, S; Casasnovas, R; Muñoz, F; Frau, J


    Theoretical and quantitative prediction of pKa values at low computational cost is a current challenge in computational chemistry. We report that the isodesmic reaction scheme provides semi-quantitative predictions (i.e. mean absolute errors of 0.5-1.0 pKa unit) for the pKa1 (α-carboxyl), pKa2 (α-amino) and pKa3 (sidechain groups) of a broad set of amino acids and peptides. This method fills the gaps of thermodynamic cycles for the computational pKa calculation of molecules that are unstable in the gas phase or undergo proton transfer reactions or large conformational changes from solution to the gas phase. We also report the key criteria to choose a reference species to make accurate predictions. This method is computationally inexpensive and makes use of standard density functional theory (DFT) and continuum solvent models. It is also conceptually simple and easy to use for researchers not specialized in theoretical chemistry methods. PMID:27052591

  2. A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.

    Hongmei Jiang

    Full Text Available The advent of next-generation sequencing technologies has greatly promoted the field of metagenomics which studies genetic material recovered directly from an environment. Characterization of genomic composition of a metagenomic sample is essential for understanding the structure of the microbial community. Multiple genomes contained in a metagenomic sample can be identified and quantitated through homology searches of sequence reads with known sequences catalogued in reference databases. Traditionally, reads with multiple genomic hits are assigned to non-specific or high ranks of the taxonomy tree, thereby impacting on accurate estimates of relative abundance of multiple genomes present in a sample. Instead of assigning reads one by one to the taxonomy tree as many existing methods do, we propose a statistical framework to model the identified candidate genomes to which sequence reads have hits. After obtaining the estimated proportion of reads generated by each genome, sequence reads are assigned to the candidate genomes and the taxonomy tree based on the estimated probability by taking into account both sequence alignment scores and estimated genome abundance. The proposed method is comprehensively tested on both simulated datasets and two real datasets. It assigns reads to the low taxonomic ranks very accurately. Our statistical approach of taxonomic assignment of metagenomic reads, TAMER, is implemented in R and available at

  3. A microfabrication-based approach to quantitative isothermal titration calorimetry.

    Wang, Bin; Jia, Yuan; Lin, Qiao


    Isothermal titration calorimetry (ITC) directly measures heat evolved in a chemical reaction to determine equilibrium binding properties of biomolecular systems. Conventional ITC instruments are expensive, use complicated design and construction, and require long analysis times. Microfabricated calorimetric devices are promising, although they have yet to allow accurate, quantitative ITC measurements of biochemical reactions. This paper presents a microfabrication-based approach to integrated, quantitative ITC characterization of biomolecular interactions. The approach integrates microfabricated differential calorimetric sensors with microfluidic titration. Biomolecules and reagents are introduced at each of a series of molar ratios, mixed, and allowed to react. The reaction thermal power is differentially measured, and used to determine the thermodynamic profile of the biomolecular interactions. Implemented in a microdevice featuring thermally isolated, well-defined reaction volumes with minimized fluid evaporation as well as highly sensitive thermoelectric sensing, the approach enables accurate and quantitative ITC measurements of protein-ligand interactions under different isothermal conditions. Using the approach, we demonstrate ITC characterization of the binding of 18-Crown-6 with barium chloride, and the binding of ribonuclease A with cytidine 2'-monophosphate within reaction volumes of approximately 0.7 µL and at concentrations down to 2mM. For each binding system, the ITC measurements were completed with considerably reduced analysis times and material consumption, and yielded a complete thermodynamic profile of the molecular interaction in agreement with published data. This demonstrates the potential usefulness of our approach for biomolecular characterization in biomedical applications. PMID:26655185

  4. EQPlanar: a maximum-likelihood method for accurate organ activity estimation from whole body planar projections

    Optimizing targeted radionuclide therapy requires patient-specific estimation of organ doses. The organ doses are estimated from quantitative nuclear medicine imaging studies, many of which involve planar whole body scans. We have previously developed the quantitative planar (QPlanar) processing method and demonstrated its ability to provide more accurate activity estimates than conventional geometric-mean-based planar (CPlanar) processing methods using physical phantom and simulation studies. The QPlanar method uses the maximum likelihood-expectation maximization algorithm, 3D organ volume of interests (VOIs), and rigorous models of physical image degrading factors to estimate organ activities. However, the QPlanar method requires alignment between the 3D organ VOIs and the 2D planar projections and assumes uniform activity distribution in each VOI. This makes application to patients challenging. As a result, in this paper we propose an extended QPlanar (EQPlanar) method that provides independent-organ rigid registration and includes multiple background regions. We have validated this method using both Monte Carlo simulation and patient data. In the simulation study, we evaluated the precision and accuracy of the method in comparison to the original QPlanar method. For the patient studies, we compared organ activity estimates at 24 h after injection with those from conventional geometric mean-based planar quantification using a 24 h post-injection quantitative SPECT reconstruction as the gold standard. We also compared the goodness of fit of the measured and estimated projections obtained from the EQPlanar method to those from the original method at four other time points where gold standard data were not available. In the simulation study, more accurate activity estimates were provided by the EQPlanar method for all the organs at all the time points compared with the QPlanar method. Based on the patient data, we concluded that the EQPlanar method provided a

  5. Quantitative texton sequences for legible bivariate maps.

    Ware, Colin


    Representing bivariate scalar maps is a common but difficult visualization problem. One solution has been to use two dimensional color schemes, but the results are often hard to interpret and inaccurately read. An alternative is to use a color sequence for one variable and a texture sequence for another. This has been used, for example, in geology, but much less studied than the two dimensional color scheme, although theory suggests that it should lead to easier perceptual separation of information relating to the two variables. To make a texture sequence more clearly readable the concept of the quantitative texton sequence (QTonS) is introduced. A QTonS is defined a sequence of small graphical elements, called textons, where each texton represents a different numerical value and sets of textons can be densely displayed to produce visually differentiable textures. An experiment was carried out to compare two bivariate color coding schemes with two schemes using QTonS for one bivariate map component and a color sequence for the other. Two different key designs were investigated (a key being a sequence of colors or textures used in obtaining quantitative values from a map). The first design used two separate keys, one for each dimension, in order to measure how accurately subjects could independently estimate the underlying scalar variables. The second key design was two dimensional and intended to measure the overall integral accuracy that could be obtained. The results show that the accuracy is substantially higher for the QTonS/color sequence schemes. A hypothesis that texture/color sequence combinations are better for independent judgments of mapped quantities was supported. A second experiment probed the limits of spatial resolution for QTonSs. PMID:19834229

  6. Accurate Load Modeling Based on Analytic Hierarchy Process

    Zhenshu Wang


    Full Text Available Establishing an accurate load model is a critical problem in power system modeling. That has significant meaning in power system digital simulation and dynamic security analysis. The synthesis load model (SLM considers the impact of power distribution network and compensation capacitor, while randomness of power load is more precisely described by traction power system load model (TPSLM. On the basis of these two load models, a load modeling method that combines synthesis load with traction power load is proposed in this paper. This method uses analytic hierarchy process (AHP to interact with two load models. Weight coefficients of two models can be calculated after formulating criteria and judgment matrixes and then establishing a synthesis model by weight coefficients. The effectiveness of the proposed method was examined through simulation. The results show that accurate load modeling based on AHP can effectively improve the accuracy of load model and prove the validity of this method.

  7. Accurate adjoint design sensitivities for nano metal optics.

    Hansen, Paul; Hesselink, Lambertus


    We present a method for obtaining accurate numerical design sensitivities for metal-optical nanostructures. Adjoint design sensitivity analysis, long used in fluid mechanics and mechanical engineering for both optimization and structural analysis, is beginning to be used for nano-optics design, but it fails for sharp-cornered metal structures because the numerical error in electromagnetic simulations of metal structures is highest at sharp corners. These locations feature strong field enhancement and contribute strongly to design sensitivities. By using high-accuracy FEM calculations and rounding sharp features to a finite radius of curvature we obtain highly-accurate design sensitivities for 3D metal devices. To provide a bridge to the existing literature on adjoint methods in other fields, we derive the sensitivity equations for Maxwell's equations in the PDE framework widely used in fluid mechanics. PMID:26368483

  8. Method for Accurately Calibrating a Spectrometer Using Broadband Light

    Simmons, Stephen; Youngquist, Robert


    A novel method has been developed for performing very fine calibration of a spectrometer. This process is particularly useful for modern miniature charge-coupled device (CCD) spectrometers where a typical factory wavelength calibration has been performed and a finer, more accurate calibration is desired. Typically, the factory calibration is done with a spectral line source that generates light at known wavelengths, allowing specific pixels in the CCD array to be assigned wavelength values. This method is good to about 1 nm across the spectrometer s wavelength range. This new method appears to be accurate to about 0.1 nm, a factor of ten improvement. White light is passed through an unbalanced Michelson interferometer, producing an optical signal with significant spectral variation. A simple theory can be developed to describe this spectral pattern, so by comparing the actual spectrometer output against this predicted pattern, errors in the wavelength assignment made by the spectrometer can be determined.

  9. Multimodal Spatial Calibration for Accurately Registering EEG Sensor Positions

    Jianhua Zhang


    Full Text Available This paper proposes a fast and accurate calibration method to calibrate multiple multimodal sensors using a novel photogrammetry system for fast localization of EEG sensors. The EEG sensors are placed on human head and multimodal sensors are installed around the head to simultaneously obtain all EEG sensor positions. A multiple views’ calibration process is implemented to obtain the transformations of multiple views. We first develop an efficient local repair algorithm to improve the depth map, and then a special calibration body is designed. Based on them, accurate and robust calibration results can be achieved. We evaluate the proposed method by corners of a chessboard calibration plate. Experimental results demonstrate that the proposed method can achieve good performance, which can be further applied to EEG source localization applications on human brain.

  10. Accurate multireference study of Si3 electronic manifold

    Goncalves, Cayo Emilio Monteiro; Braga, Joao Pedro


    Since it has been shown that the silicon trimer has a highly multi-reference character, accurate multi-reference configuration interaction calculations are performed to elucidate its electronic manifold. Emphasis is given to the long range part of the potential, aiming to understand the atom-diatom collisions dynamical aspects, to describe conical intersections and important saddle points along the reactive path. Potential energy surface main features analysis are performed for benchmarking, and highly accurate values for structures, vibrational constants and energy gaps are reported, as well as the unpublished spin-orbit coupling magnitude. The results predict that inter-system crossings will play an important role in dynamical simulations, specially in triplet state quenching, making the problem of constructing a precise potential energy surface more complicated and multi-layer dependent. The ground state is predicted to be the singlet one, but since the singlet-triplet gap is rather small (2.448 kJ/mol) bo...