WorldWideScience

Sample records for high resolution analysis

  1. A high resolution jet analysis for LEP

    International Nuclear Information System (INIS)

    Hariri, S.

    1992-11-01

    A high resolution multijet analysis of hadronic events produced in e + e - annihilation at a C.M.S. energy of 91.2 GeV is described. Hadronic events produced in e + e - annihilations are generated using the Monte Carlo program JETSET7.3 with its two options: Matrix Element (M.E.) and Parton Showers (P.S.). The shower option is used with its default parameter values while the M.E. option is used with an invariant mass cut Y CUT =0.01 instead of 0.02. This choice ensures a better continuity in the evolution of the event shape variables. (K.A.) 3 refs.; 26 figs.; 1 tab

  2. High resolution synchrotron light analysis at ELSA

    Energy Technology Data Exchange (ETDEWEB)

    Switka, Michael; Zander, Sven; Hillert, Wolfgang [Bonn Univ. (Germany). Elektronen-Stretcher Anlage ELSA-Facility (ELSA)

    2013-07-01

    The pulse stretcher ring ELSA provides polarized electrons with energies up to 3.5 GeV for external hadron experiments. In order to suffice the need of stored beam intensities towards 200 mA, advanced beam instability studies need to be carried out. An external diagnostic beamline for synchrotron light analysis has been set up and provides the space for multiple diagnostic tools including a streak camera with time resolution of <1 ps. Beam profile measurements are expected to identify instabilities and reveal their thresholds. The effect of adequate countermeasures is subject to analysis. The current status of the beamline development is presented.

  3. NOAA High-Resolution Sea Surface Temperature (SST) Analysis Products

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This archive covers two high resolution sea surface temperature (SST) analysis products developed using an optimum interpolation (OI) technique. The analyses have a...

  4. Liquid Scintillation High Resolution Spectral Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Grau Carles, A.; Grau Malonda, A.

    2010-08-06

    The CIEMAT/NIST and the TDCR methods in liquid scintillation counting are based on the determination of the efficiency for total counting. This paper tries to expand these methods analysing the pulse-height spectrum of radionuclides. To reach this objective we have to generalize the equations used in the model and to analyse the influence of ionization and chemical quench in both spectra and counting efficiency. We present equations to study the influence of different photomultipliers response in systems with one, two or three photomultipliers. We study the effect of the electronic noise discriminator level in both spectra and counting efficiency. The described method permits one to study problems that up to now was not possible to approach, such as the high uncertainty in the standardization of pure beta-ray emitter with low energy when we apply the TDCR method, or the discrepancies in the standardization of some electron capture radionuclides, when the CIEMAT/NIST method is applied. (Author) 107 refs.

  5. Liquid Scintillation High Resolution Spectral Analysis

    International Nuclear Information System (INIS)

    Grau Carles, A.; Grau Malonda, A.

    2010-01-01

    The CIEMAT/NIST and the TDCR methods in liquid scintillation counting are based on the determination of the efficiency for total counting. This paper tries to expand these methods analysing the pulse-height spectrum of radionuclides. To reach this objective we have to generalize the equations used in the model and to analyse the influence of ionization and chemical quench in both spectra and counting efficiency. We present equations to study the influence of different photomultipliers response in systems with one, two or three photomultipliers. We study the effect of the electronic noise discriminator level in both spectra and counting efficiency. The described method permits one to study problems that up to now was not possible to approach, such as the high uncertainty in the standardization of pure beta-ray emitter with low energy when we apply the TDCR method, or the discrepancies in the standardization of some electron capture radionuclides, when the CIEMAT/NIST method is applied. (Author) 107 refs.

  6. Quantitative high-resolution genomic analysis of single cancer cells.

    Science.gov (United States)

    Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

    2011-01-01

    During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

  7. Quantitative high-resolution genomic analysis of single cancer cells.

    Directory of Open Access Journals (Sweden)

    Juliane Hannemann

    Full Text Available During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

  8. Objective high Resolution Analysis over Complex Terrain with VERA

    Science.gov (United States)

    Mayer, D.; Steinacker, R.; Steiner, A.

    2012-04-01

    VERA (Vienna Enhanced Resolution Analysis) is a model independent, high resolution objective analysis of meteorological fields over complex terrain. This system consists of a special developed quality control procedure and a combination of an interpolation and a downscaling technique. Whereas the so called VERA-QC is presented at this conference in the contribution titled "VERA-QC, an approved Data Quality Control based on Self-Consistency" by Andrea Steiner, this presentation will focus on the method and the characteristics of the VERA interpolation scheme which enables one to compute grid point values of a meteorological field based on irregularly distributed observations and topography related aprior knowledge. Over a complex topography meteorological fields are not smooth in general. The roughness which is induced by the topography can be explained physically. The knowledge about this behavior is used to define the so called Fingerprints (e.g. a thermal Fingerprint reproducing heating or cooling over mountainous terrain or a dynamical Fingerprint reproducing positive pressure perturbation on the windward side of a ridge) under idealized conditions. If the VERA algorithm recognizes patterns of one or more Fingerprints at a few observation points, the corresponding patterns are used to downscale the meteorological information in a greater surrounding. This technique allows to achieve an analysis with a resolution much higher than the one of the observational network. The interpolation of irregularly distributed stations to a regular grid (in space and time) is based on a variational principle applied to first and second order spatial and temporal derivatives. Mathematically, this can be formulated as a cost function that is equivalent to the penalty function of a thin plate smoothing spline. After the analysis field has been divided into the Fingerprint components and the unexplained part respectively, the requirement of a smooth distribution is applied to the

  9. A parallel solution for high resolution histological image analysis.

    Science.gov (United States)

    Bueno, G; González, R; Déniz, O; García-Rojo, M; González-García, J; Fernández-Carrobles, M M; Vállez, N; Salido, J

    2012-10-01

    This paper describes a general methodology for developing parallel image processing algorithms based on message passing for high resolution images (on the order of several Gigabytes). These algorithms have been applied to histological images and must be executed on massively parallel processing architectures. Advances in new technologies for complete slide digitalization in pathology have been combined with developments in biomedical informatics. However, the efficient use of these digital slide systems is still a challenge. The image processing that these slides are subject to is still limited both in terms of data processed and processing methods. The work presented here focuses on the need to design and develop parallel image processing tools capable of obtaining and analyzing the entire gamut of information included in digital slides. Tools have been developed to assist pathologists in image analysis and diagnosis, and they cover low and high-level image processing methods applied to histological images. Code portability, reusability and scalability have been tested by using the following parallel computing architectures: distributed memory with massive parallel processors and two networks, INFINIBAND and Myrinet, composed of 17 and 1024 nodes respectively. The parallel framework proposed is flexible, high performance solution and it shows that the efficient processing of digital microscopic images is possible and may offer important benefits to pathology laboratories. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  10. High resolution radar satellite imagery analysis for safeguards applications

    Energy Technology Data Exchange (ETDEWEB)

    Minet, Christian; Eineder, Michael [German Aerospace Center, Remote Sensing Technology Institute, Department of SAR Signal Processing, Wessling, (Germany); Rezniczek, Arnold [UBA GmbH, Herzogenrath, (Germany); Niemeyer, Irmgard [Forschungszentrum Juelich, Institue of Energy and Climate Research, IEK-6: Nuclear Waste Management and Reactor Safety, Juelich, (Germany)

    2011-12-15

    For monitoring nuclear sites, the use of Synthetic Aperture Radar (SAR) imagery shows essential promises. Unlike optical remote sensing instruments, radar sensors operate under almost all weather conditions and independently of the sunlight, i.e. time of the day. Such technical specifications are required both for continuous and for ad-hoc, timed surveillance tasks. With Cosmo-Skymed, TerraSARX and Radarsat-2, high-resolution SAR imagery with a spatial resolution up to 1m has recently become available. Our work therefore aims to investigate the potential of high-resolution TerraSAR data for nuclear monitoring. This paper focuses on exploiting amplitude of a single acquisition, assessing amplitude changes and phase differences between two acquisitions, and PS-InSAR processing of an image stack.

  11. High resolution or optimum resolution? Spatial analysis of the Federmesser site at Andernach, Germany

    NARCIS (Netherlands)

    Stapert, D; Street, M

    1997-01-01

    This paper discusses spatial analysis at site level. It is suggested that spatial analysis has to proceed in several levels, from global to more detailed questions, and that optimum resolution should be established when applying any quantitative methods in this field. As an example, the ring and

  12. Analysis of smear in high-resolution remote sensing satellites

    Science.gov (United States)

    Wahballah, Walid A.; Bazan, Taher M.; El-Tohamy, Fawzy; Fathy, Mahmoud

    2016-10-01

    High-resolution remote sensing satellites (HRRSS) that use time delay and integration (TDI) CCDs have the potential to introduce large amounts of image smear. Clocking and velocity mismatch smear are two of the key factors in inducing image smear. Clocking smear is caused by the discrete manner in which the charge is clocked in the TDI-CCDs. The relative motion between the HRRSS and the observed object obliges that the image motion velocity must be strictly synchronized with the velocity of the charge packet transfer (line rate) throughout the integration time. During imaging an object off-nadir, the image motion velocity changes resulting in asynchronization between the image velocity and the CCD's line rate. A Model for estimating the image motion velocity in HRRSS is derived. The influence of this velocity mismatch combined with clocking smear on the modulation transfer function (MTF) is investigated by using Matlab simulation. The analysis is performed for cross-track and along-track imaging with different satellite attitude angles and TDI steps. The results reveal that the velocity mismatch ratio and the number of TDI steps have a serious impact on the smear MTF; a velocity mismatch ratio of 2% degrades the MTFsmear by 32% at Nyquist frequency when the TDI steps change from 32 to 96. In addition, the results show that to achieve the requirement of MTFsmear >= 0.95 , for TDI steps of 16 and 64, the allowable roll angles are 13.7° and 6.85° and the permissible pitch angles are no more than 9.6° and 4.8°, respectively.

  13. High-resolution analysis of the mechanical behavior of tissue

    Science.gov (United States)

    Hudnut, Alexa W.; Armani, Andrea M.

    2017-06-01

    The mechanical behavior and properties of biomaterials, such as tissue, have been directly and indirectly connected to numerous malignant physiological states. For example, an increase in the Young's Modulus of tissue can be indicative of cancer. Due to the heterogeneity of biomaterials, it is extremely important to perform these measurements using whole or unprocessed tissue because the tissue matrix contains important information about the intercellular interactions and the structure. Thus, developing high-resolution approaches that can accurately measure the elasticity of unprocessed tissue samples is of great interest. Unfortunately, conventional elastography methods such as atomic force microscopy, compression testing, and ultrasound elastography either require sample processing or have poor resolution. In the present work, we demonstrate the characterization of unprocessed salmon muscle using an optical polarimetric elastography system. We compare the results of compression testing within different samples of salmon skeletal muscle with different numbers of collagen membranes to characterize differences in heterogeneity. Using the intrinsic collagen membranes as markers, we determine the resolution of the system when testing biomaterials. The device reproducibly measures the stiffness of the tissues at variable strains. By analyzing the amount of energy lost by the sample during compression, collagen membranes that are 500 μm in size are detected.

  14. Montecarlo simulation for a new high resolution elemental analysis methodology

    Energy Technology Data Exchange (ETDEWEB)

    Figueroa S, Rodolfo; Brusa, Daniel; Riveros, Alberto [Universidad de La Frontera, Temuco (Chile). Facultad de Ingenieria y Administracion

    1996-12-31

    Full text. Spectra generated by binary, ternary and multielement matrixes when irradiated by a variable energy photon beam are simulated by means of a Monte Carlo code. Significative jumps in the counting rate are shown when the photon energy is just over the edge associated to each element, because of the emission of characteristic X rays. For a given associated energy, the net height of these jumps depends mainly on the concentration and of the sample absorption coefficient. The spectra were obtained by a monochromatic energy scan considering all the emitted radiation by the sample in a 2{pi} solid angle, associating a single multichannel spectrometer channel to each incident energy (Multichannel Scaling (MCS) mode). The simulated spectra were made with Monte Carlo simulation software adaptation of the package called PENELOPE (Penetration and Energy Loss of Positrons and Electrons in matter). The results show that it is possible to implement a new high resolution spectroscopy methodology, where a synchrotron would be an ideal source, due to the high intensity and ability to control the energy of the incident beam. The high energy resolution would be determined by the monochromating system and not by the detection system and not by the detection system, which would basicalbe a photon counter. (author)

  15. Montecarlo simulation for a new high resolution elemental analysis methodology

    International Nuclear Information System (INIS)

    Figueroa S, Rodolfo; Brusa, Daniel; Riveros, Alberto

    1996-01-01

    Full text. Spectra generated by binary, ternary and multielement matrixes when irradiated by a variable energy photon beam are simulated by means of a Monte Carlo code. Significative jumps in the counting rate are shown when the photon energy is just over the edge associated to each element, because of the emission of characteristic X rays. For a given associated energy, the net height of these jumps depends mainly on the concentration and of the sample absorption coefficient. The spectra were obtained by a monochromatic energy scan considering all the emitted radiation by the sample in a 2π solid angle, associating a single multichannel spectrometer channel to each incident energy (Multichannel Scaling (MCS) mode). The simulated spectra were made with Monte Carlo simulation software adaptation of the package called PENELOPE (Penetration and Energy Loss of Positrons and Electrons in matter). The results show that it is possible to implement a new high resolution spectroscopy methodology, where a synchrotron would be an ideal source, due to the high intensity and ability to control the energy of the incident beam. The high energy resolution would be determined by the monochromating system and not by the detection system and not by the detection system, which would basicalbe a photon counter. (author)

  16. Brain Network Analysis from High-Resolution EEG Signals

    Science.gov (United States)

    de Vico Fallani, Fabrizio; Babiloni, Fabio

    lattice and a random structure. Such a model has been designated as "small-world" network in analogy with the concept of the small-world phenomenon observed more than 30 years ago in social systems. In a similar way, many types of functional brain networks have been analyzed according to this mathematical approach. In particular, several studies based on different imaging techniques (fMRI, MEG and EEG) have found that the estimated functional networks showed small-world characteristics. In the functional brain connectivity context, these properties have been demonstrated to reflect an optimal architecture for the information processing and propagation among the involved cerebral structures. However, the performance of cognitive and motor tasks as well as the presence of neural diseases has been demonstrated to affect such a small-world topology, as revealed by the significant changes of L and C. Moreover, some functional brain networks have been mostly found to be very unlike the random graphs in their degree-distribution, which gives information about the allocation of the functional links within the connectivity pattern. It was demonstrated that the degree distributions of these networks follow a power-law trend. For this reason those networks are called "scale-free". They still exhibit the small-world phenomenon but tend to contain few nodes that act as highly connected "hubs". Scale-free networks are known to show resistance to failure, facility of synchronization and fast signal processing. Hence, it would be important to see whether the scaling properties of the functional brain networks are altered under various pathologies or experimental tasks. The present Chapter proposes a theoretical graph approach in order to evaluate the functional connectivity patterns obtained from high-resolution EEG signals. In this way, the "Brain Network Analysis" (in analogy with the Social Network Analysis that has emerged as a key technique in modern sociology) represents an

  17. Quantitative analysis of cholesteatoma using high resolution computed tomography

    International Nuclear Information System (INIS)

    Kikuchi, Shigeru; Yamasoba, Tatsuya; Iinuma, Toshitaka.

    1992-01-01

    Seventy-three cases of adult cholesteatoma, including 52 cases of pars flaccida type cholesteatoma and 21 of pars tensa type cholesteatoma, were examined using high resolution computed tomography, in both axial (lateral semicircular canal plane) and coronal sections (cochlear, vestibular and antral plane). These cases were classified into two subtypes according to the presence of extension of cholesteatoma into the antrum. Sixty cases of chronic otitis media with central perforation (COM) were also examined as controls. Various locations of the middle ear cavity were measured in terms of size in comparison with pars flaccida type cholesteatoma, pars tensa type cholesteatoma and COM. The width of the attic was significantly larger in both pars flaccida type and pars tensa type cholesteatoma than in COM. With pars flaccida type cholesteatoma there was a significantly larger distance between the malleus and lateral wall of the attic than with COM. In contrast, the distance between the malleus and medial wall of the attic was significantly larger with pars tensa type cholesteatoma than with COM. With cholesteatoma extending into the antrum, regardless of the type of cholesteatoma, there were significantly larger distances than with COM at the following sites: the width and height of the aditus ad antrum, and the width, height and anterior-posterior diameter of the antrum. However, these distances were not significantly different between cholesteatoma without extension into the antrum and COM. The hitherto demonstrated qualitative impressions of bone destruction in cholesteatoma were quantitatively verified in detail using high resolution computed tomography. (author)

  18. Analysis of the impact of spatial resolution on land/water classifications using high-resolution aerial imagery

    Science.gov (United States)

    Enwright, Nicholas M.; Jones, William R.; Garber, Adrienne L.; Keller, Matthew J.

    2014-01-01

    Long-term monitoring efforts often use remote sensing to track trends in habitat or landscape conditions over time. To most appropriately compare observations over time, long-term monitoring efforts strive for consistency in methods. Thus, advances and changes in technology over time can present a challenge. For instance, modern camera technology has led to an increasing availability of very high-resolution imagery (i.e. submetre and metre) and a shift from analogue to digital photography. While numerous studies have shown that image resolution can impact the accuracy of classifications, most of these studies have focused on the impacts of comparing spatial resolution changes greater than 2 m. Thus, a knowledge gap exists on the impacts of minor changes in spatial resolution (i.e. submetre to about 1.5 m) in very high-resolution aerial imagery (i.e. 2 m resolution or less). This study compared the impact of spatial resolution on land/water classifications of an area dominated by coastal marsh vegetation in Louisiana, USA, using 1:12,000 scale colour-infrared analogue aerial photography (AAP) scanned at four different dot-per-inch resolutions simulating ground sample distances (GSDs) of 0.33, 0.54, 1, and 2 m. Analysis of the impact of spatial resolution on land/water classifications was conducted by exploring various spatial aspects of the classifications including density of waterbodies and frequency distributions in waterbody sizes. This study found that a small-magnitude change (1–1.5 m) in spatial resolution had little to no impact on the amount of water classified (i.e. percentage mapped was less than 1.5%), but had a significant impact on the mapping of very small waterbodies (i.e. waterbodies ≤ 250 m2). These findings should interest those using temporal image classifications derived from very high-resolution aerial photography as a component of long-term monitoring programs.

  19. LSD-based analysis of high-resolution stellar spectra

    Science.gov (United States)

    Tsymbal, V.; Tkachenko, A.; Van, Reeth T.

    2014-11-01

    We present a generalization of the method of least-squares deconvolution (LSD), a powerful tool for extracting high S/N average line profiles from stellar spectra. The generalization of the method is effected by extending it towards the multiprofile LSD and by introducing the possibility to correct the line strengths from the initial mask. We illustrate the new approach by two examples: (a) the detection of astroseismic signatures from low S/N spectra of single stars, and (b) disentangling spectra of multiple stellar objects. The analysis is applied to spectra obtained with 2-m class telescopes in the course of spectroscopic ground-based support for space missions such as CoRoT and Kepler. Usually, rather high S/N is required, so smaller telescopes can only compete successfully with more advanced ones when one can apply a technique that enables a remarkable increase in the S/N of the spectra which they observe. Since the LSD profiles have a potential for reconstruction what is common in all the spectral profiles, it should have a particular practical application to faint stars observed with 2-m class telescopes and whose spectra show remarkable LPVs.

  20. High resolution melting (HRM) analysis of DNA--its role and potential in food analysis.

    Science.gov (United States)

    Druml, Barbara; Cichna-Markl, Margit

    2014-09-01

    DNA based methods play an increasing role in food safety control and food adulteration detection. Recent papers show that high resolution melting (HRM) analysis is an interesting approach. It involves amplification of the target of interest in the presence of a saturation dye by the polymerase chain reaction (PCR) and subsequent melting of the amplicons by gradually increasing the temperature. Since the melting profile depends on the GC content, length, sequence and strand complementarity of the product, HRM analysis is highly suitable for the detection of single-base variants and small insertions or deletions. The review gives an introduction into HRM analysis, covers important aspects in the development of an HRM analysis method and describes how HRM data are analysed and interpreted. Then we discuss the potential of HRM analysis based methods in food analysis, i.e. for the identification of closely related species and cultivars and the identification of pathogenic microorganisms. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Towards high resolution polarisation analysis using double polarisation and ellipsoidal analysers

    CERN Document Server

    Martin-Y-Marero, D

    2002-01-01

    Classical polarisation analysis methods lack the combination of high resolution and high count rate necessary to cope with the demand of modern condensed-matter experiments. In this work, we present a method to achieve high resolution polarisation analysis based on a double polarisation system. Coupling this method with an ellipsoidal wavelength analyser, a high count rate can be achieved whilst delivering a resolution of around 10 mu eV. This method is ideally suited to pulsed sources, although it can be adapted to continuous sources as well. (orig.)

  2. Coastal Change Analysis Program (C-CAP) High Resolution Land Cover and Change Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NOAA Coastal Change Analysis Program (C-CAP) produces national standardized high resolution land cover and change products for the coastal regions of the U.S....

  3. High-resolution analysis of cytosine methylation in ancient DNA.

    Directory of Open Access Journals (Sweden)

    Bastien Llamas

    Full Text Available Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to participate in the rapid adaptation of species to changes in environment. Any direct test of this hypothesis would require the ability to measure epigenetic states over evolutionary timescales. Here we describe the first single-base resolution of cytosine methylation patterns in an ancient mammalian genome, by bisulphite allelic sequencing of loci from late Pleistocene Bison priscus remains. Retrotransposons and the differentially methylated regions of imprinted loci displayed methylation patterns identical to those derived from fresh bovine tissue, indicating that methylation patterns are preserved in the ancient DNA. Our findings establish the biochemical stability of methylated cytosines over extensive time frames, and provide the first direct evidence that cytosine methylation patterns are retained in DNA from ancient specimens. The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution.

  4. High resolution analysis of northern Patagonia lake sediments

    Science.gov (United States)

    Jarvis, S. W.; Croudace, I. W.; Langdon, P. G.; Rindby, A.

    2009-04-01

    Sediment cores covering the period from the last glacial maximum through the Holocene to the present have been collected from sites in the Chacubuco valley, southern Chile (around 47°08'S, 72°25'W, to the east of the North Patagonian Icecap). Cores were taken from five lakes and one recently dried lake bed. Short cores (0.2 to 0.5m), covering approximately the last two hundred years, were taken from all the lakes. Additionally, long sequences were obtained from one of the lakes and from the dried lake bed, the latter sequence extending back to the last glacial maximum as indicated by thick clay at the base. Each of the lakes are small-medium sized and are open systems situated at 300-1000m above sea level. The shorter cores comprise predominantly clastic gyttja but show a number of distinct changes in colour and chemical composition that suggest major environmental changes over the period of sediment accumulation. This is also reflected in variations in the loss on ignition of samples from the cores and in elemental profiles produced by scanning the cores with the Itrax micro-XRF corescanner at 200μm resolution. The long sequence from the dried lake bed has very low organic content glacial clay at the base, interpreted as last glacial maximum basal clay following determination in the field that this layer exceeded 2m in thickness. Similar sediments occur within a stratigraphically discrete section of approximately 14cm and may relate to a stadial event. The latter section also shows a drop in organic content and appears to be glacial clay incorporating some coarse sandy components indicative of detrital input from the catchment. The second long sequence, from a carbonate lake, includes two mineral layers indicating increased detrital input from the catchment. The deeper and thicker of these layers appears similar to the 14cm layer in the first long sequence, while the upper layer comprises a fine grain size indicative of rock flour and hence also of glacial

  5. Multidimensional analysis of high resolution. gamma. -ray data

    Energy Technology Data Exchange (ETDEWEB)

    Flibotte, S.; Huettmeier, U.J.; France, G. de; Haas, B.; Romain, P.; Theisen, C.; Vivien, J.P.; Zen, J. (Centre de Recherches Nucleaires, 67 - Strasbourg (France)); Bednarczyk, P. (Inst. of Nuclear Physics, Krakow (Poland))

    1992-08-15

    Algorithms are developed to analyze high-fold {gamma}-ray coincidences. Performances of the programs have been tested in 3, 4 and 5 dimensions using events generated with a Monte Carlo simulation. (orig.).

  6. High Resolution Gamma Ray Analysis of Medical Isotopes

    Science.gov (United States)

    Chillery, Thomas

    2015-10-01

    Compton-suppressed high-purity Germanium detectors at the University of Massachusetts Lowell have been used to study medical radioisotopes produced at Brookhaven Linac Isotope Producer (BLIP), in particular isotopes such as Pt-191 used for cancer therapy in patients. The ability to precisely analyze the concentrations of such radio-isotopes is essential for both production facilities such as Brookhaven and consumer hospitals across the U.S. Without accurate knowledge of the quantities and strengths of these isotopes, it is possible for doctors to administer incorrect dosages to patients, thus leading to undesired results. Samples have been produced at Brookhaven and shipped to UML, and the advanced electronics and data acquisition capabilities at UML have been used to extract peak areas in the gamma decay spectra. Levels of Pt isotopes in diluted samples have been quantified, and reaction cross-sections deduced from the irradiation parameters. These provide both cross checks with published work, as well as a rigorous quantitative framework with high quality state-of-the-art detection apparatus in use in the experimental nuclear physics community.

  7. High resolution visualization and analysis of nasal spray drug delivery.

    Science.gov (United States)

    Inthavong, Kiao; Fung, Man Chiu; Tong, Xuwen; Yang, William; Tu, Jiyuan

    2014-08-01

    Effective nasal drug delivery of new-generation systemic drugs requires efficient devices that can achieve targeted drug delivery. It has been established that droplet size, spray plume, and droplet velocity are major contributors to drug deposition. Continual effort is needed to better understand and characterise the physical mechanisms underpinning droplet formation from nasal spray devices. High speed laser photography combined with an in-house designed automated actuation system, and a highly precise traversing unit, measurements and images magnified in small field-of-view regions within the spray was performed. The qualitative results showed a swirling liquid sheet at the near-nozzle region as the liquid is discharged before ligaments of fluid are separated off the liquid sheet. Droplets are formed and continue to deform as they travel downstream at velocities of up to 20 m/s. Increase in actuation pressure produces more rapid atomization and discharge time where finer droplets are produced. The results suggest that device designs should consider reducing droplet inertia to penetrate the nasal valve region, but find a way to deposit in the main nasal passage and not escape through to the lungs.

  8. High resolution (transformers.

    Science.gov (United States)

    Garcia-Souto, Jose A; Lamela-Rivera, Horacio

    2006-10-16

    A novel fiber-optic interferometric sensor is presented for vibrations measurements and analysis. In this approach, it is shown applied to the vibrations of electrical structures within power transformers. A main feature of the sensor is that an unambiguous optical phase measurement is performed using the direct detection of the interferometer output, without external modulation, for a more compact and stable implementation. High resolution of the interferometric measurement is obtained with this technique (transformers are also highlighted.

  9. Analysis strategies for high-resolution UHF-fMRI data.

    Science.gov (United States)

    Polimeni, Jonathan R; Renvall, Ville; Zaretskaya, Natalia; Fischl, Bruce

    2018-03-01

    Functional MRI (fMRI) benefits from both increased sensitivity and specificity with increasing magnetic field strength, making it a key application for Ultra-High Field (UHF) MRI scanners. Most UHF-fMRI studies utilize the dramatic increases in sensitivity and specificity to acquire high-resolution data reaching sub-millimeter scales, which enable new classes of experiments to probe the functional organization of the human brain. This review article surveys advanced data analysis strategies developed for high-resolution fMRI at UHF. These include strategies designed to mitigate distortion and artifacts associated with higher fields in ways that attempt to preserve spatial resolution of the fMRI data, as well as recently introduced analysis techniques that are enabled by these extremely high-resolution data. Particular focus is placed on anatomically-informed analyses, including cortical surface-based analysis, which are powerful techniques that can guide each step of the analysis from preprocessing to statistical analysis to interpretation and visualization. New intracortical analysis techniques for laminar and columnar fMRI are also reviewed and discussed. Prospects for single-subject individualized analyses are also presented and discussed. Altogether, there are both specific challenges and opportunities presented by UHF-fMRI, and the use of proper analysis strategies can help these valuable data reach their full potential. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Optimization of High-Resolution Continuous Flow Analysis for Transient Climate Signals in Ice Cores

    DEFF Research Database (Denmark)

    Bigler, Matthias; Svensson, Anders; Kettner, Ernesto

    2011-01-01

    Over the past two decades, continuous flow analysis (CFA) systems have been refined and widely used to measure aerosol constituents in polar and alpine ice cores in very high-depth resolution. Here we present a newly designed system consisting of sodium, ammonium, dust particles, and electrolytic...... meltwater conductivity detection modules. The system is optimized for high- resolution determination of transient signals in thin layers of deep polar ice cores. Based on standard measurements and by comparing sections of early Holocene and glacial ice from Greenland, we find that the new system features...

  11. ANL high resolution injector

    International Nuclear Information System (INIS)

    Minehara, E.; Kutschera, W.; Hartog, P.D.; Billquist, P.

    1985-01-01

    The ANL (Argonne National Laboratory) high-resolution injector has been installed to obtain higher mass resolution and higher preacceleration, and to utilize effectively the full mass range of ATLAS (Argonne Tandem Linac Accelerator System). Preliminary results of the first beam test are reported briefly. The design and performance, in particular a high-mass-resolution magnet with aberration compensation, are discussed. 7 refs., 5 figs., 2 tabs

  12. Report on Ultra-high Resolution Gamma-/X-ray Analysis of Uranium Skull Oxide

    International Nuclear Information System (INIS)

    Friedrich, S.; Velazquez, M.; Drury, O.; Salaymeh, S.

    2009-01-01

    We have utilized the high energy resolution and high peak-to-background ratio of superconducting TES γ-detectors at very low energies for non-destructive analysis of a skull oxide derived from reprocessed nuclear fuel. Specifically, we demonstrate that superconducting detectors can separate and analyze the strong actinide emission lines in the spectral region below 60 keV that are often obscured in γ-measurements with conventional Ge detectors.

  13. High resolution transmission electron microscopy and microdiffraction for radiation damage analysis

    International Nuclear Information System (INIS)

    Sinclair, R.

    1982-01-01

    High resolution TEM techniques have developed to quite a sophisticated level over the past few years. In addition TEM instruments with a scanning capability have become available commercially which permit in particular the formation of a small electron probe at the specimen. Thus direct resolution and microdiffraction investigations of thin specimens are now possible, neither of which have been employed to any great extent in the analysis of radiation damage. Some recent advances which are thought to be relevant to this specific area of research are highlighted

  14. Limitations to depth resolution in high-energy, heavy-ion elastic recoil detection analysis

    International Nuclear Information System (INIS)

    Elliman, R.G.; Palmer, G.R.; Ophel, T.R.; Timmers, H.

    1998-01-01

    The depth resolution of heavy-ion elastic recoil detection analysis was examined for Al and Co thin films ranging in thickness from 100 to 400 nm. Measurements were performed with 154 MeV Au ions as the incident beam, and recoils were detected using a gas ionisation detector. Energy spectra were extracted for the Al and Co recoils and the depth resolution determined as a function of film thickness from the width of the high- and low- energy edges. These results were compared with theoretical estimates calculated using the computer program DEPTH. (authors)

  15. A High-Resolution Continuous Flow Analysis System for Polar Ice Cores

    DEFF Research Database (Denmark)

    Dallmayr, Remi; Goto-Azuma, Kumiko; Kjær, Helle Astrid

    2016-01-01

    of Polar Research (NIPR) in Tokyo. The system allows the continuous analysis of stable water isotopes and electrical conductivity, as well as the collection of discrete samples from both inner and outer parts of the core. This CFA system was designed to have sufficiently high temporal resolution to detect...... signals of abrupt climate change in deep polar ice cores. To test its performance, we used the system to analyze different climate intervals in ice drilled at the NEEM (North Greenland Eemian Ice Drilling) site, Greenland. The quality of our continuous measurement of stable water isotopes has been......In recent decades, the development of continuous flow analysis (CFA) technology for ice core analysis has enabled greater sample throughput and greater depth resolution compared with the classic discrete sampling technique. We developed the first Japanese CFA system at the National Institute...

  16. High Resolution Melting Analysis for fast and cheap polymorphism screening of marine populations

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Anne-Leila Meistertzheim, Isabelle Calves, Sébastien Artigaud, Carolyn S. Friedman, Christine Paillard, Jean Laroche & Claude Ferec ### Abstract This protocol permits the mutation scanning of PCR products by high-resolution DNA melting analysis requiring the inclusion of a saturating intercalating dye in the PCR mix without labelled probe. During a scanning process, fluorescent melting curves of PCR amplicons are analyzed. Mutations modifying melting curve shapes, are allowed...

  17. High Resolution Elevation Contours

    Data.gov (United States)

    Minnesota Department of Natural Resources — This dataset contains contours generated from high resolution data sources such as LiDAR. Generally speaking this data is 2 foot or less contour interval.

  18. High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

    DEFF Research Database (Denmark)

    Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob

    2014-01-01

    In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High......-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized...... that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide...

  19. Compressed sensing cine imaging with high spatial or high temporal resolution for analysis of left ventricular function.

    Science.gov (United States)

    Goebel, Juliane; Nensa, Felix; Schemuth, Haemi P; Maderwald, Stefan; Gratz, Marcel; Quick, Harald H; Schlosser, Thomas; Nassenstein, Kai

    2016-08-01

    To assess two compressed sensing cine magnetic resonance imaging (MRI) sequences with high spatial or high temporal resolution in comparison to a reference steady-state free precession cine (SSFP) sequence for reliable quantification of left ventricular (LV) volumes. LV short axis stacks of two compressed sensing breath-hold cine sequences with high spatial resolution (SPARSE-SENSE HS: temporal resolution: 40 msec, in-plane resolution: 1.0 × 1.0 mm(2) ) and high temporal resolution (SPARSE-SENSE HT: temporal resolution: 11 msec, in-plane resolution: 1.7 × 1.7 mm(2) ) and of a reference cine SSFP sequence (standard SSFP: temporal resolution: 40 msec, in-plane resolution: 1.7 × 1.7 mm(2) ) were acquired in 16 healthy volunteers on a 1.5T MR system. LV parameters were analyzed semiautomatically twice by one reader and once by a second reader. The volumetric agreement between sequences was analyzed using paired t-test, Bland-Altman plots, and Passing-Bablock regression. Small differences were observed between standard SSFP and SPARSE-SENSE HS for stroke volume (SV; -7 ± 11 ml; P = 0.024), ejection fraction (EF; -2 ± 3%; P = 0.019), and myocardial mass (9 ± 9 g; P = 0.001), but not for end-diastolic volume (EDV; P = 0.079) and end-systolic volume (ESV; P = 0.266). No significant differences were observed between standard SSFP and SPARSE-SENSE HT regarding EDV (P = 0.956), SV (P = 0.088), and EF (P = 0.103), but for ESV (3 ± 5 ml; P = 0.039) and myocardial mass (8 ± 10 ml; P = 0.007). Bland-Altman analysis showed good agreement between the sequences (maximum bias ≤ -8%). Two compressed sensing cine sequences, one with high spatial resolution and one with high temporal resolution, showed good agreement with standard SSFP for LV volume assessment. J. Magn. Reson. Imaging 2016;44:366-374. © 2016 Wiley Periodicals, Inc.

  20. A compact high resolution ion mobility spectrometer for fast trace gas analysis.

    Science.gov (United States)

    Kirk, Ansgar T; Allers, Maria; Cochems, Philipp; Langejuergen, Jens; Zimmermann, Stefan

    2013-09-21

    Drift tube ion mobility spectrometers (IMS) are widely used for fast trace gas detection in air, but portable compact systems are typically very limited in their resolving power. Decreasing the initial ion packet width improves the resolution, but is generally associated with a reduced signal-to-noise-ratio (SNR) due to the lower number of ions injected into the drift region. In this paper, we present a refined theory of IMS operation which employs a combined approach for the analysis of the ion drift and the subsequent amplification to predict both the resolution and the SNR of the measured ion current peak. This theoretical analysis shows that the SNR is not a function of the initial ion packet width, meaning that compact drift tube IMS with both very high resolution and extremely low limits of detection can be designed. Based on these implications, an optimized combination of a compact drift tube with a length of just 10 cm and a transimpedance amplifier has been constructed with a resolution of 183 measured for the positive reactant ion peak (RIP(+)), which is sufficient to e.g. separate the RIP(+) from the protonated acetone monomer, even though their drift times only differ by a factor of 1.007. Furthermore, the limits of detection (LODs) for acetone are 180 pptv within 1 s of averaging time and 580 pptv within only 100 ms.

  1. Multi-scale Analysis of High Resolution Topography: Feature Extraction and Identification of Landscape Characteristic Scales

    Science.gov (United States)

    Passalacqua, P.; Sangireddy, H.; Stark, C. P.

    2015-12-01

    With the advent of digital terrain data, detailed information on terrain characteristics and on scale and location of geomorphic features is available over extended areas. Our ability to observe landscapes and quantify topographic patterns has greatly improved, including the estimation of fluxes of mass and energy across landscapes. Challenges still remain in the analysis of high resolution topography data; the presence of features such as roads, for example, challenges classic methods for feature extraction and large data volumes require computationally efficient extraction and analysis methods. Moreover, opportunities exist to define new robust metrics of landscape characterization for landscape comparison and model validation. In this presentation we cover recent research in multi-scale and objective analysis of high resolution topography data. We show how the analysis of the probability density function of topographic attributes such as slope, curvature, and topographic index contains useful information for feature localization and extraction. The analysis of how the distributions change across scales, quantified by the behavior of modal values and interquartile range, allows the identification of landscape characteristic scales, such as terrain roughness. The methods are introduced on synthetic signals in one and two dimensions and then applied to a variety of landscapes of different characteristics. Validation of the methods includes the analysis of modeled landscapes where the noise distribution is known and features of interest easily measured.

  2. Ultra high resolution tomography

    Energy Technology Data Exchange (ETDEWEB)

    Haddad, W.S.

    1994-11-15

    Recent work and results on ultra high resolution three dimensional imaging with soft x-rays will be presented. This work is aimed at determining microscopic three dimensional structure of biological and material specimens. Three dimensional reconstructed images of a microscopic test object will be presented; the reconstruction has a resolution on the order of 1000 A in all three dimensions. Preliminary work with biological samples will also be shown, and the experimental and numerical methods used will be discussed.

  3. Genotyping of Listeria monocytogenes isolates from poultry carcasses using high resolution melting (HRM) analysis.

    Science.gov (United States)

    Sakaridis, Ioannis; Ganopoulos, Ioannis; Madesis, Panagiotis; Tsaftaris, Athanasios; Argiriou, Anagnostis

    2014-01-02

    An outbreak situation of human listeriosis requires a fast and accurate protocol for typing Listeria monocytogenes . Existing techniques are either characterized by low discriminatory power or are laborious and require several days to give a final result. Polymerase chain reaction (PCR) coupled with high resolution melting (HRM) analysis was investigated in this study as an alternative tool for a rapid and precise genotyping of L. monocytogenes isolates. Fifty-five isolates of L. monocytogenes isolated from poultry carcasses and the environment of four slaughterhouses were typed by HRM analysis using two specific markers, internalin B and ssrA genes. The analysis of genotype confidence percentage of L. monocytogenes isolates produced by HRM analysis generated dendrograms with two major groups and several subgroups. Furthermore, the analysis of the HRM curves revealed that all L. monocytogenes isolates could easily be distinguished. In conclusion, HRM was proven to be a fast and powerful tool for genotyping isolates of L. monocytogenes .

  4. High resolution gamma-ray spectroscopy applied to bulk sample analysis

    International Nuclear Information System (INIS)

    Kosanke, K.L.; Koch, C.D.; Wilson, R.D.

    1980-01-01

    A high resolution Ge(Li) gamma-ray spectrometer has been installed and made operational for use in routine bulk sample analysis by the Bendix Field Engineering Corporation (BFEC) geochemical analysis department. The Ge(Li) spectrometer provides bulk sample analyses for potassium, uranium, and thorium that are superior to those obtained by the BFEC sodium iodide spectrometer. The near term analysis scheme permits a direct assay for uranium that corrects for bulk sample self-absorption effects and is independent of the uranium/radium disequilibrium condition of the sample. A more complete analysis scheme has been developed that fully utilizes the gamma-ray data provided by the Ge(Li) spectrometer and that more properly accounts for the sample self-absorption effect. This new analysis scheme should be implemented on the BFEC Ge(Li) spectrometer at the earliest date

  5. High resolution solar observations

    International Nuclear Information System (INIS)

    Title, A.

    1985-01-01

    Currently there is a world-wide effort to develop optical technology required for large diffraction limited telescopes that must operate with high optical fluxes. These developments can be used to significantly improve high resolution solar telescopes both on the ground and in space. When looking at the problem of high resolution observations it is essential to keep in mind that a diffraction limited telescope is an interferometer. Even a 30 cm aperture telescope, which is small for high resolution observations, is a big interferometer. Meter class and above diffraction limited telescopes can be expected to be very unforgiving of inattention to details. Unfortunately, even when an earth based telescope has perfect optics there are still problems with the quality of its optical path. The optical path includes not only the interior of the telescope, but also the immediate interface between the telescope and the atmosphere, and finally the atmosphere itself

  6. Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers.

    Science.gov (United States)

    Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S; Garcia-Closas, Montserrat; Sherman, Mark E; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P; Khan, Javed; Chanock, Stephen

    2011-01-17

    Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

  7. Detection of somatic mutations by high-resolution DNA melting (HRM analysis in multiple cancers.

    Directory of Open Access Journals (Sweden)

    Jesus Gonzalez-Bosquet

    Full Text Available Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each. HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

  8. Analysis of Chinese women with primary ovarian insufficiency by high resolution array-comparative genomic hybridization.

    Science.gov (United States)

    Liao, Can; Fu, Fang; Yang, Xin; Sun, Yi-Min; Li, Dong-Zhi

    2011-06-01

    Primary ovarian insufficiency (POI) is defined as a primary ovarian defect characterized by absent menarche (primary amenorrhea) or premature depletion of ovarian follicles before the age of 40 years. The etiology of primary ovarian insufficiency in human female patients is still unclear. The purpose of this study is to investigate the potential genetic causes in primary amenorrhea patients by high resolution array based comparative genomic hybridization (array-CGH) analysis. Following the standard karyotyping analysis, genomic DNA from whole blood of 15 primary amenorrhea patients and 15 normal control women was hybridized with Affymetrix cytogenetic 2.7M arrays following the standard protocol. Copy number variations identified by array-CGH were confirmed by real time polymerase chain reaction. All the 30 samples were negative by conventional karyotyping analysis. Microdeletions on chromosome 17q21.31-q21.32 with approximately 1.3 Mb were identified in four patients by high resolution array-CGH analysis. This included the female reproductive secretory pathway related factor N-ethylmaleimide-sensitive factor (NSF) gene. The results of the present study suggest that there may be critical regions regulating primary ovarian insufficiency in women with a 17q21.31-q21.32 microdeletion. This effect might be due to the loss of function of the NSF gene/genes within the deleted region or to effects on contiguous genes.

  9. Isotopomer analysis of lipid biosynthesis by high resolution mass spectrometry and NMR

    Energy Technology Data Exchange (ETDEWEB)

    Lane, Andrew N., E-mail: anlane01@louisville.edu [JG Brown Cancer Center, 529 S. Jackson Street, Louisville, KY 40202 (United States); Center for Regulatory and Environmental Analytical Metabolomics (CREAM), University of Louisville, Louisville, KY (United States); Fan, Teresa W.-M. [JG Brown Cancer Center, 529 S. Jackson Street, Louisville, KY 40202 (United States); Center for Regulatory and Environmental Analytical Metabolomics (CREAM), University of Louisville, Louisville, KY (United States); Department of Chemistry, University of Louisville, Louisville, KY 40292 (United States); Xie, Zhengzhi; Moseley, Hunter N.B.; Higashi, Richard M. [Center for Regulatory and Environmental Analytical Metabolomics (CREAM), University of Louisville, Louisville, KY (United States); Department of Chemistry, University of Louisville, Louisville, KY 40292 (United States)

    2009-10-05

    We have coupled 2D-NMR and infusion FT-ICR-MS with computer-assisted assignment to profile {sup 13}C-isotopologues of glycerophospholipids (GPL) directly in crude cell extracts, resulting in very high information throughput of >3000 isobaric molecules in a few minutes. A mass accuracy of better than 1 ppm combined with a resolution of 100,000 at the measured m/z was required to distinguish isotopomers from other GPL structures. Isotopologue analysis of GPLs extracted from LCC2 breast cancer cells grown on [U-{sup 13}C]-glucose provided a rich trove of information about the biosynthesis and turnover of the GPLs. The isotopologue intensity ratios from the FT-ICR-MS were accurate to {approx}1% or better based on natural abundance background, and depended on the signal-to-nose ratio. The time course of incorporation of {sup 13}C from [U-{sup 13}C]-glucose into a particular phosphatidylcholine was analyzed in detail, to provide a quantitative measure of the sizes of glycerol, acetyl CoA and total GPL pools in growing LCC2 cells. Independent and complementary analysis of the positional {sup 13}C enrichment in the glycerol and fatty acyl chains obtained from high resolution 2D NMR was used to verify key aspects of the model. This technology enables simple and rapid sample preparation, has rapid analysis, and is generally applicable to unfractionated GPLs of almost any head group, and to mixtures of other classes of metabolites.

  10. Isotopomer analysis of lipid biosynthesis by high resolution mass spectrometry and NMR

    International Nuclear Information System (INIS)

    Lane, Andrew N.; Fan, Teresa W.-M.; Xie, Zhengzhi; Moseley, Hunter N.B.; Higashi, Richard M.

    2009-01-01

    We have coupled 2D-NMR and infusion FT-ICR-MS with computer-assisted assignment to profile 13 C-isotopologues of glycerophospholipids (GPL) directly in crude cell extracts, resulting in very high information throughput of >3000 isobaric molecules in a few minutes. A mass accuracy of better than 1 ppm combined with a resolution of 100,000 at the measured m/z was required to distinguish isotopomers from other GPL structures. Isotopologue analysis of GPLs extracted from LCC2 breast cancer cells grown on [U- 13 C]-glucose provided a rich trove of information about the biosynthesis and turnover of the GPLs. The isotopologue intensity ratios from the FT-ICR-MS were accurate to ∼1% or better based on natural abundance background, and depended on the signal-to-nose ratio. The time course of incorporation of 13 C from [U- 13 C]-glucose into a particular phosphatidylcholine was analyzed in detail, to provide a quantitative measure of the sizes of glycerol, acetyl CoA and total GPL pools in growing LCC2 cells. Independent and complementary analysis of the positional 13 C enrichment in the glycerol and fatty acyl chains obtained from high resolution 2D NMR was used to verify key aspects of the model. This technology enables simple and rapid sample preparation, has rapid analysis, and is generally applicable to unfractionated GPLs of almost any head group, and to mixtures of other classes of metabolites.

  11. Interactive desktop analysis of high resolution simulations: application to turbulent plume dynamics and current sheet formation

    International Nuclear Information System (INIS)

    Clyne, John; Mininni, Pablo; Norton, Alan; Rast, Mark

    2007-01-01

    The ever increasing processing capabilities of the supercomputers available to computational scientists today, combined with the need for higher and higher resolution computational grids, has resulted in deluges of simulation data. Yet the computational resources and tools required to make sense of these vast numerical outputs through subsequent analysis are often far from adequate, making such analysis of the data a painstaking, if not a hopeless, task. In this paper, we describe a new tool for the scientific investigation of massive computational datasets. This tool (VAPOR) employs data reduction, advanced visualization, and quantitative analysis operations to permit the interactive exploration of vast datasets using only a desktop PC equipped with a commodity graphics card. We describe VAPORs use in the study of two problems. The first, motivated by stellar envelope convection, investigates the hydrodynamic stability of compressible thermal starting plumes as they descend through a stratified layer of increasing density with depth. The second looks at current sheet formation in an incompressible helical magnetohydrodynamic flow to understand the early spontaneous development of quasi two-dimensional (2D) structures embedded within the 3D solution. Both of the problems were studied at sufficiently high spatial resolution, a grid of 504 2 by 2048 points for the first and 1536 3 points for the second, to overwhelm the interactive capabilities of typically available analysis resources

  12. The spa typing of methicillin-resistant Staphylococcus aureus isolates by High Resolution Melting (HRM) analysis.

    Science.gov (United States)

    Fasihi, Yasser; Fooladi, Saba; Mohammadi, Mohammad Ali; Emaneini, Mohammad; Kalantar-Neyestanaki, Davood

    2017-09-06

    Molecular typing is an important tool for control and prevention of infection. A suitable molecular typing method for epidemiological investigation must be easy to perform, highly reproducible, inexpensive, rapid and easy to interpret. In this study, two molecular typing methods including the conventional PCR-sequencing method and high resolution melting (HRM) analysis were used for staphylococcal protein A (spa) typing of 30 Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from clinical samples. Based on PCR-sequencing method results, 16 different spa types were identified among the 30 MRSA isolates. Among the 16 different spa types, 14 spa types separated by HRM method. Two spa types including t4718 and t2894 were not separated from each other. According to our results, spa typing based on HRM analysis method is very rapid, easy to perform and cost-effective, but this method must be standardized for different regions, spa types, and real-time machinery.

  13. High resolution drift chambers

    International Nuclear Information System (INIS)

    Va'vra, J.

    1985-07-01

    High precision drift chambers capable of achieving less than or equal to 50 μm resolutions are discussed. In particular, we compare so called cool and hot gases, various charge collection geometries, several timing techniques and we also discuss some systematic problems. We also present what we would consider an ''ultimate'' design of the vertex chamber. 50 refs., 36 figs., 6 tabs

  14. High-resolution three-dimensional imaging and analysis of rock falls in Yosemite valley, California

    Science.gov (United States)

    Stock, Gregory M.; Bawden, G.W.; Green, J.K.; Hanson, E.; Downing, G.; Collins, B.D.; Bond, S.; Leslar, M.

    2011-01-01

    We present quantitative analyses of recent large rock falls in Yosemite Valley, California, using integrated high-resolution imaging techniques. Rock falls commonly occur from the glacially sculpted granitic walls of Yosemite Valley, modifying this iconic landscape but also posing signifi cant potential hazards and risks. Two large rock falls occurred from the cliff beneath Glacier Point in eastern Yosemite Valley on 7 and 8 October 2008, causing minor injuries and damaging structures in a developed area. We used a combination of gigapixel photography, airborne laser scanning (ALS) data, and ground-based terrestrial laser scanning (TLS) data to characterize the rock-fall detachment surface and adjacent cliff area, quantify the rock-fall volume, evaluate the geologic structure that contributed to failure, and assess the likely failure mode. We merged the ALS and TLS data to resolve the complex, vertical to overhanging topography of the Glacier Point area in three dimensions, and integrated these data with gigapixel photographs to fully image the cliff face in high resolution. Three-dimensional analysis of repeat TLS data reveals that the cumulative failure consisted of a near-planar rock slab with a maximum length of 69.0 m, a mean thickness of 2.1 m, a detachment surface area of 2750 m2, and a volume of 5663 ?? 36 m3. Failure occurred along a surfaceparallel, vertically oriented sheeting joint in a clear example of granitic exfoliation. Stress concentration at crack tips likely propagated fractures through the partially attached slab, leading to failure. Our results demonstrate the utility of high-resolution imaging techniques for quantifying far-range (>1 km) rock falls occurring from the largely inaccessible, vertical rock faces of Yosemite Valley, and for providing highly accurate and precise data needed for rock-fall hazard assessment. ?? 2011 Geological Society of America.

  15. Bivariable analysis of ventricular late potentials in high resolution ECG records

    International Nuclear Information System (INIS)

    Orosco, L; Laciar, E

    2007-01-01

    In this study the bivariable analysis for ventricular late potentials detection in high-resolution electrocardiographic records is proposed. The standard time-domain analysis and the application of the time-frequency technique to high-resolution ECG records are briefly described as well as their corresponding results. In the proposed technique the time-domain parameter, QRSD and the most significant time-frequency index, EN QRS are used like variables. A bivariable index is defined, that combines the previous parameters. The propose technique allows evaluating the risk of ventricular tachycardia in post-myocardial infarct patients. The results show that the used bivariable index allows discriminating between the patient's population with ventricular tachycardia and the subjects of the control group. Also, it was found that the bivariable technique obtains a good valuation as diagnostic test. It is concluded that comparatively, the valuation of the bivariable technique as diagnostic test is superior to that of the time-domain method and the time-frequency technique evaluated individually

  16. The investigation of Martian dune fields using very high resolution photogrammetric measurements and time series analysis

    Science.gov (United States)

    Kim, J.; Park, M.; Baik, H. S.; Choi, Y.

    2016-12-01

    At the present time, arguments continue regarding the migration speeds of Martian dune fields and their correlation with atmospheric circulation. However, precisely measuring the spatial translation of Martian dunes has rarely conducted only a very few times Therefore, we developed a generic procedure to precisely measure the migration of dune fields with recently introduced 25-cm resolution High Resolution Imaging Science Experimen (HIRISE) employing a high-accuracy photogrammetric processor and sub-pixel image correlator. The processor was designed to trace estimated dune migration, albeit slight, over the Martian surface by 1) the introduction of very high resolution ortho images and stereo analysis based on hierarchical geodetic control for better initial point settings; 2) positioning error removal throughout the sensor model refinement with a non-rigorous bundle block adjustment, which makes possible the co-alignment of all images in a time series; and 3) improved sub-pixel co-registration algorithms using optical flow with a refinement stage conducted on a pyramidal grid processor and a blunder classifier. Moreover, volumetric changes of Martian dunes were additionally traced by means of stereo analysis and photoclinometry. The established algorithms have been tested using high-resolution HIRISE images over a large number of Martian dune fields covering whole Mars Global Dune Database. Migrations over well-known crater dune fields appeared to be almost static for the considerable temporal periods and were weakly correlated with wind directions estimated by the Mars Climate Database (Millour et al. 2015). Only over a few Martian dune fields, such as Kaiser crater, meaningful migration speeds (>1m/year) compared to phtotogrammetric error residual have been measured. Currently a technical improved processor to compensate error residual using time series observation is under developing and expected to produce the long term migration speed over Martian dune

  17. CEST ANALYSIS: AUTOMATED CHANGE DETECTION FROM VERY-HIGH-RESOLUTION REMOTE SENSING IMAGES

    Directory of Open Access Journals (Sweden)

    M. Ehlers

    2012-08-01

    Full Text Available A fast detection, visualization and assessment of change in areas of crisis or catastrophes are important requirements for coordination and planning of help. Through the availability of new satellites and/or airborne sensors with very high spatial resolutions (e.g., WorldView, GeoEye new remote sensing data are available for a better detection, delineation and visualization of change. For automated change detection, a large number of algorithms has been proposed and developed. From previous studies, however, it is evident that to-date no single algorithm has the potential for being a reliable change detector for all possible scenarios. This paper introduces the Combined Edge Segment Texture (CEST analysis, a decision-tree based cooperative suite of algorithms for automated change detection that is especially designed for the generation of new satellites with very high spatial resolution. The method incorporates frequency based filtering, texture analysis, and image segmentation techniques. For the frequency analysis, different band pass filters can be applied to identify the relevant frequency information for change detection. After transforming the multitemporal images via a fast Fourier transform (FFT and applying the most suitable band pass filter, different methods are available to extract changed structures: differencing and correlation in the frequency domain and correlation and edge detection in the spatial domain. Best results are obtained using edge extraction. For the texture analysis, different 'Haralick' parameters can be calculated (e.g., energy, correlation, contrast, inverse distance moment with 'energy' so far providing the most accurate results. These algorithms are combined with a prior segmentation of the image data as well as with morphological operations for a final binary change result. A rule-based combination (CEST of the change algorithms is applied to calculate the probability of change for a particular location. CEST

  18. Automated Microfluidic Platform for Serial Polymerase Chain Reaction and High-Resolution Melting Analysis.

    Science.gov (United States)

    Cao, Weidong; Bean, Brian; Corey, Scott; Coursey, Johnathan S; Hasson, Kenton C; Inoue, Hiroshi; Isano, Taisuke; Kanderian, Sami; Lane, Ben; Liang, Hongye; Murphy, Brian; Owen, Greg; Shinoda, Nobuhiko; Zeng, Shulin; Knight, Ivor T

    2016-06-01

    We report the development of an automated genetic analyzer for human sample testing based on microfluidic rapid polymerase chain reaction (PCR) with high-resolution melting analysis (HRMA). The integrated DNA microfluidic cartridge was used on a platform designed with a robotic pipettor system that works by sequentially picking up different test solutions from a 384-well plate, mixing them in the tips, and delivering mixed fluids to the DNA cartridge. A novel image feedback flow control system based on a Canon 5D Mark II digital camera was developed for controlling fluid movement through a complex microfluidic branching network without the use of valves. The same camera was used for measuring the high-resolution melt curve of DNA amplicons that were generated in the microfluidic chip. Owing to fast heating and cooling as well as sensitive temperature measurement in the microfluidic channels, the time frame for PCR and HRMA was dramatically reduced from hours to minutes. Preliminary testing results demonstrated that rapid serial PCR and HRMA are possible while still achieving high data quality that is suitable for human sample testing. © 2015 Society for Laboratory Automation and Screening.

  19. High resolution data acquisition

    Science.gov (United States)

    Thornton, Glenn W.; Fuller, Kenneth R.

    1993-01-01

    A high resolution event interval timing system measures short time intervals such as occur in high energy physics or laser ranging. Timing is provided from a clock (38) pulse train (37) and analog circuitry (44) for generating a triangular wave (46) synchronously with the pulse train (37). The triangular wave (46) has an amplitude and slope functionally related to the time elapsed during each clock pulse in the train. A converter (18, 32) forms a first digital value of the amplitude and slope of the triangle wave at the start of the event interval and a second digital value of the amplitude and slope of the triangle wave at the end of the event interval. A counter (26) counts the clock pulse train (37) during the interval to form a gross event interval time. A computer (52) then combines the gross event interval time and the first and second digital values to output a high resolution value for the event interval.

  20. The application of computer technique in routine neutron activation analysis using high resolution gamma ray spectrometry

    International Nuclear Information System (INIS)

    Szopa, Z.; Plejewska, M.; Staszelis, J.

    1982-01-01

    A full system of four computer programs for routine - qualitative and quantitative - neutron activation analysis (NAA) using high resolution gamma ray-spectrometry had been elaborated. The structure and possibilities of the ''data flow'' programs i.e. programs DIDPDP and DIDCDC, dedicated for fast and reliable ''off line'' data transfer between the buffer memory of the spectrometric line (9-track magnetic tape) and the fast access memory (disc) of the used computers PDP-11/45 and CYBER-73 had been presented. The structure and organization of the ''data processing'' programs i.e. programs SAWAPS and MAZYG had been presented as well. The utility and reliability of these programs in the case of the large-scale, routine NAA, exampled by analysis of filters with air polutants, had been tested and discussed. Programs are written mainly in FORTRAN. (author)

  1. Differentiation of minute virus of mice and mouse parvovirus by high resolution melting curve analysis.

    Science.gov (United States)

    Rao, Dan; Wu, Miaoli; Wang, Jing; Yuan, Wen; Zhu, Yujun; Cong, Feng; Xu, Fengjiao; Lian, Yuexiao; Huang, Bihong; Wu, Qiwen; Chen, Meili; Zhang, Yu; Huang, Ren; Guo, Pengju

    2017-12-01

    Murine parvovirus is one of the most prevalent infectious pathogens in mouse colonies. A specific primer pair targeting the VP2 gene of minute virus of mice (MVM) and mouse parvovirus (MPV) was utilized for high resolution melting (HRM) analysis. The resulting melting curves could distinguish these two virus strains and there was no detectable amplification of the other mouse pathogens which included rat parvovirus (KRV), ectromelia virus (ECT), mouse adenovirus (MAD), mouse cytomegalovirus (MCMV), polyoma virus (Poly), Helicobactor hepaticus (H. hepaticus) and Salmonella typhimurium (S. typhimurium). The detection limit of the standard was 10 copies/μL. This study showed that the PCR-HRM assay could be an alternative useful method with high specificity and sensitivity for differentiating murine parvovirus strains MVM and MPV. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Ultra-high resolution water window x ray microscope optics design and analysis

    Science.gov (United States)

    Shealy, David L.; Wang, C.

    1993-01-01

    This project has been focused on the design and analysis of an ultra-high resolution water window soft-x-ray microscope. These activities have been accomplished by completing two tasks contained in the statement of work of this contract. The new results from this work confirm: (1) that in order to achieve resolutions greater than three times the wavelength of the incident radiation, it will be necessary to use spherical mirror surfaces and to use graded multilayer coatings on the secondary in order to accommodate the large variations of the angle of incidence over the secondary when operating the microscope at numerical apertures of 0.35 or greater; (2) that surface contour errors will have a significant effect on the optical performance of the microscope and must be controlled to a peak-to-valley variation of 50-100 A and a frequency of 8 periods over the surface of a mirror; and (3) that tolerance analysis of the spherical Schwarzschild microscope has been shown that the water window operations will require 2-3 times tighter tolerances to achieve a similar performance of operations with 130 A radiation. These results have been included in a manuscript included in the appendix.

  3. High resolution terahertz spectroscopy of a whispering gallery mode bubble resonator using Hilbert analysis.

    Science.gov (United States)

    Vogt, Dominik Walter; Leonhardt, Rainer

    2017-07-10

    We report on data processing for continuous wave (CW) terahertz (THz) spectroscopy measurements based on a Hilbert spectral analysis to achieve MHz resolution. As an example we investigate the spectral properties of a whispering gallery mode (WGM) THz bubble resonator at critical coupling. The experimental verification clearly demonstrates the significant advantages in relative frequency resolution and required acquisition time of the proposed method over the traditional data analysis. An effective frequency resolution, only limited by the precision and stability of the laser beat signal, can be achieved without complex extensions to a standard commercially available CW THz spectrometer.

  4. Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

    Directory of Open Access Journals (Sweden)

    Zhao Patrick X

    2011-07-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L., a species with high economic value but limited genomic resources. Results The alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A sample of candidate SNPs were evaluated and validated using high resolution melting (HRM analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1 chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories. Conclusions We describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.

  5. High resolution photoelectron spectroscopy

    International Nuclear Information System (INIS)

    Arko, A.J.

    1988-01-01

    Photoelectron Spectroscopy (PES) covers a very broad range of measurements, disciplines, and interests. As the next generation light source, the FEL will result in improvements over the undulator that are larger than the undulater improvements over bending magnets. The combination of high flux and high inherent resolution will result in several orders of magnitude gain in signal to noise over measurements using synchrotron-based undulators. The latter still require monochromators. Their resolution is invariably strongly energy-dependent so that in the regions of interest for many experiments (h upsilon > 100 eV) they will not have a resolving power much over 1000. In order to study some of the interesting phenomena in actinides (heavy fermions e.g.) one would need resolving powers of 10 4 to 10 5 . These values are only reachable with the FEL

  6. Genetic high throughput screening in Retinitis Pigmentosa based on high resolution melting (HRM) analysis.

    Science.gov (United States)

    Anasagasti, Ander; Barandika, Olatz; Irigoyen, Cristina; Benitez, Bruno A; Cooper, Breanna; Cruchaga, Carlos; López de Munain, Adolfo; Ruiz-Ederra, Javier

    2013-11-01

    Retinitis Pigmentosa (RP) involves a group of genetically determined retinal diseases caused by a large number of mutations that result in rod photoreceptor cell death followed by gradual death of cone cells. Most cases of RP are monogenic, with more than 80 associated genes identified so far. The high number of genes and variants involved in RP, among other factors, is making the molecular characterization of RP a real challenge for many patients. Although HRM has been used for the analysis of isolated variants or single RP genes, as far as we are concerned, this is the first study that uses HRM analysis for a high-throughput screening of several RP genes. Our main goal was to test the suitability of HRM analysis as a genetic screening technique in RP, and to compare its performance with two of the most widely used NGS platforms, Illumina and PGM-Ion Torrent technologies. RP patients (n = 96) were clinically diagnosed at the Ophthalmology Department of Donostia University Hospital, Spain. We analyzed a total of 16 RP genes that meet the following inclusion criteria: 1) size: genes with transcripts of less than 4 kb; 2) number of exons: genes with up to 22 exons; and 3) prevalence: genes reported to account for, at least, 0.4% of total RP cases worldwide. For comparison purposes, RHO gene was also sequenced with Illumina (GAII; Illumina), Ion semiconductor technologies (PGM; Life Technologies) and Sanger sequencing (ABI 3130xl platform; Applied Biosystems). Detected variants were confirmed in all cases by Sanger sequencing and tested for co-segregation in the family of affected probands. We identified a total of 65 genetic variants, 15 of which (23%) were novel, in 49 out of 96 patients. Among them, 14 (4 novel) are probable disease-causing genetic variants in 7 RP genes, affecting 15 patients. Our HRM analysis-based study, proved to be a cost-effective and rapid method that provides an accurate identification of genetic RP variants. This approach is effective for

  7. Marvel Analysis of the Measured High-resolution Rovibronic Spectra of TiO

    Science.gov (United States)

    McKemmish, Laura K.; Masseron, Thomas; Sheppard, Samuel; Sandeman, Elizabeth; Schofield, Zak; Furtenbacher, Tibor; Császár, Attila G.; Tennyson, Jonathan; Sousa-Silva, Clara

    2017-02-01

    Accurate, experimental rovibronic energy levels, with associated labels and uncertainties, are reported for 11 low-lying electronic states of the diatomic {}48{{Ti}}16{{O}} molecule, determined using the Marvel (Measured Active Rotational-Vibrational Energy Levels) algorithm. All levels are based on lines corresponding to critically reviewed and validated high-resolution experimental spectra taken from 24 literature sources. The transition data are in the 2-22,160 cm-1 region. Out of the 49,679 measured transitions, 43,885 are triplet-triplet, 5710 are singlet-singlet, and 84 are triplet-singlet transitions. A careful analysis of the resulting experimental spectroscopic network (SN) allows 48,590 transitions to be validated. The transitions determine 93 vibrational band origins of {}48{{Ti}}16{{O}}, including 71 triplet and 22 singlet ones. There are 276 (73) triplet-triplet (singlet-singlet) band-heads derived from Marvel experimental energies, 123(38) of which have never been assigned in low- or high-resolution experiments. The highest J value, where J stands for the total angular momentum, for which an energy level is validated is 163. The number of experimentally derived triplet and singlet {}48{{Ti}}16{{O}} rovibrational energy levels is 8682 and 1882, respectively. The lists of validated lines and levels for {}48{{Ti}}16{{O}} are deposited in the supporting information to this paper.

  8. High spatial resolution and high brightness ion beam probe for in-situ elemental and isotopic analysis

    Science.gov (United States)

    Long, Tao; Clement, Stephen W. J.; Bao, Zemin; Wang, Peizhi; Tian, Di; Liu, Dunyi

    2018-03-01

    A high spatial resolution and high brightness ion beam from a cold cathode duoplasmatron source and primary ion optics are presented and applied to in-situ analysis of micro-scale geological material with complex structural and chemical features. The magnetic field in the source as well as the influence of relative permeability of magnetic materials on source performance was simulated using COMSOL to confirm the magnetic field strength of the source. Based on SIMION simulation, a high brightness and high spatial resolution negative ion optical system has been developed to achieve Critical (Gaussian) illumination mode. The ion source and primary column are installed on a new Time-of-Flight secondary ion mass spectrometer for analysis of geological samples. The diameter of the ion beam was measured by the knife-edge method and a scanning electron microscope (SEM). Results show that an O2- beam of ca. 5 μm diameter with a beam intensity of ∼5 nA and an O- beam of ca. 5 μm diameter with a beam intensity of ∼50 nA were obtained, respectively. This design will open new possibilities for in-situ elemental and isotopic analysis in geological studies.

  9. Feasibility of high-resolution quantitative perfusion analysis in patients with heart failure.

    Science.gov (United States)

    Sammut, Eva; Zarinabad, Niloufar; Wesolowski, Roman; Morton, Geraint; Chen, Zhong; Sohal, Manav; Carr-White, Gerry; Razavi, Reza; Chiribiri, Amedeo

    2015-02-12

    Cardiac magnetic resonance (CMR) is playing an expanding role in the assessment of patients with heart failure (HF). The assessment of myocardial perfusion status in HF can be challenging due to left ventricular (LV) remodelling and wall thinning, coexistent scar and respiratory artefacts. The aim of this study was to assess the feasibility of quantitative CMR myocardial perfusion analysis in patients with HF. A group of 58 patients with heart failure (HF; left ventricular ejection fraction, LVEF ≤ 50%) and 33 patients with normal LVEF (LVEF >50%), referred for suspected coronary artery disease, were studied. All subjects underwent quantitative first-pass stress perfusion imaging using adenosine according to standard acquisition protocols. The feasibility of quantitative perfusion analysis was then assessed using high-resolution, 3 T kt perfusion and voxel-wise Fermi deconvolution. 30/58 (52%) subjects in the HF group had underlying ischaemic aetiology. Perfusion abnormalities were seen amongst patients with ischaemic HF and patients with normal LV function. No regional perfusion defect was observed in the non-ischaemic HF group. Good agreement was found between visual and quantitative analysis across all groups. Absolute stress perfusion rate, myocardial perfusion reserve (MPR) and endocardial-epicardial MPR ratio identified areas with abnormal perfusion in the ischaemic HF group (p = 0.02; p = 0.04; p = 0.02, respectively). In the Normal LV group, MPR and endocardial-epicardial MPR ratio were able to distinguish between normal and abnormal segments (p = 0.04; p = 0.02 respectively). No significant differences of absolute stress perfusion rate or MPR were observed comparing visually normal segments amongst groups. Our results demonstrate the feasibility of high-resolution voxel-wise perfusion assessment in patients with HF.

  10. Feasibility analysis of high resolution tissue image registration using 3-D synthetic data

    Directory of Open Access Journals (Sweden)

    Yachna Sharma

    2011-01-01

    Full Text Available Background: Registration of high-resolution tissue images is a critical step in the 3D analysis of protein expression. Because the distance between images (~4-5μm thickness of a tissue section is nearly the size of the objects of interest (~10-20μm cancer cell nucleus, a given object is often not present in both of two adjacent images. Without consistent correspondence of objects between images, registration becomes a difficult task. This work assesses the feasibility of current registration techniques for such images. Methods: We generated high resolution synthetic 3-D image data sets emulating the constraints in real data. We applied multiple registration methods to the synthetic image data sets and assessed the registration performance of three techniques (i.e., mutual information (MI, kernel density estimate (KDE method [1], and principal component analysis (PCA at various slice thicknesses (with increments of 1μm in order to quantify the limitations of each method. Results: Our analysis shows that PCA, when combined with the KDE method based on nuclei centers, aligns images corresponding to 5μm thick sections with acceptable accuracy. We also note that registration error increases rapidly with increasing distance between images, and that the choice of feature points which are conserved between slices improves performance. Conclusions: We used simulation to help select appropriate features and methods for image registration by estimating best-case-scenario errors for given data constraints in histological images. The results of this study suggest that much of the difficulty of stained tissue registration can be reduced to the problem of accurately identifying feature points, such as the center of nuclei.

  11. Computer simulation of high resolution transmission electron micrographs: theory and analysis

    International Nuclear Information System (INIS)

    Kilaas, R.

    1985-03-01

    Computer simulation of electron micrographs is an invaluable aid in their proper interpretation and in defining optimum conditions for obtaining images experimentally. Since modern instruments are capable of atomic resolution, simulation techniques employing high precision are required. This thesis makes contributions to four specific areas of this field. First, the validity of a new method for simulating high resolution electron microscope images has been critically examined. Second, three different methods for computing scattering amplitudes in High Resolution Transmission Electron Microscopy (HRTEM) have been investigated as to their ability to include upper Laue layer (ULL) interaction. Third, a new method for computing scattering amplitudes in high resolution transmission electron microscopy has been examined. Fourth, the effect of a surface layer of amorphous silicon dioxide on images of crystalline silicon has been investigated for a range of crystal thicknesses varying from zero to 2 1/2 times that of the surface layer

  12. Evaluation of PCR and high-resolution melt curve analysis for differentiation of Salmonella isolates.

    Science.gov (United States)

    Saeidabadi, Mohammad Sadegh; Nili, Hassan; Dadras, Habibollah; Sharifiyazdi, Hassan; Connolly, Joanne; Valcanis, Mary; Raidal, Shane; Ghorashi, Seyed Ali

    2017-06-01

    Consumption of poultry products contaminated with Salmonella is one of the major causes of foodborne diseases worldwide and therefore detection and differentiation of Salmonella spp. in poultry is important. In this study, oligonucleotide primers were designed from hemD gene and a PCR followed by high-resolution melt (HRM) curve analysis was developed for rapid differentiation of Salmonella isolates. Amplicons of 228 bp were generated from 16 different Salmonella reference strains and from 65 clinical field isolates mainly from poultry farms. HRM curve analysis of the amplicons differentiated Salmonella isolates and analysis of the nucleotide sequence of the amplicons from selected isolates revealed that each melting curve profile was related to a unique DNA sequence. The relationship between reference strains and tested specimens was also evaluated using a mathematical model without visual interpretation of HRM curves. In addition, the potential of the PCR-HRM curve analysis was evaluated for genotyping of additional Salmonella isolates from different avian species. The findings indicate that PCR followed by HRM curve analysis provides a rapid and robust technique for genotyping of Salmonella isolates to determine the serovar/serotype.

  13. High resolution respirometry analysis of polyethylenimine-mediated mitochondrial energy crisis and cellular stress

    DEFF Research Database (Denmark)

    Hall, Arnaldur; Larsen, Anna Karina; Parhamifar, Ladan

    2013-01-01

    and spectrophotometry analysis of cytochrome c oxidase activity we were able to identify complex IV (cytochrome c oxidase) as a likely specific site of PEI mediated inhibition within the electron transport system. Unraveling the mechanisms of PEI-mediated mitochondrial energy crisis is central for combinatorial design...... of PEI-mediated plasma membrane damage and subsequent ATP leakage to the extracellular medium. Studies with freshly isolated mouse liver mitochondria corroborated with bioenergetic findings and demonstrated parallel polycation concentration- and time-dependent changes in state 2 and state 4o oxygen flux...... as well as lowered ADP phosphorylation (state 3) and mitochondrial ATP synthesis. Polycation-mediated reduction of electron transport system activity was further demonstrated in 'broken mitochondria' (freeze-thawed mitochondrial preparations). Moreover, by using both high-resolution respirometry...

  14. High Spatial Resolution Analysis of Fungal Cell Biochemistry: Bridging the Analytical Gap using Synchrotron FTIR Spectromicroscopy

    International Nuclear Information System (INIS)

    Kaminskyj, S.; Konstantin, J.; Szeghalmi, A.; Gough, K.

    2008-01-01

    Fungi impact humans and the environment in many ways, for good and ill. Some fungi support the growth of terrestrial plants or are used in biotechnology, and yet others are established or emerging pathogens. In some cases, the same organism may play different roles depending on the context or the circumstance. A better understanding of the relationship between fungal biochemical composition as related to the fungal growth environment is essential if we are to support or control their activities. Synchrotron FTIR (sFTIR) spectromicroscopy of fungal hyphae is a major new tool for exploring cell composition at a high spatial resolution. Brilliant synchrotron light is essential for this analysis due to the small size of fungal hyphae. sFTIR biochemical characterization of subcellular variation in hyphal composition will allow detailed exploration of fungal responses to experimental treatments and to environmental factors.

  15. Neutron activation analysis of high purity silver using high resolution gamma-spectrometry

    International Nuclear Information System (INIS)

    Gilbert, E.N.; Veriovkin, G.V.; Botchkaryov, B.N.; Godovikov, A.A.; Zhavoronkov, V.Ya.; Mikhailov, V.A.

    1975-01-01

    A method of neutron activation determination of microimpurities in high purity silver has been developed. For matrix activity separation the extraction of silver by dibuthylsulfide /DBS/ was employed. The purification coefficient was 10 8 after triple extraction. To study the behaviour of microimpurities in the extraction procedure and to determine their chemical yields some tracer experiments were undertaken with radionuclides of Na, Se, Fe, Co, Cu, As, Sc, Te, Zr, Hf, Mo, W, Cd, In, Sb, La, Ce, Eu, Ta, Re, Ir, Ru. All the elements studied were found to remain in the aqueous phase up to 96-99% after triple extraction with DBS. To estimate the accuracy of the method and to study the mutual influence of the elements in the sample in various relative amounts on the accuracy of the analysis, a number of experiments of ''added-found'' type was performed and the results were treated statistically. In these experiments model mixtures of 30 nuclides were analysed after triple DBS extraction. The t-criterion values for the confidence interval at P=0.95 show the absence of systematic errors. Variation coefficient values do not exceed 15%. Using Ge/Li/ detector it was possible to determine 30 elements simultaneously in silver samples. (T.G.)

  16. Multi-group transport methods for high-resolution neutron activation analysis

    International Nuclear Information System (INIS)

    Burns, K. A.; Smith, L. E.; Gesh, C. J.; Shaver, M. W.

    2009-01-01

    The accurate and efficient simulation of coupled neutron-photon problems is necessary for several important radiation detection applications. Examples include the detection of nuclear threats concealed in cargo containers and prompt gamma neutron activation analysis for nondestructive determination of elemental composition of unknown samples. In these applications, high-resolution gamma-ray spectrometers are used to preserve as much information as possible about the emitted photon flux, which consists of both continuum and characteristic gamma rays with discrete energies. Monte Carlo transport is the most commonly used modeling tool for this type of problem, but computational times for many problems can be prohibitive. This work explores the use of multi-group deterministic methods for the simulation of neutron activation problems. Central to this work is the development of a method for generating multi-group neutron-photon cross-sections in a way that separates the discrete and continuum photon emissions so that the key signatures in neutron activation analysis (i.e., the characteristic line energies) are preserved. The mechanics of the cross-section preparation method are described and contrasted with standard neutron-gamma cross-section sets. These custom cross-sections are then applied to several benchmark problems. Multi-group results for neutron and photon flux are compared to MCNP results. Finally, calculated responses of high-resolution spectrometers are compared. Preliminary findings show promising results when compared to MCNP. A detailed discussion of the potential benefits and shortcomings of the multi-group-based approach, in terms of accuracy, and computational efficiency, is provided. (authors)

  17. High-resolution copy number variation analysis of schizophrenia in Japan.

    Science.gov (United States)

    Kushima, I; Aleksic, B; Nakatochi, M; Shimamura, T; Shiino, T; Yoshimi, A; Kimura, H; Takasaki, Y; Wang, C; Xing, J; Ishizuka, K; Oya-Ito, T; Nakamura, Y; Arioka, Y; Maeda, T; Yamamoto, M; Yoshida, M; Noma, H; Hamada, S; Morikawa, M; Uno, Y; Okada, T; Iidaka, T; Iritani, S; Yamamoto, T; Miyashita, M; Kobori, A; Arai, M; Itokawa, M; Cheng, M-C; Chuang, Y-A; Chen, C-H; Suzuki, M; Takahashi, T; Hashimoto, R; Yamamori, H; Yasuda, Y; Watanabe, Y; Nunokawa, A; Someya, T; Ikeda, M; Toyota, T; Yoshikawa, T; Numata, S; Ohmori, T; Kunimoto, S; Mori, D; Iwata, N; Ozaki, N

    2017-03-01

    Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (history of congenital/developmental phenotypes, and the rate of treatment resistance was significantly higher (odds ratio=2.79, P=0.0036). We found more severe clinical manifestations in patients with two clinically significant CNVs. Gene set analysis replicated previous findings (e.g., synapse, calcium signaling) and identified novel biological pathways including oxidative stress response, genomic integrity, kinase and small GTPase signaling. Furthermore, involvement of multiple SCZ candidate genes and biological pathways in the pathogenesis of SCZ was suggested in established SCZ-associated CNV loci. Our study shows the high genetic heterogeneity of SCZ and its clinical features and raises the possibility that genomic instability is involved in its pathogenesis, which may be related to the increased burden of de novo CNVs and variable expressivity of CNVs.

  18. SAMPO 90 - High resolution interactive gamma spectrum analysis including automation with macros

    International Nuclear Information System (INIS)

    Aarnio, P.A.; Nikkinen, M.T.; Routti, J.T.

    1991-01-01

    SAMPO 90 is a high performance gamma spectrum analysis program for personal computers. It uses high resolution color graphics to display calibrations, spectra, fitting results as multiplet components, and analysis results. All the analysis phases can be done either under full interactive user control or by using macros for automated measurement and analysis sequences including the control of MCAs and sample changers. Semi-automated calibrations for peak shapes (Gaussian with exponential tails), detector efficiency, and energy are available with a possibility for user intervention through interactive graphics. Accurate peak area determination of even the most complex multiplets, of up to 32 components, is accomplished using linear, non-linear and mixed mode fitting, where the component energies and areas can be either frozen or allowed to float in arbitrary combinations. Nuclide identification is done using associated lines techniques which allow interference correction for fully overlapping peaks. Peaked Background Subtraction can be performed and Minimum Detectable Activities calculated. Attenuation corrections can be taken into account in detector efficiency calculation. The most common PC-based MCA spectrum formats (Canberra S100, Ortec ACE, Nucleus PCA, ND AccuSpec) are supported as well as ASCII spectrum files. A gamma-line library is included together with an editor for user configurable libraries. The analysis reports and program parameters are fully customizable. Function key macros can be used to automate the most common analysis procedures. Small batch type modules are additionally available for routine work. SAMPO 90 is a result of over twenty man years of programming and contains 25,000 lines of Fortran, 10,000 lines of C, and 12,000 lines of assembler

  19. High-resolution melting analysis for prenatal diagnosis of beta-thalassemia in northern Thailand.

    Science.gov (United States)

    Charoenkwan, Pimlak; Sirichotiyakul, Supatra; Phusua, Arunee; Suanta, Sudjai; Fanhchaksai, Kanda; Sae-Tung, Rattika; Sanguansermsri, Torpong

    2017-12-01

    High-resolution melting (HRM) analysis is a rapid mutation analysis which assesses the pattern of reduction of fluorescence signal after subjecting the amplified PCR product with saturated fluorescence dye to an increasing temperature. We used HRM analysis for prenatal diagnosis of beta-thalassemia disease in northern Thailand. Five PCR-HRM protocols were used to detect point mutations in five different segments of the beta-globin gene, and one protocol to detect the 3.4 kb beta-globin deletion. We sought to characterize the mutations in carriers and to enable prenatal diagnosis in 126 couples at risk of having a fetus with beta-thalassemia disease. The protocols identified 18 common mutations causing beta-thalassemia, including the rare codon 132 (A-T) mutation. Each mutation showed a specific HRM pattern and all results were in concordance with those from direct DNA sequencing or gap-PCR methods. In cases of beta-thalassemia disease resulting from homozygosity for a mutation or compound heterozygosity for two mutations on the same amplified segment, the HRM patterns were different to those of a single mutation and were specific for each combination. HRM analysis is a simple and useful method for mutation identification in beta-thalassemia carriers and prenatal diagnosis of beta-thalassemia in northern Thailand.

  20. High resolution backscattering instruments

    International Nuclear Information System (INIS)

    Coldea, R.

    2001-01-01

    The principle of operation of indirect-geometry time-of-flight spectrometers are presented, including the IRIS at the ISIS spallation neutron source. The key features that make those types of spectrometers ideally suited for low-energy spectroscopy are: high energy resolution over a wide dynamic range, and simultaneous measurement over a large momentum transfer range provided by the wide angular detector coverage. To exemplify these features are discussed of single-crystal experiments of the spin dynamics in the two-dimensional frustrated quantum magnet Cs 2 CuCl 4 . (R.P.)

  1. Ames S-32 O-16 O-18 Line List for High-Resolution Experimental IR Analysis

    Science.gov (United States)

    Huang, Xinchuan; Schwenke, David W.; Lee, Timothy J.

    2016-01-01

    By comparing to the most recent experimental data and spectra of the SO2 628 ?1/?3 bands (see Ulenikov et al., JQSRT 168 (2016) 29-39), this study illustrates the reliability and accuracy of the Ames-296K SO2 line list, which is accurate enough to facilitate such high-resolution spectroscopic analysis. The SO2 628 IR line list is computed on a recently improved potential energy surface (PES) refinement, denoted Ames-Pre2, and the published purely ab initio CCSD(T)/aug-cc-pVQZ dipole moment surface. Progress has been made in both energy level convergence and rovibrational quantum number assignments agreeing with laboratory analysis models. The accuracy of the computed 628 energy levels and line list is similar to what has been achieved and reported for SO2 626 and 646, i.e. 0.01-0.03 cm(exp -1) for bands up to 5500 cm(exp -1). During the comparison, we found some discrepancies in addition to overall good agreements. The three-IR-list based feature-by-feature analysis in a 0.25 cm(exp -1) spectral window clearly demonstrates the power of the current Ames line lists with new assignments, correction of some errors, and intensity contributions from varied sources including other isotopologues. We are inclined to attribute part of detected discrepancies to an incomplete experimental analysis and missing intensity in the model. With complete line position, intensity, and rovibrational quantum numbers determined at 296 K, spectroscopic analysis is significantly facilitated especially for a spectral range exhibiting such an unusually high density of lines. The computed 628 rovibrational levels and line list are accurate enough to provide alternatives for the missing bands or suspicious assignments, as well as helpful to identify these isotopologues in various celestial environments. The next step will be to revisit the SO2 828 and 646 spectral analyses.

  2. An Object-Based Image Analysis Approach for Detecting Penguin Guano in very High Spatial Resolution Satellite Images

    OpenAIRE

    Chandi Witharana; Heather J. Lynch

    2016-01-01

    The logistical challenges of Antarctic field work and the increasing availability of very high resolution commercial imagery have driven an interest in more efficient search and classification of remotely sensed imagery. This exploratory study employed geographic object-based analysis (GEOBIA) methods to classify guano stains, indicative of chinstrap and Adélie penguin breeding areas, from very high spatial resolution (VHSR) satellite imagery and closely examined the transferability of knowle...

  3. NLTE ANALYSIS OF HIGH-RESOLUTION H -BAND SPECTRA. II. NEUTRAL MAGNESIUM

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Junbo; Shi, Jianrong; Liu, Chao [Key Laboratory of Optical Astronomy, National Astronomical Observatories, Chinese Academy of Sciences, A20 Datun Road, Chaoyang District, Beijing 100012 (China); Pan, Kaike [Apache Point Observatory and New Mexico State University, P.O. Box 59, Sunspot, NM 88349-0059 (United States); Prieto, Carlos Allende, E-mail: sjr@bao.ac.cn [Instituto de Astrofísica de Canarias, E-38205 La Laguna, Tenerife (Spain)

    2017-01-20

    Aiming at testing the validity of our magnesium atomic model and investigating the effects of non-local thermodynamical equilibrium (NLTE) on the formation of the H -band neutral magnesium lines, we derive the differential Mg abundances from selected transitions for 13 stars either adopting or relaxing the assumption of local thermodynamical equilibrium (LTE). Our analysis is based on high-resolution and high signal-to-noise ratio H -band spectra from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) and optical spectra from several instruments. The absolute differences between the Mg abundances derived from the two wavelength bands are always less than 0.1 dex in the NLTE analysis, while they are slightly larger for the LTE case. This suggests that our Mg atomic model is appropriate for investigating the NLTE formation of the H -band Mg lines. The NLTE corrections for the Mg i H -band lines are sensitive to the surface gravity, becoming larger for smaller log g values, and strong lines are more susceptible to departures from LTE. For cool giants, NLTE corrections tend to be negative, and for the strong line at 15765 Å they reach −0.14 dex in our sample, and up to −0.22 dex for other APOGEE stars. Our results suggest that it is important to include NLTE corrections in determining Mg abundances from the H -band Mg i transitions, especially when strong lines are used.

  4. Identification of Uvaria sp by barcoding coupled with high-resolution melting analysis (Bar-HRM).

    Science.gov (United States)

    Osathanunkul, M; Madesis, P; Ounjai, S; Pumiputavon, K; Somboonchai, R; Lithanatudom, P; Chaowasku, T; Wipasa, J; Suwannapoom, C

    2016-01-13

    DNA barcoding, which was developed about a decade ago, relies on short, standardized regions of the genome to identify plant and animal species. This method can be used to not only identify known species but also to discover novel ones. Numerous sequences are stored in online databases worldwide. One of the ways to save cost and time (by omitting the sequencing step) in species identification is to use available barcode data to design optimized primers for further analysis, such as high-resolution melting analysis (HRM). This study aimed to determine the effectiveness of the hybrid method Bar-HRM (DNA barcoding combined with HRM) to identify species that share similar external morphological features, rather than conduct traditional taxonomic identification that require major parts (leaf, flower, fruit) of the specimens. The specimens used for testing were those, which could not be identified at the species level and could either be Uvaria longipes or Uvaria wrayias, indicated by morphological identification. Primer pairs derived from chloroplast regions (matK, psbA-trnH, rbcL, and trnL) were used in the Bar-HRM. The results obtained from psbA-trnH primers were good enough to help in identifying the specimen while the rest were not. Bar-HRM analysis was proven to be a fast and cost-effective method for plant species identification.

  5. Application of high-resolution melting analysis for authenticity testing of valuable Dendrobium commercial products.

    Science.gov (United States)

    Dong, Xiaoman; Jiang, Chao; Yuan, Yuan; Peng, Daiyin; Luo, Yuqin; Zhao, Yuyang; Huang, Luqi

    2018-01-01

    The accurate identification of botanical origin in commercial products is important to ensure food authenticity and safety for consumers. The Dendrobium species have long been commercialised as functional food supplements and herbal medicines in Asia. Three valuable Dendrobium species, namely Dendrobium officinale, D. huoshanense and D. moniliforme, are often mutually adulterated in trade products in pursuit of higher profit. In this paper, a rapid and reliable semi-quantitative method for identifying the botanical origin of Dendrobium products in terminal markets was developed using high-resolution melting (HRM) analysis with specific primer pairs to target the trnL-F region. The HRM analysis method detected amounts of D. moniliforme adulterants as low as 1% in D. huoshanense or D. officinale products. The results have demonstrated that HRM analysis is a fast and effective tool for the differentiation of these Dendrobium species both for their authenticity as well as for the semi-quantitative determination of the purity of their processed products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  6. Analysis of corrosion layers in ancient Roman silver coins with high resolution surface spectroscopic techniques

    Energy Technology Data Exchange (ETDEWEB)

    Keturakis, Christopher J. [Operando Molecular Spectroscopy and Catalysis Research Laboratory, Department of Chemical Engineering, Lehigh University, Bethlehem, PA 18015 (United States); Notis, Ben [Brandeis University, Waltham, MA 02453 (United States); Blenheim, Alex [Department of Mechanical Engineering, Pennsylvania State University, College Park, PA 16802 (United States); Miller, Alfred C.; Pafchek, Rob [Zettlemoyer Center for Surface Studies, Lehigh University, Bethlehem, PA 18015 (United States); Notis, Michael R., E-mail: mrn1@lehigh.edu [Department of Materials Science and Engineering, Lehigh University, Bethlehem, PA 18015 (United States); Wachs, Israel E., E-mail: iew0@lehigh.edu [Operando Molecular Spectroscopy and Catalysis Research Laboratory, Department of Chemical Engineering, Lehigh University, Bethlehem, PA 18015 (United States)

    2016-07-15

    Highlights: • Five ancient silver alloy coins (225 BCE–244 CE) were analyzed using surface characterization techniques. • Both destructive and non-destructive surface characterization methods were developed. • Alloying with copper, even in small amounts, leads to the formation of an outer Cu{sub 2}O corrosion layer. - Abstract: Determination of the microchemistry of surface corrosion layers on ancient silver alloy coins is important both in terms of understanding the nature of archaeological environmental conditions to which these ancient coins were exposed and also to help in their conservation. In this present study, five ancient silver alloy coins (225 BCE–244 CE) were used as test vehicles to measure their immediate surface microchemistry and evaluate the appropriateness and limitations of High Sensitivity-Low Energy Ion Scattering Spectroscopy (HS-LEIS, 0.3 nm depth analysis), High Resolution-X-ray Photoelectron Spectroscopy (HR-XPS, 1–3 nm depth analysis) and High Resolution-Raman Spectroscopy (HR-Raman, ∼1000 nm depth analysis). Additional information about the deeper corrosion layers, up to ∼300–1000 nm, was provided by dynamic HS-LEIS and HR-Raman spectroscopy. While not archeologically significant, the use of these coins of small commercial value provides data that is more representative of the weaker signals typically obtained from ancient corroded objects, which can be in stark contrast to pristine data often obtained from carefully prepared alloys of known composition. The oldest coins, from 225 to 214 BCE, possessed an outermost surface layer containing Cu{sub 2}O, Na, Al, Pb, and adsorbed hydrocarbons, while the more recent coins, from 98 to 244 CE, contained Cu{sub 2}O, Ag, N, F, Na, Al, S, Cl, and adsorbed hydrocarbons in similar corresponding surface layers. It thus appears that alloying with copper, even in small amounts, leads to the formation of an outer Cu{sub 2}O layer. Depth profiling revealed the presence of K, Na, Cl, and

  7. Analysis of corrosion layers in ancient Roman silver coins with high resolution surface spectroscopic techniques

    International Nuclear Information System (INIS)

    Keturakis, Christopher J.; Notis, Ben; Blenheim, Alex; Miller, Alfred C.; Pafchek, Rob; Notis, Michael R.; Wachs, Israel E.

    2016-01-01

    Highlights: • Five ancient silver alloy coins (225 BCE–244 CE) were analyzed using surface characterization techniques. • Both destructive and non-destructive surface characterization methods were developed. • Alloying with copper, even in small amounts, leads to the formation of an outer Cu 2 O corrosion layer. - Abstract: Determination of the microchemistry of surface corrosion layers on ancient silver alloy coins is important both in terms of understanding the nature of archaeological environmental conditions to which these ancient coins were exposed and also to help in their conservation. In this present study, five ancient silver alloy coins (225 BCE–244 CE) were used as test vehicles to measure their immediate surface microchemistry and evaluate the appropriateness and limitations of High Sensitivity-Low Energy Ion Scattering Spectroscopy (HS-LEIS, 0.3 nm depth analysis), High Resolution-X-ray Photoelectron Spectroscopy (HR-XPS, 1–3 nm depth analysis) and High Resolution-Raman Spectroscopy (HR-Raman, ∼1000 nm depth analysis). Additional information about the deeper corrosion layers, up to ∼300–1000 nm, was provided by dynamic HS-LEIS and HR-Raman spectroscopy. While not archeologically significant, the use of these coins of small commercial value provides data that is more representative of the weaker signals typically obtained from ancient corroded objects, which can be in stark contrast to pristine data often obtained from carefully prepared alloys of known composition. The oldest coins, from 225 to 214 BCE, possessed an outermost surface layer containing Cu 2 O, Na, Al, Pb, and adsorbed hydrocarbons, while the more recent coins, from 98 to 244 CE, contained Cu 2 O, Ag, N, F, Na, Al, S, Cl, and adsorbed hydrocarbons in similar corresponding surface layers. It thus appears that alloying with copper, even in small amounts, leads to the formation of an outer Cu 2 O layer. Depth profiling revealed the presence of K, Na, Cl, and S as key

  8. High-resolution melting-curve (HRM) analysis for C. meleagridis identification in stool samples.

    Science.gov (United States)

    Chelbi, Hanen; Essid, Rym; Jelassi, Refka; Bouzekri, Nesrine; Zidi, Ines; Ben Salah, Hamza; Mrad, Ilhem; Ben Sghaier, Ines; Abdelmalek, Rym; Aissa, Sameh; Bouratbine, Aida; Aoun, Karim

    2018-02-01

    Cryptosporidiosis represents a major public health problem. This infection, caused by a protozoan parasite of the genus Cryptosporidium, has been reported worldwide as a frequent cause of diarrhoea. In the immunocompetent host, the typical watery diarrhea can be self-limiting. However, it is severe and chronic, in the immunocompromised host and may cause death. Cryptosporidium spp. are coccidians, which complete their life cycle in both humans and animals. The two species C. hominis and C. parvum are the major cause of human infection. Compared to studies on C. hominis and C. parvum, only a few studies have developed methods to identify C. meleagridis. To develop a new real time PCR-coupled High resolution melting assay allowing the detection for C. meleagridis, in addition of the other dominant species (C. hominis and C. parvum). The polymorphic sequence on the dihydrofolate reductase gene (DHFR) of three species was sequenced to design primers pair and establish a sensitive real-time PCR coupled to a high-resolution melting-curve (HRM) analysis method, allowing the detection of Cryptosporidium sp. and discrimination between three prevalent species in Tunisia. We analyzed a collection of 42 archived human isolates of the three studied species. Real-time PCR coupled to HRM assay allowed detection of Cryptosporidium, using the new designed primers, and basing on melting profile, we can distinguish C. meleagridis species in addition to C. parvum and C. hominis. We developed a qPCR-HRM assay that allows Cryptosporidium genotyping. This method is sensitive and able to distinguish three Cryptosporidium species. Copyright © 2017. Published by Elsevier Ltd.

  9. MARVEL analysis of the measured high-resolution spectra of 14NH3

    International Nuclear Information System (INIS)

    Al Derzi, Afaf R.; Furtenbacher, Tibor; Tennyson, Jonathan; Yurchenko, Sergei N.; Császár, Attila G.

    2015-01-01

    Accurate, experimental rotational–vibrational energy levels and line positions, with associated labels and uncertainties, are reported for the ground electronic state of the symmetric-top 14 NH 3 molecule. All levels and lines are based on critically reviewed and validated high-resolution experimental spectra taken from 56 literature sources. The transition data are in the 0.7–17 000 cm −1 region, with a large gap between 7000 and 15 000 cm −1 . The MARVEL (Measured Active Rotational–Vibrational Energy Levels) algorithm is used to determine the energy levels. Out of the 29 450 measured transitions 10 041 and 18 947 belong to ortho- and para- 14 NH 3 , respectively. A careful analysis of the related experimental spectroscopic network (SN) allows 28 530 of the measured transitions to be validated, 18 178 of these are unique, while 462 transitions belong to floating components. Despite the large number of spectroscopic measurements published over the last 80 years, the transitions determine only 30 vibrational band origins of 14 NH 3 , 8 for ortho- and 22 for para- 14 NH 3 . The highest J value, where J stands for the rotational quantum number, for which an energy level is validated is 31. The number of experimental-quality ortho- and para- 14 NH 3 rovibrational energy levels is 1724 and 3237, respectively. The MARVEL energy levels are checked against ones in the BYTe first-principles database, determined previously. The lists of validated lines and levels for 14 NH 3 are deposited in the Supporting Information to this paper. Combination of the MARVEL energy levels with first-principles absorption intensities yields a huge number of experimental-quality rovibrational lines, which should prove to be useful for the understanding of future complex high-resolution spectroscopy on 14 NH 3 ; these lines are also deposited in the Supporting Information to this paper

  10. MARVEL analysis of the measured high-resolution spectra of 14NH3

    Science.gov (United States)

    Al Derzi, Afaf R.; Furtenbacher, Tibor; Tennyson, Jonathan; Yurchenko, Sergei N.; Császár, Attila G.

    2015-08-01

    Accurate, experimental rotational-vibrational energy levels and line positions, with associated labels and uncertainties, are reported for the ground electronic state of the symmetric-top 14NH3 molecule. All levels and lines are based on critically reviewed and validated high-resolution experimental spectra taken from 56 literature sources. The transition data are in the 0.7-17 000 cm-1 region, with a large gap between 7000 and 15 000 cm-1. The MARVEL (Measured Active Rotational-Vibrational Energy Levels) algorithm is used to determine the energy levels. Out of the 29 450 measured transitions 10 041 and 18 947 belong to ortho- and para-14NH3, respectively. A careful analysis of the related experimental spectroscopic network (SN) allows 28 530 of the measured transitions to be validated, 18 178 of these are unique, while 462 transitions belong to floating components. Despite the large number of spectroscopic measurements published over the last 80 years, the transitions determine only 30 vibrational band origins of 14NH3, 8 for ortho- and 22 for para-14NH3. The highest J value, where J stands for the rotational quantum number, for which an energy level is validated is 31. The number of experimental-quality ortho- and para-14NH3 rovibrational energy levels is 1724 and 3237, respectively. The MARVEL energy levels are checked against ones in the BYTe first-principles database, determined previously. The lists of validated lines and levels for 14NH3 are deposited in the Supporting Information to this paper. Combination of the MARVEL energy levels with first-principles absorption intensities yields a huge number of experimental-quality rovibrational lines, which should prove to be useful for the understanding of future complex high-resolution spectroscopy on 14NH3; these lines are also deposited in the Supporting Information to this paper.

  11. Reliability of an Automated High-Resolution Manometry Analysis Program across Expert Users, Novice Users, and Speech-Language Pathologists

    Science.gov (United States)

    Jones, Corinne A.; Hoffman, Matthew R.; Geng, Zhixian; Abdelhalim, Suzan M.; Jiang, Jack J.; McCulloch, Timothy M.

    2014-01-01

    Purpose: The purpose of this study was to investigate inter- and intrarater reliability among expert users, novice users, and speech-language pathologists with a semiautomated high-resolution manometry analysis program. We hypothesized that all users would have high intrarater reliability and high interrater reliability. Method: Three expert…

  12. ERIC First Analysis: Agricultural Policy. 1986-87 National High School Debate Resolutions.

    Science.gov (United States)

    Wagner, David L.; Fraleigh, Douglas

    Designed to serve as a framework in which high school debate students, coaches, and judges can evaluate the issues, arguments, and evidence concerning which agricultural policies best serve the United States, this booklet provides guidelines for research on the 1986-87 debate resolutions selected by the National Federation of State High School…

  13. Targeting high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction-nuclear magnetic resonance analysis with high-resolution radical scavenging profiles - bioactive secondary metabolites from the endophytic fungus Penicillium namyslowskii

    DEFF Research Database (Denmark)

    Wubshet, Sileshi Gizachew; Nyberg, Nils; Tejesvi, Mysore V.

    2013-01-01

    The high-resolution radical scavenging profile of an extract of the endophytic fungus Penicillium namyslowskii was used to target analysis by high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction-nuclear magnetic resonance spectroscopy, i.e., HPLC...... NMR probe designed for 1.7-mm NMR tubes. To further explore the potential of the above HPLC-HRMS-SPE-NMR platform for analysis of endophytic extracts, six peaks displaying no radical scavenging activity were also analyzed. This allowed unambiguous identification of six metabolites, i...... and griseofulvin, directly from crude extract via HPLC-HRMS-SPE-NMR. Dechlorodehydrogriseofulvin was reported for the first time from nature....

  14. High-resolution SNP array analysis of patients with developmental disorder and normal array CGH results

    Directory of Open Access Journals (Sweden)

    Siggberg Linda

    2012-09-01

    Full Text Available Abstract Background Diagnostic analysis of patients with developmental disorders has improved over recent years largely due to the use of microarray technology. Array methods that facilitate copy number analysis have enabled the diagnosis of up to 20% more patients with previously normal karyotyping results. A substantial number of patients remain undiagnosed, however. Methods and Results Using the Genome-Wide Human SNP array 6.0, we analyzed 35 patients with a developmental disorder of unknown cause and normal array comparative genomic hybridization (array CGH results, in order to characterize previously undefined genomic aberrations. We detected no seemingly pathogenic copy number aberrations. Most of the vast amount of data produced by the array was polymorphic and non-informative. Filtering of this data, based on copy number variant (CNV population frequencies as well as phenotypically relevant genes, enabled pinpointing regions of allelic homozygosity that included candidate genes correlating to the phenotypic features in four patients, but results could not be confirmed. Conclusions In this study, the use of an ultra high-resolution SNP array did not contribute to further diagnose patients with developmental disorders of unknown cause. The statistical power of these results is limited by the small size of the patient cohort, and interpretation of these negative results can only be applied to the patients studied here. We present the results of our study and the recurrence of clustered allelic homozygosity present in this material, as detected by the SNP 6.0 array.

  15. High resolution melting analysis: a rapid and accurate method to detect CALR mutations.

    Directory of Open Access Journals (Sweden)

    Cristina Bilbao-Sieyro

    Full Text Available The recent discovery of CALR mutations in essential thrombocythemia (ET and primary myelofibrosis (PMF patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN. We tested the feasibility of high-resolution melting (HRM as a screening method for rapid detection of CALR mutations.CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET.Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34, 14% of persistent thrombocytosis suggestive of MPN (3/21 and none of the secondary thrombocytosis (0/98. Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%.This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations.

  16. High-resolution DNA content analysis of microbiopsy samples in oral lichen planus.

    Science.gov (United States)

    Pentenero, M; Monticone, M; Marino, R; Aiello, C; Marchitto, G; Malacarne, D; Giaretti, W; Gandolfo, S; Castagnola, P

    2017-04-01

    DNA aneuploidy has been reported to be a predictor of poor prognosis in both premalignant and malignant lesions. In oral lichen planus (OLP), this hypothesis remains to be proved. This study aimed to determine the rate of occurrence of DNA aneuploidy in patients with OLP by high-resolution DNA flow cytometry. Patients with OLP were consecutively enrolled. Tissue samples were subdivided for formalin fixation and routine histological assessment and for immediate storage at -20°C for later DNA ploidy analysis, which was performed by DAPI staining of the extracted nuclei and excitation with a UV lamp. The DNA aneuploid sublines were characterized by the DNA Index. A DNA aneuploid status was observed in two of 77 patients with OLP (2.6%). When considering the clinical aspect of the OLP lesions, both DNA aneuploid cases had a reticular clinical aspect. DNA aneuploidy is an uncommon event in OLP and less frequent compared to other non-dysplastic and non-OLP oral potentially malignant disorders. The extremely low rate of DNA aneuploidy could represent an occasional finding or reflect the low rate of malignant transformation observed in patients with OLP even if the real prognostic value of DNA ploidy analysis in patients with OLP remains to be confirmed. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  17. Abundance Analysis of 17 Planetary Nebulae from High-Resolution Optical Spectroscopy

    Science.gov (United States)

    Sherrard, Cameroun G.; Sterling, Nicholas C.; Dinerstein, Harriet L.; Madonna, Simone; Mashburn, Amanda

    2017-06-01

    We present an abundance analysis of 17 planetary nebulae (PNe) observed with the 2D-coudé echelle spectrograph on the 2.7-m Harlan J. Smith telescope at McDonald Observatory. The spectra cover the wavelength range 3600--10,400 Å at a resolution R = 36,700, and are the first high-resolution optical spectra for many objects in our sample. The number of emission lines detected in individual nebulae range from ~125 to over 600. We derive temperatures, densities, and abundances from collisionally-excited lines using the PyNeb package (Luridiana et al. 2015, A&A, 573, A42) and the ionization correction factor scheme of Delgado-Inglada et al. (2014, MNRAS, 440, 536). The abundances of light elements agree with previous estimates for most of the PNe. Several objects exhibit emission lines of refractory elements such as K and Fe, and neutron-capture elements that can be enriched by the s-process. We find that K and Fe are depleted relative to solar by ~0.3--0.7~dex and 1-2 dex, respectively, and find evidence for s-process enrichments in 10 objects. Several objects in our sample exhibit C, N, and O recombination lines that are useful for abundance determinations. These transitions are used to compute abundance discrepancy factors (ADFs), the ratio of ionic abundances derived from permitted lines to those from collisionally-excited transitions. We explore relations among depletion factors, ADFs, s-process enrichment factors, and other nebular stellar and nebular properties. We acknowledge support from NSF awards AST-901432 and AST-0708429.

  18. The dynamics of cyclone clustering in re-analysis and a high-resolution climate model

    Science.gov (United States)

    Priestley, Matthew; Pinto, Joaquim; Dacre, Helen; Shaffrey, Len

    2017-04-01

    Extratropical cyclones have a tendency to occur in groups (clusters) in the exit of the North Atlantic storm track during wintertime, potentially leading to widespread socioeconomic impacts. The Winter of 2013/14 was the stormiest on record for the UK and was characterised by the recurrent clustering of intense extratropical cyclones. This clustering was associated with a strong, straight and persistent North Atlantic 250 hPa jet with Rossby wave-breaking (RWB) on both flanks, pinning the jet in place. Here, we provide for the first time an analysis of all clustered events in 36 years of the ERA-Interim Re-analysis at three latitudes (45˚ N, 55˚ N, 65˚ N) encompassing various regions of Western Europe. The relationship between the occurrence of RWB and cyclone clustering is studied in detail. Clustering at 55˚ N is associated with an extended and anomalously strong jet flanked on both sides by RWB. However, clustering at 65(45)˚ N is associated with RWB to the south (north) of the jet, deflecting the jet northwards (southwards). A positive correlation was found between the intensity of the clustering and RWB occurrence to the north and south of the jet. However, there is considerable spread in these relationships. Finally, analysis has shown that the relationships identified in the re-analysis are also present in a high-resolution coupled global climate model (HiGEM). In particular, clustering is associated with the same dynamical conditions at each of our three latitudes in spite of the identified biases in frequency and intensity of RWB.

  19. High Time Resolution Astrophysics

    CERN Document Server

    Phelan, Don; Shearer, Andrew

    2008-01-01

    High Time Resolution Astrophysics (HTRA) is an important new window to the universe and a vital tool in understanding a range of phenomena from diverse objects and radiative processes. This importance is demonstrated in this volume with the description of a number of topics in astrophysics, including quantum optics, cataclysmic variables, pulsars, X-ray binaries and stellar pulsations to name a few. Underlining this science foundation, technological developments in both instrumentation and detectors are described. These instruments and detectors combined cover a wide range of timescales and can measure fluxes, spectra and polarisation. These advances make it possible for HTRA to make a big contribution to our understanding of the Universe in the next decade.

  20. High resolution ultrasonic densitometer

    International Nuclear Information System (INIS)

    Dress, W.B.

    1983-01-01

    The velocity of torsional stress pulses in an ultrasonic waveguide of non-circular cross section is affected by the temperature and density of the surrounding medium. Measurement of the transit times of acoustic echoes from the ends of a sensor section are interpreted as level, density, and temperature of the fluid environment surrounding that section. This paper examines methods of making these measurements to obtain high resolution, temperature-corrected absolute and relative density and level determinations of the fluid. Possible applications include on-line process monitoring, a hand-held density probe for battery charge state indication, and precise inventory control for such diverse fluids as uranium salt solutions in accountability storage and gasoline in service station storage tanks

  1. Sensitive rapid analysis of iodine-labelled protein mixture on flat substrates with high spatial resolution

    International Nuclear Information System (INIS)

    Zanevskij, Yu.V.; Ivanov, A.B.; Movchan, S.A.; Peshekhonov, V.D.; Chan Dyk Tkhan'; Chernenko, S.P.; Kaminir, L.B.; Krejndlin, Eh.Ya.; Chernyj, A.A.

    1983-01-01

    Usability of rapid analysis by electrophoresis of the admixture of I 125 -labelled proteins on flat samples by means of URAN type installation developed using a multiwire proportional chamber is studied. The sensitivity of the method is better than 200 cpm/cm 2 and the spatial resolution is approximately 1 mm. The procedure of the rapid analysis is no longer than several tens of minutes

  2. High-resolution abundance analysis of red giants in the globular cluster NGC 6522

    Science.gov (United States)

    Barbuy, B.; Chiappini, C.; Cantelli, E.; Depagne, E.; Pignatari, M.; Hirschi, R.; Cescutti, G.; Ortolani, S.; Hill, V.; Zoccali, M.; Minniti, D.; Trevisan, M.; Bica, E.; Gómez, A.

    2014-10-01

    Context. The [Sr/Ba] and [Y/Ba] scatter observed in some galactic halo stars that are very metal-poor and in a few individual stars of the oldest known Milky Way globular cluster NGC 6522 have been interpreted as evidence of early enrichment by massive fast-rotating stars (spinstars). Because NGC 6522 is a bulge globular cluster, the suggestion was that not only the very-metal poor halo stars, but also bulge stars at [Fe/H] ~ -1 could be used as probes of the stellar nucleosynthesis signatures from the earlier generations of massive stars, but at much higher metallicity. For the bulge the suggestions were based on early spectra available for stars in NGC 6522, with a medium resolution of R ~ 22 000 and a moderate signal-to-noise ratio. Aims: The main purpose of this study is to re-analyse the NGC 6522 stars reported previously by using new high-resolution (R ~ 45 000) and high signal-to-noise spectra (S/N > 100). We aim at re-deriving their stellar parameters and elemental ratios, in particular the abundances of the neutron-capture s-process-dominated elements such as Sr, Y, Zr, La, and Ba, and of the r-element Eu. Methods: High-resolution spectra of four giants belonging to the bulge globular cluster NGC 6522 were obtained at the 8m VLT UT2-Kueyen telescope with the UVES spectrograph in FLAMES-UVES configuration. The spectroscopic parameters were derived based on the excitation and ionization equilibrium of Fe i and Fe ii. Results: Our analysis confirms a metallicity [Fe/H] = -0.95 ± 0.15 for NGC 6522 and the overabundance of the studied stars in Eu (with +0.2 < [Eu/Fe] < + 0.4) and alpha-elements O and Mg. The neutron-capture s-element-dominated Sr, Y, Zr, Ba, and La now show less pronounced variations from star to star. Enhancements are in the range 0.0 < [Sr/Fe] < +0.4, +0.23 < [Y/Fe] < +0.43, 0.0 < [Zr/Fe] < +0.4, 0.0 < [La/Fe] < +0.35, and 0.05 < [Ba/Fe] < +0.55. Conclusions: The very high overabundances of [Y/Fe] previously reported for the four studied

  3. Erythrocyte orientation and lung conductivity analysis with a high temporal resolution FEM model for bioimpedance measurements

    NARCIS (Netherlands)

    Ulbrich, M.; Paluchowski, P.; Muehlsteff, J.; Leonhardt, S.

    2012-01-01

    Impedance cardiography (ICG) is a simple and cheap method to acquirehemodynamic parameters. In this work, the influence of three dynamic physiological sources has been analyzed using a model of the humanthorax with a high temporal resolution. Therefore, simulations havebeen conducted using the

  4. Analysis of high resolution satellite digital data for land use studies ...

    African Journals Online (AJOL)

    High-resolution satellite data can give vital information about land cover, which can lead to better interpretation and classification of land resources. This study examined the relationship between Systeme Probatoire d'Observation de la Terre (SPOT) digital data and land use types in the derived savanna ecosystem of ...

  5. High sensitivity and high resolution element 3D analysis by a combined SIMS–SPM instrument

    Directory of Open Access Journals (Sweden)

    Yves Fleming

    2015-04-01

    Full Text Available Using the recently developed SIMS–SPM prototype, secondary ion mass spectrometry (SIMS data was combined with topographical data from the scanning probe microscopy (SPM module for five test structures in order to obtain accurate chemical 3D maps: a polystyrene/polyvinylpyrrolidone (PS/PVP polymer blend, a nickel-based super-alloy, a titanium carbonitride-based cermet, a reticle test structure and Mg(OH2 nanoclusters incorporated inside a polymer matrix. The examples illustrate the potential of this combined approach to track and eliminate artefacts related to inhomogeneities of the sputter rates (caused by samples containing various materials, different phases or having a non-flat surface and inhomogeneities of the secondary ion extraction efficiencies due to local field distortions (caused by topography with high aspect ratios. In this respect, this paper presents the measured relative sputter rates between PVP and PS as well as in between the different phases of the TiCN cermet.

  6. Cardiovascular coupling analysis with high-resolution joint symbolic dynamics in patients suffering from acute schizophrenia

    International Nuclear Information System (INIS)

    Schulz, Steffen; Tupaika, Nadine; Voss, Andreas; Berger, Sandy; Bär, Karl-Jürgen; Haueisen, Jens

    2013-01-01

    Besides the well-known cardiac risk factors for schizophrenia, increasing concerns have been raised regarding the cardiac side-effects of antipsychotic medications. A bivariate analysis of autonomic regulation, based on cardiovascular coupling, can provide additional information about heart rate (HR) and blood pressure regulatory patterns within the complex interactions of the cardiovascular system. We introduce a new high-resolution coupling analysis method (HRJSD) based on joint symbolic dynamics (JSD), which is characterized by three symbols, a threshold (individual dynamic variability, physiological) for time series transformation and eight coupling pattern families. This is based on a redundancy reduction strategy used to quantify and characterize cardiovascular couplings. In this study, short-term (30 min) HR and systolic blood pressure (SP) time series of 42 unmedicated (UNMED) and 42 medicated patients (MED) suffering from acute schizophrenia were analysed to establish the suitability of the new method for quantifying the effects of antipsychotics on cardiovascular couplings. We were able to demonstrate that HRJSD, applying the threshold based on spontaneous baroreflex sensitivity (BRS) estimation, revealed eight significant pattern families that were able to quantify the anti-cholinergic effects of antipsychotics and the related changes of cardiovascular regulation (coupling) in MED in comparison to UNMED. This was in contrast to the simple JSD, BRS (sequence method) and only partly to standard linear HR variability indices. HRJSD provides strong evidence that autonomic regulation in MED seems to be, to some extent, predominated by invariable HR responses in combination with alternating SP values in contrast to UNMED, indicating an impairment of the baroreflex control feedback loop in MED. Surrogate data analysis was applied to test for the significance and nonlinearity of cardiovascular couplings in the original data due to medical treatment with

  7. High resolution melting analysis (HRM) for the assessment of clonality in feline B-cell lymphomas.

    Science.gov (United States)

    Henrich, Manfred; Scheffold, Svenja; Hecht, Werner; Reinacher, Manfred

    2018-06-01

    Analysis of clonality is gaining importance in diagnosing lymphomas in veterinary medicine. Usually, PCR for the analysis of antigen receptor rearrangement (PARR) is followed by electrophoretic separation of the PCR products. Aim of this study was to test the feasibility of HRM for the assessment of clonality in B-cell lymphomas of cats. High resolution melting analysis differentiates PCR products by their different melting point using the decrease in fluorescence of an intercalating dye during melting of the PCR product. Additionally, the method is easy to use with no post-PCR manipulation of the samples. Forty-seven feline B-cell lymphomas and 31 reactive lymphatic proliferations of cats were investigated by PARR followed either by capillary electrophoresis or an HRM assay. To objectify the interpretation of the HRM results a recently published mathematical approach was applied to the melting curve. To overcome discrepancies between the visual interpretation and the mathematical approach, the latter was modified to include testing of reproducibility and recognition of pseudoclonality. In 11 of 47 lymphoma cases clonal populations were detectable by HRM assay compared to 14 of 47 lymphomas in which clonal populations were detected by capillary electrophoresis assay. Neither of the methods showed a clonal pattern in any of the reactive samples. However, the HRM assay showed a unique pattern in cases of follicular lymphatic hyperplasia that had no corresponding pattern in capillary electrophoresis. The capillary electrophoresis assay could identify 3 lymphomas that were not detected by the HRM assay and is therefore regarded superior to the HRM assay. The comparison however, was hampered by the overall bad performance of the PARR, that might be the consequence of insufficient primer binding due to somatic hypermutation of the binding sites during antigen stimulated proliferation of the B lymphocytes. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. Differentiation of five enterohepatic Helicobacter species by nested PCR with high-resolution melting curve analysis.

    Science.gov (United States)

    Wu, Miaoli; Rao, Dan; Zhu, Yujun; Wang, Jing; Yuan, Wen; Zhang, Yu; Huang, Ren; Guo, Pengju

    2017-04-01

    Enterohepatic Helicobacter species (EHS) are widespread in rodent species around the world. Several studies have demonstrated that infection with EHS can interfere with the outcomes of animal experiments in cancer research and significantly influence the study results. Therefore, it is essential to establish a rapid detection and identification of EHS for biomedical research using laboratory rodents. Our study aimed to develop a rapid and sensitive method to detect and distinguish five enterohepatic Helicobacter species. Nested PCR followed by high-resolution melting curve analysis (HRM) was developed for identification of H. bilis, H. rodentium, H. muridarum, H. typhlonius, as well as H. hepaticus. To validate the accuracy of nested PCR-HRM analysis, quantitative real-time PCR methods for five different enterohepatic Helicobacter species were developed. A total of 50 cecal samples were tested using both nested PCR-HRM analysis and qPCR method. The nested PCR-HRM method could distinguish five enterohepatic Helicobacter species by different melting temperatures. The melting curve were characterized by peaks of 78.7 ± 0.12°C for H. rodentium, 80.51 ± 0.09°C for H. bilis, 81.6 ± 0.1°C for H. typhlonius, 82.11 ± 0.18°C for H. muridarum, and 82.95 ± 0.09°C for H. hepaticus. The nested PCR-HRM assay is a simple, rapid, and cost-effective assay. This assay could be a useful tool for molecular epidemiology study of enterohepatic Helicobacter infection and an attractive alternative for genotyping of enterohepatic Helicobacter species. © 2016 John Wiley & Sons Ltd.

  9. A High Resolution Hydrodynamic Model of Puget Sound to Support Nearshore Restoration Feasibility Analysis and Design

    International Nuclear Information System (INIS)

    Khangaonkar, Tarang; Yang, Zhaoqing

    2011-01-01

    Estuarine and coastal hydrodynamic processes are sometimes neglected in the design and planning of nearshore restoration actions. Despite best intentions, efforts to restore nearshore habitats can result in poor outcomes if circulation and transport which also affect freshwater-saltwater interactions are not properly addressed. Limitations due to current land use can lead to selection of sub-optimal restoration alternatives that may result in undesirable consequences, such as flooding, deterioration of water quality, and erosion, requiring immediate remedies and costly repairs. Uncertainty with achieving restoration goals, such as recovery of tidal exchange, supply of sediment and nutrients, and establishment of fish migration pathways, may be minimized by using numerical models designed for application to the nearshore environment. A high resolution circulation and transport model of the Puget Sound, in the state of Washington, was developed to assist with nearshore habitat restoration design and analysis, and to answer the question 'can we achieve beneficial restoration outcomes at small local scale, as well as at a large estuary-wide scale?' The Puget Sound model is based on an unstructured grid framework to define the complex Puget Sound shoreline using a finite volume coastal ocean model (FVCOM). The capability of the model for simulating the important nearshore processes, such as circulation in complex multiple tidal channels, wetting and drying of tide flats, and water quality and sediment transport as part of restoration feasibility, are illustrated through examples of restoration projects in Puget Sound.

  10. Crackle analysis for chest auscultation and comparison with high-resolution CT findings.

    Science.gov (United States)

    Kawamura, Takeo; Matsumoto, Tsuneo; Tanaka, Nobuyuki; Kido, Shoji; Jiang, Zhongwei; Matsunaga, Naofumi

    2003-01-01

    The purpose of our study was to clarify the correlation between respiratory sounds and the high-resolution CT (HRCT) findings of lung diseases. Respiratory sounds were recorded using a stethoscope in 41 patients with crackles. All had undergone inspiratory and expiratory CT. Subjects included 18 patients with interstitial pneumonia and 23 without interstitial pneumonia. Two parameters, two-cycle duration (2CD) and initial deflection width (IDW) of the "crackle," were induced by time-expanded waveform analysis. Two radiologists independently assessed 11 HRCT findings. An evaluation was carried out to determine whether there was a significant difference in the two parameters between the presence and absence of each HRCT finding. The two parameters of crackles were significantly shorter in the interstitial pneumonia group than the non-interstitial pneumonia group. Ground-glass opacity, honeycombing, lung volume reduction, traction bronchiectasis, centrilobular nodules, emphysematous change, and attenuation and volume change between inspiratory and expiratory CT were correlated with one or two parameters in all patients, whereas the other three findings were not. Among the interstitial pneumonia group, traction bronchiectasis, emphysematous change, and attenuation and volume change between inspiratory and expiratory CT were significantly correlated with one or two parameters. Abnormal respiratory sounds were correlated with some HRCT findings.

  11. Crackle analysis for chest auscultation and comparison with high-resolution CT findings

    International Nuclear Information System (INIS)

    Kawamura, Takeo; Matsumoto, Tsuneo; Tanaka, Nobuyuki; Matsunaga, Naofumi; Kido, Shoji; Jiang Zhongwei

    2003-01-01

    The purpose of our study was to clarify the correlation between respiratory sounds and the high-resolution CT (HRCT) findings of lung diseases. Respiratory sounds were recorded using a stethoscope in 41 patients with crackles. All had undergone inspiratory and expiratory CT. Subjects included 18 patients with interstitial pneumonia and 23 without interstitial pneumonia. Two parameters, two-cycle duration (2CD) and initial deflection width (IDW) of the ''crackle,'' were induced by time-expanded waveform analysis. Two radiologists independently assessed 11 HRCT findings. An evaluation was carried out to determine whether there was a significant difference in the two parameters between the presence and absence of each HRCT finding. The two parameters of crackles were significantly shorter in the interstitial pneumonia group than the non-interstitial pneumonia group. Ground-glass opacity, honeycombing, lung volume reduction, traction bronchiectasis, centrilobular nodules, emphysematous change, and attenuation and volume change between inspiratory and expiratory CT were correlated with one or two parameters in all patients, whereas the other three findings were not. Among the interstitial pneumonia group, traction bronchiectasis, emphysematous change, and attenuation and volume change between inspiratory and expiratory CT were significantly correlated with one or two parameters. Abnormal respiratory sounds were correlated with some HRCT findings. (author)

  12. The high resolution melting analysis (HRM) as a molecular tool for monitoring parasites of the wildlife.

    Science.gov (United States)

    Héritier, Laurent; Verneau, Olivier; Breuil, Gregory; Meistertzheim, Anne-Leila

    2017-04-01

    In an interconnected world, the international pet trade on wild animals is becoming increasingly important. As a consequence, non-native parasite species are introduced, which affect the health of wildlife and contribute to the loss of biodiversity. Because the investigation of parasite diversity within vulnerable host species implies the molecular identification of large samples of parasite eggs, the sequencing of DNA barcodes is time-consuming and costly. Thereby, the objectives of our study were to apply the high resolution melting (HRM) approach for species determination from pools of parasite eggs. Molecular assays were validated on flatworm parasites (polystomes) infecting the Mediterranean pond turtle Mauremys leprosa and the invasive red-eared slider Trachemys scripta elegans in French natural environments. HRM analysis results indicated that double or multiple parasitic infections could be detected from wild animal populations. They also showed that the cycle of parasite eggs production was not regular over time and may depend on several factors, among which the ecological niche and the target species. Thereby, monitoring parasites from wild endangered animals implies periodic parasitological surveys to avoid false negative diagnostics, based solely on eggs production.

  13. Rapid detection and identification of four major Schistosoma species by high-resolution melt (HRM) analysis.

    Science.gov (United States)

    Li, Juan; Zhao, Guang-Hui; Lin, RuiQing; Blair, David; Sugiyama, Hiromu; Zhu, Xing-Quan

    2015-11-01

    Schistosomiasis, caused by blood flukes belonging to several species of the genus Schistosoma, is a serious and widespread parasitic disease. Accurate and rapid differentiation of these etiological agents of animal and human schistosomiasis to species level can be difficult. We report a real-time PCR assay coupled with a high-resolution melt (HRM) assay targeting a portion of the nuclear 18S rDNA to detect, identify, and distinguish between four major blood fluke species (Schistosoma japonicum, Schistosoma mansoni, Schistosoma haematobium, and Schistosoma mekongi). Using this system, the Schistosoma spp. was accurately identified and could also be distinguished from all other trematode species with which they were compared. As little as 10(-5) ng genomic DNA from a Schistosoma sp. could be detected. This process is inexpensive, easy, and can be completed within 3 h. Examination of 21 representative Schistosoma samples from 15 geographical localities in seven endemic countries validated the value of the HRM detection assay and proved its reliability. The melting curves were characterized by peaks of 83.65 °C for S. japonicum and S. mekongi, 85.65 °C for S. mansoni, and 85.85 °C for S. haematobium. The present study developed a real-time PCR coupled with HRM analysis assay for detection and differential identification of S. mansoni, S. haematobium, S. japonicum, and S. mekongi. This method is rapid, sensitive, and inexpensive. It has important implications for epidemiological studies of Schistosoma.

  14. High-resolution surface analysis for extended-range downscaling with limited-area atmospheric models

    Science.gov (United States)

    Separovic, Leo; Husain, Syed Zahid; Yu, Wei; Fernig, David

    2014-12-01

    High-resolution limited-area model (LAM) simulations are frequently employed to downscale coarse-resolution objective analyses over a specified area of the globe using high-resolution computational grids. When LAMs are integrated over extended time frames, from months to years, they are prone to deviations in land surface variables that can be harmful to the quality of the simulated near-surface fields. Nudging of the prognostic surface fields toward a reference-gridded data set is therefore devised in order to prevent the atmospheric model from diverging from the expected values. This paper presents a method to generate high-resolution analyses of land-surface variables, such as surface canopy temperature, soil moisture, and snow conditions, to be used for the relaxation of lower boundary conditions in extended-range LAM simulations. The proposed method is based on performing offline simulations with an external surface model, forced with the near-surface meteorological fields derived from short-range forecast, operational analyses, and observed temperatures and humidity. Results show that the outputs of the surface model obtained in the present study have potential to improve the near-surface atmospheric fields in extended-range LAM integrations.

  15. Geographic information system for fusion and analysis of high-resolution remote sensing and ground data

    Science.gov (United States)

    Freeman, Anthony; Way, Jo Bea; Dubois, Pascale; Leberl, Franz

    1993-01-01

    We seek to combine high-resolution remotely sensed data with models and ground truth measurements, in the context of a Geographical Information System (GIS), integrated with specialized image processing software. We will use this integrated system to analyze the data from two Case Studies, one at a boreal forest site, the other a tropical forest site. We will assess the information content of the different components of the data, determine the optimum data combinations to study biogeophysical changes in the forest, assess the best way to visualize the results, and validate the models for the forest response to different radar wavelengths/polarizations. During the 1990's, unprecedented amounts of high-resolution images from space of the Earth's surface will become available to the applications scientist from the LANDSAT/TM series, European and Japanese ERS-1 satellites, RADARSAT and SIR-C missions. When the Earth Observation Systems (EOS) program is operational, the amount of data available for a particular site can only increase. The interdisciplinary scientist, seeking to use data from various sensors to study his site of interest, may be faced with massive difficulties in manipulating such large data sets, assessing their information content, determining the optimum combinations of data to study a particular parameter, visualizing his results and validating his model of the surface. The techniques to deal with these problems are also needed to support the analysis of data from NASA's current program of Multi-sensor Airborne Campaigns, which will also generate large volumes of data. In the Case Studies outlined in this proposal, we will have somewhat unique data sets. For the Bonanza Creek Experimental Forest (Case 1) calibrated DC-8 SAR (Synthetic Aperture Radar) data and extensive ground truth measurement are already at our disposal. The data set shows documented evidence to temporal change. The Belize Forest Experiment (Case 2) will produce calibrated DC-8 SAR

  16. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer.

    Directory of Open Access Journals (Sweden)

    Shin-ichi Hashimoto

    Full Text Available Massively parallel, tag-based sequencing systems, such as the SOLiD system, hold the promise of revolutionizing the study of whole genome gene expression due to the number of data points that can be generated in a simple and cost-effective manner. We describe the development of a 5'-end transcriptome workflow for the SOLiD system and demonstrate the advantages in sensitivity and dynamic range offered by this tag-based application over traditional approaches for the study of whole genome gene expression. 5'-end transcriptome analysis was used to study whole genome gene expression within a colon cancer cell line, HT-29, treated with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5Aza. More than 20 million 25-base 5'-end tags were obtained from untreated and 5Aza-treated cells and matched to sequences within the human genome. Seventy three percent of the mapped unique tags were associated with RefSeq cDNA sequences, corresponding to approximately 14,000 different protein-coding genes in this single cell type. The level of expression of these genes ranged from 0.02 to 4,704 transcripts per cell. The sensitivity of a single sequence run of the SOLiD platform was 100-1,000 fold greater than that observed from 5'end SAGE data generated from the analysis of 70,000 tags obtained by Sanger sequencing. The high-resolution 5'end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology.

  17. Rapid Detection and Identification of Human Hookworm Infections through High Resolution Melting (HRM) Analysis

    Science.gov (United States)

    Ngui, Romano; Lim, Yvonne A. L.; Chua, Kek Heng

    2012-01-01

    Background Hookworm infections are still endemic in low and middle income tropical countries with greater impact on the socioeconomic and public health of the bottom billion of the world's poorest people. In this study, a real-time polymerase chain reaction (PCR) coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on the five human hookworm species. Methods Real-time PCR coupled with HRM analysis targeting the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA as the genetic marker was used to identify and distinguish hookworm species in human samples. Unique and distinct characteristics of HRM patterns were produced for each of the five hookworm species. The melting curves were characterized by peaks of 79.24±0.05°C and 83.00±0.04°C for Necator americanus, 79.12±0.10°C for Ancylostoma duodenale, 79.40±0.10°C for Ancylostoma ceylanicum, 79.63±0.05°C for Ancylostoma caninum and 79.70±0.14°C for Ancylostoma braziliense. An evaluation of the method's sensitivity and specificity revealed that this assay was able to detect as low as 0.01 ng/µl hookworm DNA and amplification was only recorded for hookworm positive samples. Conclusion The HRM assay developed in this study is a rapid and straightforward method for the diagnosis, identification and discrimination of five human hookworms. This assay is simple compared to other probe-based genotyping methods as it does not require multiplexing, DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of human hookworm species. PMID:22844538

  18. Rapid detection and identification of human hookworm infections through high resolution melting (HRM analysis.

    Directory of Open Access Journals (Sweden)

    Romano Ngui

    Full Text Available BACKGROUND: Hookworm infections are still endemic in low and middle income tropical countries with greater impact on the socioeconomic and public health of the bottom billion of the world's poorest people. In this study, a real-time polymerase chain reaction (PCR coupled with high resolution melting-curve (HRM analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on the five human hookworm species. METHODS: Real-time PCR coupled with HRM analysis targeting the second internal transcribed spacer (ITS-2 of nuclear ribosomal DNA as the genetic marker was used to identify and distinguish hookworm species in human samples. Unique and distinct characteristics of HRM patterns were produced for each of the five hookworm species. The melting curves were characterized by peaks of 79.24±0.05°C and 83.00±0.04°C for Necator americanus, 79.12±0.10°C for Ancylostoma duodenale, 79.40±0.10°C for Ancylostoma ceylanicum, 79.63±0.05°C for Ancylostoma caninum and 79.70±0.14°C for Ancylostoma braziliense. An evaluation of the method's sensitivity and specificity revealed that this assay was able to detect as low as 0.01 ng/µl hookworm DNA and amplification was only recorded for hookworm positive samples. CONCLUSION: The HRM assay developed in this study is a rapid and straightforward method for the diagnosis, identification and discrimination of five human hookworms. This assay is simple compared to other probe-based genotyping methods as it does not require multiplexing, DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of human hookworm species.

  19. Functional exploratory data analysis for high-resolution measurements of urban particulate matter.

    Science.gov (United States)

    Ranalli, M Giovanna; Rocco, Giorgia; Jona Lasinio, Giovanna; Moroni, Beatrice; Castellini, Silvia; Crocchianti, Stefano; Cappelletti, David

    2016-09-01

    In this work we propose the use of functional data analysis (FDA) to deal with a very large dataset of atmospheric aerosol size distribution resolved in both space and time. Data come from a mobile measurement platform in the town of Perugia (Central Italy). An OPC (Optical Particle Counter) is integrated on a cabin of the Minimetrò, an urban transportation system, that moves along a monorail on a line transect of the town. The OPC takes a sample of air every six seconds and counts the number of particles of urban aerosols with a diameter between 0.28 μm and 10 μm and classifies such particles into 21 size bins according to their diameter. Here, we adopt a 2D functional data representation for each of the 21 spatiotemporal series. In fact, space is unidimensional since it is measured as the distance on the monorail from the base station of the Minimetrò. FDA allows for a reduction of the dimensionality of each dataset and accounts for the high space-time resolution of the data. Functional cluster analysis is then performed to search for similarities among the 21 size channels in terms of their spatiotemporal pattern. Results provide a good classification of the 21 size bins into a relatively small number of groups (between three and four) according to the season of the year. Groups including coarser particles have more similar patterns, while those including finer particles show a more different behavior according to the period of the year. Such features are consistent with the physics of atmospheric aerosol and the highlighted patterns provide a very useful ground for prospective model-based studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. High-resolution melt PCR analysis for genotyping of Ureaplasma parvum isolates directly from clinical samples.

    Science.gov (United States)

    Payne, Matthew S; Tabone, Tania; Kemp, Matthew W; Keelan, Jeffrey A; Spiller, O Brad; Newnham, John P

    2014-02-01

    Ureaplasma sp. infection in neonates and adults underlies a variety of disease pathologies. Of the two human Ureaplasma spp., Ureaplasma parvum is clinically the most common. We have developed a high-resolution melt (HRM) PCR assay for the differentiation of the four serovars of U. parvum in a single step. Currently U. parvum strains are separated into four serovars by sequencing the promoter and coding region of the multiple-banded antigen (MBA) gene. We designed primers to conserved sequences within this region for PCR amplification and HRM analysis to generate reproducible and distinct melt profiles that distinguish clonal representatives of serovars 1, 3, 6, and 14. Furthermore, our HRM PCR assay could classify DNA extracted from 74 known (MBA-sequenced) test strains with 100% accuracy. Importantly, HRM PCR was also able to identify U. parvum serovars directly from 16 clinical swabs. HRM PCR performed with DNA consisting of mixtures of combined known serovars yielded profiles that were easily distinguished from those for single-serovar controls. These profiles mirrored clinical samples that contained mixed serovars. Unfortunately, melt curve analysis software is not yet robust enough to identify the composition of mixed serovar samples, only that more than one serovar is present. HRM PCR provides a single-step, rapid, cost-effective means to differentiate the four serovars of U. parvum that did not amplify any of the known 10 serovars of Ureaplasma urealyticum tested in parallel. Choice of reaction reagents was found to be crucial to allow sufficient sensitivity to differentiate U. parvum serovars directly from clinical swabs rather than requiring cell enrichment using microbial culture techniques.

  1. High angular resolution at LBT

    Science.gov (United States)

    Conrad, A.; Arcidiacono, C.; Bertero, M.; Boccacci, P.; Davies, A. G.; Defrere, D.; de Kleer, K.; De Pater, I.; Hinz, P.; Hofmann, K. H.; La Camera, A.; Leisenring, J.; Kürster, M.; Rathbun, J. A.; Schertl, D.; Skemer, A.; Skrutskie, M.; Spencer, J. R.; Veillet, C.; Weigelt, G.; Woodward, C. E.

    2015-12-01

    High angular resolution from ground-based observatories stands as a key technology for advancing planetary science. In the window between the angular resolution achievable with 8-10 meter class telescopes, and the 23-to-40 meter giants of the future, LBT provides a glimpse of what the next generation of instruments providing higher angular resolution will provide. We present first ever resolved images of an Io eruption site taken from the ground, images of Io's Loki Patera taken with Fizeau imaging at the 22.8 meter LBT [Conrad, et al., AJ, 2015]. We will also present preliminary analysis of two data sets acquired during the 2015 opposition: L-band fringes at Kurdalagon and an occultation of Loki and Pele by Europa (see figure). The light curves from this occultation will yield an order of magnitude improvement in spatial resolution along the path of ingress and egress. We will conclude by providing an overview of the overall benefit of recent and future advances in angular resolution for planetary science.

  2. Analysis of X-Band Very High Resolution Persistent Scatterer Interferometry Data Over Urban Areas

    Science.gov (United States)

    Crosetto, M.; Monserrat, O.; Cuevas-González, M.; Devanthéry, N.; Crippa, B.

    2013-04-01

    Persistent Scatterer Interferometry (PSI) is a satellite-based Synthetic Aperture Radar (SAR) remote sensing technique used to measure and monitor land deformation from a stack of interferometric SAR images. This work concerns X-band PSI and, in particular, PSI based on very high resolution (VHR) StripMap CosmoSkyMed and TerraSAR-X SAR imagery. In fact, it mainly focuses on the technical aspects of deformation measurement and monitoring over urban areas. A key technical aspect analysed in this paper is the thermal expansion component of PSI observations, which is a result of temperature differences in the imaged area between SAR acquisitions. This component of PSI observations is particularly important in the urban environment. This is an interesting feature of PSI, which can be surely used to illustrate the high sensitivity of X-band PSI to very subtle displacements. Thermal expansion can have a strong impact on the PSI products, especially on the deformation velocity maps and deformation time series, if not properly handled during the PSI data processing and analysis, and a comprehensive discussion of this aspect will be provided in this paper. The importance of thermal expansion is related to the fact that the PSI analyses are often performed using limited stacks of images, which may cover a limited time period, e.g. several months only. These two factors (limited number of images and short period) make the impact of a non-modelled thermal expansion particularly critical. This issue will be illustrated considering different case studies based on TerraSAR-X and CosmoSkyMed PSI data. Besides, an extended PSI model which alleviates this problem will be described and case studies from the Barcelona metropolitan area will demonstrate the effectiveness of the proposed strategy.

  3. ANALYSIS OF X-BAND VERY HIGH RESOLUTION PERSISTENT SCATTERER INTERFEROMETRY DATA OVER URBAN AREAS

    Directory of Open Access Journals (Sweden)

    M. Crosetto

    2013-04-01

    Full Text Available Persistent Scatterer Interferometry (PSI is a satellite-based Synthetic Aperture Radar (SAR remote sensing technique used to measure and monitor land deformation from a stack of interferometric SAR images. This work concerns X-band PSI and, in particular, PSI based on very high resolution (VHR StripMap CosmoSkyMed and TerraSAR-X SAR imagery. In fact, it mainly focuses on the technical aspects of deformation measurement and monitoring over urban areas. A key technical aspect analysed in this paper is the thermal expansion component of PSI observations, which is a result of temperature differences in the imaged area between SAR acquisitions. This component of PSI observations is particularly important in the urban environment. This is an interesting feature of PSI, which can be surely used to illustrate the high sensitivity of X-band PSI to very subtle displacements. Thermal expansion can have a strong impact on the PSI products, especially on the deformation velocity maps and deformation time series, if not properly handled during the PSI data processing and analysis, and a comprehensive discussion of this aspect will be provided in this paper. The importance of thermal expansion is related to the fact that the PSI analyses are often performed using limited stacks of images, which may cover a limited time period, e.g. several months only. These two factors (limited number of images and short period make the impact of a non-modelled thermal expansion particularly critical. This issue will be illustrated considering different case studies based on TerraSAR-X and CosmoSkyMed PSI data. Besides, an extended PSI model which alleviates this problem will be described and case studies from the Barcelona metropolitan area will demonstrate the effectiveness of the proposed strategy.

  4. Near-field electromagnetic holography for high-resolution analysis of network interactions in neuronal tissue.

    Science.gov (United States)

    Kjeldsen, Henrik D; Kaiser, Marcus; Whittington, Miles A

    2015-09-30

    Brain function is dependent upon the concerted, dynamical interactions between a great many neurons distributed over many cortical subregions. Current methods of quantifying such interactions are limited by consideration only of single direct or indirect measures of a subsample of all neuronal population activity. Here we present a new derivation of the electromagnetic analogy to near-field acoustic holography allowing high-resolution, vectored estimates of interactions between sources of electromagnetic activity that significantly improves this situation. In vitro voltage potential recordings were used to estimate pseudo-electromagnetic energy flow vector fields, current and energy source densities and energy dissipation in reconstruction planes at depth into the neural tissue parallel to the recording plane of the microelectrode array. The properties of the reconstructed near-field estimate allowed both the utilization of super-resolution techniques to increase the imaging resolution beyond that of the microelectrode array, and facilitated a novel approach to estimating causal relationships between activity in neocortical subregions. The holographic nature of the reconstruction method allowed significantly better estimation of the fine spatiotemporal detail of neuronal population activity, compared with interpolation alone, beyond the spatial resolution of the electrode arrays used. Pseudo-energy flow vector mapping was possible with high temporal precision, allowing a near-realtime estimate of causal interaction dynamics. Basic near-field electromagnetic holography provides a powerful means to increase spatial resolution from electrode array data with careful choice of spatial filters and distance to reconstruction plane. More detailed approaches may provide the ability to volumetrically reconstruct activity patterns on neuronal tissue, but the ability to extract vectored data with the method presented already permits the study of dynamic causal interactions

  5. Quantitative Analysis of Swallowing Function Between Dysphagia Patients and Healthy Subjects Using High-Resolution Manometry

    OpenAIRE

    Park, Chul-Hyun; Kim, Don-Kyu; Lee, Yong-Taek; Yi, Youbin; Lee, Jung-Sang; Kim, Kunwoo; Park, Jung Ho; Yoon, Kyung Jae

    2017-01-01

    Objective To compare swallowing function between healthy subjects and patients with pharyngeal dysphagia using high resolution manometry (HRM) and to evaluate the usefulness of HRM for detecting pharyngeal dysphagia. Methods Seventy-five patients with dysphagia and 28 healthy subjects were included in this study. Diagnosis of dysphagia was confirmed by a videofluoroscopy. HRM was performed to measure pressure and timing information at the velopharynx (VP), tongue base (TB), and upper esophage...

  6. High-resolution computed tomography of the lung in smokers: Visual and computer-based analysis

    International Nuclear Information System (INIS)

    Mueller-Leisse, C.; Otto, A.; Berger, F.; Schmitz, E.; Guenther, R.W.

    1997-01-01

    Purpose: It has been the aim of the study to assess parenchymal changes in the lung with high-resolution CT in healthy heavy, moderate, and non-smokers. Material and methods: We prospectively evaluated CT changes in 42 healthy heavy smokers (gr. (group) 2, ≥30 pack-years), 40 moderate smokers (gr. 1, R , Kontron GmbH, Munich, Germany). Results: Productive cough, dyspnoea and chronic bronchitis were more common in smokers than in non-smokers (p [de

  7. High Resolution Topography Analysis on Threading Edge Dislocations in 4H-SiC Epilayers

    International Nuclear Information System (INIS)

    Kamata, I.; Nagano, M.; Tsuchida, H.; Chen, Y.; Dudley, M.

    2009-01-01

    Threading edge dislocations (TEDs) in a 4H-SiC epitaxial layer are investigated using high-resolution synchrotron topography. Six types of TED image are confirmed to correspond to the Burgers vector directions by a comparison of computer simulated images and observed topography images in crystal boundaries. Using a mapping method, a wide spatial distribution of the six types of TED is examined in a quarter section of a 2-inch wafer.

  8. High resolution positron tomography

    International Nuclear Information System (INIS)

    Brownell, G.L.; Burnham, C.A.

    1982-01-01

    The limits of spatial resolution in practical positron tomography are examined. The four factors that limit spatial resolution are: positron range; small angle deviation; detector dimensions and properties; statistics. Of these factors, positron range may be considered the fundamental physical limitation since it is independent of instrument properties. The other factors are to a greater or lesser extent dependent on the design of the tomograph

  9. Molecular identification of broomrape species from a single seed by High Resolution Melting analysis

    Directory of Open Access Journals (Sweden)

    Mathieu Rolland

    2016-12-01

    Full Text Available Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species. The aim of this study was to develop and evaluate a High Resolution Melting assay identifying the eight most noxious and common broomrape species (P. aegyptiaca, O. cernua, O. crenata, O. cumana, O. foetida, O. hederae, O. minor, and P. ramosa from a single seed. Based on trnL and rbcL plastidial genes amplification, the designed assay successfully identifies O. cumana, O. cernua, O. crenata, O. minor, O. hederae, and O. foetida; P. ramosa and P. aegyptiaca can be differentiated from other species but not from each other. Tested on 50 seed lots, obtained results perfectly matched identifications performed by sequencing. Through the analysis of common seed lots by different analysts, the reproducibility of the assay was evaluated at 90 %. Despite an original sample preparation process it was not possible to extract enough DNA from some seeds (10% of the samples. The described assay fulfils its objectives and allows an accurate identification of the targeted broomrape species. It can be used to identify contaminants in commercial seed lots or for any other purpose. The assay might be extended to vegetative material.

  10. Rapid Determination of Lymphogranuloma Venereum Serovars of Chlamydia trachomatis by Quantitative High-Resolution Melt Analysis (HRMA)

    Science.gov (United States)

    Stevens, Matthew P.; Garland, Suzanne M.; Zaia, Angelo M.; Tabrizi, Sepehr N.

    2012-01-01

    A quantitative high-resolution melt analysis assay was developed to differentiate lymphogranuloma venereum-causing serovars of Chlamydia trachomatis (L1 to L3) from other C. trachomatis serovars (D to K). The detection limit of this assay is approximately 10 copies per reaction, comparable to the limits of other quantitative-PCR-based methods. PMID:22933594

  11. Simplifying the detection of MUTYH mutations by high resolution melting analysis

    International Nuclear Information System (INIS)

    López-Villar, Isabel; Martínez-López, Joaquín; Ayala, Rosa; Wesselink, Jan; Morillas, Juan Diego; López, Elena; Marín, José Carlos; Díaz-Tasende, José; González, Sara; Robles, Luis

    2010-01-01

    MUTYH-associated polyposis (MAP) is a disorder caused by bi-allelic germline MUTYH mutation, characterized by multiple colorectal adenomas. In order to identify mutations in MUTYH gene we applied High Resolution Melting (HRM) genotyping. HRM analysis is extensively employed as a scanning method for the detection of heterozygous mutations. Therefore, we applied HRM to show effectiveness in detecting homozygous mutations for these clinically important and frequent patients. In this study, we analyzed phenotype and genotype data from 82 patients, with multiple (>= 10) synchronous (19/82) or metachronous (63/82) adenomas and negative APC study (except one case). Analysis was performed by HRM-PCR and direct sequencing, in order to identify mutations in MUTYH exons 7, 12 and 13, where the most prevalent mutations are located. In monoallelic mutation carriers, we evaluated entire MUTYH gene in search of another possible alteration. HRM-PCR was performed with strict conditions in several rounds: the first one to discriminate the heteroduplex patterns and homoduplex patterns and the next ones, in order to refine and confirm parameters. The genotypes obtained were correlated to phenotypic features (number of adenomas (synchronous or metachronous), colorectal cancer (CRC) and family history). MUTYH germline mutations were found in 15.8% (13/82) of patients. The hot spots, Y179C (exon 7) and G396D (exon 13), were readily identified and other mutations were also detected. Each mutation had a reproducible melting profile by HRM, both heterozygous mutations and homozygous mutations. In our study of 82 patients, biallelic mutation is associated with being a carrier of ≥10 synchronous polyps (p = 0.05) and there is no association between biallelic mutation and CRC (p = 0.39) nor family history (p = 0.63). G338H non-pathogenic polymorphism (exon 12) was found in 23.1% (19/82) of patients. In all cases there was concordance between HRM (first and subsequent rounds) and sequencing

  12. High-resolution spectral analysis of light from neutral beams and ion source plasmas

    International Nuclear Information System (INIS)

    McNeill, D.H.; Kim, J.

    1980-05-01

    The spectral distributions of Balmer alpha emission from 7- and 22-cm-diam neutral hydrogen beams have been measured with a Fabry-Perot interferometer to obtain information on the beam energy, divergence, and species composition. Results of these measurements are compared with other data on the beam properties to evaluate high-resolution spectroscopy as a beam diagnostic technique. Measurements on ion source plasmas and on beam-produced background plasmas yield average neutral atom energies of approximately 0.3 and 2.5 eV, respectively

  13. PC-SEAPAK - ANALYSIS OF COASTAL ZONE COLOR SCANNER AND ADVANCED VERY HIGH RESOLUTION RADIOMETER DATA

    Science.gov (United States)

    Mcclain, C. R.

    1994-01-01

    PC-SEAPAK is a user-interactive satellite data analysis software package specifically developed for oceanographic research. The program is used to process and interpret data obtained from the Nimbus-7/Coastal Zone Color Scanner (CZCS), and the NOAA Advanced Very High Resolution Radiometer (AVHRR). PC-SEAPAK is a set of independent microcomputer-based image analysis programs that provide the user with a flexible, user-friendly, standardized interface, and facilitates relatively low-cost analysis of oceanographic satellite data. Version 4.0 includes 114 programs. PC-SEAPAK programs are organized into categories which include CZCS and AVHRR level-1 ingest, level-2 analyses, statistical analyses, data extraction, remapping to standard projections, graphics manipulation, image board memory manipulation, hardcopy output support and general utilities. Most programs allow user interaction through menu and command modes and also by the use of a mouse. Most programs also provide for ASCII file generation for further analysis in spreadsheets, graphics packages, etc. The CZCS scanning radiometer aboard the NIMBUS-7 satellite was designed to measure the concentration of photosynthetic pigments and their degradation products in the ocean. AVHRR data is used to compute sea surface temperatures and is supported for the NOAA 6, 7, 8, 9, 10, 11, and 12 satellites. The CZCS operated from November 1978 to June 1986. CZCS data may be obtained free of charge from the CZCS archive at NASA/Goddard Space Flight Center. AVHRR data may be purchased through NOAA's Satellite Data Service Division. Ordering information is included in the PC-SEAPAK documentation. Although PC-SEAPAK was developed on a COMPAQ Deskpro 386/20, it can be run on most 386-compatible computers with an AT bus, EGA controller, Intel 80387 coprocessor, and MS-DOS 3.3 or higher. A Matrox MVP-AT image board with appropriate monitor and cables is also required. Note that the authors have received some reports of

  14. Multi-dimensional analysis of high resolution {gamma}-ray data

    Energy Technology Data Exchange (ETDEWEB)

    Flibotte, S.; Huettmeier, U.J.; France, G. de; Haas, B.; Romain, P.; Theisen, Ch.; Vivien, J.P.; Zen, J. [Strasbourg-1 Univ., 67 (France). Centre de Recherches Nucleaires

    1992-12-31

    A new generation of high resolution {gamma}-ray spectrometers capable of recording high-fold coincidence events with a large efficiency will soon be available. Algorithms are developed to analyze high-fold {gamma}-ray coincidences. As a contribution to the software development associated with the EUROGAM spectrometer, the performances of computer codes designed to select multi-dimensional gates from 3-, 4- and 5-fold coincidence databases were tested. The tests were performed on events generated with a Monte Carlo simulation and also on real experimental triple data recorded with the 8{pi} spectrometer and with a preliminary version of the EUROGAM array. (R.P.) 14 refs.; 3 figs.; 3 tabs.

  15. Multi-dimensional analysis of high resolution γ-ray data

    International Nuclear Information System (INIS)

    Flibotte, S.; Huettmeier, U.J.; France, G. de; Haas, B.; Romain, P.; Theisen, Ch.; Vivien, J.P.; Zen, J.

    1992-01-01

    A new generation of high resolution γ-ray spectrometers capable of recording high-fold coincidence events with a large efficiency will soon be available. Algorithms are developed to analyze high-fold γ-ray coincidences. As a contribution to the software development associated with the EUROGAM spectrometer, the performances of computer codes designed to select multi-dimensional gates from 3-, 4- and 5-fold coincidence databases were tested. The tests were performed on events generated with a Monte Carlo simulation and also on real experimental triple data recorded with the 8π spectrometer and with a preliminary version of the EUROGAM array. (R.P.) 14 refs.; 3 figs.; 3 tabs

  16. Rapid Detection and Differentiation of Clonorchis sinensis and Opisthorchis viverrini Using Real-Time PCR and High Resolution Melting Analysis

    OpenAIRE

    Cai, Xian-Quan; Yu, Hai-Qiong; Li, Rong; Yue, Qiao-Yun; Liu, Guo-Hua; Bai, Jian-Shan; Deng, Yan; Qiu, De-Yi; Zhu, Xing-Quan

    2014-01-01

    Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA...

  17. Transmission and selection of macrolide resistant Mycoplasma genitalium infections detected by rapid high resolution melt analysis.

    Directory of Open Access Journals (Sweden)

    Jimmy Twin

    Full Text Available BACKGROUND: Mycoplasma genitalium (MG causes urethritis, cervicitis and pelvic inflammatory disease. The MG treatment failure rate using 1 g azithromycin at an Australian Sexual Health clinic in 2007-9 was 31% (95%CI 23-40%. We developed a rapid high resolution melt analysis (HRMA assay targeting resistance mutations in the MG 23S rRNA gene, and validated it against DNA sequencing by examining pre- and post-treatment archived samples from MG-infected patients. METHODOLOGY/PRINCIPAL FINDINGS: Available MG-positive pre-treatment (n = 82 and post-treatment samples from individuals with clinical treatment failure (n = 20 were screened for 23S rRNA gene mutations. Sixteen (20% pre-treatment samples possessed resistance mutations (A2058G, A2059G, A2059C, which were significantly more common in patients with symptomatic azithromycin-treatment failure (12/26; 44% than in those clinically cured (4/56; 7%, p<0.001. All 20 patients experiencing azithromycin-failure had detectable mutations in their post-treatment samples. In 9 of these cases, the same mutational types were present in both pre- and post-treatment samples indicating transmitted resistance, whilst in 11 of these cases (55%, mutations were absent in pre-treatment samples indicating likely selection of resistant isolates have occurred. HRMA was able to detect all mutational changes determined in this study by DNA sequencing. An additional HRMA assay incorporating an unlabelled probe was also developed to detect type 4 single-nucleotide polymorphisms found in other populations, with a slightly lower sensitivity of 90%. CONCLUSIONS/SIGNIFICANCE: Treatment failure is associated with the detection of macrolide resistance mutations, which appear to be almost equally due to selection of resistant isolates following exposure to 1 g azithromycin and pre-existing transmitted resistance. The application of a rapid molecular assay to detect resistance at the time of initial detection of infection allows

  18. Analysis of lipid experiments (ALEX: a software framework for analysis of high-resolution shotgun lipidomics data.

    Directory of Open Access Journals (Sweden)

    Peter Husen

    Full Text Available Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of lipidomics data in "database table format" which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1. The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.

  19. Analysis of lipid experiments (ALEX): a software framework for analysis of high-resolution shotgun lipidomics data.

    Science.gov (United States)

    Husen, Peter; Tarasov, Kirill; Katafiasz, Maciej; Sokol, Elena; Vogt, Johannes; Baumgart, Jan; Nitsch, Robert; Ekroos, Kim; Ejsing, Christer S

    2013-01-01

    Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of lipidomics data in "database table format" which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF) from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1). The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.

  20. [Analysis of the characteristic of pharyngeal paraesthesia patients by high resolution manometry].

    Science.gov (United States)

    Gu, Yun; Qian, Wei

    2015-09-01

    To discuss the pressure changing characteristics of upper esophageal sphincter (UES), lower esophageal sphincter (LES) and the esophagus kinetic characteristics of pharyngeal paraesthesia patients. To take high resolution manometry in 44 cases of pharyngeal paraesthesia patients and 23 normal subjects separately. According to the RSI score,the 44 patients were divided into group A (the group without reflux, RSI 0.05). The esophagus DCI of group B was lower than that of group A and control group (P 0.05). The pharyngeal paresthesia symptoms of'patients was associated with the increasing of UES pressure. The pharyngeal paresthesia symptoms of group with reflux was related to low pressure of LES and high pressure of UES. The last part of esophagus of group with reflux had obstacles in powers, which weaken the peristalsis and declined the ability to clear the bolus and gastric reflux material.

  1. Optical Analysis of an Ultra-High resolution Two-Mirror Soft X-Ray Microscope

    Science.gov (United States)

    Shealy, David L.; Wang, Cheng; Hoover, Richard B.

    1994-01-01

    This work has summarized for a Schwarzschild microscope some relationships between numerical aperture (NA), magnification, diameter of the primary mirror, radius of curvature of the secondary mirror, and the total length of the microscope. To achieve resolutions better than a spherical Schwarzschild microscope of 3.3 Lambda for a perfectly aligned and fabricated system. it is necessary to use aspherical surfaces to control higher-order aberrations. For an NA of 0.35, the aspherical Head microscope provides diffraction limited resolution of 1.4 Lambda where the aspherical surfaces differ from the best fit spherical surface by approximately 1 micrometer. However, the angle of incidence varies significantly over the primary and the secondary mirrors, which will require graded multilayer coatings to operate near peak reflectivities. For higher numerical apertures, the variation of the angle of incidence over the secondary mirror surface becomes a serious problem which must be solved before multilayer coatings can be used for this application. Tolerance analysis of the spherical Schwarzschild microscope has shown that water window operations will require 2-3 times tighter tolerances to achieve a similar performance for operations with 130 A radiation. Surface contour errors have been shown to have a significant impact on the MTF and must be controlled to a peak-to-valley variation of 50-100 A and a frequency of 8 periods over the surface of a mirror.

  2. High resolution hadron calorimetry

    International Nuclear Information System (INIS)

    Wigmans, R.

    1987-01-01

    The components that contribute to the signal of a hadron calorimeter and the factors that affect its performance are discussed, concentrating on two aspects; energy resolution and signal linearity. Both are decisively dependent on the relative response to the electromagnetic and the non-electromagnetic shower components, the e/h signal ratio, which should be equal to 1.0 for optimal performance. The factors that determine the value of this ratio are examined. The calorimeter performance is crucially determined by its response to the abundantly present soft neutrons in the shower. The presence of a considerable fraction of hydrogen atoms in the active medium is essential for achieving the best possible results. Firstly, this allows one to tune e/h to the desired value by choosing the appropriate sampling fraction. And secondly, the efficient neutron detection via recoil protons in the readout medium itself reduces considerably the effect of fluctuations in binding energy losses at the nuclear level, which dominate the intrinsic energy resolution. Signal equalization, or compensation (e/h = 1.0) does not seem to be a property unique to 238 U, but can also be achieved with lead and probably even iron absorbers. 21 refs.; 19 figs

  3. Extraction of Terraces on the Loess Plateau from High-Resolution DEMs and Imagery Utilizing Object-Based Image Analysis

    Directory of Open Access Journals (Sweden)

    Hanqing Zhao

    2017-05-01

    Full Text Available Abstract: Terraces are typical artificial landforms on the Loess Plateau, with ecological functions in water and soil conservation, agricultural production, and biodiversity. Recording the spatial distribution of terraces is the basis of monitoring their extent and understanding their ecological effects. The current terrace extraction method mainly relies on high-resolution imagery, but its accuracy is limited due to vegetation coverage distorting the features of terraces in imagery. High-resolution topographic data reflecting the morphology of true terrace surfaces are needed. Terraces extraction on the Loess Plateau is challenging because of the complex terrain and diverse vegetation after the implementation of “vegetation recovery”. This study presents an automatic method of extracting terraces based on 1 m resolution digital elevation models (DEMs and 0.3 m resolution Worldview-3 imagery as auxiliary information used for object-based image analysis (OBIA. A multi-resolution segmentation method was used where slope, positive and negative terrain index (PN, accumulative curvature slope (AC, and slope of slope (SOS were determined as input layers for image segmentation by correlation analysis and Sheffield entropy method. The main classification features based on DEMs were chosen from the terrain features derived from terrain factors and texture features by gray-level co-occurrence matrix (GLCM analysis; subsequently, these features were determined by the importance analysis on classification and regression tree (CART analysis. Extraction rules based on DEMs were generated from the classification features with a total classification accuracy of 89.96%. The red band and near-infrared band of images were used to exclude construction land, which is easily confused with small-size terraces. As a result, the total classification accuracy was increased to 94%. The proposed method ensures comprehensive consideration of terrain, texture, shape, and

  4. In vitro analysis of integrated global high-resolution DNA methylation profiling with genomic imbalance and gene expression in osteosarcoma.

    Directory of Open Access Journals (Sweden)

    Bekim Sadikovic

    Full Text Available Genetic and epigenetic changes contribute to deregulation of gene expression and development of human cancer. Changes in DNA methylation are key epigenetic factors regulating gene expression and genomic stability. Recent progress in microarray technologies resulted in developments of high resolution platforms for profiling of genetic, epigenetic and gene expression changes. OS is a pediatric bone tumor with characteristically high level of numerical and structural chromosomal changes. Furthermore, little is known about DNA methylation changes in OS. Our objective was to develop an integrative approach for analysis of high-resolution epigenomic, genomic, and gene expression profiles in order to identify functional epi/genomic differences between OS cell lines and normal human osteoblasts. A combination of Affymetrix Promoter Tilling Arrays for DNA methylation, Agilent array-CGH platform for genomic imbalance and Affymetrix Gene 1.0 platform for gene expression analysis was used. As a result, an integrative high-resolution approach for interrogation of genome-wide tumour-specific changes in DNA methylation was developed. This approach was used to provide the first genomic DNA methylation maps, and to identify and validate genes with aberrant DNA methylation in OS cell lines. This first integrative analysis of global cancer-related changes in DNA methylation, genomic imbalance, and gene expression has provided comprehensive evidence of the cumulative roles of epigenetic and genetic mechanisms in deregulation of gene expression networks.

  5. Analysis and Application of High Resolution Numerical Perturbation Algorithm for Convective-Diffusion Equation

    International Nuclear Information System (INIS)

    Gao Zhi; Shen Yi-Qing

    2012-01-01

    The high resolution numerical perturbation (NP) algorithm is analyzed and tested using various convective-diffusion equations. The NP algorithm is constructed by splitting the second order central difference schemes of both convective and diffusion terms of the convective-diffusion equation into upstream and downstream parts, then the perturbation reconstruction functions of the convective coefficient are determined using the power-series of grid interval and eliminating the truncated errors of the modified differential equation. The important nature, i.e. the upwind dominance nature, which is the basis to ensuring that the NP schemes are stable and essentially oscillation free, is firstly presented and verified. Various numerical cases show that the NP schemes are efficient, robust, and more accurate than the original second order central scheme

  6. Analysis and realization of a high resolution trigger for DM2 experiment

    International Nuclear Information System (INIS)

    Bertrand, J.L.

    1984-01-01

    The construction of a high resolution trigger has been carried out from its theoretical design to building. The term trigger is applied to an almost real-time system for track filtering in particle detection. Curved tracks are detected (with a magnetic field) and the detector is of a revolution symmetry type. The concept of a ''hybrid'' trigger with features in between those of the so-called ''CELLO R0'' and ''MARK II'' types is launched. It allows a positive versatility for the optimization of the different features. Besides a specific structure, some hardware and software implements have been designed for development and tests. The ''TRIGGER LENT'' is presently in operation in the DM2 experiment [fr

  7. High resolution analysis of tropical forest fragmentation and its impact on the global carbon cycle

    Science.gov (United States)

    Brinck, Katharina; Fischer, Rico; Groeneveld, Jürgen; Lehmann, Sebastian; Dantas de Paula, Mateus; Pütz, Sandro; Sexton, Joseph O.; Song, Danxia; Huth, Andreas

    2017-03-01

    Deforestation in the tropics is not only responsible for direct carbon emissions but also extends the forest edge wherein trees suffer increased mortality. Here we combine high-resolution (30 m) satellite maps of forest cover with estimates of the edge effect and show that 19% of the remaining area of tropical forests lies within 100 m of a forest edge. The tropics house around 50 million forest fragments and the length of the world's tropical forest edges sums to nearly 50 million km. Edge effects in tropical forests have caused an additional 10.3 Gt (2.1-14.4 Gt) of carbon emissions, which translates into 0.34 Gt per year and represents 31% of the currently estimated annual carbon releases due to tropical deforestation. Fragmentation substantially augments carbon emissions from tropical forests and must be taken into account when analysing the role of vegetation in the global carbon cycle.

  8. Multi-dimensional analysis of high resolution γ-ray data

    International Nuclear Information System (INIS)

    Flibotte, S.; Huttmeier, U.J.; France, G. de; Haas, B.; Romain, P.; Theisen, Ch.; Vivien, J.P.; Zen, J.; Bednarczyk, P.

    1992-01-01

    High resolution γ-ray multi-detectors capable of measuring high-fold coincidences with a large efficiency are presently under construction (EUROGAM, GASP, GAMMASPHERE). The future experimental progress in our understanding of nuclear structure at high spin critically depends on our ability to analyze the data in a multi-dimensional space and to resolve small photopeaks of interest from the generally large background. Development of programs to process such high-fold events is still in its infancy and only the 3-fold case has been treated so far. As a contribution to the software development associated with the EUROGAM spectrometer, we have written and tested the performances of computer codes designed to select multi-dimensional gates from 3-, 4- and 5-fold coincidence databases. The tests were performed on events generated with a Monte Carlo simulation and also on experimental data (triples) recorded with the 8π spectrometer and with a preliminary version of the EUROGAM array. (author). 7 refs., 3 tabs., 1 fig

  9. Multi-dimensional analysis of high resolution {gamma}-ray data

    Energy Technology Data Exchange (ETDEWEB)

    Flibotte, S; Huttmeier, U J; France, G de; Haas, B; Romain, P; Theisen, Ch; Vivien, J P; Zen, J [Centre National de la Recherche Scientifique (CNRS), 67 - Strasbourg (France); Bednarczyk, P [Institute of Nuclear Physics, Cracow (Poland)

    1992-08-01

    High resolution {gamma}-ray multi-detectors capable of measuring high-fold coincidences with a large efficiency are presently under construction (EUROGAM, GASP, GAMMASPHERE). The future experimental progress in our understanding of nuclear structure at high spin critically depends on our ability to analyze the data in a multi-dimensional space and to resolve small photopeaks of interest from the generally large background. Development of programs to process such high-fold events is still in its infancy and only the 3-fold case has been treated so far. As a contribution to the software development associated with the EUROGAM spectrometer, we have written and tested the performances of computer codes designed to select multi-dimensional gates from 3-, 4- and 5-fold coincidence databases. The tests were performed on events generated with a Monte Carlo simulation and also on experimental data (triples) recorded with the 8{pi} spectrometer and with a preliminary version of the EUROGAM array. (author). 7 refs., 3 tabs., 1 fig.

  10. Analysis of Ground Displacements in Taipei Area by Using High Resolution X-band SAR Interferometry

    Science.gov (United States)

    Tung, H.; Chen, H. Y.; Hu, J. C.

    2014-12-01

    Located at the northern part of Taiwan, Taipei is the most densely populated city and the center of politic, economic, and culture of this island. North of the Taipei basin, the active Tatun volcano group with the eruptive potential to devastate the entire Taipei is only 15 km away from the capital Taipei. Furthermore, the active Shanchiao fault located in the western margin of Taipei basin. Therefore, it is not only an interesting scientific topic but also a strong social impact to better understand the assessment and mitigation of geological hazard in the metropolitan Taipei city. In this study, we use 12 high resolution X-band SAR images from the new generation COSMO-SkyMed (CSK) constellation for associating with leveling and GPS data to monitor surface deformation around the Shanchiao fault and the Tatun volcano group. The stripmap mode of CSK SAR images provides spatial resolution of 3 m x 3 m, which is one order of magnitude better than the previous available satellite SAR data. Furthermore, the more frequent revisit of the same Area of Interest (AOI) of the present X-band missions provides massive datasets to avoid the baseline limitation and temporal decorrelation to improve the temporal resolution of deformation in time series. After transferring the GPS vectors and leveling data to the LOS direction by referring to continuous GPS station BANC, the R square between PS velocities and GPS velocities is approximate to 0.9, which indicates the high reliability of our PSInSAR result. In addition, the well-fitting profiles between leveling data and PSInSAR result along two leveling routes both demonstrate that the significant deformation gradient mainly occurs along the Shanchiao fault. The severe land subsidence area is located in the western part of Taipei basin just next to the Shanchiao fault with a maximum of SRD rate of 30 mm/yr. However, the severe subsidence area, Wuku, is also one industrial area in Taipei which could be attributed to anthropogenic

  11. Non- invasive in vivo analysis of a murine aortic graft using high resolution ultrasound microimaging

    International Nuclear Information System (INIS)

    Rowinska, Zuzanna; Zander, Simone; Zernecke, Alma; Jacobs, Michael; Langer, Stephan; Weber, Christian; Merx, Marc W.; Koeppel, Thomas A.

    2012-01-01

    Introduction: As yet, murine aortic grafts have merely been monitored histopathologically. The aim of our study was to examine how these grafts can be monitored in vivo and non-invasively by using high-resolution ultrasound microimaging to evaluate function and morphology. A further aim was to prove if this in vivo monitoring can be correlated to immunohistological data that indicates graft integrity. Methods: Murine infrarenal aortic isografts were orthotopically transplanted into 14 female mice (C57BL/6-Background) whereas a group of sham-operated animals (n = 10) served as controls. To assess the graft morphology and hemodynamics, we examined the mice over a post-operative period of 8 weeks with a sophisticated ultrasound system (Vevo 770, Visual Sonics). Results: The non-invasive graft monitoring was feasible in all transplanted mice. We could demonstrate a regular post-transplant graft function and morphology, such as anterior/posterior wall displacement and wall thickness. Mild alterations of anterior wall motion dynamics could only be observed at the site of distal graft anastomosis (8 weeks after grafting (transplant vs. sham mice: 0.02 mm ± 0.01 vs. 0.03 mm ± 0.01, p < 0.05). However, the integrity of the entire graft wall could be confirmed by histopathological evaluation of the grafts. Conclusions: With regard to graft patency, function and morphology, high resolution ultrasound microimaging has proven to be a valuable tool for longitudinal, non-invasive, in vivo graft monitoring in this murine aortic transplantation model. Consequently, this experimental animal model provides an excellent basis for molecular and pharmacological studies using genetically engineered mice.

  12. Identification of Brucella spp. isolated from human brucellosis in Malaysia using high-resolution melt (HRM) analysis.

    Science.gov (United States)

    Mohamed Zahidi, Jama'ayah; Bee Yong, Tay; Hashim, Rohaidah; Mohd Noor, Azura; Hamzah, Siti Hawa; Ahmad, Norazah

    2015-04-01

    Molecular approaches have been investigated to overcome difficulties in identification and differentiation of Brucella spp. using conventional phenotypic methods. In this study, high-resolution melt (HRM) analysis was used for rapid identification and differentiation of members of Brucella genus. A total of 41 Brucella spp. isolates from human brucellosis were subjected to HRM analysis using 4 sets of primers, which identified 40 isolates as Brucella melitensis and 1 as Brucella canis. The technique utilized low DNA concentration and was highly reproducible. The assay is shown to be a useful diagnostic tool, which can rapidly differentiate Brucella up to species level. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  13. High-resolution electron microscope image analysis approach for superconductor YBa2Cu3O7-x

    International Nuclear Information System (INIS)

    Xu, J.; Lu, F.; Jia, C.; Hua, Z.

    1991-01-01

    In this paper, an HREM (High-resolution electron microscope) image analysis approach has been developed. The image filtering, segmentation and particles extraction based on gray-scale mathematical morphological operations, are performed on the original HREM image. The final image is a pseudocolor image, with the background removed, relatively uniform brightness, filtered slanting elongation, regular shape for every kind of particle, and particle boundaries that no longer touch each other so that the superconducting material structure can be shown clearly

  14. Remotely Sensed Data for High Resolution Agro-Environmental Policy Analysis

    Science.gov (United States)

    Welle, Paul

    Policy analyses of agricultural and environmental systems are often limited due to data constraints. Measurement campaigns can be costly, especially when the area of interest includes oceans, forests, agricultural regions or other dispersed spatial domains. Satellite based remote sensing offers a way to increase the spatial and temporal resolution of policy analysis concerning these systems. However, there are key limitations to the implementation of satellite data. Uncertainty in data derived from remote-sensing can be significant, and traditional methods of policy analysis for managing uncertainty on large datasets can be computationally expensive. Moreover, while satellite data can increasingly offer estimates of some parameters such as weather or crop use, other information regarding demographic or economic data is unlikely to be estimated using these techniques. Managing these challenges in practical policy analysis remains a challenge. In this dissertation, I conduct five case studies which rely heavily on data sourced from orbital sensors. First, I assess the magnitude of climate and anthropogenic stress on coral reef ecosystems. Second, I conduct an impact assessment of soil salinity on California agriculture. Third, I measure the propensity of growers to adapt their cropping practices to soil salinization in agriculture. Fourth, I analyze whether small-scale desalination units could be applied on farms in California in order mitigate the effects of drought and salinization as well as prevent agricultural drainage from entering vulnerable ecosystems. And fifth, I assess the feasibility of satellite-based remote sensing for salinity measurement at global scale. Through these case studies, I confront both the challenges and benefits associated with implementing satellite based-remote sensing for improved policy analysis.

  15. Analysis of X-ray Spectra of High-Z Elements obtained on Nike with high spectral and spatial resolution

    Science.gov (United States)

    Aglitskiy, Yefim; Weaver, J. L.; Karasik, M.; Serlin, V.; Obenschain, S. P.; Ralchenko, Yu.

    2014-10-01

    The spectra of multi-charged ions of Hf, Ta, W, Pt, Au and Bi have been studied on Nike krypton-fluoride laser facility with the help of two kinds of X-ray spectrometers. First, survey instrument covering a spectral range from 0.5 to 19.5 angstroms which allows simultaneous observation of both M- and N- spectra of above mentioned elements with high spectral resolution. Second, an imaging spectrometer with interchangeable spherically bent Quartz crystals that added higher efficiency, higher spectral resolution and high spatial resolution to the qualities of the former one. Multiple spectral lines with X-ray energies as high as 4 keV that belong to the isoelectronic sequences of Fe, Co, Ni, Cu and Zn were identified with the help of NOMAD package developed by Dr. Yu. Ralchenko and colleagues. In our continuous effort to support DOE-NNSA's inertial fusion program, this campaign covered a wide range of plasma conditions that result in production of relatively energetic X-rays. Work supported by the US DOE/NNSA.

  16. A high-resolution, empirical approach to climate impact assessment for regulatory analysis

    Science.gov (United States)

    Delgado, M.; Simcock, J. G.; Greenstone, M.; Hsiang, S. M.; Kopp, R. E.; Carleton, T.; Hultgren, A.; Jina, A.; Rising, J. A.; Nath, I.; Yuan, J.; Rode, A.; Chong, T.; Dobbels, G.; Hussain, A.; Wang, J.; Song, Y.; Mohan, S.; Larsen, K.; Houser, T.

    2017-12-01

    Recent breakthroughs in computing, data availability, and methodology have precipitated significant advances in the understanding of the relationship between climate and socioeconomic outcomes [1]. And while the use of estimates of the global marginal costs of greenhouse gas emissions (e.g. the SCC) are a mandatory component of regulatory policy in many jurisdictions, existing SCC-IAMs have lagged advances in impact assessment and valuation [2]. Recent work shows that incorporating high spatial and temporal resolution can significantly affect the observed relationships of economic outcomes to climate and socioeconomic factors [3] and that maintaining this granularity is critical to understanding the sensitivity of aggregate measures of valuation to inequality and risk adjustment methodologies [4]. We propose a novel framework that decomposes uncertainty in the SCC along multiple sources, including aggregate climate response parameters, the translation of global climate into local weather, the effect of weather on physical and economic systems, human and macro-economic responses, and impact valuation methodologies. This work extends Hsiang et al. (2017) [4] to directly estimate local response functions for multiple sectors in each of 24,378 global regions and to estimate impacts at this resolution daily, incorporating endogenous, empirically-estimated adaptation and costs. The goal of this work is to provide insight into the heterogeneity of climate impacts and to work with other modeling teams to enhance the empirical grounding of integrated climate impact assessment in more complex energy-environment-economics models. [1] T. Carleton and S. Hsiang (2016), DOI: 10.1126/science.aad9837. [2] National Academies of Sciences, Engineering, and Medicine (2017), DOI: 10.17226/24651. [3] Burke, M., S. Hsiang, and E. Miguel (2015), DOI: 10.1038/nature15725. [4] S. Hsiang et al. (2017), DOI: 10.1126/science.aal4369.

  17. SAMPO 90 high resolution interactive gamma-spectrum analysis including automation with macros

    International Nuclear Information System (INIS)

    Aarnio, P.A.; Nikkinen, M.T.; Routti, J.T.

    1992-01-01

    SAMPO 90 is high performance gamma-spectrum analysis program for personal computers. It uses color graphics to display calibrations, spectra, fitting results as multiplet components, and analysis results. All the analysis phases can be done either under full interactive user control or macros and programmable function keys can be used for completely automated measurement and analysis sequences including the control of MACs and sample changers. Accurate peak area determination of even the most complex multiplets, of up to 32 components, is accomplished using linear and mixed mode fitting. Nuclide identification is done using associated lines techniques allowing interference correction for fully overlapping peaks. Peaked Background Subtraction can be performed and Minimum Detectable Activities calculated. The analysis reports and program parameters are fully customizable. (author) 13 refs.; 1 fig

  18. High resolution x-ray diffraction analysis of annealed low-temperature gallium arsenide

    Science.gov (United States)

    Matyi, R. J.; Melloch, M. R.; Woodall, J. M.

    1992-05-01

    High resolution x-ray diffraction methods have been used to characterize GaAs grown at low substrate temperatures by molecular beam epitaxy and to examine the effects of post-growth annealing on the structure of the layers. Double crystal rocking curves from the as-deposited epitaxial layer show well-defined interference fringes, indicating a high level of structural perfection despite the presence of excess arsenic. Annealing at temperatures from 700 to 900 °C resulted in a decrease in the perpendicular lattice mismatch between the GaAs grown at low temperature and the substrate from 0.133% to 0.016% and a decrease (but not total elimination) of the visibility of the interference fringes. Triple-crystal diffraction scans around the 004 point in reciprocal space exhibited an increase in the apparent mosaic spread of the epitaxial layer with increasing anneal temperature. The observations are explained in terms of the growth of arsenic precipitates in the epitaxial layer.

  19. High-resolution photoelectron spectroscopy analysis of sulfidation of brass at the rubber/brass interface

    International Nuclear Information System (INIS)

    Ozawa, Kenichi; Kakubo, Takashi; Shimizu, Katsunori; Amino, Naoya; Mase, Kazuhiko; Komatsu, Takayuki

    2013-01-01

    Highlights: ► Chemical composition at the rubber/brass interface is investigated. ► The 2-min vulcanization reaction is enough to convert the interface composition. ► Five S-containing species are identified at the interface. ► Strong rubber–brass adhesion is related to the Cu 2 S/CuS ratio. ► Degradation of adhesion proceeds along with desulfidation of the interface. - Abstract: High resolution photoelectron spectroscopy is utilized to investigate the chemical composition at the rubber/brass interface to elucidate the origin of strong adhesion as well as the degradation between rubber and brass. Special attention has been given to copper sulfides formed at the interface during the vulcanization reaction at 170 °C. At least five sulfur-containing species are identified in the adhesive interlayer including crystalline CuS and amorphous Cu x S (x ≃ 2). These copper sulfide species are not uniformly distributed within the layer, but there exits the concentration gradation; the concentration of Cu x S is high in the region on the rubber side and is diminished in the deeper region, while vice versa for that of CuS. Degradation of the interface adhesive strength by prolonged vulcanization arises from the decrease in the Cu x S/CuS ratio accompanying desulfurization of the adhesive layer.

  20. PV Hosting Capacity Analysis and Enhancement Using High Resolution Stochastic Modeling

    Directory of Open Access Journals (Sweden)

    Emilio J. Palacios-Garcia

    2017-09-01

    Full Text Available Reduction of CO2 emissions is a main target in the future smart grid. This goal is boosting the installation of renewable energy resources (RES, as well as a major consumer engagement that seeks for a more efficient utilization of these resources toward the figure of ‘prosumers’. Nevertheless, these resources present an intermittent nature, which requires the presence of an energy storage system and an energy management system (EMS to ensure an uninterrupted power supply. Moreover, network-related issues might arise due to the increasing power of renewable resources installed in the grid, the storage systems also being capable of contributing to the network stability. However, to assess these future scenarios and test the control strategies, a simulation system is needed. The aim of this paper is to analyze the interaction between residential consumers with high penetration of PV generation and distributed storage and the grid by means of a high temporal resolution simulation scenario based on a stochastic residential load model and PV production records. Results of the model are presented for different PV power rates and storage capacities, as well as a two-level charging strategy as a mechanism for increasing the hosting capacity (HC of the network.

  1. High-resolution photoelectron spectroscopy analysis of sulfidation of brass at the rubber/brass interface

    Energy Technology Data Exchange (ETDEWEB)

    Ozawa, Kenichi, E-mail: ozawa.k.ab@m.titech.ac.jp [Department of Chemistry and Materials Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8551 (Japan); Kakubo, Takashi; Shimizu, Katsunori; Amino, Naoya [Yokohama Rubber Co., Ltd., Oiwake, Hiratsuka 254-8601 (Japan); Mase, Kazuhiko [Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801 (Japan); Komatsu, Takayuki [Department of Chemistry and Materials Science, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8551 (Japan)

    2013-01-01

    Highlights: Black-Right-Pointing-Pointer Chemical composition at the rubber/brass interface is investigated. Black-Right-Pointing-Pointer The 2-min vulcanization reaction is enough to convert the interface composition. Black-Right-Pointing-Pointer Five S-containing species are identified at the interface. Black-Right-Pointing-Pointer Strong rubber-brass adhesion is related to the Cu{sub 2}S/CuS ratio. Black-Right-Pointing-Pointer Degradation of adhesion proceeds along with desulfidation of the interface. - Abstract: High resolution photoelectron spectroscopy is utilized to investigate the chemical composition at the rubber/brass interface to elucidate the origin of strong adhesion as well as the degradation between rubber and brass. Special attention has been given to copper sulfides formed at the interface during the vulcanization reaction at 170 Degree-Sign C. At least five sulfur-containing species are identified in the adhesive interlayer including crystalline CuS and amorphous Cu{sub x}S (x Asymptotically-Equal-To 2). These copper sulfide species are not uniformly distributed within the layer, but there exits the concentration gradation; the concentration of Cu{sub x}S is high in the region on the rubber side and is diminished in the deeper region, while vice versa for that of CuS. Degradation of the interface adhesive strength by prolonged vulcanization arises from the decrease in the Cu{sub x}S/CuS ratio accompanying desulfurization of the adhesive layer.

  2. Reliable discrimination of 10 ungulate species using high resolution melting analysis of faecal DNA.

    Directory of Open Access Journals (Sweden)

    Ana Ramón-Laca

    Full Text Available Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat from swabs of faecal pellets. A high resolution melting (HRM assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA.

  3. Advances In very high resolution satellite imagery analysis for Monitoring human settlements

    Energy Technology Data Exchange (ETDEWEB)

    Vatsavai, Raju [ORNL; Cheriyadat, Anil M [ORNL; Bhaduri, Budhendra L [ORNL

    2014-01-01

    The high rate of urbanization, political conflicts and ensuing internal displacement of population, and increased poverty in the 20th century has resulted in rapid increase of informal settlements. These unplanned, unauthorized, and/or unstructured homes, known as informal settlements, shantytowns, barrios, or slums, pose several challenges to the nations, as these settlements are often located in most hazardous regions and lack basic services. Though several World Bank and United Nations sponsored studies stress the importance of poverty maps in designing better policies and interventions, mapping slums of the world is a daunting and challenging task. In this paper, we summarize our ongoing research on settlement mapping through the utilization of Very high resolution (VHR) remote sensing imagery. Most existing approaches used to classify VHR images are single instance (or pixel-based) learning algorithms, which are inadequate for analyzing VHR imagery, as single pixels do not contain sufficient contextual information (see Figure 1). However, much needed spatial contextual information can be captured via feature extraction and/or through newer machine learning algorithms in order to extract complex spatial patterns that distinguish informal settlements from formal ones. In recent years, we made significant progress in advancing the state of art in both directions. This paper summarizes these results.

  4. Elemental analysis of chamber organic aerosol using an aerodyne high-resolution aerosol mass spectrometer

    Directory of Open Access Journals (Sweden)

    P. S. Chhabra

    2010-05-01

    Full Text Available The elemental composition of laboratory chamber secondary organic aerosol (SOA from glyoxal uptake, α-pinene ozonolysis, isoprene photooxidation, single-ring aromatic photooxidation, and naphthalene photooxidation is evaluated using Aerodyne high-resolution time-of-flight mass spectrometer data. SOA O/C ratios range from 1.13 for glyoxal uptake experiments to 0.30–0.43 for α-pinene ozonolysis. The elemental composition of α-pinene and naphthalene SOA is also confirmed by offline mass spectrometry. The fraction of organic signal at m/z 44 is generally a good measure of SOA oxygenation for α-pinene/O3, isoprene/high-NOx, and naphthalene SOA systems. The agreement between measured and estimated O/C ratios tends to get closer as the fraction of organic signal at m/z 44 increases. This is in contrast to the glyoxal uptake system, in which m/z 44 substantially underpredicts O/C. Although chamber SOA has generally been considered less oxygenated than ambient SOA, single-ring aromatic- and naphthalene-derived SOA can reach O/C ratios upward of 0.7, well within the range of ambient PMF component OOA, though still not as high as some ambient measurements. The spectra of aromatic and isoprene-high-NOx SOA resemble that of OOA, but the spectrum of glyoxal uptake does not resemble that of any ambient organic aerosol PMF component.

  5. High Spatial Resolution Airborne Multispectral Thermal Infrared Remote Sensing Data for Analysis of Urban Landscape Characteristics

    Science.gov (United States)

    Quattrochi, Dale A.; Luvall, Jeffrey C.; Estes, Maurice G., Jr.; Arnold, James E. (Technical Monitor)

    2000-01-01

    We have used airborne multispectral thermal infrared (TIR) remote sensing data collected at a high spatial resolution (i.e., 10m) over several cities in the United States to study thermal energy characteristics of the urban landscape. These TIR data provide a unique opportunity to quantify thermal responses from discrete surfaces typical of the urban landscape and to identify both the spatial arrangement and patterns of thermal processes across the city. The information obtained from these data is critical to understanding how urban surfaces drive or force development of the Urban Heat Island (UHI) effect, which exists as a dome of elevated air temperatures that presides over cities in contrast to surrounding non-urbanized areas. The UHI is most pronounced in the summertime where urban surfaces, such as rooftops and pavement, store solar radiation throughout the day, and release this stored energy slowly after sunset creating air temperatures over the city that are in excess of 2-4'C warmer in contrast with non-urban or rural air temperatures. The UHI can also exist as a daytime phenomenon with surface temperatures in downtown areas of cities exceeding 38'C. The implications of the UHI are significant, particularly as an additive source of thermal energy input that exacerbates the overall production of ground level ozone over cities. We have used the Airborne Thermal and Land Applications Sensor (ATLAS), flown onboard a Lear 23 jet aircraft from the NASA Stennis Space Center, to acquire high spatial resolution multispectral TIR data (i.e., 6 bandwidths between 8.2-12.2 (um) over Huntsville, Alabama, Atlanta, Georgia, Baton Rouge, Louisiana, Salt Lake City, Utah, and Sacramento, California. These TIR data have been used to produce maps and other products, showing the spatial distribution of heating and cooling patterns over these cities to better understand how the morphology of the urban landscape affects development of the UHI. In turn, these data have been used

  6. Absolute high-resolution Se+ photoionization cross-section measurements with Rydberg-series analysis

    International Nuclear Information System (INIS)

    Esteves, D. A.; Bilodeau, R. C.; Sterling, N. C.; Phaneuf, R. A.; Kilcoyne, A. L. D.; Red, E. C.; Aguilar, A.

    2011-01-01

    Absolute single photoionization cross-section measurements for Se + ions were performed at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory using the photo-ion merged-beams technique. Measurements were made at a photon energy resolution of 5.5 meV from 17.75 to 21.85 eV spanning the 4s 2 4p 3 4 S 3/2 o ground-state ionization threshold and the 2 P 3/2 o , 2 P 1/2 o , 2 D 5/2 o , and 2 D 3/2 o metastable state thresholds. Extensive analysis of the complex resonant structure in this region identified numerous Rydberg series of resonances and obtained the Se 2+ 4s 2 4p 23 P 2 and 4s 2 4p 21 S 0 state energies. In addition, particular attention was given to removing significant effects in the measurements due to a small percentage of higher-order undulator radiation.

  7. Development of a parallel zoomed EVI sequence for high temporal resolution analysis of the BOLD response

    International Nuclear Information System (INIS)

    Rabrait, C.

    2006-01-01

    The hemodynamic impulse response to any short stimulus typically lasts around 20 seconds. Thus, the detection of the Blood Oxygenation Level Dependent (BOLD) effect is usually performed using a 2D Echo Planar Imaging (EPI) sequence, with repetition times on the order of 1 or 2 seconds. This temporal resolution is generally enough for detection purposes. Nevertheless, when trying to accurately estimate the hemodynamic response functions (HRF), higher scanning rates represent a real advantage. Thus, in order to reach a temporal resolution around 200 ms, we developed a new acquisition method, based on Echo Volumar Imaging and 2D parallel acquisition (1). Echo Volumar Imaging (EVI) has been proposed in 1977 by Mansfield (2). EVI intrinsically possesses a lot of advantages for functional neuroimaging, as a 3 D single shot acquisition method. Nevertheless, to date, only a few applications have been reported (3, 4). Actually, very restricting hardware requirements make EVI difficult to perform in satisfactory experimental conditions, even today. The critical point in EVI is the echo train duration, which is longer than in EPI, due to 3D acquisition. Indeed, at equal field of view and spatial resolutions, EVI echo train duration must be approximately equal to EPI echo train duration multiplied by the number of slices acquired in EPI. Consequently, EVI is much more sensitive than EPI to geometric distortions, which are related to phase errors, and also to signal losses, which are due to long echo times (TE). Thus, a first improvement has been brought by 'zoomed' or 'localized' EVI (5), which allows to focus on a small volume of interest and thus limit echo train durations compared to full FOV acquisitions.To reduce echo train durations, we chose to apply parallel acquisition. Moreover, since EVI is a 3D acquisition method, we are able to perform parallel acquisition and SENSE reconstruction along the two phase directions (6). The R = 4 under-sampling consists in the

  8. Analysis of high resolution scatter images from laser damage experiments performed on KDP

    International Nuclear Information System (INIS)

    Runkel, M.; Woods, B.; Yan, M.

    1996-01-01

    Interest in producing high damage threshold KH 2 PO 4 (KDP) and (D x H 1-x ) 2 PO 4 (KD*P, DKDP) for optical switching and frequency conversion applications is being driven by the system requirements for the National Ignition Facility (NIF) at Lawrence Livermore National Lab (LLNL). Historically, the path to achieving higher damage thresholds has been to improve the purity of crystal growth solutions. Application of advanced filtration technology has increased the damage threshold, but gives little insight into the actual mechanisms of laser damage. We have developed a laser scatter diagnostic to better study bulk defects and laser damage mechanisms in KDP and KD*P crystals. This diagnostic consists of a cavity doubled, kilohertz class, Nd:YLF laser (527 nm) and high dynamic range CCD camera which allows imaging of bulk scatter signals. With it, we have performed damage tests at 355 nm on four different open-quotes vintagesclose quotes of KDP crystals, concentrating on crystals produced via fast growth methods. We compare the diagnostic's resolution to LLNL's standard damage detection method of 100X darkfield microscopy and discuss its impact on damage threshold determination. We have observed the disappearance of scatter sites upon exposure to subthreshold irradiation. In contrast, we have seen scatterers appear where none previously existed. This includes isolated, large (high signal) sites as well as multiple small scatter sites which appear at fluences above 7 J/cm 2 (fine tracking). However, we have not observed a strong correlation of preexisting scatter sites and laser damage sites. We speculate on the connection between the laser-induced disappearance of scatter sites and the observed increase in damage threshold with laser conditioning

  9. Quantitative image analysis of vertebral body architecture - improved diagnosis in osteoporosis based on high-resolution computed tomography

    International Nuclear Information System (INIS)

    Mundinger, A.; Wiesmeier, B.; Dinkel, E.; Helwig, A.; Beck, A.; Schulte Moenting, J.

    1993-01-01

    71 women, 64 post-menopausal, were examined by single-energy quantitative computed tomography (SEQCT) and by high-resolution computed tomography (HRCT) scans through the middle of lumbar vertebral bodies. Computer-assisted image analysis of the high-resolution images assessed trabecular morphometry of the vertebral spongiosa texture. Texture parameters differed in women with and without age-reduced bone density, and in the former group also in patients with and without vertebral fractures. Discriminating parameters were the total number, diameter and variance of trabecular and intertrabecular spaces as well as the trabecular surface (p < 0.05)). A texture index based on these statistically selected morphometric parameters identified a subgroup of patients suffering from fractures due to abnormal spongiosal architecture but with a bone mineral content not indicative for increased fracture risk. The combination of osteodensitometric and trabecular morphometry improves the diagnosis of osteoporosis and may contribute to the prediction of individual fracture risk. (author)

  10. Diagnosis of genetic predisposition for lactose intolerance by high resolution melting analysis.

    Science.gov (United States)

    Delacour, Hervé; Leduc, Amandine; Louçano-Perdriat, Andréa; Plantamura, Julie; Ceppa, Franck

    2017-02-01

    Lactose, the principle sugar in milk, is a disaccharide hydrolyzed by intestinal lactase into glucose and galactose, which are absorbed directly by diffusion in the intestine. The decline of lactase expression (or hypolactasia) in intestinal microvilli after weaning is a normal phenomenon in mammals known as lactase deficiency. It is observed in nearly 75% of the world population and is an inherited autosomal recessive trait with incomplete penetrance. It is caused by SNPs in a regulatory element for lactase gene. In Indo-European, lactase deficiency is associated with rs4982235 SNP (or -13910C>T). The aim of this study is to describe a method based on high resolution melting for rapidly detecting genetic predisposition to lactose intolerance. Analytical performance of the assay was assessed by evaluating within and betwwen-run precision and by comparing the results (n = 50 patients) obtained with the HRM assay to those obtained with the gold standard (Sanger sequencing of the region of interest). In silico prediction of HRM curves was performed to evaluate the potential impact of the other SNPs described within the PCR product on the HRM analytical performances. The assay has good performance (CV lactose intolerance.

  11. NLTE ANALYSIS OF HIGH-RESOLUTION H -BAND SPECTRA. I. NEUTRAL SILICON

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Junbo; Shi, Jianrong; Liu, Chao [Key Laboratory of Optical Astronomy, National Astronomical Observatories, Chinese Academy of Sciences, A20 Datun Road, Chaoyang District, Beijing 100012 (China); Pan, Kaike [Apache Point Observatory and New Mexico State University, P.O. Box 59, Sunspot, NM, 88349-0059 (United States); Prieto, Carlos Allende, E-mail: sjr@bao.ac.cn [Instituto de Astrofísica de Canarias, E-38205 La Laguna, Tenerife (Spain)

    2016-12-20

    We investigated the reliability of our silicon atomic model and the influence of non-local thermodynamical equilibrium (NLTE) on the formation of neutral silicon (Si i) lines in the near-infrared (near-IR) H -band. We derived the differential Si abundances for 13 sample stars with high-resolution H -band spectra from the Apache Point Observatory Galactic Evolution Experiment (APOGEE), as well as from optical spectra, both under local thermodynamical equilibrium (LTE) and NLTE conditions. We found that the differences between the Si abundances derived from the H -band and from optical lines for the same stars are less than 0.1 dex when the NLTE effects are included, and that NLTE reduces the line-to-line scatter in the H -band spectra for most sample stars. These results suggest that our Si atomic model is appropriate for studying the formation of H -band Si lines. Our calculations show that the NLTE corrections of the Si i H -band lines are negative, i.e., the final Si abundances will be overestimated in LTE. The corrections for strong lines depend on surface gravity, and tend to be larger for giants, reaching ∼−0.2 dex in our sample, and up to ∼−0.4 dex in extreme cases of APOGEE targets. Thus, the NLTE effects should be included in deriving silicon abundances from H -band Si i lines, especially for the cases where only strong lines are available.

  12. System analysis of a tilted field-widened Michelson interferometer for high spectral resolution lidar.

    Science.gov (United States)

    Liu, Dong; Hostetler, Chris; Miller, Ian; Cook, Anthony; Hair, Johnathan

    2012-01-16

    High spectral resolution lidars (HSRLs) have shown great value in aircraft aerosol remote sensing application and are planned for future satellite missions. A compact, robust, quasi-monolithic tilted field-widened Michelson interferometer is being developed as the spectral discrimination filter for an second-generation HSRL(HSRL-2) at NASA Langley Research Center. The Michelson interferometer consists of a cubic beam splitter, a solid arm and an air arm. Piezo stacks connect the air arm mirror to the body of the interferometer and can tune the interferometer within a small range. The whole interferometer is tilted so that the standard Michelson output and the reflected complementary output can both be obtained. In this paper, the transmission ratio is proposed to evaluate the performance of the spectral filter for HSRL. The transmission ratios over different types of system imperfections, such as cumulative wavefront error, locking error, reflectance of the beam splitter and anti-reflection coatings, system tilt, and depolarization angle are analyzed. The requirements of each imperfection for good interferometer performance are obtained.

  13. Identification of chlorinated solvents degradation zones in clay till by high resolution chemical, microbial and compound specific isotope analysis

    DEFF Research Database (Denmark)

    Damgaard, Ida; Bjerg, Poul Løgstrup; Bælum, Jacob

    2013-01-01

    subsampling of the clay till cores. The study demonstrates that an integrated approach combining chemical analysis, molecular microbial tools and compound specific isotope analysis (CSIA) was required in order to document biotic and abiotic degradations in the clay till system. © 2013 Elsevier B.V.......The degradation of chlorinated ethenes and ethanes in clay till was investigated at a contaminated site (Vadsby, Denmark) by high resolution sampling of intact cores combined with groundwater sampling. Over decades of contamination, bioactive zones with degradation of trichloroethene (TCE) and 1...

  14. Experimental analysis of high-resolution soft x-ray microscopy

    International Nuclear Information System (INIS)

    Chao, Weilun; Anderson, Erik H.; Denbeaux, Gregory; Harteneck, Bruce; Pearson, Angelic L.; Olynick, Deirdre; Schneider, Gerd; Attwood, David

    2001-01-01

    The soft x-ray, full-field microscope XM-1 at Lawrence Berkeley National Laboratory's (LBNL) Advanced Light Source has already demonstrated its capability to resolve 25-nm features. This was accomplished using a micro zone plate (MZP) with an outer zone width of 25 nm. Limited by the aspect ratio of the resist used in the fabrication, the gold-plating thickness of that zone plate is around 40 nm. However, some applications, in particular, biological imaging, prefer improved efficiency, which can be achieved by high-aspect-ratio zone plates. We accomplish this by using a bilayer-resist process in the zone plate fabrication. As our first attempt, a 40-nm-outer-zone-width MZP with a nickel-plating thickness of 150 nm (aspect ratio of 4:1) was successfully fabricated. Relative to the 25-nm MZP, this zone plate is ten times more efficient. Using this high-efficiency MZP, a line test pattern with half period of 30 nm is resolved by the microscope at photon energy of 500 eV. Furthermore, with a new multilayer mirror, the XM-1 can now perform imaging up to 1.8 keV. An image of a line test pattern with half period of 40 nm has a measured modulation of 90%. The image was taken at 1.77 keV with the high-efficiency MZP with an outer zone width of 35 nm and a nickel-plating thickness of 180 nm (aspect ratio of 5:1). XM-1 provides a gateway to high-resolution imaging at high energy. To measure frequency response of the XM-1, a partially annealed gold ''island'' pattern was chosen as a test object. After comparison with the SEM image of the pattern, the microscope has the measured cutoff of 19 nm, close to the theoretical one of 17 nm. The normalized frequency response, which is the ratio of the power density of the soft x-ray image to that of the SEM image, is shown in this paper

  15. High-resolution melting curve analysis for rapid detection of mutations in a Medaka TILLING library

    Directory of Open Access Journals (Sweden)

    Deguchi Tomonori

    2010-09-01

    Full Text Available Abstract Background During the last two decades, DNA sequencing has led to the identification of numerous genes in key species; however, in most cases, their functions are still unknown. In this situation, reverse genetics is the most suitable method to assign function to a gene. TILLING (Targeting Induced Local Lesions IN Genomes is a reverse-genetic strategy that combines random chemical mutagenesis with high-throughput discovery of the induced mutations in target genes. The method has been applied to a variety of plant and animal species. Screening of the induced mutations is the most important step in TILLING. Currently, direct sequencing or nuclease-mediated screening of heteroduplexes is widely used for detection of mutations in TILLING. Both methods are useful, but the costs are substantial and turnaround times are relatively long. Thus, there is a need for an alternative method that is of higher throughput and more cost effective. Results In this study, we developed a high resolution melting (HRM assay and evaluated its effectiveness for screening ENU-induced mutations in a medaka TILLING library. We had previously screened mutations in the p53 gene by direct sequencing. Therefore, we first tested the efficiency of the HRM assay by screening mutations in p53, which indicated that the HRM assay is as useful as direct sequencing. Next, we screened mutations in the atr and atm genes with the HRM assay. Nonsense mutations were identified in each gene, and the phenotypes of these nonsense mutants confirmed their loss-of-function nature. Conclusions These results demonstrate that the HRM assay is useful for screening mutations in TILLING. Furthermore, the phenotype of the obtained mutants indicates that medaka is an excellent animal model for investigating genome stability and gene function, especially when combined with TILLING.

  16. High-resolution ultrasonic spectroscopy

    Directory of Open Access Journals (Sweden)

    V. Buckin

    2018-03-01

    Full Text Available High-resolution ultrasonic spectroscopy (HR-US is an analytical technique for direct and non-destructive monitoring of molecular and micro-structural transformations in liquids and semi-solid materials. It is based on precision measurements of ultrasonic velocity and attenuation in analysed samples. The application areas of HR-US in research, product development, and quality and process control include analysis of conformational transitions of polymers, ligand binding, molecular self-assembly and aggregation, crystallisation, gelation, characterisation of phase transitions and phase diagrams, and monitoring of chemical and biochemical reactions. The technique does not require optical markers or optical transparency. The HR-US measurements can be performed in small sample volumes (down to droplet size, over broad temperature range, at ambient and elevated pressures, and in various measuring regimes such as automatic temperature ramps, titrations and measurements in flow.

  17. Modern, PC based, high resolution portable EDXRF analyzer offers laboratory performance for field, in-situ analysis of environmental contaminants

    International Nuclear Information System (INIS)

    Piorek, Stanislaw

    1994-01-01

    The introduction of a new, high resolution, portable probe that has improved the sensitivity of the conventional field portable X-ray fluorescence (FPXRF) by up to an order of magnitude had been reported earlier [S. Piorek and J.R. Pasmore, Proc. 2nd Int. Symp. on Field Screening Methods for Hazardous Wastes and Toxic Chemicals, Las Vegas, 1991, p. 737]. A high resolution Si(Li) detector probe operates connected to a multichannel X-ray analyzer (2048 channels) which is housed in a portable, battery powered industrial computer. An improved energy resolution of the detector allows the implementation of more sophisticated data treatment methods to convert the measured intensities into mass concentrations of the analytes. A backscatter with a fundamental parameters approach (BFP) is one of the best methods, specifically for metallic contaminants in soil. A program has been written based on the BFP method for use with the new probe. The new software/probe combination enables one to quickly assess levels of contaminants on the site without the need of analyzed samples for instrument calibration. The performance of the EDXRF system in application to analysis of metals in contaminated soil is discussed in this paper. Also discussed is the extension of this method in the analysis of other types of environmental samples such as air particulates collected on filter paper. ((orig.))

  18. High resolution melt curve analysis based on methylation status for human semen identification.

    Science.gov (United States)

    Fachet, Caitlyn; Quarino, Lawrence; Karnas, K Joy

    2017-03-01

    A high resolution melt curve assay to differentiate semen from blood, saliva, urine, and vaginal fluid based on methylation status at the Dapper Isoform 1 (DACT1) gene was developed. Stains made from blood, saliva, urine, semen, and vaginal fluid were obtained from volunteers and DNA was isolated using either organic extraction (saliva, urine, and vaginal fluid) or Chelex ® 100 extraction (blood and semen). Extracts were then subjected to bisulfite modification in order to convert unmethylated cytosines to uracil, consequently creating sequences whose amplicons have melt curves that vary depending on their initial methylation status. When primers designed to amplify the promoter region of the DACT1 gene were used, DNA from semen samples was distinguishable from other fluids by a having a statistically significant lower melting temperature. The assay was found to be sperm-significant since semen from a vasectomized man produced a melting temperature similar to the non-semen body fluids. Blood and semen stains stored up to 5 months and tested at various intervals showed little variation in melt temperature indicating the methylation status was stable during the course of the study. The assay is a more viable method for forensic science practice than most molecular-based methods for body fluid stain identification since it is time efficient and utilizes instrumentation common to forensic biology laboratories. In addition, the assay is advantageous over traditional presumptive chemical methods for body fluid identification since results are confirmatory and the assay offers the possibility of multiplexing which may test for multiple body fluids simultaneously.

  19. High spatial resolution analysis of ferromanganese concretions by LA-ICP-MS†

    Directory of Open Access Journals (Sweden)

    Ingri Johan

    2002-06-01

    Full Text Available A procedure was developed for the determination of element distributions in cross-sections of ferromanganese concretions using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS. The effects of carrier flow rates, rf forward power, ablation energy, ablation spot size, repetition rate and number of shots per point on analyte intensity were studied. It is shown that different carrier gas flow rates are required in order to obtain maximum sensitivities for different groups of elements, thus complicating the optimisation of ICP parameters. On the contrary, LA parameters have very similar effects on almost all elements studied, thus providing a common optimum parameter set for the entire mass range. However, for selected LA parameters, the use of compromise conditions was necessary in order to compensate for relatively slow data acquisition by ICP-MS and maintain high spatial resolution without sacrificing the multielemental capabilities of the technique. Possible variations in ablation efficiency were corrected for mathematically using the sum of Fe and Mn intensities. Quantification by external calibration against matrix-matched standards was successfully used for more than 50 elements. These standards, in the form of pressed pellets (no binder, were prepared in-house using ferromanganese concentrates from a deep-sea nodule reference material as well as from shallow-marine concretions varying in size and having different proportions of three major phases: aluminosilicates, Fe- and Mn-oxyhydroxides. Element concentrations in each standard were determined by means of conventional solution nebulisation ICP-MS following acid digestion. Examples of selected inter-element correlations in distribution patterns along the cross-section of a concretion are given.

  20. High-resolution proteomic and lipidomic analysis of exosomes and microvesicles from different cell sources

    Directory of Open Access Journals (Sweden)

    Reka A. Haraszti

    2016-11-01

    Full Text Available Extracellular vesicles (EVs, including exosomes and microvesicles (MVs, are explored for use in diagnostics, therapeutics and drug delivery. However, little is known about the relationship of protein and lipid composition of EVs and their source cells. Here, we report high-resolution lipidomic and proteomic analyses of exosomes and MVs derived by differential ultracentrifugation from 3 different cell types: U87 glioblastoma cells, Huh7 hepatocellular carcinoma cells and human bone marrow-derived mesenchymal stem cells (MSCs. We identified 3,532 proteins and 1,961 lipid species in the screen. Exosomes differed from MVs in several different areas: (a The protein patterns of exosomes were more likely different from their cells of origin than were the protein patterns of MVs; (b The proteomes of U87 and Huh7 exosomes were similar to each other but different from the proteomes of MSC exosomes, whereas the lipidomes of Huh7 and MSC exosomes were similar to each other but different from the lipidomes of U87 exosomes; (c exosomes exhibited proteins of extracellular matrix, heparin-binding, receptors, immune response and cell adhesion functions, whereas MVs were enriched in endoplasmic reticulum, proteasome and mitochondrial proteins. Exosomes and MVs also differed in their types of lipid contents. Enrichment in glycolipids and free fatty acids characterized exosomes, whereas enrichment in ceramides and sphingomyelins characterized MVs. Furthermore, Huh7 and MSC exosomes were specifically enriched in cardiolipins; U87 exosomes were enriched in sphingomyelins. This study comprehensively analyses the protein and lipid composition of exosomes, MVs and source cells in 3 different cell types.

  1. Quantitative Analysis of Swallowing Function Between Dysphagia Patients and Healthy Subjects Using High-Resolution Manometry

    Science.gov (United States)

    2017-01-01

    Objective To compare swallowing function between healthy subjects and patients with pharyngeal dysphagia using high resolution manometry (HRM) and to evaluate the usefulness of HRM for detecting pharyngeal dysphagia. Methods Seventy-five patients with dysphagia and 28 healthy subjects were included in this study. Diagnosis of dysphagia was confirmed by a videofluoroscopy. HRM was performed to measure pressure and timing information at the velopharynx (VP), tongue base (TB), and upper esophageal sphincter (UES). HRM parameters were compared between dysphagia and healthy groups. Optimal threshold values of significant HRM parameters for dysphagia were determined. Results VP maximal pressure, TB maximal pressure, UES relaxation duration, and UES resting pressure were lower in the dysphagia group than those in healthy group. UES minimal pressure was higher in dysphagia group than in the healthy group. Receiver operating characteristic (ROC) analyses were conducted to validate optimal threshold values for significant HRM parameters to identify patients with pharyngeal dysphagia. With maximal VP pressure at a threshold value of 144.0 mmHg, dysphagia was identified with 96.4% sensitivity and 74.7% specificity. With maximal TB pressure at a threshold value of 158.0 mmHg, dysphagia was identified with 96.4% sensitivity and 77.3% specificity. At a threshold value of 2.0 mmHg for UES minimal pressure, dysphagia was diagnosed at 74.7% sensitivity and 60.7% specificity. Lastly, UES relaxation duration of dysphagia. Conclusion We present evidence that HRM could be a useful evaluation tool for detecting pharyngeal dysphagia. PMID:29201816

  2. Rapid screening for targeted genetic variants via high-resolution melting curve analysis.

    Science.gov (United States)

    Chambliss, Allison B; Resnick, Molly; Petrides, Athena K; Clarke, William A; Marzinke, Mark A

    2017-03-01

    Current methods for the detection of single nucleotide polymorphisms (SNPs) associated with aberrant drug-metabolizing enzyme function are hindered by long turnaround times and specialized techniques and instrumentation. In this study, we describe the development and validation of a high-resolution melting (HRM) curve assay for the rapid screening of variant genotypes for targeted genetic polymorphisms in the cytochrome P450 enzymes CYP2C9, CYP2C19, and CYP3A5. Sequence-specific primers were custom-designed to flank nine SNPs within the genetic regions of aforementioned drug metabolizing enzymes. PCR amplification was performed followed by amplicon denaturation by precise temperature ramping in order to distinguish genotypes by melting temperature (Tm). A standardized software algorithm was used to assign amplicons as 'reference' or 'variant' as compared to duplicate reference sequence DNA controls for each SNP. Intra-assay (n=5) precision of Tms for all SNPs was ≤0.19%, while inter-assay (n=20) precision ranged from 0.04% to 0.21%. When compared to a reference method of Sanger sequencing, the HRM assay produced no false negative results, and overcall frequency ranged from 0% to 26%, depending on the SNP. Furthermore, HRM genotyping displayed accuracy over input DNA concentrations ranging from 10 to 200 ng/μL. The presented assay provides a rapid method for the screening for genetic variants in targeted CYP450 regions with a result of 'reference' or 'variant' available within 2 h from receipt of extracted DNA. The method can serve as a screening approach to rapidly identify individuals with variant sequences who should be further investigated by reflexed confirmatory testing for aberrant cytochrome P450 enzymatic activity. Rapid knowledge of variant status may aid in the avoidance of adverse clinical events by allowing for dosing of normal metabolizer patients immediately while identifying the need to wait for confirmatory testing in those patients who are

  3. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology

    Science.gov (United States)

    Mazars, Edith; Lesjean, Sarah; Banuls, Anne-Laure; Gilbert, Michèle; Vincent, Véronique; Gicquel, Brigitte; Tibayrenc, Michel; Locht, Camille; Supply, Philip

    2001-01-01

    The worldwide threat of tuberculosis to human health emphasizes the need to develop novel approaches to a global epidemiological surveillance. The current standard for Mycobacterium tuberculosis typing based on IS6110 restriction fragment length polymorphism (RFLP) suffers from the difficulty of comparing data between independent laboratories. Here, we propose a high-resolution typing method based on variable number tandem repeats (VNTRs) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) in 12 human minisatellite-like regions of the M. tuberculosis genome. MIRU-VNTR profiles of 72 different M. tuberculosis isolates were established by PCR analysis of all 12 loci. From 2 to 8 MIRU-VNTR alleles were identified in the 12 regions in these strains, which corresponds to a potential of over 16 million different combinations, yielding a resolution power close to that of IS6110-RFLP. All epidemiologically related isolates tested were perfectly clustered by MIRU-VNTR typing, indicating that the stability of these MIRU-VNTRs is adequate to track outbreak episodes. The correlation between genetic relationships inferred from MIRU-VNTR and IS6110-RFLP typing was highly significant. Compared with IS6110-RFLP, high-resolution MIRU-VNTR typing has the considerable advantages of being fast, appropriate for all M. tuberculosis isolates, including strains that have a few IS6110 copies, and permitting easy and rapid comparison of results from independent laboratories. This typing method opens the way to the construction of digital global databases for molecular epidemiology studies of M. tuberculosis. PMID:11172048

  4. TOPOGRAPHIC LOCAL ROUGHNESS EXTRACTION AND CALIBRATION OVER MARTIAN SURFACE BY VERY HIGH RESOLUTION STEREO ANALYSIS AND MULTI SENSOR DATA FUSION

    Directory of Open Access Journals (Sweden)

    J. R. Kim

    2012-08-01

    Full Text Available The planetary topography has been the main focus of the in-orbital remote sensing. In spite of the recent development in active and passive sensing technologies to reconstruct three dimensional planetary topography, the resolution limit of range measurement is theoretically and practically obvious. Therefore, the extraction of inner topographical height variation within a measurement spot is very challengeable and beneficial topic for the many application fields such as the identification of landform, Aeolian process analysis and the risk assessment of planetary lander. In this study we tried to extract the topographic height variation over martian surface so called local roughness with different approaches. One method is the employment of laser beam broadening effect and the other is the multi angle optical imaging. Especially, in both cases, the precise pre processing employing high accuracy DTM (Digital Terrain Model were introduced to minimise the possible errors. Since a processing routine to extract very high resolution DTMs up to 0.5–4m grid-spacing from HiRISE (High Resolution Imaging Science Experiment and 20–10m DTM from CTX (Context Camera stereo pair has been developed, it is now possible to calibrate the local roughness compared with the calculated height variation from very high resolution topographic products. Three testing areas were chosen and processed to extract local roughness with the co-registered multi sensor data sets. Even though, the extracted local roughness products are still showing the strong correlation with the topographic slopes, we demonstrated the potentials of the height variations extraction and calibration methods.

  5. Explorative analysis of long time series of very high resolution spatial rainfall

    DEFF Research Database (Denmark)

    Thomassen, Emma Dybro; Sørup, Hjalte Jomo Danielsen; Scheibel, Marc

    2017-01-01

    . For each method a set of 17 variables are used to describe the properties of each event, e.g. duration, maximum volumes, spatial coverage and heterogeneity, and movement of cells. A total of 5-9 dimensions can be found in the data, which can be interpreted as a rough indication of how many independent...... simple scaling across the set of variables, i.e. the level of each variable varies signicantly, but not the overall structure of the spatial precipitation. The analysis show that there is a good potential for making a spatial weather generator for high spatio-temporal precipitation for precipitation...

  6. Exploring high-resolution magic angle spinning (HR-MAS) NMR spectroscopy for metabonomic analysis of apples.

    Science.gov (United States)

    Vermathen, Martina; Marzorati, Mattia; Vermathen, Peter

    2012-01-01

    Classical liquid-state high-resolution (HR) NMR spectroscopy has proved a powerful tool in the metabonomic analysis of liquid food samples like fruit juices. In this paper the application of (1)H high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to apple tissue is presented probing its potential for metabonomic studies. The (1)H HR-MAS NMR spectra are discussed in terms of the chemical composition of apple tissue and compared to liquid-state NMR spectra of apple juice. Differences indicate that specific metabolic changes are induced by juice preparation. The feasibility of HR-MAS NMR-based multivariate analysis is demonstrated by a study distinguishing three different apple cultivars by principal component analysis (PCA). Preliminary results are shown from subsequent studies comparing three different cultivation methods by means of PCA and partial least squares discriminant analysis (PLS-DA) of the HR-MAS NMR data. The compounds responsible for discriminating organically grown apples are discussed. Finally, an outlook of our ongoing work is given including a longitudinal study on apples.

  7. Identification of TNIP1 Polymorphisms by High Resolution Melting Analysis with Unlabelled Probe: Association with Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Jie Zhang

    2012-01-01

    Full Text Available Background. TNFα-induced protein 3 (TNFAIP3 interacting with protein 1 (TNIP1 acts as a negative regulator of NF-κB and plays an important role in maintaining the homeostasis of immune system. A recent genome-wide association study (GWAS showed that the polymorphism of TNIP1 was associated with the disease risk of SLE in Caucasian. In this study, we investigated whether the association of TNIP1 with SLE was replicated in Chinese population. Methods. The association of TNIP1 SNP rs7708392 (G/C was determined by high resolution melting (HRM analysis with unlabeled probe in 285 SLE patients and 336 healthy controls. Results. A new SNP rs79937737 located on 5 bp upstream of rs7708392 was discovered during the HRM analysis. No association of rs7708392 or rs79937737 with the disease risk of SLE was found. Furthermore, rs7708392 and rs79937737 were in weak linkage disequilibrium (LD. Hypotypes analysis of the two SNPs also showed no association with SLE in Chinese population. Conclusions. High resolution melting analysis with unlabeled probes proves to be a powerful and efficient genotyping method for identifying and screening SNPs. No association of rs7708392 or rs79937737 with the disease risk of SLE was observed in Chinese population.

  8. Surface Wind Regionalization over Complex Terrain: Evaluation and Analysis of a High-Resolution WRF Simulation

    NARCIS (Netherlands)

    Jiménez, P.A.; González-Rouco, J.F.; García-Bustamante, E.; Navarro, J.; Montávez, J.P.; Vilà-Guerau de Arellano, J.; Dudhia, J.; Muñoz-Roldan, A.

    2010-01-01

    This study analyzes the daily-mean surface wind variability over an area characterized by complex topography through comparing observations and a 2-km-spatial-resolution simulation performed with the Weather Research and Forecasting (WRF) model for the period 1992–2005. The evaluation focuses on the

  9. Tidal analysis of GNSS data from a high resolution sensor network at Helheim Glacier

    Science.gov (United States)

    Martin, Ian; Aspey, Robin; Baugé, Tim; Edwards, Stuart; Everett, Alistair; James, Timothy; Loskot, Pavel; Murray, Tavi; O'Farrell, Tim; Rutt, Ian

    2014-05-01

    Changes in Greenland and Antarctic ice sheets due to ice flow/ice-berg calving are a major uncertainty affecting sea-level rise forecasts. Latterly GNSS (Global Navigation Satellite Systems) have been employed extensively to monitor such glacier dynamics. Until recently however, the favoured methodology has been to deploy sensors onto the glacier surface, collect data for a period of time, then retrieve and download the sensors. This approach works well in less dynamic environments where the risk of sensor loss is low. In more extreme environments e.g. approaching the glacial calving front, the risk of sensor loss and hence data loss increases dramatically. In order to provide glaciologists with new insights into flow dynamics and calving processes we have developed a novel sensor network to increase the robustness of data capture. We present details of the technological requirements for an in-situ Zigbee wireless streaming network infrastructure supporting instantaneous data acquisition from high resolution GNSS sensors thereby increasing data capture robustness. The data obtained offers new opportunities to investigate the interdependence of mass flow, uplift, velocity and geometry and the network architecture has been specifically designed for deployment by helicopter close to the calving front to yield unprecedented detailed information. Following successful field trials of a pilot three node network during 2012, a larger 20 node network was deployed on the fast-flowing Helheim glacier, south-east Greenland over the summer months of 2013. The utilisation of dual wireless transceivers in each glacier node, multiple frequencies and four 'collector' stations located on the valley sides creates overlapping networks providing enhanced capacity, diversity and redundancy of data 'back-haul', even close to 'floor' RSSI (Received Signal Strength Indication) levels around -100 dBm. Data loss through radio packet collisions within sub-networks are avoided through the

  10. Derivation and analysis of a high-resolution estimate of global permafrost zonation

    Directory of Open Access Journals (Sweden)

    S. Gruber

    2012-02-01

    Full Text Available Permafrost underlies much of Earth's surface and interacts with climate, eco-systems and human systems. It is a complex phenomenon controlled by climate and (sub- surface properties and reacts to change with variable delay. Heterogeneity and sparse data challenge the modeling of its spatial distribution. Currently, there is no data set to adequately inform global studies of permafrost. The available data set for the Northern Hemisphere is frequently used for model evaluation, but its quality and consistency are difficult to assess. Here, a global model of permafrost extent and dataset of permafrost zonation are presented and discussed, extending earlier studies by including the Southern Hemisphere, by consistent data and methods, by attention to uncertainty and scaling. Established relationships between air temperature and the occurrence of permafrost are re-formulated into a model that is parametrized using published estimates. It is run with a high-resolution (<1 km global elevation data and air temperatures based on the NCAR-NCEP reanalysis and CRU TS 2.0. The resulting data provide more spatial detail and a consistent extrapolation to remote regions, while aggregated values resemble previous studies. The estimated uncertainties affect regional patterns and aggregate number, and provide interesting insight. The permafrost area, i.e. the actual surface area underlain by permafrost, north of 60° S is estimated to be 13–18 × 106 km2 or 9–14 % of the exposed land surface. The global permafrost area including Antarctic and sub-sea permafrost is estimated to be 16–21 × 106 km2. The global permafrost region, i.e. the exposed land surface below which some permafrost can be expected, is estimated to be 22 ± 3 × 106 km2. A large proportion of this exhibits considerable topography and spatially-discontinuous permafrost, underscoring the importance of attention to scaling issues

  11. An analysis of MM5 sensitivity to different parameterizations for high-resolution climate simulations

    Science.gov (United States)

    Argüeso, D.; Hidalgo-Muñoz, J. M.; Gámiz-Fortis, S. R.; Esteban-Parra, M. J.; Castro-Díez, Y.

    2009-04-01

    An evaluation of MM5 mesoscale model sensitivity to different parameterizations schemes is presented in terms of temperature and precipitation for high-resolution integrations over Andalusia (South of Spain). As initial and boundary conditions ERA-40 Reanalysis data are used. Two domains were used, a coarse one with dimensions of 55 by 60 grid points with spacing of 30 km and a nested domain of 48 by 72 grid points grid spaced 10 km. Coarse domain fully covers Iberian Peninsula and Andalusia fits loosely in the finer one. In addition to parameterization tests, two dynamical downscaling techniques have been applied in order to examine the influence of initial conditions on RCM long-term studies. Regional climate studies usually employ continuous integration for the period under survey, initializing atmospheric fields only at the starting point and feeding boundary conditions regularly. An alternative approach is based on frequent re-initialization of atmospheric fields; hence the simulation is divided in several independent integrations. Altogether, 20 simulations have been performed using varying physics options, of which 4 were fulfilled applying the re-initialization technique. Surface temperature and accumulated precipitation (daily and monthly scale) were analyzed for a 5-year period covering from 1990 to 1994. Results have been compared with daily observational data series from 110 stations for temperature and 95 for precipitation Both daily and monthly average temperatures are generally well represented by the model. Conversely, daily precipitation results present larger deviations from observational data. However, noticeable accuracy is gained when comparing with monthly precipitation observations. There are some especially conflictive subregions where precipitation is scarcely captured, such as the Southeast of the Iberian Peninsula, mainly due to its extremely convective nature. Regarding parameterization schemes performance, every set provides very

  12. Coastal change analysis of Lovells Island using high resolution ground based LiDAR imagery

    Science.gov (United States)

    Ly, Jennifer K.

    Many methods have been employed to study coastline change. These methods range from historical map analysis to GPS surveys to modern airborne LiDAR and satellite imagery. These previously used methods can be time consuming, labor intensive, and expensive and have varying degrees of accuracy and temporal coverage. Additionally, it is often difficult to apply such techniques in direct response to an isolated event within an appropriate temporal framework. Here we utilize a new ground based Canopy Biomass LiDAR (CBL) system built at The University of Massachusetts Boston (in collaboration with the Rochester Institute of Technology) in order to identify and analyze coastal change on Lovells Island, Boston Harbor. Surveys of a bluff developing in an eroding drumlin and beach cusps on a high-energy cobble beach on Lovells Island were conducted in June, September and December of 2013. At each site for each survey, the CBL was set up and multiple scans of each feature were taken on a predetermined transect that was established parallel to the high-water mark at distances relative to the scale of the bluff and cusps. The scans from each feature were compiled, integrated and visualized using Meshlab. Results from our surveys indicate that the highly portable and easy to deploy CBL system produces images of exceptional clarity, with the capacity to resolve small-scale changes to coastal features and systems. The CBL, while still under development (and coastal surveying protocols with it are just being established), appears to be an ideal tool for analyzing coastal geological features and is anticipated to prove to be a useful tool for the observation and analysis of coastal change. Furthermore, there is significant potential for utilizing the low cost ultra-portable CBL in frequent deployments to develop small-scale erosion rate and sediment budget analyses.

  13. ‘‘Blind'' mapping of genic DNA sequence polymorphisms in Lolium perenne L. by high resolution melting curve analysis

    DEFF Research Database (Denmark)

    Studer, Bruno; Jensen, Louise Bach; Fiil, Alice

    2009-01-01

    High resolution melting curve analysis (HRM) measures dissociation of double stranded DNA of a PCR product amplified in the presence of a saturating fluorescence dye. Recently, HRM proved successful to genotype DNA sequence polymorphisms such as SSRs and SNPs based on the shape of the melting...... curves. In this study, HRM was used for simultaneous screening and genotyping of genic DNA sequence polymorphisms identified in the Lolium perenne F2 mapping population VrnA. Melting profiles of PCR products amplified from previously published gene loci and from a novel gene putatively involved...

  14. High resolution metric imaging payload

    Science.gov (United States)

    Delclaud, Y.

    2017-11-01

    Alcatel Space Industries has become Europe's leader in the field of high and very high resolution optical payloads, in the frame work of earth observation system able to provide military government with metric images from space. This leadership allowed ALCATEL to propose for the export market, within a French collaboration frame, a complete space based system for metric observation.

  15. Flow-Signature Analysis of Water Consumption in Nonresidential Building Water Networks Using High-Resolution and Medium-Resolution Smart Meter Data: Two Case Studies

    Science.gov (United States)

    Clifford, Eoghan; Mulligan, Sean; Comer, Joanne; Hannon, Louise

    2018-01-01

    Real-time monitoring of water consumption activities can be an effective mechanism to achieve efficient water network management. This approach, largely enabled by the advent of smart metering technologies, is gradually being practiced in domestic and industrial contexts. In particular, identifying water consumption habits from flow-signatures, i.e., the specific end-usage patterns, is being investigated as a means for conservation in both the residential and nonresidential context. However, the quality of meter data is bivariate (dependent on number of meters and data temporal resolution) and as a result, planning a smart metering scheme is relatively difficult with no generic design approach available. In this study, a comprehensive medium-resolution to high-resolution smart metering program was implemented at two nonresidential trial sites to evaluate the effect of spatial and temporal data aggregation. It was found that medium-resolution water meter data were capable of exposing regular, continuous, peak use, and diurnal patterns which reflect group wide end-usage characteristics. The high-resolution meter data permitted flow-signature at a personal end-use level. Through this unique opportunity to observe water usage characteristics via flow-signature patterns, newly defined hydraulic-based design coefficients determined from Poisson rectangular pulse were developed to intuitively aid in the process of pattern discovery with implications for automated activity recognition applications. A smart meter classification and siting index was introduced which categorizes meter resolution in terms of their suitable application.

  16. Identification case of evidence in timber tracing of Pinus radiate, using high-resolution melting (HRM) analysis.

    Science.gov (United States)

    Solano, Jaime; Anabalón, Leonardo; Encina, Francisco

    2016-03-01

    Fast, accurate detection of plant species and their hybrids using molecular tools will facilitate assessment and monitoring of timber tracing evidence. In this study the origin of unknown pine samples is determined for a case of timber theft in the region of Araucania southern Chile. We evaluate the utility of the trnL marker region for species identification applied to pine wood based on High Resolution Melting. This efficient tracing methods can be incorporated into forestry applications such as certification of origin. The object of this work was genotype identification using high-resolution melting (HRM) and trnL approaches for Pinus radiata (Don) in timber tracing evidence. Our results indicate that trnL is a very sensitive marker for delimiting species and HRM analysis was used successfully for genotyping Pinus samples for timber tracing purposes. Genotyping samples by HRM analysis with the trnL1 approach allowed us to differentiate two wood samples from the Pinaceae family: Pinus radiata (Don) and Pseudotsuga menziesii (Mirb.) Franco. The same approach with Pinus trnL wood was not able to discriminate between samples of Pinus radiata, indicating that the samples were genetically indistinguishable, possibly because they have the same genotype at this locus. Timber tracing with HRM analysis is expected to contribute to future forest certification schemes, control of illegal trading, and molecular traceability of Pinus spp. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  17. Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled High-Resolution Gamma Spectrometry Systems Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Dreyer, Jonathan G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wang, Tzu-Fang [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vo, Duc T. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Funk, Pierre F. [Inst. for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses (France); Weber, Anne-Laure [Inst. for Radiological Protection and Nuclear Safety (IRSN), Fontenay-aux-Roses (France)

    2017-07-20

    Under a 2006 agreement between the Department of Energy (DOE) of the United States of America and the Institut de Radioprotection et de Sûreté Nucléaire (IRSN) of France, the National Nuclear Security Administration (NNSA) within DOE and IRSN initiated a collaboration to improve isotopic identification and analysis of nuclear material [i.e., plutonium (Pu) and uranium (U)]. The specific aim of the collaborative project was to develop new versions of two types of isotopic identification and analysis software: (1) the fixed-energy response-function analysis for multiple energies (FRAM) codes and (2) multi-group analysis (MGA) codes. The project is entitled Action Sheet 4 – Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled, High-Resolution Gamma Spectrometry Systems (Action Sheet 4). FRAM and MGA/U235HI are software codes used to analyze isotopic ratios of U and Pu. FRAM is an application that uses parameter sets for the analysis of U or Pu. MGA and U235HI are two separate applications that analyze Pu or U, respectively. They have traditionally been used by safeguards practitioners to analyze gamma spectra acquired with high-resolution gamma spectrometry (HRGS) systems that are cooled by liquid nitrogen. However, it was discovered that these analysis programs were not as accurate when used on spectra acquired with a newer generation of more portable, electrically cooled HRGS (ECHRGS) systems. In response to this need, DOE/NNSA and IRSN collaborated to update the FRAM and U235HI codes to improve their performance with newer ECHRGS systems. Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL) performed this work for DOE/NNSA.

  18. Berkeley High-Resolution Ball

    International Nuclear Information System (INIS)

    Diamond, R.M.

    1984-10-01

    Criteria for a high-resolution γ-ray system are discussed. Desirable properties are high resolution, good response function, and moderate solid angle so as to achieve not only double- but triple-coincidences with good statistics. The Berkeley High-Resolution Ball involved the first use of bismuth germanate (BGO) for anti-Compton shield for Ge detectors. The resulting compact shield permitted rather close packing of 21 detectors around a target. In addition, a small central BGO ball gives the total γ-ray energy and multiplicity, as well as the angular pattern of the γ rays. The 21-detector array is nearly complete, and the central ball has been designed, but not yet constructed. First results taken with 9 detector modules are shown for the nucleus 156 Er. The complex decay scheme indicates a transition from collective rotation (prolate shape) to single- particle states (possibly oblate) near spin 30 h, and has other interesting features

  19. A comparative analysis of pixel- and object-based detection of landslides from very high-resolution images

    Science.gov (United States)

    Keyport, Ren N.; Oommen, Thomas; Martha, Tapas R.; Sajinkumar, K. S.; Gierke, John S.

    2018-02-01

    A comparative analysis of landslides detected by pixel-based and object-oriented analysis (OOA) methods was performed using very high-resolution (VHR) remotely sensed aerial images for the San Juan La Laguna, Guatemala, which witnessed widespread devastation during the 2005 Hurricane Stan. A 3-band orthophoto of 0.5 m spatial resolution together with a 115 field-based landslide inventory were used for the analysis. A binary reference was assigned with a zero value for landslide and unity for non-landslide pixels. The pixel-based analysis was performed using unsupervised classification, which resulted in 11 different trial classes. Detection of landslides using OOA includes 2-step K-means clustering to eliminate regions based on brightness; elimination of false positives using object properties such as rectangular fit, compactness, length/width ratio, mean difference of objects, and slope angle. Both overall accuracy and F-score for OOA methods outperformed pixel-based unsupervised classification methods in both landslide and non-landslide classes. The overall accuracy for OOA and pixel-based unsupervised classification was 96.5% and 94.3%, respectively, whereas the best F-score for landslide identification for OOA and pixel-based unsupervised methods: were 84.3% and 77.9%, respectively.Results indicate that the OOA is able to identify the majority of landslides with a few false positive when compared to pixel-based unsupervised classification.

  20. The digital structural analysis of cadmium selenide crystals by a method of ion beam thinning for high resolution electron microscopy

    International Nuclear Information System (INIS)

    Kanaya, Koichi; Baba, Norio; Naka, Michiaki; Kitagawa, Yukihisa; Suzuki, Kunio

    1986-01-01

    A digital processing method using a scanning densitometer system for structural analysis of electron micrographs was successfully applied to a study of cadmium selenide crystals, which were prepared by an argon-ion beam thinning method. Based on Fourier techniques for structural analysis from a computer-generated diffractogram, it was demonstrated that when cadmium selenide crystals were sufficiently thin to display the higher order diffraction spots at a high resolution approaching the atomic level, they constitute an alternative hexagonal lattice of imperfect wurtzite phase from a superposition of individual harmonic images by the enhanced scattering amplitude and corrected phase. From the structural analysis data, a Fourier synthetic lattice image was reconstructed, representing the precise location and three-dimensional arrangement of each of the atoms in the unit cell. Extensively enhanced lattice defect images of dislocations and stacking faults were also derived and shown graphically. (author)

  1. High-resolution melting analysis using unlabeled probe and amplicon scanning simultaneously detects several lactase persistence variants

    DEFF Research Database (Denmark)

    Janukonyté, Jurgita; Vestergaard, Else M; Ladefoged, Søren A

    2010-01-01

    Lactase persistence and thereby tolerance to lactose is a common trait in people of Northern European descent. It is linked to the LCT -13910C>T variant located in intron 13 of the MCM6 gene 13.9 kb upstream of the lactase (LCT) gene. In people of African and Middle Eastern descent, lactase...... persistence can be associated with other variants nearby the -13910C>T variant, limiting the use of the -13910C>T-based SNP analysis, e.g. TaqMan assays for the diagnosis of lactose intolerance. Using high-resolution melting analysis, we identified five samples that were heterozygous for the -13915T>G variant...... the -13910C>T and -13915T>G variants in addition to rarer variants surrounding the -13910 site. This new method may contribute to improve the diagnostic performance of the genetic analysis for lactose intolerance....

  2. Variability Extraction and Synthesis via Multi-Resolution Analysis using Distribution Transformer High-Speed Power Data

    Energy Technology Data Exchange (ETDEWEB)

    Chamana, Manohar [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Mather, Barry A [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-10-19

    A library of load variability classes is created to produce scalable synthetic data sets using historical high-speed raw data. These data are collected from distribution monitoring units connected at the secondary side of a distribution transformer. Because of the irregular patterns and large volume of historical high-speed data sets, the utilization of current load characterization and modeling techniques are challenging. Multi-resolution analysis techniques are applied to extract the necessary components and eliminate the unnecessary components from the historical high-speed raw data to create the library of classes, which are then utilized to create new synthetic load data sets. A validation is performed to ensure that the synthesized data sets contain the same variability characteristics as the training data sets. The synthesized data sets are intended to be utilized in quasi-static time-series studies for distribution system planning studies on a granular scale, such as detailed PV interconnection studies.

  3. Three-dimensional reconstruction and modeling of middle ear biomechanics by high-resolution computed tomography and finite element analysis.

    Science.gov (United States)

    Lee, Chia-Fone; Chen, Peir-Rong; Lee, Wen-Jeng; Chen, Jyh-Horng; Liu, Tien-Chen

    2006-05-01

    To present a systematic and practical approach that uses high-resolution computed tomography to derive models of the middle ear for finite element analysis. This prospective study included 31 subjects with normal hearing and no previous otologic disorders. Temporal bone images obtained from 15 right ears and 16 left ears were used for evaluation and reconstruction. High-resolution computed tomography of temporal bone was performed using simultaneous acquisition of 16 sections with a collimated slice thickness of 0.625 mm. All images were transferred to an Amira visualization system for three-dimensional reconstruction. The created three-dimensional model was translated into two commercial modeling packages, Patran and ANSYS, for finite element analysis. The characteristic dimensions of the model were measured and compared with previously published histologic section data. This result confirms that the geometric model created by the proposed method is accurate except that the tympanic membrane is thicker than when measured by the histologic section method. No obvious difference in the geometrical dimension between right and left ossicles was found (P > .05). The three-dimensional model created by finite element method and predicted umbo and stapes displacements are close to the bounds of the experimental curves of Nishihara's, Huber's, Gan's, and Sun's data across the frequency range of 100 to 8000 Hz. The model includes a description of the geometry of the middle ear components and dynamic equations of vibration. The proposed method is quick, practical, low-cost, and, most importantly, noninvasive as compared with histologic section methods.

  4. High-resolution tree canopy mapping for New York City using LIDAR and object-based image analysis

    Science.gov (United States)

    MacFaden, Sean W.; O'Neil-Dunne, Jarlath P. M.; Royar, Anna R.; Lu, Jacqueline W. T.; Rundle, Andrew G.

    2012-01-01

    Urban tree canopy is widely believed to have myriad environmental, social, and human-health benefits, but a lack of precise canopy estimates has hindered quantification of these benefits in many municipalities. This problem was addressed for New York City using object-based image analysis (OBIA) to develop a comprehensive land-cover map, including tree canopy to the scale of individual trees. Mapping was performed using a rule-based expert system that relied primarily on high-resolution LIDAR, specifically its capacity for evaluating the height and texture of aboveground features. Multispectral imagery was also used, but shadowing and varying temporal conditions limited its utility. Contextual analysis was a key part of classification, distinguishing trees according to their physical and spectral properties as well as their relationships to adjacent, nonvegetated features. The automated product was extensively reviewed and edited via manual interpretation, and overall per-pixel accuracy of the final map was 96%. Although manual editing had only a marginal effect on accuracy despite requiring a majority of project effort, it maximized aesthetic quality and ensured the capture of small, isolated trees. Converting high-resolution LIDAR and imagery into usable information is a nontrivial exercise, requiring significant processing time and labor, but an expert system-based combination of OBIA and manual review was an effective method for fine-scale canopy mapping in a complex urban environment.

  5. Extending the scope of diagnostic chromosome analysis: detection of single gene defects using high-resolution SNP microarrays.

    Science.gov (United States)

    Bruno, Damien L; Stark, Zornitza; Amor, David J; Burgess, Trent; Butler, Kathy; Corrie, Sylvea; Francis, David; Ganesamoorthy, Devika; Hills, Louise; James, Paul A; O'Rielly, Darren; Oertel, Ralph; Savarirayan, Ravi; Prabhakara, Krishnamurthy; Salce, Nicholas; Slater, Howard R

    2011-12-01

    Microarray analysis has provided significant advances in the diagnosis of conditions resulting from submicroscopic chromosome abnormalities. It has been recommended that array testing should be a "first tier" test in the evaluation of individuals with intellectual disability, developmental delay, congenital anomalies, and autism. The availability of arrays with increasingly high probe coverage and resolution has increased the detection of decreasingly small copy number changes (CNCs) down to the intragenic or even exon level. Importantly, arrays that genotype SNPs also detect extended regions of homozygosity. We describe 14 examples of single gene disorders caused by intragenic changes from a consecutive set of 6,500 tests using high-resolution SNP microarrays. These cases illustrate the increased scope of cytogenetic testing beyond dominant chromosome rearrangements that typically contain many genes. Nine of the cases confirmed the clinical diagnosis, that is, followed a "phenotype to genotype" approach. Five were diagnosed by the laboratory analysis in the absence of a specific clinical diagnosis, that is, followed a "genotype to phenotype" approach. Two were clinically significant, incidental findings. The importance of astute clinical assessment and laboratory-clinician consultation is emphasized to optimize the value of microarrays in the diagnosis of disorders caused by single gene copy number and sequence mutations. © 2011 Wiley-Liss, Inc.

  6. A novel typing method for Listeria monocytogenes using high-resolution melting analysis (HRMA) of tandem repeat regions.

    Science.gov (United States)

    Ohshima, Chihiro; Takahashi, Hajime; Iwakawa, Ai; Kuda, Takashi; Kimura, Bon

    2017-07-17

    Listeria monocytogenes, which is responsible for causing food poisoning known as listeriosis, infects humans and animals. Widely distributed in the environment, this bacterium is known to contaminate food products after being transmitted to factories via raw materials. To minimize the contamination of products by food pathogens, it is critical to identify and eliminate factory entry routes and pathways for the causative bacteria. High resolution melting analysis (HRMA) is a method that takes advantage of differences in DNA sequences and PCR product lengths that are reflected by the disassociation temperature. Through our research, we have developed a multiple locus variable-number tandem repeat analysis (MLVA) using HRMA as a simple and rapid method to differentiate L. monocytogenes isolates. While evaluating our developed method, the ability of MLVA-HRMA, MLVA using capillary electrophoresis, and multilocus sequence typing (MLST) was compared for their ability to discriminate between strains. The MLVA-HRMA method displayed greater discriminatory ability than MLST and MLVA using capillary electrophoresis, suggesting that the variation in the number of repeat units, along with mutations within the DNA sequence, was accurately reflected by the melting curve of HRMA. Rather than relying on DNA sequence analysis or high-resolution electrophoresis, the MLVA-HRMA method employs the same process as PCR until the analysis step, suggesting a combination of speed and simplicity. The result of MLVA-HRMA method is able to be shared between different laboratories. There are high expectations that this method will be adopted for regular inspections at food processing facilities in the near future. Copyright © 2017. Published by Elsevier B.V.

  7. Requirements on high resolution detectors

    Energy Technology Data Exchange (ETDEWEB)

    Koch, A. [European Synchrotron Radiation Facility, Grenoble (France)

    1997-02-01

    For a number of microtomography applications X-ray detectors with a spatial resolution of 1 {mu}m are required. This high spatial resolution will influence and degrade other parameters of secondary importance like detective quantum efficiency (DQE), dynamic range, linearity and frame rate. This note summarizes the most important arguments, for and against those detector systems which could be considered. This article discusses the mutual dependencies between the various figures which characterize a detector, and tries to give some ideas on how to proceed in order to improve present technology.

  8. High Resolution 3D Earth Observation Data Analysis for Safeguards Activities

    International Nuclear Information System (INIS)

    D'Angelo, P.; Eineder, M.; Rossi, C.

    2015-01-01

    This paper provides an overview of the investigations performed in the last three years at DLR and highlights the application of SAR and optical data for 3D analysis in the context of Safeguards. The Research Center Juelich and the adjacent open cut mines were used as main test site, and a comprehensive stack of ascending and descending TerraSAR data was acquired over two years. TerraSAR data acquisition was performed, and various ways to visualize stacks of radar images were evaluated. Building height estimation was performed using a combination of ascending-descending radar images, as well as height-form-shadow, height-from-layover. A tutorial on building signatures from SAR images highlighted the sensor specific imaging characteristics. These topics were particularly relevant in safeguards activity with a ''small-budget'' as only a single image - or a couple - were employed. Interferometric coherence map interpretation allows the detection of used dirt roads. Digital surface models (DSM) were generated from TanDEM-X interferometric data and from optical VHR data. Sub-meterWorldview-2 and GeoEye-1 data was processed into highly detailed DSM with a grid spacing of 1 m, showing building structures. 3D change and volume detection was performed with both optical and radar DSMs. The TanDEM-X DSMs proved useful for volume change detection and computation in mining areas, and down to building level with optical data. Virtual fly-through were found to be a good tool to provide an intuitive understanding of site structure and might be useful for inspector briefing. Tools for most of the above mentioned tasks have been developed for the ENVI environment and can be used by IAEA internally. (author)

  9. Application of high resolution x-ray spectrometry preceded by neutron activation for elemental analysis of soil samples

    International Nuclear Information System (INIS)

    Hernandez Rivero, A.; Capote Rodriguez, G.; Padilla Alvarez, R.; Herrera Peraza, E.

    1997-01-01

    Utilization of High Resolution X-Ray Spectrometry preceded by activation of the samples by irradiation with neutron fluxes (NAA-RX) is a relatively modern trend in application of nuclear techniques. This method may complement advantageously the usual Neutron Activation Analysis by means of Gamma Spectrometry (NAA-G). In this work results obtained by the application of NAA-RX for non-destructive analysis of Cuban soil samples are discussed. The samples were irradiated with reactor neutron fluxes and the induced characteristic X-rays were measured by using Si(Li)-detector. Concentrations of Fe, Zn and Eu as determined by NAA-RX are compared with both NAA-G and XRF data. For the elaboration of X-Ray and Gamma Spectra the computer programs AXIL and ACTAN were used respectively. (author) [es

  10. Application of high resolution x-ray spectrometry preceded by neutron activation for elemental analysis of soil samples

    International Nuclear Information System (INIS)

    Hernandez Rivero, A.; Capote Rodriguez, G.; Herrera Peraza, E.

    1996-01-01

    Utilization of High Resolution X-Ray Spectrometry preceded by activation of the samples by irradiation with neutron fluxes (NAA R X) is a relatively modern trend in application of nuclear techniques. This method may complement advantageously the usual Neutron Activation Analysis by means of Gamma Spectrometry (NAA-G) In this work results obtained by the application of NAA-RX for non-destructive analysis of Cuban soil samples are discussed. The samples were irradiated with reactor neutron fluxes and the induced characteristic X-rays were measured by using Si(li)-detector. Concentrations of Fe, Zn and Eu as determined by NAA-RX are compared with both NAA-G and XRF data. For the elaboration of X-ray and Gamma Spectra the computer programs AXIL and ACTAN were used respectively

  11. High resolution optical DNA mapping

    Science.gov (United States)

    Baday, Murat

    Many types of diseases including cancer and autism are associated with copy-number variations in the genome. Most of these variations could not be identified with existing sequencing and optical DNA mapping methods. We have developed Multi-color Super-resolution technique, with potential for high throughput and low cost, which can allow us to recognize more of these variations. Our technique has made 10--fold improvement in the resolution of optical DNA mapping. Using a 180 kb BAC clone as a model system, we resolved dense patterns from 108 fluorescent labels of two different colors representing two different sequence-motifs. Overall, a detailed DNA map with 100 bp resolution was achieved, which has the potential to reveal detailed information about genetic variance and to facilitate medical diagnosis of genetic disease.

  12. Automated analysis of heterogeneous carbon nanostructures by high-resolution electron microscopy and on-line image processing

    International Nuclear Information System (INIS)

    Toth, P.; Farrer, J.K.; Palotas, A.B.; Lighty, J.S.; Eddings, E.G.

    2013-01-01

    High-resolution electron microscopy is an efficient tool for characterizing heterogeneous nanostructures; however, currently the analysis is a laborious and time-consuming manual process. In order to be able to accurately and robustly quantify heterostructures, one must obtain a statistically high number of micrographs showing images of the appropriate sub-structures. The second step of analysis is usually the application of digital image processing techniques in order to extract meaningful structural descriptors from the acquired images. In this paper it will be shown that by applying on-line image processing and basic machine vision algorithms, it is possible to fully automate the image acquisition step; therefore, the number of acquired images in a given time can be increased drastically without the need for additional human labor. The proposed automation technique works by computing fields of structural descriptors in situ and thus outputs sets of the desired structural descriptors in real-time. The merits of the method are demonstrated by using combustion-generated black carbon samples. - Highlights: ► The HRTEM analysis of heterogeneous nanostructures is a tedious manual process. ► Automatic HRTEM image acquisition and analysis can improve data quantity and quality. ► We propose a method based on on-line image analysis for the automation of HRTEM image acquisition. ► The proposed method is demonstrated using HRTEM images of soot particles

  13. Desorption atmospheric pressure photoionization high-resolution mass spectrometry: a complementary approach for the chemical analysis of atmospheric aerosols.

    Science.gov (United States)

    Parshintsev, Jevgeni; Vaikkinen, Anu; Lipponen, Katriina; Vrkoslav, Vladimir; Cvačka, Josef; Kostiainen, Risto; Kotiaho, Tapio; Hartonen, Kari; Riekkola, Marja-Liisa; Kauppila, Tiina J

    2015-07-15

    On-line chemical characterization methods of atmospheric aerosols are essential to increase our understanding of physicochemical processes in the atmosphere, and to study biosphere-atmosphere interactions. Several techniques, including aerosol mass spectrometry, are nowadays available, but they all suffer from some disadvantages. In this research, desorption atmospheric pressure photoionization high-resolution (Orbitrap) mass spectrometry (DAPPI-HRMS) is introduced as a complementary technique for the fast analysis of aerosol chemical composition without the need for sample preparation. Atmospheric aerosols from city air were collected on a filter, desorbed in a DAPPI source with a hot stream of toluene and nitrogen, and ionized using a vacuum ultraviolet lamp at atmospheric pressure. To study the applicability of the technique for ambient aerosol analysis, several samples were collected onto filters and analyzed, with the focus being on selected organic acids. To compare the DAPPI-HRMS data with results obtained by an established method, each filter sample was divided into two equal parts, and the second half of the filter was extracted and analyzed by liquid chromatography/mass spectrometry (LC/MS). The DAPPI results agreed with the measured aerosol particle number. In addition to the targeted acids, the LC/MS and DAPPI-HRMS methods were found to detect different compounds, thus providing complementary information about the aerosol samples. DAPPI-HRMS showed several important oxidation products of terpenes, and numerous compounds were tentatively identified. Thanks to the soft ionization, high mass resolution, fast analysis, simplicity and on-line applicability, the proposed methodology has high potential in the field of atmospheric research. Copyright © 2015 John Wiley & Sons, Ltd.

  14. High-resolution melt-curve analysis of random-amplified-polymorphic-DNA markers, for the characterisation of pathogenic Leptospira

    DEFF Research Database (Denmark)

    Tulsiani, Suhella; Craig, S B; Graham, G C

    2010-01-01

    A new test for pathogenic Leptospira isolates, based on RAPD-PCR and high-resolution melt (HRM) analysis (which measures the melting temperature of amplicons in real time, using a fluorescent DNA-binding dye), has recently been developed. A characteristic profile of the amplicons can be used...... typed against 13 previously published RAPD primers, using a real-time cycler (the Corbett Life Science RotorGene 6000) and the optimised reagents from a commercial kit (Quantace SensiMix). RAPD-HRM at specific temperatures generated defining amplicon melt profiles for each of the tested serovars....... These profiles were evaluated as difference-curve graphs generated using the RotorGene software package, with a cut-off of at least 8 'U' (plus or minus). The results demonstrated that RAPD-HRM can be used to measure serovar diversity and establish identity, with a high degree of stability. The characterisation...

  15. A study on the microstructure of Pt/TaN/Si films by high resolution TEM analysis

    CERN Document Server

    Cho, K N; Oh, J E; Park, C S; Lee, S I; Lee, M Y

    1998-01-01

    The microstructure change of Pt/amorphous TaN/Si films after various heat treatments has been investigated by high resolution transmission electron microscopy (HR-TEM) analysis. TaN thin films are deposited by remote plasma metalorganic chemical vapor deposition (RP-MOCVD) using pentakis-dimethyl-amino-tantalum (PDMATa) and radical sources, hydrogen and ammonia plasma. Deposited TaN thin film shows excellent barrier properties such as good resistance against oxidation after post-heat treatment at high temperature. In the case of hydrogen plasma, however, diffusion of Pt into TaN layer was observed, which was caused by the out-diffusion of carbon through the grain boundaries of Pt. In the case of ammonia plasma, the formation of thin oxide layer at the Pt/TaN interface was observed.

  16. Next-generation technologies for spatial proteomics: Integrating ultra-high speed MALDI-TOF and high mass resolution MALDI FTICR imaging mass spectrometry for protein analysis.

    Science.gov (United States)

    Spraggins, Jeffrey M; Rizzo, David G; Moore, Jessica L; Noto, Michael J; Skaar, Eric P; Caprioli, Richard M

    2016-06-01

    MALDI imaging mass spectrometry is a powerful analytical tool enabling the visualization of biomolecules in tissue. However, there are unique challenges associated with protein imaging experiments including the need for higher spatial resolution capabilities, improved image acquisition rates, and better molecular specificity. Here we demonstrate the capabilities of ultra-high speed MALDI-TOF and high mass resolution MALDI FTICR IMS platforms as they relate to these challenges. High spatial resolution MALDI-TOF protein images of rat brain tissue and cystic fibrosis lung tissue were acquired at image acquisition rates >25 pixels/s. Structures as small as 50 μm were spatially resolved and proteins associated with host immune response were observed in cystic fibrosis lung tissue. Ultra-high speed MALDI-TOF enables unique applications including megapixel molecular imaging as demonstrated for lipid analysis of cystic fibrosis lung tissue. Additionally, imaging experiments using MALDI FTICR IMS were shown to produce data with high mass accuracy (z 5000) for proteins up to ∼20 kDa. Analysis of clear cell renal cell carcinoma using MALDI FTICR IMS identified specific proteins localized to healthy tissue regions, within the tumor, and also in areas of increased vascularization around the tumor. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Resolution analysis by random probing

    NARCIS (Netherlands)

    Fichtner, Andreas; van Leeuwen, T.

    2015-01-01

    We develop and apply methods for resolution analysis in tomography, based on stochastic probing of the Hessian or resolution operators. Key properties of our methods are (i) low algorithmic complexity and easy implementation, (ii) applicability to any tomographic technique, including full‐waveform

  18. Recognition of anesthetic barbiturates by a protein binding site: a high resolution structural analysis.

    Directory of Open Access Journals (Sweden)

    Simon Oakley

    Full Text Available Barbiturates potentiate GABA actions at the GABA(A receptor and act as central nervous system depressants that can induce effects ranging from sedation to general anesthesia. No structural information has been available about how barbiturates are recognized by their protein targets. For this reason, we tested whether these drugs were able to bind specifically to horse spleen apoferritin, a model protein that has previously been shown to bind many anesthetic agents with affinities that are closely correlated with anesthetic potency. Thiopental, pentobarbital, and phenobarbital were all found to bind to apoferritin with affinities ranging from 10-500 µM, approximately matching the concentrations required to produce anesthetic and GABAergic responses. X-ray crystal structures were determined for the complexes of apoferritin with thiopental and pentobarbital at resolutions of 1.9 and 2.0 Å, respectively. These structures reveal that the barbiturates bind to a cavity in the apoferritin shell that also binds haloalkanes, halogenated ethers, and propofol. Unlike these other general anesthetics, however, which rely entirely upon van der Waals interactions and the hydrophobic effect for recognition, the barbiturates are recognized in the apoferritin site using a mixture of both polar and nonpolar interactions. These results suggest that any protein binding site that is able to recognize and respond to the chemically and structurally diverse set of compounds used as general anesthetics is likely to include a versatile mixture of both polar and hydrophobic elements.

  19. High resolution mass spectrometry method and system for analysis of whole proteins and other large molecules

    Science.gov (United States)

    Reilly, Peter T. A. [Knoxville, TN; Harris, William A [Naperville, IL

    2010-03-02

    A matrix assisted laser desorption/ionization (MALDI) method and related system for analyzing high molecular weight analytes includes the steps of providing at least one matrix-containing particle inside an ion trap, wherein at least one high molecular weight analyte molecule is provided within the matrix-containing particle, and MALDI on the high molecular weight particle while within the ion trap. A laser power used for ionization is sufficient to completely vaporize the particle and form at least one high molecular weight analyte ion, but is low enough to avoid fragmenting the high molecular weight analyte ion. The high molecular weight analyte ion is extracted out from the ion trap, and is then analyzed using a detector. The detector is preferably a pyrolyzing and ionizing detector.

  20. Design and analysis of a cross-type structured-illumination confocal microscope for high speed and high resolution

    International Nuclear Information System (INIS)

    Kim, Young-Duk; Ahn, MyoungKi; Kim, Taejoong; Gweon, DaeGab; Yoo, Hongki

    2012-01-01

    There have been many studies about a super resolution microscope for many years. A super resolution microscope can detect the physical phenomena or morphology of a biological sample more precisely than conventional microscopes. The structured-illumination microscope (SIM) is one of the technologies that demonstrate super resolution. However, the conventional SIM requires more time to obtain one resolution-enhanced image than other super resolution microscopes. More specifically, the conventional SIM uses three images with a 120° phase difference for each direction and three different directions are image-processed to make one resolution enhancement by increasing the optical transfer function in three directions. In this paper, we present a novel cross structured-illumination confocal microscope (CSICM) that takes the advantage of the technology of both SIM and the confocal microscope. The CSICM uses only two directions with three phase difference images, for a total of six images. By reducing the number of images that must be obtained, the total image acquisition time and image reconstruction time in obtaining the final output images can be decreased, and the confocal microscope provides axial information of the sample automatically. We demonstrate our method of cross illumination and evaluate the performance of the CSICM and compare it to the conventional SIM and the confocal microscope. (paper)

  1. Fluorine determination in coal using high-resolution graphite furnace molecular absorption spectrometry and direct solid sample analysis

    Energy Technology Data Exchange (ETDEWEB)

    Machado, Patrícia M.; Morés, Silvane; Pereira, Éderson R. [Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC (Brazil); Welz, Bernhard, E-mail: w.bernardo@terra.com.br [Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador, BA (Brazil); Carasek, Eduardo [Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC (Brazil); Andrade, Jailson B. de [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, 40170-115 Salvador, BA (Brazil)

    2015-03-01

    The absorption of the calcium mono-fluoride (CaF) molecule has been employed in this study for the determination of fluorine in coal using direct solid sample analysis and high-resolution continuum source graphite furnace molecular absorption spectrometry (HR-CS GF MAS). The rotational line at 606.440 nm was used for measuring the molecular absorption in the gas phase. The pyrolysis and vaporization temperatures were 700 °C and 2100 °C, respectively. Different chemical modifiers have been studied, such as Pd and Ir as permanent modifiers, and Pd and the mixed Pd/Mg modifier in solution. The limit of detection and the characteristic mass were 0.3 and 0.1 ng F, respectively. One certified reference material (CRM) of coal (NIST 1635) and four CRMs with a non-certified value for F (SARM 18, SARM 20, BCR 40, BCR 180) were used to evaluate the accuracy and precision of the method, obtaining good agreement (104%) with the certified value and with the informed values (ranging from 90 to 103%). - Highlights: • High-resolution Graphite Furnace Molecular Absorption Spectrometry (HR-GF MAS) • Fluorine has been determined using HR-GF MAS of the CaF molecule. • The CaF molecule was generated in a graphite furnace at a temperature of 2100 °C • Coal samples have been analyzed using direct solid sample introduction. • Aqueous standard solutions have been used for calibration.

  2. An Object-Based Image Analysis Approach for Detecting Penguin Guano in very High Spatial Resolution Satellite Images

    Directory of Open Access Journals (Sweden)

    Chandi Witharana

    2016-04-01

    Full Text Available The logistical challenges of Antarctic field work and the increasing availability of very high resolution commercial imagery have driven an interest in more efficient search and classification of remotely sensed imagery. This exploratory study employed geographic object-based analysis (GEOBIA methods to classify guano stains, indicative of chinstrap and Adélie penguin breeding areas, from very high spatial resolution (VHSR satellite imagery and closely examined the transferability of knowledge-based GEOBIA rules across different study sites focusing on the same semantic class. We systematically gauged the segmentation quality, classification accuracy, and the reproducibility of fuzzy rules. A master ruleset was developed based on one study site and it was re-tasked “without adaptation” and “with adaptation” on candidate image scenes comprising guano stains. Our results suggest that object-based methods incorporating the spectral, textural, spatial, and contextual characteristics of guano are capable of successfully detecting guano stains. Reapplication of the master ruleset on candidate scenes without modifications produced inferior classification results, while adapted rules produced comparable or superior results compared to the reference image. This work provides a road map to an operational “image-to-assessment pipeline” that will enable Antarctic wildlife researchers to seamlessly integrate VHSR imagery into on-demand penguin population census.

  3. High-resolution gas chromatographic analysis of polycyclic aromatic hydrocarbons and aliphatic hydrocarbons

    International Nuclear Information System (INIS)

    Perez, M.; Gonzalez, D.

    1988-01-01

    A study of the analysis by gas chromatography of aromatic polycyclic hydrocarbons and aliphatic hydrocarbons is presented. The separation has been carried out by glass and fused silica capillary column in two different polar stationary phases OV-1 and SE-54. The limitation and the advantages of the procedure are discussed in terms of separation, sensitivity and precision. (Author) 20 refs

  4. High resolution tomographic instrument development

    International Nuclear Information System (INIS)

    1992-01-01

    Our recent work has concentrated on the development of high-resolution PET instrumentation reflecting in part the growing importance of PET in nuclear medicine imaging. We have developed a number of positron imaging instruments and have the distinction that every instrument has been placed in operation and has had an extensive history of application for basic research and clinical study. The present program is a logical continuation of these earlier successes. PCR-I, a single ring positron tomograph was the first demonstration of analog coding using BGO. It employed 4 mm detectors and is currently being used for a wide range of biological studies. These are of immense importance in guiding the direction for future instruments. In particular, PCR-II, a volume sensitive positron tomograph with 3 mm spatial resolution has benefited greatly from the studies using PCR-I. PCR-II is currently in the final stages of assembly and testing and will shortly be placed in operation for imaging phantoms, animals and ultimately humans. Perhaps the most important finding resulting from our previous study is that resolution and sensitivity must be carefully balanced to achieve a practical high resolution system. PCR-II has been designed to have the detection characteristics required to achieve 3 mm resolution in human brain under practical imaging situations. The development of algorithms by the group headed by Dr. Chesler is based on a long history of prior study including his joint work with Drs. Pelc and Reiderer and Stearns. This body of expertise will be applied to the processing of data from PCR-II when it becomes operational

  5. High resolution tomographic instrument development

    Energy Technology Data Exchange (ETDEWEB)

    1992-08-01

    Our recent work has concentrated on the development of high-resolution PET instrumentation reflecting in part the growing importance of PET in nuclear medicine imaging. We have developed a number of positron imaging instruments and have the distinction that every instrument has been placed in operation and has had an extensive history of application for basic research and clinical study. The present program is a logical continuation of these earlier successes. PCR-I, a single ring positron tomograph was the first demonstration of analog coding using BGO. It employed 4 mm detectors and is currently being used for a wide range of biological studies. These are of immense importance in guiding the direction for future instruments. In particular, PCR-II, a volume sensitive positron tomograph with 3 mm spatial resolution has benefited greatly from the studies using PCR-I. PCR-II is currently in the final stages of assembly and testing and will shortly be placed in operation for imaging phantoms, animals and ultimately humans. Perhaps the most important finding resulting from our previous study is that resolution and sensitivity must be carefully balanced to achieve a practical high resolution system. PCR-II has been designed to have the detection characteristics required to achieve 3 mm resolution in human brain under practical imaging situations. The development of algorithms by the group headed by Dr. Chesler is based on a long history of prior study including his joint work with Drs. Pelc and Reiderer and Stearns. This body of expertise will be applied to the processing of data from PCR-II when it becomes operational.

  6. High resolution tomographic instrument development

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    Our recent work has concentrated on the development of high-resolution PET instrumentation reflecting in part the growing importance of PET in nuclear medicine imaging. We have developed a number of positron imaging instruments and have the distinction that every instrument has been placed in operation and has had an extensive history of application for basic research and clinical study. The present program is a logical continuation of these earlier successes. PCR-I, a single ring positron tomograph was the first demonstration of analog coding using BGO. It employed 4 mm detectors and is currently being used for a wide range of biological studies. These are of immense importance in guiding the direction for future instruments. In particular, PCR-II, a volume sensitive positron tomograph with 3 mm spatial resolution has benefited greatly from the studies using PCR-I. PCR-II is currently in the final stages of assembly and testing and will shortly be placed in operation for imaging phantoms, animals and ultimately humans. Perhaps the most important finding resulting from our previous study is that resolution and sensitivity must be carefully balanced to achieve a practical high resolution system. PCR-II has been designed to have the detection characteristics required to achieve 3 mm resolution in human brain under practical imaging situations. The development of algorithms by the group headed by Dr. Chesler is based on a long history of prior study including his joint work with Drs. Pelc and Reiderer and Stearns. This body of expertise will be applied to the processing of data from PCR-II when it becomes operational.

  7. Development of numerical simulation technology for high resolution thermal hydraulic analysis

    International Nuclear Information System (INIS)

    Yoon, Han Young; Kim, K. D.; Kim, B. J.; Kim, J. T.; Park, I. K.; Bae, S. W.; Song, C. H.; Lee, S. W.; Lee, S. J.; Lee, J. R.; Chung, S. K.; Chung, B. D.; Cho, H. K.; Choi, S. K.; Ha, K. S.; Hwang, M. K.; Yun, B. J.; Jeong, J. J.; Sul, A. S.; Lee, H. D.; Kim, J. W.

    2012-04-01

    A realistic simulation of two phase flows is essential for the advanced design and safe operation of a nuclear reactor system. The need for a multi dimensional analysis of thermal hydraulics in nuclear reactor components is further increasing with advanced design features, such as a direct vessel injection system, a gravity driven safety injection system, and a passive secondary cooling system. These features require more detailed analysis with enhanced accuracy. In this regard, KAERI has developed a three dimensional thermal hydraulics code, CUPID, for the analysis of transient, multi dimensional, two phase flows in nuclear reactor components. The code was designed for use as a component scale code, and/or a three dimensional component, which can be coupled with a system code. This report presents an overview of the CUPID code development and preliminary assessment, mainly focusing on the numerical solution method and its verification and validation. It was shown that the CUPID code was successfully verified. The results of the validation calculations show that the CUPID code is very promising, but a systematic approach for the validation and improvement of the physical models is still needed

  8. Scanning SRXF analysis and isotopes of uranium series from bottom sediments of Siberian lakes for high-resolution climate reconstructions

    International Nuclear Information System (INIS)

    Goldberg, E.L.; Grachev, M.A.; Chebykin, E.P.; Phedorin, M.A.; Kalugin, I.A.; Khlystov, O.M.; Zolotarev, K.V.

    2005-01-01

    High-resolution scanning X-ray Fluorescence Analysis with Synchrotron Radiation (SRXFA) was applied to investigate the downcore distribution of elements in Lake Baikal and Lake Teletskoye. Physical modeling of river runoff taking into account the chemistry of U series isotopes and their concentrations in sediments allowed a decade-scale reconstruction of Holocene (0-11 ky) river input to Lake Baikal. Holocene moisture peaks in East Siberia are synchronous with abrupt spells in the Atlantic. The multi-element data from Lake Teletskoye were used to predict the function of geochemical response to climate change in plainland Altai and to reconstruct the trends of annual (winter) air temperatures and atmospheric precipitation for the past 500 years

  9. Prepared for the thirtieth annual conference on bioassay analytical and environmental chemistry. Reliable analysis of high resolution gamma spectra

    International Nuclear Information System (INIS)

    Spitz, H.B.; Buschbom, R.; Rieksts, G.A.; Palmer, H.E.

    1985-01-01

    A new method has been developed to reliably analyze pulse height-energy spectra obtained from measurements employing high resolution germanium detectors. The method employs a simple data transformation and smoothing function to calculate background and identify photopeaks and isotopic analysis. This technique is elegant in its simplicity because it avoids dependence upon complex spectrum deconvolution, stripping, or other least-square-fitting techniques which complicate the assessment of measurement reliability. A moving median was chosen for data smoothing because, unlike moving averages, medians are not dominated by extreme data points. Finally, peaks are identified whenever the difference between the background spectrum and the transformed spectrum exceeds a pre-determined number of standard deviations

  10. Chemical state analysis of oxide thin films using a high resolution double crystal X-ray fluorescence spectrometer

    International Nuclear Information System (INIS)

    Masuda, Hirohisa; Morinaga, Kenji; Ohta, Yoshio.

    1995-01-01

    The chemical state analysis of r.f.-sputtered amorphous oxide thin films was determined by a high resolution X-ray fluorescence spectrometer with double crystals. The polymerization degree of silicate anions in the silicate film was as same as a target (α-Quartz). The oxygen coordination number of Al 3+ ions in the aluminate film was different from a target (α-Al 2 O 3 ), and it was a mixture of 4 and 6 in a spinel-like structure. In CaO-SiO 2 and CaO-Al 2 O 3 films, when the film thickness is thin at the beginning of sputtering, the composition of films are in the shortage of CaO. But when the film thickness become thicker, the composition of films become as same as the target. From the results above, the chemical state of films and their variations with film thickness can be clarified by using the apparatus. (author)

  11. High-resolution measurements and multichannel quantum defect analysis of spectral line shapes of autoionizing Rydberg series

    International Nuclear Information System (INIS)

    Ueda, Kiyoshi

    1997-01-01

    Spectral line shapes for autoionizing Rydberg series are briefly reviewed within the framework of multichannel quantum defect theory (MQDT). Recent high-resolution measurements and MQDT analysis for the spectra line shapes are reviewed for the mp 5 ( 2 P 1/2 )ns ' and nd ' J=1 odd spectra of the Ar, Kr, and Xe atoms (m=3,4,5 for Ar, Kr, and Xe) and the 3p 5 ( 2 P 1/2 )nd ' J=2 and 3 odd spectra of Ar*3p 5 4p excited atoms. Some results are also discussed for the Ca 4p( 2 P 1/2,3/2 )ns and nd J=1 odd spectrum and the Ba 5d( 2 P 5/2 )nd J=1 odd spectrum

  12. Nuclear forensic applications involving high spatial resolution analysis of Trinitite cross-sections

    International Nuclear Information System (INIS)

    Donohue, P.H.; Antonio Simonetti; Koeman, E.C.; Sara Mana; University of Iowa, Iowa City, IA; Burns, P.C.; University of Notre Dame, Notre Dame, IN

    2015-01-01

    This study reports a comprehensive cross-sectional analysis of major and trace element abundances and 240 Pu/ 239 Pu ratios within vertically oriented Trinitite thin sections. The upper glassy layer (∼2 mm thick) represents fused desert sand combined with devolatilized fallout from the debris cloud. The vertical distribution of 240 Pu/ 239 Pu ratios indicates that residual fuel was incorporated deeper (up to ∼10 mm depth) into Trinitite than previously reported. This requires thorough mixing and disturbance of the upper cm of the blast site prior to or during the initial melting of the desert sand resulting from the nuclear explosion. (author)

  13. Quantitative chemical analysis for the standardization of copaiba oil by high resolution gas chromatography

    International Nuclear Information System (INIS)

    Tappin, Marcelo R.R.; Pereira, Jislaine F.G.; Lima, Lucilene A.; Siani, Antonio C.; Mazzei, Jose L.; Ramos, Monica F.S.

    2004-01-01

    Quantitative GC-FID was evaluated for analysis of methylated copaiba oils, using trans-(-)-caryophyllene or methyl copalate as external standards. Analytical curves showed good linearity and reproducibility in terms of correlation coefficients (0.9992 and 0.996, respectively) and relative standard deviation (< 3%). Quantification of sesquiterpenes and diterpenic acids were performed with each standard, separately. When compared with the integrator response normalization, the standardization was statistically similar for the case of methyl copalate, but the response of trans-(-)-caryophyllene was statistically (P < 0.05) different. This method showed to be suitable for classification and quality control of commercial samples of the oils. (author)

  14. LiDAR derived high resolution topography: the next challenge for the analysis of terraces stability and vineyard soil erosion

    Directory of Open Access Journals (Sweden)

    Federico Preti

    2013-09-01

    Full Text Available The soil erosion in the vineyards is a critical issue that could affect their productivity, but also, when the cultivation is organized in terraces, increase the risk due to derived slope failure processes. If terraces are not correctly designed or maintained, a progressively increasing of gully erosion affects the structure of the walls. The results of this process is the increasing of connectivity and runoff. In order to overcome such issues it is really important to recognize in detail all the surface drainage paths, thus providing a basis upon which develop a suitable drainage system or provide structural measures for the soil erosion risk mitigation. In the last few years, the airborne LiDAR technology led to a dramatic increase in terrain information. Airborne LiDAR and Terrestrial Laser Scanner derived high-resolution Digital Terrain Models (DTMs have opened avenues for hydrologic and geomorphologic studies (Tarolli et al., 2009. In general, all the main surface process signatures are correctly recognized using a DTM with cell sizes of 1 m. However sub-meter grid sizes may be more suitable in those situations where the analysis of micro topography related to micro changes is critical for slope failures risk assessment or for the design of detailed drainage flow paths. The Terrestrial Laser Scanner (TLS has been proven to be an useful tool for such detailed field survey. In this work, we test the effectiveness of high resolution topography derived by airborne LiDAR and TLS for the recognition of areas subject to soil erosion risk in a typical terraced vineyard landscape of “Chianti Classico” (Tuscany, Italy. The algorithm proposed by Tarolli et al. (2013, for the automatic recognition of anthropic feature induced flow direction changes, has been tested. The results underline the effectiveness of LiDAR and TLS data in the analysis of soil erosion signatures in vineyards, and indicate the high resolution topography as a useful tool to

  15. Novel approaches in analysis of Fusarium mycotoxins in cereals employing ultra performance liquid chromatography coupled with high resolution mass spectrometry

    International Nuclear Information System (INIS)

    Zachariasova, M.; Lacina, O.; Malachova, A.; Kostelanska, M.; Poustka, J.; Godula, M.; Hajslova, J.

    2010-01-01

    Rapid, simple and cost-effective analytical methods with performance characteristics matching regulatory requirements are needed for effective control of occurrence of Fusarium toxins in cereals and cereal-based products to which they might be transferred during processing. Within this study, two alternative approaches enabling retrospective data analysis and identification of unknown signals in sample extracts have been implemented and validated for determination of 11 major Fusarium toxins. In both cases, ultra-high performance liquid chromatography (U-HPLC) coupled with high resolution mass spectrometry (HR MS) was employed. 13 C isotopically labeled surrogates as well as matrix-matched standards were employed for quantification. As far as time of flight mass analyzer (TOF-MS) was a detection tool, the use of modified QuEChERS (quick easy cheap effective rugged and safe) sample preparation procedure, widely employed in multi-pesticides residue analysis, was shown as an optimal approach to obtain low detection limits. The second challenging alternative, enabling direct analysis of crude extract, was the use of mass analyzer based on Orbitrap technology. In addition to demonstration of full compliance of the new methods with Commission Regulation (EC) No. 401/2006, also their potential to be used for confirmatory purposes according to Commission Decision 2002/657/EC has been critically assessed.

  16. High Resolution Spatio Temporal Moments Analysis of Solute Migration Captured using Pre-clinical Medical Imaging Techniques

    Science.gov (United States)

    Dogan, M.; Moysey, S. M.; Powell, B. A.; DeVol, T. A.

    2016-12-01

    Advances in medical imaging technologies are continuously expanding the range of applications enabled within the earth sciences. While computed x-ray tomography (CT) scans have traditionally been used for investigating the structure of geologic materials, it is now possible to perform 3D time-lapse imaging of dynamic processes, such as monitoring the infiltration of water into a soil, with sub-millimeter resolution. Likewise, single photon emission computed tomography (SPECT) can provide information on the evolution of solute transport with spatial resolution on the order of a millimeter by tracking the migration of gamma-ray emitting isotopes like 99mTc and 111In. While these imaging techniques are revolutionizing our ability to look within porous media, techniques for the analysis of such rich and large data sets are limited. The spatial and temporal moments of a plume have long been used to provide quantitative measures to describe plume movement in a wide range of settings from the lab to field. Moment analysis can also be used to estimate the hydrologic properties of the porous media. In this research, we investigate the use of moments for analyzing a high resolution 4D SPECT data set collected during a 99mTc transport experiment performed in a heterogeneous column. The 4D nature of the data set makes it amenable to the use of data mining and pattern recognition methods, such as cluster analysis, to identify regions or zones within the data that exhibit abnormal or unexpected behaviors. We then compare anomalous features within the SPECT data to similar features identified within the CT image to relate the flow behavior to pore-scale structures, such as porosity differences and macropores. Such comparisons help to identify whether these features are good predictors of preferential transport. Likewise, we evaluate whether local analysis of moments can be used to infer apparent parameters governing non-conservative transport in a heterogeneous porous media, such

  17. Analysis of the Emitted Wavelet of High-Resolution Bowtie GPR Antennas

    Directory of Open Access Journals (Sweden)

    Manuel Pereira

    2009-06-01

    Full Text Available Most Ground Penetrating Radars (GPR cover a wide frequency range by emitting very short time wavelets. In this work, we study in detail the wavelet emitted by two bowtie GPR antennas with nominal frequencies of 800 MHz and 1 GHz. Knowledge of this emitted wavelet allows us to extract as much information as possible from recorded signals, using advanced processing techniques and computer simulations. Following previously published methodology used by Rial et al. [1], which ensures system stability and reliability in data acquisition, a thorough analysis of the wavelet in both time and frequency domain is performed. Most of tests were carried out with air as propagation medium, allowing a proper analysis of the geometrical attenuation factor. Furthermore, we attempt to determine, for each antenna, a time zero in the records to allow us to correctly assign a position to the reflectors detected by the radar. Obtained results indicate that the time zero is not a constant value for the evaluated antennas, but instead depends on the characteristics of the material in contact with the antenna.

  18. Liquid chromatography-high resolution mass spectrometry for the analysis of phytochemicals in vegetal-derived food and beverages.

    Science.gov (United States)

    La Barbera, Giorgia; Capriotti, Anna Laura; Cavaliere, Chiara; Montone, Carmela Maria; Piovesana, Susy; Samperi, Roberto; Zenezini Chiozzi, Riccardo; Laganà, Aldo

    2017-10-01

    The recent years witnessed a change in the perception of nutrition. Diet does not only provide nutrients to meet the metabolic requirements of the body, but it also constitutes an active way for the consumption of compounds beneficial for human health. Fruit and vegetables are an excellent source of such compounds, thus the growing interest in characterizing phytochemical sources, structures and activities. Given the interest for phytochemicals in food, the development of advanced and suitable analytical techniques for their identification is fundamental for the advancement of food research. In this review, the state of the art of phytochemical research in food plants is described, starting from sample preparation, throughout extract clean-up and compound separation techniques, to the final analysis, considering both qualitative and quantitative investigations. In this regard, from an analytical point of view, fruit and vegetable extracts are complex matrices, which greatly benefit from the use of modern hyphenated techniques, in particular from the combination of high performance liquid chromatography separation and high resolution mass spectrometry, powerful tools which are being increasingly used in the recent years. Therefore, selected applications to real samples are presented and discussed, in particular for the analysis of phenols, polyphenols and phenolic acids. Finally, some hot points are discussed, such as waste characterization for high value-compounds recovery and the untargeted metabolomics approach. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Classification of brain tumor extracts by high resolution ¹H MRS using partial least squares discriminant analysis

    Directory of Open Access Journals (Sweden)

    A.V. Faria

    2011-02-01

    Full Text Available High resolution proton nuclear magnetic resonance spectroscopy (¹H MRS can be used to detect biochemical changes in vitro caused by distinct pathologies. It can reveal distinct metabolic profiles of brain tumors although the accurate analysis and classification of different spectra remains a challenge. In this study, the pattern recognition method partial least squares discriminant analysis (PLS-DA was used to classify 11.7 T ¹H MRS spectra of brain tissue extracts from patients with brain tumors into four classes (high-grade neuroglial, low-grade neuroglial, non-neuroglial, and metastasis and a group of control brain tissue. PLS-DA revealed 9 metabolites as the most important in group differentiation: γ-aminobutyric acid, acetoacetate, alanine, creatine, glutamate/glutamine, glycine, myo-inositol, N-acetylaspartate, and choline compounds. Leave-one-out cross-validation showed that PLS-DA was efficient in group characterization. The metabolic patterns detected can be explained on the basis of previous multimodal studies of tumor metabolism and are consistent with neoplastic cell abnormalities possibly related to high turnover, resistance to apoptosis, osmotic stress and tumor tendency to use alternative energetic pathways such as glycolysis and ketogenesis.

  20. Towards high resolution analysis of metabolic flux in cells and tissues.

    Science.gov (United States)

    Sims, James K; Manteiga, Sara; Lee, Kyongbum

    2013-10-01

    Metabolism extracts chemical energy from nutrients, uses this energy to form building blocks for biosynthesis, and interconverts between various small molecules that coordinate the activities of cellular pathways. The metabolic state of a cell is increasingly recognized to determine the phenotype of not only metabolically active cell types such as liver, muscle, and adipose, but also other specialized cell types such as neurons and immune cells. This review focuses on methods to quantify intracellular reaction flux as a measure of cellular metabolic activity, with emphasis on studies involving cells of mammalian tissue. Two key areas are highlighted for future development, single cell metabolomics and noninvasive imaging, which could enable spatiotemporally resolved analysis and thereby overcome issues of heterogeneity, a distinctive feature of tissue metabolism. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Method for high resolution magnetic resonance analysis using magic angle technique

    Science.gov (United States)

    Wind, Robert A.; Hu, Jian Zhi

    2003-12-30

    A method of performing a magnetic resonance analysis of a biological object that includes placing the object in a main magnetic field (that has a static field direction) and in a radio frequency field; rotating the object at a frequency of less than about 100 Hz around an axis positioned at an angle of about 54.degree.44' relative to the main magnetic static field direction; pulsing the radio frequency to provide a sequence that includes a phase-corrected magic angle turning pulse segment; and collecting data generated by the pulsed radio frequency. The object may be reoriented about the magic angle axis between three predetermined positions that are related to each other by 120.degree.. The main magnetic field may be rotated mechanically or electronically. Methods for magnetic resonance imaging of the object are also described.

  2. High resolution melting curve analysis, a rapid and affordable method for mutation analysis in childhood acute myeloid leukemia

    Directory of Open Access Journals (Sweden)

    Yin eLiu

    2014-09-01

    Full Text Available Background: Molecular genetic alterations with prognostic significance have been described in childhood acute myeloid leukemia (AML. The aim of this study was to establish cost-effective techniques to detect mutations of FMS-like tyrosine kinase 3 (FLT3, Nucleophosmin 1 (NPM1, and a partial tandem duplication within the mixed lineage leukemia (MLL-PTD genes in childhood AML. Procedure: Ninety-nine children with newly diagnosed AML were included in this study. We developed a fluoresent dye SYTO-82 based high resolution melting curve (HRM anaylsis to detect FLT3 internal tandem duplication (FLT3-ITD, FLT3 tyrosine kinase domain (FLT3-TKD and NPM1 mutations. MLL-PTD was screened by real-time quantitative PCR. Results: The HRM methodology correlated well with gold standard Sanger sequencing with less cost. Among the 99 patients studied, the FLT3-ITD mutation was associated with significantly worse event free survival (EFS. Patients with the NPM1 mutation had significantly better EFS and overall survival. However, HRM was not sensitive enough for minimal residual disease monitoring. Conclusions: HRM was a rapid and efficient method for screening of FLT3 and NPM1 gene mutations. It was both affordable and accurate, especially in resource underprivileged regions. Our results indicated that HRM could be a useful clinical tool for rapid and cost effective screening of the FLT3 and NPM1 mutations in AML patients.

  3. High-resolution sedimentological and subsidence analysis of the Late Neogene, Pannonian Basin, Hungary

    Science.gov (United States)

    Juhasz, E.; Muller, P.; Toth-Makk, A.; Hamor, T.; Farkas-Bulla, J.; Suto-Szentai, M.; Phillips, R.L.; Ricketts, B.

    1996-01-01

    Detailed sedimentological and paleontological analyses were carried out on more than 13,000 m of core from ten boreholes in the Late Neogene sediments of the Pannonian Basin, Hungary. These data provide the basis for determining the character of high-order depositional cycles and their stacking patterns. In the Late Neogene sediments of the Pannonian Basin there are two third-order sequences: the Late Miocene and the Pliocene ones. The Miocene sequence shows a regressive, upward-coarsening trend. There are four distinguishable sedimentary units in this sequence: the basal transgressive, the lower aggradational, the progradational and the upper aggradational units. The Pliocene sequence is also of aggradational character. The progradation does not coincide in time in the wells within the basin. The character of the relative water-level curves is similar throughout the basin but shows only very faint similarity to the sea-level curve. Therefore, it is unlikely that eustasy played any significant role in the pattern of basin filling. Rather, the dominant controls were the rapidly changing basin subsidence and high sedimentation rates, together with possible climatic factors.

  4. High resolution t-LiDAR scanning of an active bedrock fault scarp for palaeostress analysis

    Science.gov (United States)

    Reicherter, Klaus; Wiatr, Thomas; Papanikolaou, Ioannis; Fernández-Steeger, Tomas

    2013-04-01

    Palaeostress analysis of an active bedrock normal fault scarp based on kinematic indicators is carried applying terrestrial laser scanning (t-LiDAR or TLS). For this purpose three key elements are necessary for a defined region on the fault plane: (i) the orientation of the fault plane, (ii) the orientation of the slickenside lineation or other kinematic indicators and (iii) the sense of motion of the hanging wall. We present a workflow to obtain palaeostress data from point cloud data using terrestrial laser scanning. The entire case-study was performed on a continuous limestone bedrock normal fault scarp on the island of Crete, Greece, at four different locations along the WNW-ESE striking Spili fault. At each location we collected data with a mobile terrestrial light detection and ranging system and validated the calculated three-dimensional palaeostress results by comparison with the conventional palaeostress method with compass at three of the locations. Numerous kinematics indicators for normal faulting were discovered on the fault plane surface using t-LiDAR data and traditional methods, like Riedel shears, extensional break-outs, polished corrugations and many more. However, the kinematic indicators are more or less unidirectional and almost pure dip-slip. No oblique reactivations have been observed. But, towards the tips of the fault, inclination of the striation tends to point towards the centre of the fault. When comparing all reconstructed palaeostress data obtained from t-LiDAR to that obtained through manual compass measurements, the degree of fault plane orientation divergence is around ±005/03 for dip direction and dip. The degree of slickenside lineation variation is around ±003/03 for dip direction and dip. Therefore, the percentage threshold error of the individual vector angle at the different investigation site is lower than 3 % for the dip direction and dip for planes, and lower than 6 % for strike. The maximum mean variation of the complete

  5. Landslide Detection in the Carlyon Beach, WA Peninsula: Analysis Of High Resolution DEMs

    Science.gov (United States)

    Fayne, J.; Tran, C.; Mora, O. E.

    2017-12-01

    Landslides are geological events caused by slope instability and degradation, leading to the sliding of large masses of rock and soil down a mountain or hillside. These events are influenced by topography, geology, weather and human activity, and can cause extensive damage to the environment and infrastructure, such as the destruction of transportation networks, homes, and businesses. It is therefore imperative to detect early-warning signs of landslide hazards as a means of mitigation and disaster prevention. Traditional landslide surveillance consists of field mapping, but the process is expensive and time consuming. This study uses Light Detection and Ranging (LiDAR) derived Digital Elevation Models (DEMs) and k-means clustering and Gaussian Mixture Model (GMM) to analyze surface roughness and extract spatial features and patterns of landslides and landslide-prone areas. The methodology based on several feature extractors employs an unsupervised classifier on the Carlyon Beach Peninsula in the state of Washington to attempt to identify slide potential terrain. When compared with the independently compiled landslide inventory map, the proposed algorithm correctly classifies up to 87% of the terrain. These results suggest that the proposed methods and LiDAR-derived DEMs can provide important surface information and be used as efficient tools for digital terrain analysis to create accurate landslide maps.

  6. Application of Object Based Classification and High Resolution Satellite Imagery for Savanna Ecosystem Analysis

    Directory of Open Access Journals (Sweden)

    Jane Southworth

    2010-12-01

    Full Text Available Savanna ecosystems are an important component of dryland regions and yet are exceedingly difficult to study using satellite imagery. Savannas are composed are varying amounts of trees, shrubs and grasses and typically traditional classification schemes or vegetation indices cannot differentiate across class type. This research utilizes object based classification (OBC for a region in Namibia, using IKONOS imagery, to help differentiate tree canopies and therefore woodland savanna, from shrub or grasslands. The methodology involved the identification and isolation of tree canopies within the imagery and the creation of tree polygon layers had an overall accuracy of 84%. In addition, the results were scaled up to a corresponding Landsat image of the same region, and the OBC results compared to corresponding pixel values of NDVI. The results were not compelling, indicating once more the problems of these traditional image analysis techniques for savanna ecosystems. Overall, the use of the OBC holds great promise for this ecosystem and could be utilized more frequently in studies of vegetation structure.

  7. Section on High Resolution Optical Imaging (HROI)

    Data.gov (United States)

    Federal Laboratory Consortium — The Section on High Resolution Optical Imaging (HROI) develops novel technologies for studying biological processes at unprecedented speed and resolution. Research...

  8. High Resolution Thermometry for EXACT

    Science.gov (United States)

    Panek, J. S.; Nash, A. E.; Larson, M.; Mulders, N.

    2000-01-01

    High Resolution Thermometers (HRTs) based on SQUID detection of the magnetization of a paramagnetic salt or a metal alloy has been commonly used for sub-nano Kelvin temperature resolution in low temperature physics experiments. The main applications to date have been for temperature ranges near the lambda point of He-4 (2.177 K). These thermometers made use of materials such as Cu(NH4)2Br4 *2H2O, GdCl3, or PdFe. None of these materials are suitable for EXACT, which will explore the region of the He-3/He-4 tricritical point at 0.87 K. The experiment requirements and properties of several candidate paramagnetic materials will be presented, as well as preliminary test results.

  9. High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling.

    Science.gov (United States)

    Irigoyen, Nerea; Firth, Andrew E; Jones, Joshua D; Chung, Betty Y-W; Siddell, Stuart G; Brierley, Ian

    2016-02-01

    Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global "snap-shot" of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59), a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the ribosomal

  10. High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling.

    Directory of Open Access Journals (Sweden)

    Nerea Irigoyen

    2016-02-01

    Full Text Available Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV, are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global "snap-shot" of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59, a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the

  11. Update from the Analysis of High Resolution Propane Spectra and the Interpretation of Titan's Infrared Spectra

    Science.gov (United States)

    Klavans, V.; Nixon, C.; Hewagama, T.; Jennings, D. E.

    2012-01-01

    Titan has an extremely thick atmosphere dominated by nitrogen, but includes a range of trace species such as hydrocarbons and nitriles. One such hydrocarbon is propane (C3H8). Propane has 21 active IR bands covering broad regions of the mid-infrared. Therefore, its ubiquitous signature may potentially mask weaker signatures of other undetected species with important roles in Titan's chemistry. Cassini's Composite Infrared Spectrometer (CIRS) observations of Titan's atmosphere hint at the presence of such molecules. Unfortunately, C3H8 line atlases for the vibration bands V(sub 8), V(sub 21), V(sub 20), and V(sub 7) (869, 922, 1054, and 1157 per centimeter, respectively) are not currently available for subtracting the C3H8 signal to reveal, or constrain, the signature of underlying chemical species. Using spectra previously obtained by Jennings, D. E., et al. at the McMath-Pierce FTIR at Kitt Peak, AZ, as the source and automated analysis utilities developed for this application, we are compiling an atlas of spectroscopic parameters for propane that characterize the ro-vibrational transitions in the above bands. In this paper, we will discuss our efforts for inspecting and fitting the aforementioned bands, present updated results for spectroscopic parameters including absolute line intensities and transition frequencies in HITRAN and GEISA formats, and show how these optical constants will be used in searching for other trace chemical species in Titan's atmosphere. Our line atlas for the V(sub 21) band contains a total number of 2971 lines. The band integrated strength calculated for the V(sub 21) band is 1.003 per centimeter per (centimeter-atm).

  12. High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes.

    Science.gov (United States)

    Lochlainn, Seosamh Ó; Amoah, Stephen; Graham, Neil S; Alamer, Khalid; Rios, Juan J; Kurup, Smita; Stoute, Andrew; Hammond, John P; Østergaard, Lars; King, Graham J; White, Phillip J; Broadley, Martin R

    2011-12-08

    Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.

  13. High Resolution Melt (HRM analysis is an efficient tool to genotype EMS mutants in complex crop genomes

    Directory of Open Access Journals (Sweden)

    Lochlainn Seosamh Ó

    2011-12-01

    Full Text Available Abstract Background Targeted Induced Loci Lesions IN Genomes (TILLING is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs and insertion/deletions (IN/DELs enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. Results We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. Conclusions Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.

  14. High resolution genome-wide analysis of chromosomal alterations in Burkitt's lymphoma.

    Directory of Open Access Journals (Sweden)

    Saloua Toujani

    Full Text Available Additional chromosomal abnormalities are currently detected in Burkitt's lymphoma. They play major roles in the progression of BL and in prognosis. The genes involved remain elusive. A whole-genome oligonucleotide array CGH analysis correlated with karyotype and FISH was performed in a set of 27 Burkitt's lymphoma-derived cell lines and primary tumors. More than half of the 145 CNAs2 Mb, gains were found in 1q (12/27, 13q (7/27, 7q (6/27, 8q(4/27, 2p (3/27, 11q (2/27 and 15q (2/27. Losses were found in 3p (5/27, 4p (4/27, 4q (4/27, 9p (4/27, 13q (4/27, 6p (3/27, 17p (3/27, 6q (2/27,11pterp13 (2/27 and 14q12q21.3 (2/27. Twenty one minimal critical regions (MCR, (range 0.04-71.36 Mb, were delineated in tumors and cell lines. Three MCRs were localized to 1q. The proximal one was mapped to 1q21.1q25.2 with a 6.3 Mb amplicon (1q21.1q21.3 harboring BCA2 and PIAS3. In the other 2 MCRs, 1q32.1 and 1q44, MDM4 and AKT3 appeared as possible drivers of these gains respectively. The 13q31.3q32.1 MCR contained an amplicon and ABCC4 might be the driver of this amplicon. The 40 Kb 2p16.1 MCR was the smallest gained MCR and specifically encompassed the REL oncogene which is already implicated in B cell lymphomas. The most frequently deleted MCR was 3p14.1 that removed the fifth exon of FHIT. Further investigations which combined gene expression and functional studies are essential to understand the lymphomagenesis mechanism and for the development of more effective, targeted therapeutic strategies.

  15. High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity

    Directory of Open Access Journals (Sweden)

    Rouet Fabien

    2009-10-01

    Full Text Available Abstract Background Commercially available microarrays have been used in many settings to generate expression profiles for a variety of applications, including target selection for disease detection, classification, profiling for pharmacogenomic response to therapeutics, and potential disease staging. However, many commercially available microarray platforms fail to capture transcript diversity produced by alternative splicing, a major mechanism for driving proteomic diversity through transcript heterogeneity. Results The human Genome-Wide SpliceArray™ (GWSA, a novel microarray platform, utilizes an existing probe design concept to monitor such transcript diversity on a genome scale. The human GWSA allows the detection of alternatively spliced events within the human genome through the use of exon body and exon junction probes to provide a direct measure of each transcript, through simple calculations derived from expression data. This report focuses on the performance and validation of the array when measured against standards recently published by the Microarray Quality Control (MAQC Project. The array was shown to be highly quantitative, and displayed greater than 85% correlation with the HG-U133 Plus 2.0 array at the gene level while providing more extensive coverage of each gene. Almost 60% of splice events among genes demonstrating differential expression of greater than 3 fold also contained extensive splicing alterations. Importantly, almost 10% of splice events within the gene set displaying constant overall expression values had evidence of transcript diversity. Two examples illustrate the types of events identified: LIM domain 7 showed no differential expression at the gene level, but demonstrated deregulation of an exon skip event, while erythrocyte membrane protein band 4.1 -like 3 was differentially expressed and also displayed deregulation of a skipped exon isoform. Conclusion Significant changes were detected independent of

  16. High speed, High resolution terahertz spectrometers

    International Nuclear Information System (INIS)

    Kim, Youngchan; Yee, Dae Su; Yi, Miwoo; Ahn, Jaewook

    2008-01-01

    A variety of sources and methods have been developed for terahertz spectroscopy during almost two decades. Terahertz time domain spectroscopy (THz TDS)has attracted particular attention as a basic measurement method in the fields of THz science and technology. Recently, asynchronous optical sampling (AOS)THz TDS has been demonstrated, featuring rapid data acquisition and a high spectral resolution. Also, terahertz frequency comb spectroscopy (TFCS)possesses attractive features for high precision terahertz spectroscopy. In this presentation, we report on these two types of terahertz spectrometer. Our high speed, high resolution terahertz spectrometer is demonstrated using two mode locked femtosecond lasers with slightly different repetition frequencies without a mechanical delay stage. The repetition frequencies of the two femtosecond lasers are stabilized by use of two phase locked loops sharing the same reference oscillator. The time resolution of our terahertz spectrometer is measured using the cross correlation method to be 270 fs. AOS THz TDS is presented in Fig. 1, which shows a time domain waveform rapidly acquired on a 10ns time window. The inset shows a zoom into the signal with 100ps time window. The spectrum obtained by the fast Fourier Transformation (FFT)of the time domain waveform has a frequency resolution of 100MHz. The dependence of the signal to noise ratio (SNR)on the measurement time is also investigated

  17. Line width and line shape analysis in the inductively coupled plasma by high resolution Fourier transform spectrometry

    International Nuclear Information System (INIS)

    Faires, L.M.; Palmer, B.A.; Brault, J.W.

    1984-01-01

    High resolution Fourier transform spectrometry has been used to perform line width and line shape analysis of eighty-one iron I emision lines in the spectral range 290 to 390nm originating in the normal analytical zone of an inductively coupled plasma. Computer programs using non-linear least squares fitting techniques for line shape analysis were applied to the fully resolved spectra to determine Gaussian and Lorentzian components of the total observed line width. The effect of noise in the spectrum on the precision of the line fitting technique was assessed, and the importance of signal to noise ratio for line shape analysis is discussed. Translational (Doppler) temperatures were calculated from the Gaussian components of the line width and were found to be on the order of 6300 0 K. The excitation temperature of iron I was also determined from the same spectral data by the spectroscopic slope method based on the Einstein-Boltzmann expression for spectral intensity and was found to be on the order of 4700 0 K. 31 references

  18. High-resolution melting (HRM) analysis as a feasible method for detecting spinal muscular atrophy via dried blood spots.

    Science.gov (United States)

    Er, Tze-Kiong; Kan, Tzu-Min; Su, Yu-Fa; Liu, Ta-Chih; Chang, Jan-Gowth; Hung, Shih-Ya; Jong, Yuh-Jyh

    2012-11-12

    Spinal muscular atrophy (SMA) is a neurodegenerative disease with the leading genetic cause of infant mortality. More than 95% of patients with SMA have a homozygous disruption in the survival motor neuron1 (SMN1) gene, caused by mutation, deletion, or rearrangement. Recently, treatment in humans in the immediate postnatal period, prior to the development of weakness or very early in the course of the disease, may be effective. Therefore, our objective was to establish a feasible method for SMA screening. High-resolution melting (HRM) analysis is rapidly becoming the most important mutation-scanning methodology that allows mutation scanning and genotyping without the need for costly labeled oligonucleotides. In the current study, we aim to develop a method for identifying the substitution of single nucleotide in SMN1 exon 7 (c.840C>T) by HRM analysis. Genomic DNA was extracted from peripheral blood samples and dried blood spots obtained from 30 patients with SMA and 30 normal individuals. All results were previously confirmed by denaturing high-performance liquid chromatography (DHPLC). In order to identify the substitution of single nucleotide in SMN1 exon 7 (c.840C>T) by HRM analysis, a primer set was used in HRM analysis. At first, we failed to identify the substitution of single nucleotide in SMN1 exon 7 (c.840C>T) by HRM analysis because the homozygous CC and homozygous TT cannot be distinguished by HRM analysis. Therefore, all samples were mixed with a known SMN1/SMN2 copy number (SMN1/SMN2=0:3), which we may call driver. This strategy is used to differentiate between homozygous CC and homozygous TT. After mixing with driver, the melting profile of homozygous CC becomes heteroduplex; however, the homozygous TT remains the same in the normalized and temperature-shifted difference plots. HRM analysis can be successfully applied to screen SMA via DNA obtained from whole blood and dried blood spots. We strongly believe that HRM analysis, a high-throughput method

  19. Identification of the GST-T1 and GST-M1 null genotypes using high resolution melting analysis.

    Science.gov (United States)

    Drobná, Zuzana; Del Razo, Luz Maria; Garcia-Vargas, Gonzalo; Sánchez-Ramírez, Blanca; González-Horta, Carmen; Ballinas-Casarrubias, Lourdes; Loomis, Dana; Stýblo, Miroslav

    2012-01-13

    Glutathione S-transferases, including GST-T1 and GST-M1, are known to be involved in the phase II detoxification pathways for xenobiotics as well as in the metabolism of endogenous compounds. Polymorphisms in these genes have been linked to an increased susceptibility to carcinogenesis and associated with risk factors that predispose to certain inflammatory diseases. In addition, GST-T1 and GST-M1 null genotypes have been shown to be responsible for interindividual variations in the metabolism of arsenic, a known human carcinogen. To assess the specific GST genotypes in the Mexican population chronically exposed to arsenic, we have developed a multiplex High Resolution Melting PCR (HRM-PCR) analysis using a LightCycler480 instrument. This method is based on analysis of the PCR product melting curve that discriminates PCR products according to their lengths and base sequences. Three pairs of primers that specifically recognize GST-T1, GST-M1, and β-globin, an internal control, to produce amplicons of different length were designed and combined with LightCycler480 High Resolution Melting Master Mix containing ResoLight, a completely saturating DNA dye. Data collected from melting curve analysis were evaluated using LightCycler480 software to determine specific melting temperatures of individual melting curves representing target genes. Using this newly developed multiplex HRM-PCR analysis, we evaluated GST-T1 and GST-M1 genotypes in 504 DNA samples isolated from the blood of individuals residing in Zimapan, Lagunera, and Chihuahua regions in Mexico. We found that the Zimapan and Lagunera populations have similar GST-T1 and GST-M1 genotype frequencies which differ from those of the Chihuahua population. In addition, 14 individuals have been identified as carriers of the double null genotype, i.e., null genotypes in both GST-T1 and GST-M1 genes. Although this procedure does not distinguish between biallelic (+/+) and monoallelic (+/-) genotypes, it can be used in an

  20. Analysis of High Resolution Satellite imagery to acsees Glacier Mass Balance and Lake Hazards in Sikkim Himalayas

    Science.gov (United States)

    Bhushan, S.; Shean, D. E.; Haritashya, U. K.; Arendt, A. A.; Syed, T. H.; Setiawan, L.

    2017-12-01

    Glacial lake outburst floods can impact downstream communities due to the sudden outflux of huge quantities of stored water. In this study, we develop a hazard assessment of the moraine dammed glacial lakes in Sikkim Himalayas by analyzing the morphometry of proglacial features, and the surface velocity and mass balance of glaciers. We generated high-resolution digital elevation models (DEMs) using the open-source NASA Ames Stereo Pipeline (ASP) and use other open-source tools to calculate surface velocity and patterns of glacier downwasting over time. Geodetic glacier mass balance is obtained for three periods using high-resolution WorldView/GeoEye stereo DEMs (8 m posting, 2014-2016), Cartosat-1 stereo DEMs (10 m, 2006-2008) and SRTM (30 m, 2000). Initial results reveal a region-wide mass balance of -0.31±0.13 m w.eq.a-1 for the 2007-2015 period, with some debris covered glaciers showing a very low mass loss rate. Additionally, 12 annual glacier velocity fields spanning from 1991 to 2017.derived from Landsat imagery are used to explore the relationship between glacier dynamics and changes in proglacial lakes. Multi-temporal glacial lake mapping is conducted using Landsat and Cartosat imagery. Avalanche and rockfall modeling are combined with morphometric analysis of the proglacial lake area to assess the likelihood of glacial lake dam failure. The above parameters are integrated into a decision tree approach enabling categorization of moraine-dammed lakes according to their potential for outburst events.

  1. Detection of Crater Rims by Image Analysis in Very High Resolution Images of Mars, Mercury and the Moon

    Science.gov (United States)

    Pina, P.; Marques, J. S.; Bandeira, L.

    2013-12-01

    The adaptive nature of automated crater detection algorithms permits achieving a high level of autonomous detections in different surfaces and consequently becoming an important tool in the update of crater catalogues. Nevertheless, the available approaches assume all craters as circular and only provide as output the radius and location of each crater. However, the delineation of impact craters following the local variability of the rims is also important to, among others, evaluate their degree of degradation or preservation, namely those studies related to ancient climate analysis. This contour determination is normally prepared in a manual way but can advantageously be done by image analysis methods, eliminating subjectivity and allowing large scale delineations. We have recently proposed a pair of independent approaches to tackle with this problem, one based on processing the crater image in polar coordinates [1], the other using morphological operators [2], which achieved a good degree of success on very high resolution images from Mars [3-4], but where enough room for improvement was still available. Thus, the integration of both approaches into a single one, suppressing the individual drawbacks of the previous approaches, permitted to strength the detection procedure. We describe now the novel sequence of processing that we have built and test it intensively in a wider variety of planetary surfaces, namely, those of Mars, Mercury and the Moon, using the very high resolution images provided by HiRISE, MDIS and LROC cameras. The automated delineations of the craters are compared to a ground-truth reference (manually delineated contours), so a quantitative evaluation can be performed; on a dataset constituted by more than one thousand impact craters we have obtained a global high delineation rate. The breakdown by crater size on each surface is performed. The whole processing procedure works on raster images and also delivers the output in the same image format

  2. Validation of high-resolution DNA melting analysis for mutation scanning of the CDKL5 gene: identification of novel mutations.

    Science.gov (United States)

    Raymond, Laure; Diebold, Bertrand; Leroux, Céline; Maurey, Hélène; Drouin-Garraud, Valérie; Delahaye, Andre; Dulac, Olivier; Metreau, Julia; Melikishvili, Gia; Toutain, Annick; Rivier, François; Bahi-Buisson, Nadia; Bienvenu, Thierry

    2013-01-01

    Mutations in the cyclin-dependent kinase-like 5 gene (CDKL5) have been predominantly described in epileptic encephalopathies of female, including infantile spasms with Rett-like features. Up to now, detection of mutations in this gene was made by laborious, expensive and/or time consuming methods. Here, we decided to validate high-resolution melting analysis (HRMA) for mutation scanning of the CDKL5 gene. Firstly, using a large DNA bank consisting to 34 samples carrying different mutations and polymorphisms, we validated our analytical conditions to analyse the different exons and flanking intronic sequences of the CDKL5 gene by HRMA. Secondly, we screened CDKL5 by both HRMA and denaturing high performance liquid chromatography (dHPLC) in a cohort of 135 patients with early-onset seizures. Our results showed that point mutations and small insertions and deletions can be reliably detected by HRMA. Compared to dHPLC, HRMA profiles are more discriminated, thereby decreasing unnecessary sequencing. In this study, we identified eleven novel sequence variations including four pathogenic mutations (2.96% prevalence). HRMA appears cost-effective, easy to set up, highly sensitive, non-toxic and rapid for mutation screening, ideally suited for large genes with heterogeneous mutations located along the whole coding sequence, such as the CDKL5 gene. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Rapid detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini using real-time PCR and high resolution melting analysis.

    Science.gov (United States)

    Cai, Xian-Quan; Yu, Hai-Qiong; Li, Rong; Yue, Qiao-Yun; Liu, Guo-Hua; Bai, Jian-Shan; Deng, Yan; Qiu, De-Yi; Zhu, Xing-Quan

    2014-01-01

    Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA extracted from the two flukes yielded specific amplification and their identity was confirmed by sequencing, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit below 1 pg of purified genomic DNA, 5 EPG, or 1 metacercaria of C. sinensis. Moreover, C. sinensis and O. viverrini were able to be differentiated by their HRM profiles. The method can reduce labor of microscopic examination and the contamination of agarose electrophoresis. Moreover, it can differentiate these two flukes which are difficult to be distinguished using other methods. The established method provides an alternative tool for rapid, simple, and duplex detection of C. sinensis and O. viverrini.

  4. Rapid Detection and Differentiation of Clonorchis sinensis and Opisthorchis viverrini Using Real-Time PCR and High Resolution Melting Analysis

    Directory of Open Access Journals (Sweden)

    Xian-Quan Cai

    2014-01-01

    Full Text Available Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA extracted from the two flukes yielded specific amplification and their identity was confirmed by sequencing, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit below 1 pg of purified genomic DNA, 5 EPG, or 1 metacercaria of C. sinensis. Moreover, C. sinensis and O. viverrini were able to be differentiated by their HRM profiles. The method can reduce labor of microscopic examination and the contamination of agarose electrophoresis. Moreover, it can differentiate these two flukes which are difficult to be distinguished using other methods. The established method provides an alternative tool for rapid, simple, and duplex detection of C. sinensis and O. viverrini.

  5. Analysis of stationary fuel cell dynamic ramping capabilities and ultra capacitor energy storage using high resolution demand data

    Science.gov (United States)

    Meacham, James R.; Jabbari, Faryar; Brouwer, Jacob; Mauzey, Josh L.; Samuelsen, G. Scott

    Current high temperature fuel cell (HTFC) systems used for stationary power applications (in the 200-300 kW size range) have very limited dynamic load following capability or are simply base load devices. Considering the economics of existing electric utility rate structures, there is little incentive to increase HTFC ramping capability beyond 1 kWs -1 (0.4% s -1). However, in order to ease concerns about grid instabilities from utility companies and increase market adoption, HTFC systems will have to increase their ramping abilities, and will likely have to incorporate electrical energy storage (EES). Because batteries have low power densities and limited lifetimes in highly cyclic applications, ultra capacitors may be the EES medium of choice. The current analyses show that, because ultra capacitors have a very low energy storage density, their integration with HTFC systems may not be feasible unless the fuel cell has a ramp rate approaching 10 kWs -1 (4% s -1) when using a worst-case design analysis. This requirement for fast dynamic load response characteristics can be reduced to 1 kWs -1 by utilizing high resolution demand data to properly size ultra capacitor systems and through demand management techniques that reduce load volatility.

  6. Experimental investigation on spontaneously active hippocampal cultures recorded by means of high-density MEAs: analysis of the spatial resolution effects

    Directory of Open Access Journals (Sweden)

    Alessandro Maccione

    2010-05-01

    Full Text Available Based on experiments performed with high-resolution Active Pixel Sensor microelectrode arrays (APS-MEAs coupled with spontaneously active hippocampal cultures, this work investigates the spatial resolution effects of the neuroelectronic interface on the analysis of the recorded electrophysiological signals. The adopted methodology consists, first, in recording the spontaneous activity at the highest spatial resolution (inter-electrode separation of 21 µm from the whole array of 4096 microelectrodes. Then, the full resolution dataset is spatially down sampled in order to evaluate the effects on raster plot representation, array-wide spike rate (AWSR, mean firing rate (MFR and mean bursting rate (MBR. Furthermore, the effects of the array-to-network relative position are evaluated by shifting a subset of equally spaced electrodes on the entire recorded area. Results highlight that MFR and MBR are particularly influenced by the spatial resolution provided by the neuroelectronic interface. On high-resolution large MEAs, such analysis better represent the time-based parameterization of the network dynamics. Finally, this work suggest interesting capabilities of high-resolution MEAs for spatial-based analysis in dense and low-dense neuronal preparation for investigating signalling at both local and global neuronal circuitries.

  7. High-resolution continuous flow analysis setup for water isotopic measurement from ice cores using laser spectroscopy

    Science.gov (United States)

    Emanuelsson, B. D.; Baisden, W. T.; Bertler, N. A. N.; Keller, E. D.; Gkinis, V.

    2014-12-01

    Here we present an experimental setup for water stable isotopes (δ18O and δD) continuous flow measurements. It is the first continuous flow laser spectroscopy system that is using Off-Axis Integrated Cavity Output Spectroscopy (OA-ICOS; analyzer manufactured by Los Gatos Research - LGR) in combination with an evaporation unit to continuously analyze sample from an ice core. A Water Vapor Isotopic Standard Source (WVISS) calibration unit, manufactured by LGR, was modified to: (1) increase the temporal resolution by reducing the response time (2) enable measurements on several water standards, and (3) to reduce the influence from memory effects. While this setup was designed for the Continuous Flow Analysis (CFA) of ice cores, it can also continuously analyze other liquid or vapor sources. The modified setup provides a shorter response time (~54 and 18 s for 2013 and 2014 setup, respectively) compared to the original WVISS unit (~62 s), which is an improvement in measurement resolution. Another improvement compared to the original WVISS is that the modified setup has a reduced memory effect. Stability tests comparing the modified WVISS and WVISS setups were performed and Allan deviations (σAllan) were calculated to determine precision at different averaging times. For the 2013 modified setup the precision after integration times of 103 s are 0.060 and 0.070‰ for δ18O and δD, respectively. For the WVISS setup the corresponding σAllan values are 0.030, 0.060 and 0.043‰ for δ18O, δD and δ17O, respectively. For the WVISS setup the precision is 0.035, 0.070 and 0.042‰ after 103 s for δ18O, δD and δ17O, respectively. Both the modified setups and WVISS setup are influenced by instrumental drift with δ18O being more drift sensitive than δD. The σAllan values for δ18O of 0.30 and 0.18‰ for the modified (2013) and WVISS setup, respectively after averaging times of 104 s (2.78 h). The Isotopic Water Analyzer (IWA)-modified WVISS setup used during the

  8. Using object-based image analysis to conduct high-resolution conifer extraction at regional spatial scales

    Science.gov (United States)

    Coates, Peter S.; Gustafson, K. Benjamin; Roth, Cali L.; Chenaille, Michael P.; Ricca, Mark A.; Mauch, Kimberly; Sanchez-Chopitea, Erika; Kroger, Travis J.; Perry, William M.; Casazza, Michael L.

    2017-08-10

    The distribution and abundance of pinyon (Pinus monophylla) and juniper (Juniperus osteosperma, J. occidentalis) trees (hereinafter, "pinyon-juniper") in sagebrush (Artemisia spp.) ecosystems of the Great Basin in the Western United States has increased substantially since the late 1800s. Distributional expansion and infill of pinyon-juniper into sagebrush ecosystems threatens the ecological function and economic viability of these ecosystems within the Great Basin, and is now a major contemporary challenge facing land and wildlife managers. Particularly, pinyon-juniper encroachment into intact sagebrush ecosystems has been identified as a primary threat facing populations of greater sage-grouse (Centrocercus urophasianus; hereinafter, "sage-grouse"), which is a sagebrush obligate species. Even seemingly innocuous scatterings of isolated pinyon-juniper in an otherwise intact sagebrush landscape can negatively affect survival and reproduction of sage-grouse. Therefore, accurate and high-resolution maps of pinyon-juniper distribution and abundance (indexed by canopy cover) across broad geographic extents would help guide land management decisions that better target areas for pinyon-juniper removal projects (for example, fuel reduction, habitat improvement for sage-grouse, and other sagebrush species) and facilitate science that further quantifies ecological effects of pinyon-juniper encroachment on sage-grouse populations and sagebrush ecosystem processes. Hence, we mapped pinyon-juniper (referred to as conifers for actual mapping) at a 1 × 1-meter (m) high resolution across the entire range of previously mapped sage-grouse habitat in Nevada and northeastern California.We used digital orthophoto quad tiles from National Agriculture Imagery Program (2010, 2013) as base imagery, and then classified conifers using automated feature extraction methodology with the program Feature Analyst™. This method relies on machine learning algorithms that extract features from

  9. Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2

    Directory of Open Access Journals (Sweden)

    Sinilnikova Olga

    2011-05-01

    Full Text Available Abstract Background The gene CHEK2 encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though CHEK2 has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk families have been explained by genetic variants located in its coding region. Alteration in gene expression regulation provides a potential mechanism for generating disease susceptibility. The detection of differential allelic expression (DAE represents a sensitive assay to direct the search for a functional sequence variant within the transcriptional regulatory elements of a candidate gene. We aimed to assess whether CHEK2 was subject to DAE in lymphoblastoid cell lines (LCLs from high-risk breast cancer patients for whom no mutation in BRCA1 or BRCA2 had been identified. Methods We implemented an assay based on high-resolution melting (HRM curve analysis and developed an analysis tool for DAE assessment. Results We observed allelic expression imbalance in 4 of the 41 LCLs examined. All four were carriers of the truncating mutation 1100delC. We confirmed previous findings that this mutation induces non-sense mediated mRNA decay. In our series, we ruled out the possibility of a functional sequence variant located in the promoter region or in a regulatory element of CHEK2 that would lead to DAE in the transcriptional regulatory milieu of freely proliferating LCLs. Conclusions Our results support that HRM is a sensitive and accurate method for DAE assessment. This approach would be of great interest for high-throughput mutation screening projects aiming to identify genes carrying functional regulatory polymorphisms.

  10. ISDoT: in situ decellularization of tissues for high-resolution imaging and proteomic analysis of native extracellular matrix

    DEFF Research Database (Denmark)

    Mayorca-Guiliani, Alejandro E.; Madsen, Chris D.; Cox, Thomas R.

    2017-01-01

    The extracellular matrix (ECM) is a master regulator of cellular phenotype and behavior. It has a crucial role in both normal tissue homeostasis and disease pathology. Here we present a fast and efficient approach to enhance the study of ECM composition and structure. Termed in situ...... decellularization of tissues (ISDoT), it allows whole organs to be decellularized, leaving native ECM architecture intact. These three-dimensional decellularized tissues can be studied using high-resolution fluorescence and second harmonic imaging, and can be used for quantitative proteomic interrogation of the ECM....... Our method is superior to other methods tested in its ability to preserve the structural integrity of the ECM, facilitate high-resolution imaging and quantitatively detect ECM proteins. In particular, we performed high-resolution sub-micron imaging of matrix topography in normal tissue and over...

  11. High-resolution intravital microscopy.

    Directory of Open Access Journals (Sweden)

    Volker Andresen

    Full Text Available Cellular communication constitutes a fundamental mechanism of life, for instance by permitting transfer of information through synapses in the nervous system and by leading to activation of cells during the course of immune responses. Monitoring cell-cell interactions within living adult organisms is crucial in order to draw conclusions on their behavior with respect to the fate of cells, tissues and organs. Until now, there is no technology available that enables dynamic imaging deep within the tissue of living adult organisms at sub-cellular resolution, i.e. detection at the level of few protein molecules. Here we present a novel approach called multi-beam striped-illumination which applies for the first time the principle and advantages of structured-illumination, spatial modulation of the excitation pattern, to laser-scanning-microscopy. We use this approach in two-photon-microscopy--the most adequate optical deep-tissue imaging-technique. As compared to standard two-photon-microscopy, it achieves significant contrast enhancement and up to 3-fold improved axial resolution (optical sectioning while photobleaching, photodamage and acquisition speed are similar. Its imaging depth is comparable to multifocal two-photon-microscopy and only slightly less than in standard single-beam two-photon-microscopy. Precisely, our studies within mouse lymph nodes demonstrated 216% improved axial and 23% improved lateral resolutions at a depth of 80 µm below the surface. Thus, we are for the first time able to visualize the dynamic interactions between B cells and immune complex deposits on follicular dendritic cells within germinal centers (GCs of live mice. These interactions play a decisive role in the process of clonal selection, leading to affinity maturation of the humoral immune response. This novel high-resolution intravital microscopy method has a huge potential for numerous applications in neurosciences, immunology, cancer research and

  12. High-Resolution Intravital Microscopy

    Science.gov (United States)

    Andresen, Volker; Pollok, Karolin; Rinnenthal, Jan-Leo; Oehme, Laura; Günther, Robert; Spiecker, Heinrich; Radbruch, Helena; Gerhard, Jenny; Sporbert, Anje; Cseresnyes, Zoltan; Hauser, Anja E.; Niesner, Raluca

    2012-01-01

    Cellular communication constitutes a fundamental mechanism of life, for instance by permitting transfer of information through synapses in the nervous system and by leading to activation of cells during the course of immune responses. Monitoring cell-cell interactions within living adult organisms is crucial in order to draw conclusions on their behavior with respect to the fate of cells, tissues and organs. Until now, there is no technology available that enables dynamic imaging deep within the tissue of living adult organisms at sub-cellular resolution, i.e. detection at the level of few protein molecules. Here we present a novel approach called multi-beam striped-illumination which applies for the first time the principle and advantages of structured-illumination, spatial modulation of the excitation pattern, to laser-scanning-microscopy. We use this approach in two-photon-microscopy - the most adequate optical deep-tissue imaging-technique. As compared to standard two-photon-microscopy, it achieves significant contrast enhancement and up to 3-fold improved axial resolution (optical sectioning) while photobleaching, photodamage and acquisition speed are similar. Its imaging depth is comparable to multifocal two-photon-microscopy and only slightly less than in standard single-beam two-photon-microscopy. Precisely, our studies within mouse lymph nodes demonstrated 216% improved axial and 23% improved lateral resolutions at a depth of 80 µm below the surface. Thus, we are for the first time able to visualize the dynamic interactions between B cells and immune complex deposits on follicular dendritic cells within germinal centers (GCs) of live mice. These interactions play a decisive role in the process of clonal selection, leading to affinity maturation of the humoral immune response. This novel high-resolution intravital microscopy method has a huge potential for numerous applications in neurosciences, immunology, cancer research and developmental biology

  13. Evaluation of gas chromatography – electron ionization – full scan high resolution Orbitrap mass spectrometry for pesticide residue analysis

    Energy Technology Data Exchange (ETDEWEB)

    Mol, Hans G.J., E-mail: hans.mol@wur.nl; Tienstra, Marc; Zomer, Paul

    2016-09-07

    Gas chromatography with electron ionization and full scan high resolution mass spectrometry with an Orbitrap mass analyzer (GC-EI-full scan Orbitrap HRMS) was evaluated for residue analysis. Pesticides in fruit and vegetables were taken as an example application. The relevant aspects for GC-MS based residue analysis, including the resolving power (15,000 to 120,000 FWHM at m/z 200), scan rate, dynamic range, selectivity, sensitivity, analyte identification, and utility of existing EI-libraries, are assessed and discussed in detail. The optimum acquisition conditions in full scan mode (m/z 50–500) were a resolving power of 60,000 and an automatic-gain-control target value of 3E6. These conditions provided (i) an optimum mass accuracy: within 2 ppm over a wide concentration range, with/without matrix, enabling the use of ±5 ppm mass extraction windows (ii) adequate scan speed: minimum 12 scans/peak, (iii) an intra-scan dynamic range sufficient to achieve LOD/LOQs ≤0.5 pg in fruit/vegetable matrices (corresponding to ≤0.5 μg kg{sup −1}) for most pesticides. EI-Orbitrap spectra were consistent over a very wide concentration range (5 orders) with good match values against NIST (EI-quadrupole) spectra. The applicability for quantitative residue analysis was verified by validation of 54 pesticides in three matrices (tomato, leek, orange) at 10 and 50 μg/kg. The method involved a QuEChERS-based extraction with a solvent switch into iso-octane, and 1 μL hot splitless injection into the GC-HRMS system. A recovery between 70 and 120% and a repeatability RSD <10% was obtained in most cases. Linearity was demonstrated for the range ≤5–250 μg kg{sup −1}. The pesticides could be identified according to the applicable EU criteria for GC-HRMS (SANTE/11945/2015). GC-EI-full scan Orbitrap HRMS was found to be highly suited for quantitative pesticide residue analysis. The potential of qualitative screening to extend the scope makes it an attractive

  14. Evaluation of gas chromatography – electron ionization – full scan high resolution Orbitrap mass spectrometry for pesticide residue analysis

    International Nuclear Information System (INIS)

    Mol, Hans G.J.; Tienstra, Marc; Zomer, Paul

    2016-01-01

    Gas chromatography with electron ionization and full scan high resolution mass spectrometry with an Orbitrap mass analyzer (GC-EI-full scan Orbitrap HRMS) was evaluated for residue analysis. Pesticides in fruit and vegetables were taken as an example application. The relevant aspects for GC-MS based residue analysis, including the resolving power (15,000 to 120,000 FWHM at m/z 200), scan rate, dynamic range, selectivity, sensitivity, analyte identification, and utility of existing EI-libraries, are assessed and discussed in detail. The optimum acquisition conditions in full scan mode (m/z 50–500) were a resolving power of 60,000 and an automatic-gain-control target value of 3E6. These conditions provided (i) an optimum mass accuracy: within 2 ppm over a wide concentration range, with/without matrix, enabling the use of ±5 ppm mass extraction windows (ii) adequate scan speed: minimum 12 scans/peak, (iii) an intra-scan dynamic range sufficient to achieve LOD/LOQs ≤0.5 pg in fruit/vegetable matrices (corresponding to ≤0.5 μg kg"−"1) for most pesticides. EI-Orbitrap spectra were consistent over a very wide concentration range (5 orders) with good match values against NIST (EI-quadrupole) spectra. The applicability for quantitative residue analysis was verified by validation of 54 pesticides in three matrices (tomato, leek, orange) at 10 and 50 μg/kg. The method involved a QuEChERS-based extraction with a solvent switch into iso-octane, and 1 μL hot splitless injection into the GC-HRMS system. A recovery between 70 and 120% and a repeatability RSD <10% was obtained in most cases. Linearity was demonstrated for the range ≤5–250 μg kg"−"1. The pesticides could be identified according to the applicable EU criteria for GC-HRMS (SANTE/11945/2015). GC-EI-full scan Orbitrap HRMS was found to be highly suited for quantitative pesticide residue analysis. The potential of qualitative screening to extend the scope makes it an attractive alternative to

  15. The geometric phase analysis method based on the local high resolution discrete Fourier transform for deformation measurement

    International Nuclear Information System (INIS)

    Dai, Xianglu; Xie, Huimin; Wang, Huaixi; Li, Chuanwei; Wu, Lifu; Liu, Zhanwei

    2014-01-01

    The geometric phase analysis (GPA) method based on the local high resolution discrete Fourier transform (LHR-DFT) for deformation measurement, defined as LHR-DFT GPA, is proposed to improve the measurement accuracy. In the general GPA method, the fundamental frequency of the image plays a crucial role. However, the fast Fourier transform, which is generally employed in the general GPA method, could make it difficult to locate the fundamental frequency accurately when the fundamental frequency is not located at an integer pixel position in the Fourier spectrum. This study focuses on this issue and presents a LHR-DFT algorithm that can locate the fundamental frequency with sub-pixel precision in a specific frequency region for the GPA method. An error analysis is offered and simulation is conducted to verify the effectiveness of the proposed method; both results show that the LHR-DFT algorithm can accurately locate the fundamental frequency and improve the measurement accuracy of the GPA method. Furthermore, typical tensile and bending tests are carried out and the experimental results verify the effectiveness of the proposed method. (paper)

  16. Shadow Analysis Technique for Extraction of Building Height using High Resolution Satellite Single Image and Accuracy Assessment

    Science.gov (United States)

    Raju, P. L. N.; Chaudhary, H.; Jha, A. K.

    2014-11-01

    These High resolution satellite data with metadata information is used to extract the height of the building using shadow. Proposed approach divides into two phases 1) rooftop and shadow extraction and 2) height estimation. Firstly the rooftop and shadow region were extracted by manual/ automatic methods using Example - Based and Rule - Based approaches. After feature extraction next step is estimating height of the building by taking rooftop in association with shadow using Ratio Method and by using the relation between sun-satellite geometry. The performance analysis shows the total mean error of height is 0.67 m from ratio method, 1.51 m from Example - Based Approach and 0.96 m from Rule - Based Approach. Analysis concluded that Ratio Method i.e. manual method is best for height estimation but it is time consuming so the automatic Rule Based approach is best for height estimation in comparison to Example Based Approach because it require more knowledge and selection of more training samples as well as slows the processing rate of the method.

  17. Current applications of high-resolution mass spectrometry for the analysis of new psychoactive substances: a critical review.

    Science.gov (United States)

    Pasin, Daniel; Cawley, Adam; Bidny, Sergei; Fu, Shanlin

    2017-10-01

    The proliferation of new psychoactive substances (NPS) in recent years has resulted in the development of numerous analytical methods for the detection and identification of known and unknown NPS derivatives. High-resolution mass spectrometry (HRMS) has been identified as the method of choice for broad screening of NPS in a wide range of analytical contexts because of its ability to measure accurate masses using data-independent acquisition (DIA) techniques. Additionally, it has shown promise for non-targeted screening strategies that have been developed in order to detect and identify novel analogues without the need for certified reference materials (CRMs) or comprehensive mass spectral libraries. This paper reviews the applications of HRMS for the analysis of NPS in forensic drug chemistry and analytical toxicology. It provides an overview of the sample preparation procedures in addition to data acquisition, instrumental analysis, and data processing techniques. Furthermore, it gives an overview of the current state of non-targeted screening strategies with discussion on future directions and perspectives of this technique. Graphical Abstract Missing the bullseye - a graphical respresentation of non-targeted screening. Image courtesy of Christian Alonzo.

  18. First report of Tasmanian sheep strain (G2) genotype isolated from Iranian goat using the high resolution melting (HRM) analysis.

    Science.gov (United States)

    Hosseini-Safa, Ahmad; Mohag Hegh, Mohammad Ali; Pestechian, Nader; Ganji, Maryam; Mohammadi, Rasoul; Mahmoudi Lamouki, Reza; Rostami-Nejad, Mohammad

    2016-12-01

    The present study was aimed to evaluate E. granulosus genotypes isolated from goats using HRM analysis in Isfahan province. Cystic echincoccosis, so-called hydatidosis, is widespread infection caused by the larval stage of Echinococcus granulosus . This is an important zoonotic disease worldwide, especially in the developing countries such as Iran. To date, molecular studies mainly based on the mitochondrial DNA sequences have identified distinct genotypes termed G1-G10 which can differ in some characteristics such as the growth and infectivity to different intermediate hosts or the survival rate in the definitive hosts that are important for the development of control strategies. From August to December 2014, 1341 goats were investigated and hydatid cysts were collected from the liver and lungs of 43 infected goats in Isfahan province abattoirs, Isfahan, Iran. Total genomic DNA was extracted from each sample, amplified for the presence of polymorphism of mitochondrial gene coding for cytochrome c oxidase subunit 1 (CO1), using high resolution melting curve (HRM) method. the results of HRM analysis using the sequence of CO1 gene for 43 Echinococcus granulosus isolates from goats showed 31, 2 and 10 isolates were identified as G1, G2, and G3 genotypes, respectively. G1 is the predominant genotype in the isolated goat samples in Isfahan province, and the presence of G2 strain was reported for the first time in goat in Iran.

  19. LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data.

    Science.gov (United States)

    Zhang, Wei; Zhang, Jiyang; Xu, Changming; Li, Ning; Liu, Hui; Ma, Jie; Zhu, Yunping; Xie, Hongwei

    2012-12-01

    Database searching based methods for label-free quantification aim to reconstruct the peptide extracted ion chromatogram based on the identification information, which can limit the search space and thus make the data processing much faster. The random effect of the MS/MS sampling can be remedied by cross-assignment among different runs. Here, we present a new label-free fast quantitative analysis tool, LFQuant, for high-resolution LC-MS/MS proteomics data based on database searching. It is designed to accept raw data in two common formats (mzXML and Thermo RAW), and database search results from mainstream tools (MASCOT, SEQUEST, and X!Tandem), as input data. LFQuant can handle large-scale label-free data with fractionation such as SDS-PAGE and 2D LC. It is easy to use and provides handy user interfaces for data loading, parameter setting, quantitative analysis, and quantitative data visualization. LFQuant was compared with two common quantification software packages, MaxQuant and IDEAL-Q, on the replication data set and the UPS1 standard data set. The results show that LFQuant performs better than them in terms of both precision and accuracy, and consumes significantly less processing time. LFQuant is freely available under the GNU General Public License v3.0 at http://sourceforge.net/projects/lfquant/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Analysis of a severe weather event over Mecca, Kingdom of Saudi Arabia, using observations and high-resolution modelling

    KAUST Repository

    Dasari, Hari Prasad; Attada, Raju; Knio, Omar; Hoteit, Ibrahim

    2017-01-01

    The dynamic and thermodynamic characteristics of a severe weather event that caused heavy wind and rainfall over Mecca, Kingdom of Saudi Arabia, on 11 September 2015 were investigated using available observations and the Weather Research and Forecasting model configured at 1 km resolution. Analysis of surface, upper air observations and model outputs reveals that the event was initiated by synoptic scale conditions that intensified by interaction with the local topography, triggering strong winds and high convective rainfall. The model predicted the observed characteristics of both rainfall and winds well, accurately predicting the maximum wind speed of 20–25 m s−1 that was sustained for about 2 h. A time series analysis of various atmospheric variables suggests a sudden fall in pressure, temperature and outgoing long wave radiation before the development of the storm, followed by a significant increase in wind speed, latent and moisture fluxes and change in wind direction during the mature stage of the storm. The model outputs suggest that the heavy rainfall was induced by a low-level moisture supply from the Red Sea combined with orographic lifting. Latent heat release from microphysical processes increased the vertical velocities in the mid-troposphere, further increasing the low-level convergence that strengthened the event.

  1. Analysis of a severe weather event over Mecca, Kingdom of Saudi Arabia, using observations and high-resolution modelling

    KAUST Repository

    Dasari, Hari Prasad

    2017-08-10

    The dynamic and thermodynamic characteristics of a severe weather event that caused heavy wind and rainfall over Mecca, Kingdom of Saudi Arabia, on 11 September 2015 were investigated using available observations and the Weather Research and Forecasting model configured at 1 km resolution. Analysis of surface, upper air observations and model outputs reveals that the event was initiated by synoptic scale conditions that intensified by interaction with the local topography, triggering strong winds and high convective rainfall. The model predicted the observed characteristics of both rainfall and winds well, accurately predicting the maximum wind speed of 20–25 m s−1 that was sustained for about 2 h. A time series analysis of various atmospheric variables suggests a sudden fall in pressure, temperature and outgoing long wave radiation before the development of the storm, followed by a significant increase in wind speed, latent and moisture fluxes and change in wind direction during the mature stage of the storm. The model outputs suggest that the heavy rainfall was induced by a low-level moisture supply from the Red Sea combined with orographic lifting. Latent heat release from microphysical processes increased the vertical velocities in the mid-troposphere, further increasing the low-level convergence that strengthened the event.

  2. The use of high resolution melting analysis to detect Fabry mutations in heterozygous females via dry bloodspots.

    Science.gov (United States)

    Tai, Chang-Long; Liu, Mei-Ying; Yu, Hsiao-Chi; Chiang, Chiang-Chuan; Chiang, Hung; Suen, Jeng-Hung; Kao, Shu-Min; Huang, Yu-Hsiu; Wu, Tina Jui-Ting; Yang, Chia-Feng; Tsai, Fang-Chih; Lin, Ching-Yuang; Chang, Jan-Gowth; Chen, Hong-Duo; Niu, Dau-Ming

    2012-02-18

    As an X-linked genetic disorder, Fabry disease was first thought to affect males only, and females were generally considered to be asymptomatic carriers. However, recent research suggests that female carriers of Fabry disease may still develop vital organ damage causing severe morbidity and mortality. In the previous newborn screening, from 299,007 newborns, we identified a total of 20 different Fabry mutations and 121 newborns with Fabry mutations. However, we found that most female carriers are not detected by enzyme assays. A streamlined method for high resolution melting (HRM) analysis was designed to screen for GLA gene mutations using a same PCR and melting program. Primer sets were designed to cover the 7 exons and the Chinese common intronic mutation, IVS4+919G>A of GLA gene. The HRM analysis was successful in identifying heterozygous and hemizygous patients with the 20 surveyed mutations. We were also successful in using this method to test dry blood spots of newborns afflicted with Fabry mutations without having to determine DNA concentration before PCR amplification. The results of this study show that HRM could be a reliable and sensitive method for use in the rapid screening of females for GLA mutations. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. High-Resolution Mass Spectrometers

    Science.gov (United States)

    Marshall, Alan G.; Hendrickson, Christopher L.

    2008-07-01

    Over the past decade, mass spectrometry has been revolutionized by access to instruments of increasingly high mass-resolving power. For small molecules up to ˜400 Da (e.g., drugs, metabolites, and various natural organic mixtures ranging from foods to petroleum), it is possible to determine elemental compositions (CcHhNnOoSsPp…) of thousands of chemical components simultaneously from accurate mass measurements (the same can be done up to 1000 Da if additional information is included). At higher mass, it becomes possible to identify proteins (including posttranslational modifications) from proteolytic peptides, as well as lipids, glycoconjugates, and other biological components. At even higher mass (˜100,000 Da or higher), it is possible to characterize posttranslational modifications of intact proteins and to map the binding surfaces of large biomolecule complexes. Here we review the principles and techniques of the highest-resolution analytical mass spectrometers (time-of-flight and Fourier transform ion cyclotron resonance and orbitrap mass analyzers) and describe some representative high-resolution applications.

  4. High-resolution phylogenetic analysis of residual bacterial species of fouled membranes after NaOCl cleaning.

    Science.gov (United States)

    Navarro, Ronald R; Hori, Tomoyuki; Inaba, Tomohiro; Matsuo, Kazuyuki; Habe, Hiroshi; Ogata, Atsushi

    2016-05-01

    Biofouling is one of the major problems during wastewater treatment using membrane bioreactors (MBRs). In this regard, sodium hypochlorite (NaOCl) has been widely used to wash fouled membranes for maintenance and recovery purposes. Advanced chemical and biological characterization was conducted in this work to evaluate the performance of aqueous NaOCl solutions during washing of polyacrylonitrile membranes. Fouled membranes from MBR operations supplemented with artificial wastewater were washed with 0.1% and 0.5% aqueous NaOCl solutions for 5, 10 and 30 min. The changes in organics composition on the membrane surface were directly monitored by an attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectrometer. In addition, high-throughput Illumina sequencing of 16S rRNA genes was applied to detect any residual microorganisms. Results from ATR-FT-IR analysis indicated the complete disappearance of functional groups representing different fouling compounds after at least 30 min of treatment with 0.1% NaOCl. However, the biomolecular survey revealed the presence of residual bacteria even after 30 min of treatment with 0.5% NaOCl solution. Evaluation of microbial diversity of treated samples using Chao1, Shannon and Simpson reciprocal indices showed an increase in evenness while no significant decline in richness was observed. These implied that only the population of dominant species was mainly affected. The high-resolution phylogenetic analysis revealed the presence of numerous operational taxonomic units (OTUs) whose close relatives exhibit halotolerance. Some OTUs related to thermophilic and acid-resistant strains were also identified. Finally, the taxonomic analysis of recycled membranes that were previously washed with NaOCl also showed the presence of numerous halotolerant-related OTUs in the early stage of fouling. This further suggested the possible contribution of such chemical tolerance on their survival against NaOCl washing, which in turn

  5. High-resolution Melting Analysis for Gene Scanning of Adenomatous Polyposis Coli (APC) Gene With Oral Squamous Cell Carcinoma Samples.

    Science.gov (United States)

    Chang, Ya-Sian; Lin, Chien-Yu; Yang, Shu-Fen; Ho, Cheng Mao; Chang, Jan-Gowth

    2016-02-01

    There have been many different mutations reported for the large adenomatous polyposis coli (APC) tumor suppressor gene. APC mutations result in inactivation of APC tumor suppressor action, allowing the progression of tumorigenesis. The present study utilized a highly efficient method to identify APC mutations and investigated the association between the APC genetic variants Y486Y, A545A, T1493T, and D1822V and susceptibility to oral squamous cell carcinoma (OSCC). High-resolution melting (HRM) analysis was used to characterize APC mutations. Genomic DNA was extracted from 83 patient specimens of OSCC and 50 blood samples from healthy control subjects. The 14 exons and mutation cluster region of exon 15 were screened by HRM analysis. All mutations were confirmed by direct DNA sequencing. Three mutations and 4 single nucleotide polymorphisms (SNPs) were found in this study. The mutations were c.573T>C (Y191Y) in exon 5, c.1005A>G (L335L) in exon 9, and c.1488A>T (T496T) in exon 11. Two SNPs, c.4479G>A (T1493T) and c.5465A>T (D1822V), were located in exon 15, whereas c.1458T>C (Y486Y) and c.1635G>A (A545A) were located in exon 11 and 13, respectively. There was no observed association between OSCC risk and genotype for any of the 4 APC SNPs. The mutation of APC is rare in Taiwanese patients with OSCC. HRM analysis is a reliable, accurate, and fast screening method for APC mutations.

  6. High-resolution melt analysis for species identification of coagulase-negative staphylococci derived from bovine milk.

    Science.gov (United States)

    Ajitkumar, Praseeda; Barkema, Herman W; Zadoks, Ruth N; Morck, Douglas W; van der Meer, Frank J U M; De Buck, Jeroen

    2013-03-01

    Coagulase-negative staphylococci (CNS) are the most frequently isolated pathogens isolated from bovine milk. In this study, we report a rapid assay for species identification of CNS using high-resolution melt analysis (HRMA) of 16S rDNA sequences. Real-time polymerase chain reaction amplification of 16S rRNA gene fragment, spanning the variable region V1 and V2, was performed with a resulting amplicon of 215 bp. A library of distinct melt curves of reference strains of 13 common CNS species was created using HRMA. Sequencing of 16S rRNA and rpoB genes, and, when needed, tuf gene, of 100 CNS isolates obtained from Canadian Bovine Mastitis Research Network was done to determine their species identity, allowing for subsequent evaluation of the performance of HRMA for field isolates of bovine CNS. A combination of HRMA and sequencing revealed that Staphylococcus chromogenes, S. xylosus, S. simulans, and S. sciuri had multiple genotypes, complicating their resolution by HRMA. As the 3 genotypes of S. chromogenes had distinct melt curves, the 3 distinct genotypes were employed as reference strains in a blinded trial of 156 CNS isolates to identify S. chromogenes. HRMA correctly identified all S. chromogenes isolates which were later confirmed by sequencing. Staphylococcus chromogenes (68%) was most frequently found among the CNS isolates, followed by S. haemolyticus (10%) and S. xylosus (6%). The present study revealed that HRMA of 16S rRNA gene (V1-V2) could be used as a rapid, efficient, low-cost, and minimally cumbersome technique for S. chromogenes identification, the most common CNS derived from bovine milk. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. DOTS: A High Resolution Orbitrap Mass Spectrometer for In Situ Analysis of the surface samples of Airless Planetary Bodies

    Science.gov (United States)

    Briois, Christelle; Thissen, Roland; Engrand, Cécile; Altwegg, Kathrin; Bouabdellah, Abdel; Boukrara, Amirouche; Carrasco, Nathalie; Chapuis, Claude; Cottin, Hervé; Grün, Eberhard; Grand, Noel; Henkel, Hartmut; Kempf, Sascha; Lebreton, Jean-Pierre; Makarov, Alexander A.; Postber, Frank; Srama, Ralf; Schmidt, Jürgen; Szopa, Cyril; Thirkell, Laurent; Tobie, Gabriel; Wurz, Peter; Zolotov, Mikhail Yu

    2013-04-01

    The dust detectors on board the Ulysses and Galileo spacecraft have shown that the Galilean satellites are surrounded by clouds of sub-micrometer size grains generated by impacts of interplanetary (micro-) meteoroids [1, 2]. In situ chemical analysis from orbit of these ballistic grains ejected from the surface of airless bodies provides a unique opportunity to remotely access the chemical composition of the Jovian moons' surface and subsurface. For Saturn, in situ identification by the Cassini Dust Analyzer (CDA) of sodium in icy grains in the E-Ring and in Enceladus plumes have proven a subsurface liquid water reservoir inside Enceladus [3, 4]. Noticeably, this was not accessible to other in situ or traditional remote sensing techniques. In situ measurements, either during a flyby or from orbit, of grains ejected from the surface, or emerging from the subsurface, of an airless body is a powerful tool to remotely study its surface composition and the nature of its geological activity. Crucial constraints on habitability can thus be determined. Our consortium of laboratories, in collaboration with Thermo Fischer Scientific [5, 6], is currently developing a high mass resolution Fourier Transform (FT) Orbitrap-based mass spectrometer optimized for in situ analysis of dust and icy grains in the environment of Solar System airless bodies. This new generation of dust mass spectrometer was studied in the framework of the Europa Jupiter System Mission (EJSM) instrument study in 2010-2012 and proposed in response to ESA's AO for the JUpiter ICy moons Explorer (JUICE) mission [7]. This mass analyser can provide very high mass resolution analysis (M/ΔM reaching 50 000 at m/z 50 Da). DOTS would allow identification of elemental and molecular species with excellent accuracy, in the 20-1000 Da mass range. In the context of the JUICE mission, DOTS would provide decisive information on the surface composition and on the putative liquid oceans in the subsurface of Ganymede

  8. High Resolution Melting Analysis Targeting hsp70 as a Fast and Efficient Method for the Discrimination of Leishmania Species.

    Science.gov (United States)

    Zampieri, Ricardo Andrade; Laranjeira-Silva, Maria Fernanda; Muxel, Sandra Marcia; Stocco de Lima, Ana Carolina; Shaw, Jeffrey Jon; Floeter-Winter, Lucile Maria

    2016-02-01

    Protozoan parasites of the genus Leishmania cause a large spectrum of clinical manifestations known as Leishmaniases. These diseases are increasingly important public health problems in many countries both within and outside endemic regions. Thus, an accurate differential diagnosis is extremely relevant for understanding epidemiological profiles and for the administration of the best therapeutic protocol. Exploring the High Resolution Melting (HRM) dissociation profiles of two amplicons using real time polymerase chain reaction (real-time PCR) targeting heat-shock protein 70 coding gene (hsp70) revealed differences that allowed the discrimination of genomic DNA samples of eight Leishmania species found in the Americas, including Leishmania (Leishmania) infantum chagasi, L. (L.) amazonensis, L. (L.) mexicana, L. (Viannia) lainsoni, L. (V.) braziliensis, L. (V.) guyanensis, L. (V.) naiffi and L. (V.) shawi, and three species found in Eurasia and Africa, including L. (L.) tropica, L. (L.) donovani and L. (L.) major. In addition, we tested DNA samples obtained from standard promastigote culture, naturally infected phlebotomines, experimentally infected mice and clinical human samples to validate the proposed protocol. HRM analysis of hsp70 amplicons is a fast and robust strategy that allowed for the detection and discrimination of all Leishmania species responsible for the Leishmaniases in Brazil and Eurasia/Africa with high sensitivity and accuracy. This method could detect less than one parasite per reaction, even in the presence of host DNA.

  9. High Resolution Melting Analysis Targeting hsp70 as a Fast and Efficient Method for the Discrimination of Leishmania Species.

    Directory of Open Access Journals (Sweden)

    Ricardo Andrade Zampieri

    2016-02-01

    Full Text Available Protozoan parasites of the genus Leishmania cause a large spectrum of clinical manifestations known as Leishmaniases. These diseases are increasingly important public health problems in many countries both within and outside endemic regions. Thus, an accurate differential diagnosis is extremely relevant for understanding epidemiological profiles and for the administration of the best therapeutic protocol.Exploring the High Resolution Melting (HRM dissociation profiles of two amplicons using real time polymerase chain reaction (real-time PCR targeting heat-shock protein 70 coding gene (hsp70 revealed differences that allowed the discrimination of genomic DNA samples of eight Leishmania species found in the Americas, including Leishmania (Leishmania infantum chagasi, L. (L. amazonensis, L. (L. mexicana, L. (Viannia lainsoni, L. (V. braziliensis, L. (V. guyanensis, L. (V. naiffi and L. (V. shawi, and three species found in Eurasia and Africa, including L. (L. tropica, L. (L. donovani and L. (L. major. In addition, we tested DNA samples obtained from standard promastigote culture, naturally infected phlebotomines, experimentally infected mice and clinical human samples to validate the proposed protocol.HRM analysis of hsp70 amplicons is a fast and robust strategy that allowed for the detection and discrimination of all Leishmania species responsible for the Leishmaniases in Brazil and Eurasia/Africa with high sensitivity and accuracy. This method could detect less than one parasite per reaction, even in the presence of host DNA.

  10. Ultra-high resolution AMOLED

    Science.gov (United States)

    Wacyk, Ihor; Prache, Olivier; Ghosh, Amal

    2011-06-01

    AMOLED microdisplays continue to show improvement in resolution and optical performance, enhancing their appeal for a broad range of near-eye applications such as night vision, simulation and training, situational awareness, augmented reality, medical imaging, and mobile video entertainment and gaming. eMagin's latest development of an HDTV+ resolution technology integrates an OLED pixel of 3.2 × 9.6 microns in size on a 0.18 micron CMOS backplane to deliver significant new functionality as well as the capability to implement a 1920×1200 microdisplay in a 0.86" diagonal area. In addition to the conventional matrix addressing circuitry, the HDTV+ display includes a very lowpower, low-voltage-differential-signaling (LVDS) serialized interface to minimize cable and connector size as well as electromagnetic emissions (EMI), an on-chip set of look-up-tables for digital gamma correction, and a novel pulsewidth- modulation (PWM) scheme that together with the standard analog control provides a total dimming range of 0.05cd/m2 to 2000cd/m2 in the monochrome version. The PWM function also enables an impulse drive mode of operation that significantly reduces motion artifacts in high speed scene changes. An internal 10-bit DAC ensures that a full 256 gamma-corrected gray levels are available across the entire dimming range, resulting in a measured dynamic range exceeding 20-bits. This device has been successfully tested for operation at frame rates ranging from 30Hz up to 85Hz. This paper describes the operational features and detailed optical and electrical test results for the new AMOLED WUXGA resolution microdisplay.

  11. High resolution, high speed ultrahigh vacuum microscopy

    International Nuclear Information System (INIS)

    Poppa, Helmut

    2004-01-01

    The history and future of transmission electron microscopy (TEM) is discussed as it refers to the eventual development of instruments and techniques applicable to the real time in situ investigation of surface processes with high resolution. To reach this objective, it was necessary to transform conventional high resolution instruments so that an ultrahigh vacuum (UHV) environment at the sample site was created, that access to the sample by various in situ sample modification procedures was provided, and that in situ sample exchanges with other integrated surface analytical systems became possible. Furthermore, high resolution image acquisition systems had to be developed to take advantage of the high speed imaging capabilities of projection imaging microscopes. These changes to conventional electron microscopy and its uses were slowly realized in a few international laboratories over a period of almost 40 years by a relatively small number of researchers crucially interested in advancing the state of the art of electron microscopy and its applications to diverse areas of interest; often concentrating on the nucleation, growth, and properties of thin films on well defined material surfaces. A part of this review is dedicated to the recognition of the major contributions to surface and thin film science by these pioneers. Finally, some of the important current developments in aberration corrected electron optics and eventual adaptations to in situ UHV microscopy are discussed. As a result of all the path breaking developments that have led to today's highly sophisticated UHV-TEM systems, integrated fundamental studies are now possible that combine many traditional surface science approaches. Combined investigations to date have involved in situ and ex situ surface microscopies such as scanning tunneling microscopy/atomic force microscopy, scanning Auger microscopy, and photoemission electron microscopy, and area-integrating techniques such as x-ray photoelectron

  12. Gas chromatographic quadrupole time-of-flight full scan high resolution mass spectrometric screening of human urine in antidoping analysis

    NARCIS (Netherlands)

    Abushareeda, Wadha; Lyris, Emmanouil; Kraiem, Suhail; Wahaibi, Aisha Al; Alyazidi, Sameera; Dbes, Najib; Lommen, Arjen; Nielen, Michel; Horvatovich, Peter L.; Alsayrafi, Mohammed; Georgakopoulos, Costas

    2017-01-01

    This paper presents the development and validation of a high-resolution full scan (FS) electron impact ionization (EI) gas chromatography coupled to quadrupole Time-of-Flight mass spectrometry (GC/QTOF) platform for screening anabolic androgenic steroids (AAS) in human urine samples. The World

  13. Gas chromatographic quadrupole time-of-flight full scan high resolution mass spectrometric screening of human urine in antidoping analysis

    NARCIS (Netherlands)

    Abushareeda, Wadha; Lyris, Emmanouil; Kraiem, Suhail; Wahaibi, Aisha Al; Alyazidi, Sameera; Dbes, Najib; Lommen, Arjen; Nielen, Michel; Horvatovich, Peter L.; Alsayrafi, Mohammed; Georgakopoulos, Costas

    2017-01-01

    This paper presents the development and validation of a high-resolution full scan (FS) electron impact ionization (EI) gas chromatography coupled to quadrupole Time-of-Flight mass spectrometry (GC/QTOF) platform for screening anabolic androgenic steroids (AAS) in human urine samples. The World

  14. Analysis of HIV using a high resolution melting (HRM) diversity assay: automation of HRM data analysis enhances the utility of the assay for analysis of HIV incidence.

    Science.gov (United States)

    Cousins, Matthew M; Swan, David; Magaret, Craig A; Hoover, Donald R; Eshleman, Susan H

    2012-01-01

    HIV diversity may be a useful biomarker for discriminating between recent and non-recent HIV infection. The high resolution melting (HRM) diversity assay was developed to quantify HIV diversity in viral populations without sequencing. In this assay, HIV diversity is expressed as a single numeric HRM score that represents the width of a melting peak. HRM scores are highly associated with diversity measures obtained with next generation sequencing. In this report, a software package, the HRM Diversity Assay Analysis Tool (DivMelt), was developed to automate calculation of HRM scores from melting curve data. DivMelt uses computational algorithms to calculate HRM scores by identifying the start (T1) and end (T2) melting temperatures for a DNA sample and subtracting them (T2 - T1 =  HRM score). DivMelt contains many user-supplied analysis parameters to allow analyses to be tailored to different contexts. DivMelt analysis options were optimized to discriminate between recent and non-recent HIV infection and to maximize HRM score reproducibility. HRM scores calculated using DivMelt were compared to HRM scores obtained using a manual method that is based on visual inspection of DNA melting curves. HRM scores generated with DivMelt agreed with manually generated HRM scores obtained from the same DNA melting data. Optimal parameters for discriminating between recent and non-recent HIV infection were identified. DivMelt provided greater discrimination between recent and non-recent HIV infection than the manual method. DivMelt provides a rapid, accurate method of determining HRM scores from melting curve data, facilitating use of the HRM diversity assay for large-scale studies.

  15. Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry.

    Directory of Open Access Journals (Sweden)

    Mårten Sundberg

    Full Text Available Today immunoassays are widely used in veterinary medicine, but lack of species specific assays often necessitates the use of assays developed for human applications. Mass spectrometry (MS is an attractive alternative due to high specificity and versatility, allowing for species-independent analysis. Targeted MS-based quantification methods are valuable complements to large scale shotgun analysis. A method referred to as parallel reaction monitoring (PRM, implemented on Orbitrap MS, has lately been presented as an excellent alternative to more traditional selected reaction monitoring/multiple reaction monitoring (SRM/MRM methods. The insulin-like growth factor (IGF-system is not well described in the cat but there are indications of important differences between cats and humans. In feline medicine IGF-I is mainly analyzed for diagnosis of growth hormone disorders but also for research, while the other proteins in the IGF-system are not routinely analyzed within clinical practice. Here, a PRM method for quantification of IGF-I, IGF-II, IGF binding protein (BP -3 and IGFBP-5 in feline serum is presented. Selective quantification was supported by the use of a newly launched internal standard named QPrEST™. Homology searches demonstrated the possibility to use this standard of human origin for quantification of the targeted feline proteins. Excellent quantitative sensitivity at the attomol/μL (pM level and selectivity were obtained. As the presented approach is very generic we show that high resolution mass spectrometry in combination with PRM and QPrEST™ internal standards is a versatile tool for protein quantitation across multispecies.

  16. High-resolution two-dimensional liquid chromatography analysis of key linker drug intermediate used in antibody drug conjugates.

    Science.gov (United States)

    Venkatramani, C J; Huang, Shu Rong; Al-Sayah, Mohammad; Patel, Ila; Wigman, Larry

    2017-10-27

    In this manuscript, the application of high-resolution sampling (HRS) two-dimensional liquid chromatography (2D-LC) in the detailed analysis of key linker drug intermediate is presented. Using HRS, selected regions of the primary column eluent were transferred to a secondary column with fidelity enabling qualitative and quantitative analysis of linker drugs. The primary column purity of linker drug intermediate ranged from 88.9% to 94.5% and the secondary column purity ranged from 99.6% to 99.9%, showing lot-to-lot variability, significant differences between the three lots, and substantiating the synthetic and analytical challenges of ADCs. Over 15 impurities co-eluting with the linker drug intermediate in the primary dimension were resolved in the secondary dimension. The concentrations of most of these impurities were over three orders of magnitude lower than the linker drug. Effective peak focusing and high-speed secondary column analysis resulted in sharp peaks in the secondary dimension, improving the signal-to-noise ratios. The sensitivity of 2D-LC separation was over five fold better than conventional HPLC separation. The limit of quantitation (LOQ) was less than 0.01%. Many peaks originating from primary dimension were resolved into multiple components in the complementary secondary dimension, demonstrating the complexity of these samples. The 2D-LC was highly reproducible, showing good precision between runs with%RSD of peak areas less than 0.1 for the main component. The absolute difference in the peak areas of impurities less than 0.1% were within ±0.01% and for impurities in the range of 0.1%-0.3%, the absolute difference were ±0.02%, which are comparable to 1D-LC. The overall purity of the linker drug intermediate was determined from the product of primary and secondary column purity (HPLC Purity=%peak area of main component in the primary dimension×%peak area of main component in the secondary dimension). Additionally, the 2D-LC separation enables

  17. High resolution eddy current microscopy

    Science.gov (United States)

    Lantz, M. A.; Jarvis, S. P.; Tokumoto, H.

    2001-01-01

    We describe a sensitive scanning force microscope based technique for measuring local variations in resistivity by monitoring changes in the eddy current induced damping of a cantilever with a magnetic tip oscillating above a conducting sample. To achieve a high sensitivity, we used a cantilever with an FeNdBLa particle mounted on the tip. Resistivity measurements are demonstrated on a silicon test structure with a staircase doping profile. Regions with resistivities of 0.0013, 0.0041, and 0.022 Ω cm are clearly resolved with a lateral resolution of approximately 180 nm. For this range of resistivities, the eddy current induced damping is found to depend linearly on the sample resistivity.

  18. High resolution electron back-scatter diffraction analysis of thermally and mechanically induced strains near carbide inclusions in a superalloy

    Energy Technology Data Exchange (ETDEWEB)

    Karamched, Phani S., E-mail: phani.karamched@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Wilkinson, Angus J. [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom)

    2011-01-15

    Cross-correlation-based analysis of electron back-scatter diffraction (EBSD) patterns has been used to obtain high angular resolution maps of lattice rotations and elastic strains near carbides in a directionally solidified superalloy MAR-M-002. Lattice curvatures were determined from the EBSD measurements and used to estimate the distribution of geometrically necessary dislocations (GNDs) induced by the deformation. Significant strains were induced by thermal treatment due to the lower thermal expansion coefficient of the carbide inclusions compared to that of the matrix. In addition to elastic strains the mismatch was sufficient to have induced localized plastic deformation in the matrix leading to a GND density of 3 x 10{sup 13} m{sup -2} in regions around the carbide. Three-point bending was then used to impose strain levels within the range {+-}12% across the height of the bend bar. EBSD lattice curvature measurements were then made at both carbide-containing and carbide-free regions at different heights across the bar. The average GND density increases with the magnitude of the imposed strain (both in tension and compression), and is markedly higher near the carbides particles. The higher GND densities near the carbides (order of 10{sup 14} m{sup -2}) are generated by the large strain gradients produced around the plastically rigid inclusion during mechanical deformation with some minor contribution from the pre-existing residual deformation caused by the thermal mismatch between carbide and nickel matrix.

  19. Temporal measurement and analysis of high-resolution spectral signatures of plants and relationships to biophysical characteristics

    Science.gov (United States)

    Bostater, Charles R., Jr.; Rebbman, Jan; Hall, Carlton; Provancha, Mark; Vieglais, David

    1995-11-01

    Measurements of temporal reflectance signatures as a function of growing season for sand live oak (Quercus geminata), myrtle oak (Q. myrtifolia, and saw palmetto (Serenoa repens) were collected during a two year study period. Canopy level spectral reflectance signatures, as a function of 252 channels between 368 and 1115 nm, were collected using near nadir viewing geometry and a consistent sun illumination angle. Leaf level reflectance measurements were made in the laboratory using a halogen light source and an environmental optics chamber with a barium sulfate reflectance coating. Spectral measurements were related to several biophysical measurements utilizing optimal passive ambient correlation spectroscopy (OPACS) technique. Biophysical parameters included percent moisture, water potential (MPa), total chlorophyll, and total Kjeldahl nitrogen. Quantitative data processing techniques were used to determine optimal bands based on the utilization of a second order derivative or inflection estimator. An optical cleanup procedure was then employed that computes the double inflection ratio (DIR) spectra for all possible three band combinations normalized to the previously computed optimal bands. These results demonstrate a unique approach to the analysis of high spectral resolution reflectance signatures for estimation of several biophysical measures of plants at the leaf and canopy level from optimally selected bands or bandwidths.

  20. Analysis of volatile thiols in alcoholic beverages by simultaneous derivatization/extraction and liquid chromatography-high resolution mass spectrometry.

    Science.gov (United States)

    Vichi, Stefania; Cortés-Francisco, Nuria; Caixach, Josep

    2015-05-15

    A simultaneous derivatization/extraction method followed by liquid chromatography-electrospray-high resolution mass spectrometry for the determination of volatile thiols in hydroalcoholic matrixes was optimized and used to identify and quantify volatile thiols in wine and beer samples. The method was evaluated in terms of sensitivity, precision, accuracy and selectivity. The experimental LOQs of eleven thiols tested ranged between 0.01 ng/L and 10 ng/L. Intra-day relative standard deviation (RSD) was in general lower than 10% and inter-day RSD ranged between 10% and 30%. Recovery in the model and real matrixes ranged from 45% to 129%. The method was then applied for the analysis of four white wines and six beers. Five out of the eleven reference thiols were identified and quantified in the samples analyzed. The non-target approach, carried out by monitoring the diagnostic ion at m/z 275.9922 [C13H10ONSe](+) in the fragmentation spectrum, allowed detecting, in the same samples, fourteen non-target thiols. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Vineyard Yield Estimation Based on the Analysis of High Resolution Images Obtained with Artificial Illumination at Night

    Directory of Open Access Journals (Sweden)

    Davinia Font

    2015-04-01

    Full Text Available This paper presents a method for vineyard yield estimation based on the analysis of high-resolution images obtained with artificial illumination at night. First, this paper assesses different pixel-based segmentation methods in order to detect reddish grapes: threshold based, Mahalanobis distance, Bayesian classifier, linear color model segmentation and histogram segmentation, in order to obtain the best estimation of the area of the clusters of grapes in this illumination conditions. The color spaces tested were the original RGB and the Hue-Saturation-Value (HSV. The best segmentation method in the case of a non-occluded reddish table-grape variety was the threshold segmentation applied to the H layer, with an estimation error in the area of 13.55%, improved up to 10.01% by morphological filtering. Secondly, after segmentation, two procedures for yield estimation based on a previous calibration procedure have been proposed: (1 the number of pixels corresponding to a cluster of grapes is computed and converted directly into a yield estimate; and (2 the area of a cluster of grapes is converted into a volume by means of a solid of revolution, and this volume is converted into a yield estimate; the yield errors obtained were 16% and −17%, respectively.

  2. The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology.

    Science.gov (United States)

    Ruskova, Lenka; Raclavsky, Vladislav

    2011-09-01

    Routine medical microbiology diagnostics relies on conventional cultivation followed by phenotypic techniques for identification of pathogenic bacteria and fungi. This is not only due to tradition and economy but also because it provides pure culture needed for antibiotic susceptibility testing. This review focuses on the potential of High Resolution Melting Analysis (HRMA) of double-stranded DNA for future routine medical microbiology. Search of MEDLINE database for publications showing the advantages of HRMA in routine medical microbiology for identification, strain typing and further characterization of pathogenic bacteria and fungi in particular. The results show increasing numbers of newly-developed and more tailor-made assays in this field. For microbiologists unfamiliar with technical aspects of HRMA, we also provide insight into the technique from the perspective of microbial characterization. We can anticipate that the routine availability of HRMA in medical microbiology laboratories will provide a strong stimulus to this field. This is already envisioned by the growing number of medical microbiology applications published recently. The speed, power, convenience and cost effectiveness of this technology virtually predestine that it will advance genetic characterization of microbes and streamline, facilitate and enrich diagnostics in routine medical microbiology without interfering with the proven advantages of conventional cultivation.

  3. Molecular differentiation of Opisthorchis viverrini and Clonorchis sinensis eggs by multiplex real-time PCR with high resolution melting analysis.

    Science.gov (United States)

    Kaewkong, Worasak; Intapan, Pewpan M; Sanpool, Oranuch; Janwan, Penchom; Thanchomnang, Tongjit; Laummaunwai, Porntip; Lulitanond, Viraphong; Doanh, Pham Ngoc; Maleewong, Wanchai

    2013-12-01

    Opisthorchis viverrini and Clonorchis sinensis are parasites known to be carcinogenic and causative agents of cholangiocarcinoma in Asia. The standard method for diagnosis for those parasite infections is stool examination to detect parasite eggs. However, the method has low sensitivity, and eggs of O. viverrini and C. sinensis are difficult to distinguish from each other and from those of some other trematodes. Here, we report a multiplex real-time PCR coupled with high resolution melting (HRM) analysis for the differentiation of O. viverrini and C. sinensis eggs in fecal samples. Using 2 pairs of species-specific primers, DNA sequences from a portion of the mitochondrial NADH dehydrogenase subunit 2 (nad 2) gene, were amplified to generate 209 and 165 bp products for O. viverrini and C. sinensis, respectively. The distinct characteristics of HRM patterns were analyzed, and the melting temperatures peaked at 82.4±0.09℃ and 85.9±0.08℃ for O. viverrini and C. sinensis, respectively. This technique was able to detect as few as 1 egg of O. viverrini and 2 eggs of C. sinensis in a 150 mg fecal sample, which is equivalent to 7 and 14 eggs per gram of feces, respectively. The method is species-specific, rapid, simple, and does not require fluorescent probes or post-PCR processing for discrimination of eggs of the 2 species. It offers a new tool for differentiation and detection of Asian liver fluke infections in stool specimens.

  4. Study of Grape Polyphenols by Liquid Chromatography-High-Resolution Mass Spectrometry (UHPLC/QTOF and Suspect Screening Analysis

    Directory of Open Access Journals (Sweden)

    Riccardo Flamini

    2015-01-01

    Full Text Available Suspect screening analysis is a targeted metabolomics method in which the identification of compounds relies on specific available information, such as their molecular formula and isotopic pattern. This method, coupled to liquid chromatography-high-resolution mass spectrometry, is effective in the study of grape metabolomics, in particular for characterization of flavonols, stilbene derivatives, and anthocyanins. For identification of compounds expected in the samples, a new database of putative compounds was expressly constructed by using the molecular information on potential metabolites of grape and wine from the literature and other electronic databases. Currently, this database contains around 1,100 compounds. The method allows identification of several hundred grape metabolites with two analyses (positive and negative ionization modes, and performing of data reprocessing using “untargeted” algorithms also provided the identification of some flavonols and resveratrol trimers and tetramers in grape for the first time. This approach can be potentially used in the study of metabolomics of varieties of other plant species.

  5. High-resolution dynamic imaging and quantitative analysis of lung cancer xenografts in nude mice using clinical PET/CT.

    Science.gov (United States)

    Wang, Ying Yi; Wang, Kai; Xu, Zuo Yu; Song, Yan; Wang, Chu Nan; Zhang, Chong Qing; Sun, Xi Lin; Shen, Bao Zhong

    2017-08-08

    Considering the general application of dedicated small-animal positron emission tomography/computed tomography is limited, an acceptable alternative in many situations might be clinical PET/CT. To estimate the feasibility of using clinical PET/CT with [F-18]-fluoro-2-deoxy-D-glucose for high-resolution dynamic imaging and quantitative analysis of cancer xenografts in nude mice. Dynamic clinical PET/CT scans were performed on xenografts for 60 min after injection with [F-18]-fluoro-2-deoxy-D-glucose. Scans were reconstructed with or without SharpIR method in two phases. And mice were sacrificed to extracting major organs and tumors, using ex vivo γ-counting as a reference. Strikingly, we observed that the image quality and the correlation between the all quantitive data from clinical PET/CT and the ex vivo counting was better with the SharpIR reconstructions than without. Our data demonstrate that clinical PET/CT scanner with SharpIR reconstruction is a valuable tool for imaging small animals in preclinical cancer research, offering dynamic imaging parameters, good image quality and accurate data quatification.

  6. Comparative analysis of native and permethylated human milk oligosaccharides by liquid chromatography coupled to high resolution mass spectrometry.

    Science.gov (United States)

    Oursel, Stéphanie; Cholet, Sophie; Junot, Christophe; Fenaille, François

    2017-12-15

    Human milk oligosaccharides (HMOs) represent the third most abundant components of milk after lactose and lipids. HMOs are indigestible by the suckling infant but can act as prebiotics and have significant biological functions regarding the organism defense against pathogens (such as bacteria or viruses) by preventing interactions with their receptors. Although constituted of only five distinct monosaccharide building blocks, HMOs are highly structurally diverse compounds with many co-existing structural isomers. Here we report the development and comparison of two distinct glycomic platforms based on liquid chromatography coupled to high resolution mass spectrometry (LC-MS) for analyzing HMOs. We have implemented and thoroughly compared the LC-MS of permethylated and native HMOs on reversed phase (RP) and porous graphitic carbon (PGC) columns for their ability to resolve the natural heterogeneity of milk oligosaccharides at the highest sensitivity. Our data essentially underlines the usefulness of analyzing HMOs as permethylated derivatives especially for getting more precise structural information at high sensitivity. For instance, permethylation annihilates gas-phase fucose migration during MS/MS experiments, thus facilitating spectra interpretation and giving access to relevant information regarding oligosaccharide branching and isomer distinction. At the opposite, LC-MS profiling of native HMOs (using PGC) in milk performed best in terms of detected species, while also being much faster in terms of sample preparation. Although less efficient than PGC chromatography, RPLC proved successful for separating pairs of permethylated isomeric HMOs. A key advantage of RP over PGC liquid chromatography is that retention times can be correlated to molecular weights, which can greatly facilitate further HMO identification using retention time prediction. Altogether these data lead us to think that LC-MS analysis of native HMOs (using PGC) can be used as first

  7. High Resolution Modeling of the Water Cycle to Refine GRACE Signal Analysis in the Gulf of Alaska Drainage

    Science.gov (United States)

    Beamer, J.; Hill, D. F.; Arendt, A. A.; Luthcke, S. B.; Liston, G. E.

    2015-12-01

    A comprehensive study of the Gulf of Alaska (GOA) drainage basin was carried out to improve understanding of the coastal freshwater discharge (FWD) and surface mass balance (SMB) of glaciers. Coastal FWD and SMB for all glacier surfaces were modeled using a suite of physically based, spatially distributed weather, energy-balance snow/ice melt, soil water balance, and runoff routing models at a high resolution (1 km horizontal grid; daily time step). A 35 year hind cast was performed, providing complete records of precipitation, runoff, snow water equivalent (SWE) depth, evapotranspiration, coastal FWD and glacier SMB. Meteorological forcing was provided by the North American Regional Reanalysis (NARR), Modern Era Retrospective Analysis for Research and Applications (MERRA), and NCEP Climate Forecast System Reanalysis (CFSR) datasets. A fourth dataset was created by bias-correcting the NARR data to recently-developed monthly weather grids based on PRISM climatologies (NARR-BC). Each weather dataset and model combination was individually calibrated using PRISM climatologies, streamflow, and glacier mass balance measurements from four locations in the study domain. Simulated mean annual FWD into the GOA ranged from 600 km3 yr-1 using NARR to 850 km3 yr-1 from NARR-BC. The CFSR-forced simulations with optimized model parameters produced a simulated regional water storage that compared favorably to data from the NASA/DLR Gravity Recovery and Climate Experiment (GRACE) high resolution mascon solutions (Figure). Glacier runoff, taken as the sum of rainfall, snow and ice melt occurring on glacier surfaces, ranged from 260 km3 yr-1 from MERRA to 400 km3 yr-1 from NARR-BC, approximately one half of the signal from both glaciers and surrounding terrain. The large contribution from non-glacier surfaces to the seasonal water balance is likely not being fully removed from GRACE solutions aimed at isolating the glacier signal alone. We will discuss methods to use our simulations

  8. Geographic information system for fusion and analysis of high-resolution remote sensing and ground truth data

    Science.gov (United States)

    Freeman, Anthony; Way, Jo Bea; Dubois, Pascale; Leberl, Franz

    1992-01-01

    We seek to combine high-resolution remotely sensed data with models and ground truth measurements, in the context of a Geographical Information System, integrated with specialized image processing software. We will use this integrated system to analyze the data from two Case Studies, one at a bore Al forest site, the other a tropical forest site. We will assess the information content of the different components of the data, determine the optimum data combinations to study biogeophysical changes in the forest, assess the best way to visualize the results, and validate the models for the forest response to different radar wavelengths/polarizations. During the 1990's, unprecedented amounts of high-resolution images from space of the Earth's surface will become available to the applications scientist from the LANDSAT/TM series, European and Japanese ERS-1 satellites, RADARSAT and SIR-C missions. When the Earth Observation Systems (EOS) program is operational, the amount of data available for a particular site can only increase. The interdisciplinary scientist, seeking to use data from various sensors to study his site of interest, may be faced with massive difficulties in manipulating such large data sets, assessing their information content, determining the optimum combinations of data to study a particular parameter, visualizing his results and validating his model of the surface. The techniques to deal with these problems are also needed to support the analysis of data from NASA's current program of Multi-sensor Airborne Campaigns, which will also generate large volumes of data. In the Case Studies outlined in this proposal, we will have somewhat unique data sets. For the Bonanza Creek Experimental Forest (Case I) calibrated DC-8 SAR data and extensive ground truth measurement are already at our disposal. The data set shows documented evidence to temporal change. The Belize Forest Experiment (Case II) will produce calibrated DC-8 SAR and AVIRIS data, together with

  9. Direct surface analysis coupled to high-resolution mass spectrometry reveals heterogeneous composition of the cuticle of Hibiscus trionum petals.

    Science.gov (United States)

    Giorio, Chiara; Moyroud, Edwige; Glover, Beverley J; Skelton, Paul C; Kalberer, Markus

    2015-10-06

    Plant cuticle, which is the outermost layer covering the aerial parts of all plants including petals and leaves, can present a wide range of patterns that, combined with cell shape, can generate unique physical, mechanical, or optical properties. For example, arrays of regularly spaced nanoridges have been found on the dark (anthocyanin-rich) portion at the base of the petals of Hibiscus trionum. Those ridges act as a diffraction grating, producing an iridescent effect. Because the surface of the distal white region of the petals is smooth and noniridescent, a selective chemical characterization of the surface of the petals on different portions (i.e., ridged vs smooth) is needed to understand whether distinct cuticular patterns correlate with distinct chemical compositions of the cuticle. In the present study, a rapid screening method has been developed for the direct surface analysis of Hibiscus trionum petals using liquid extraction surface analysis (LESA) coupled with high-resolution mass spectrometry. The optimized method was used to characterize a wide range of plant metabolites and cuticle monomers on the upper (adaxial) surface of the petals on both the white/smooth and anthocyanic/ridged regions, and on the lower (abaxial) surface, which is entirely smooth. The main components detected on the surface of the petals are low-molecular-weight organic acids, sugars, and flavonoids. The ridged portion on the upper surface of the petal is enriched in long-chain fatty acids, which are constituents of the wax fraction of the cuticle. These compounds were not detected on the white/smooth region of the upper petal surface or on the smooth lower surface.

  10. Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis.

    Science.gov (United States)

    Hanson, Erin K; Ballantyne, Jack

    2013-01-01

    Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive

  11. High resolution melting analysis for the detection of EMS induced mutations in wheat SbeIIa genes

    Directory of Open Access Journals (Sweden)

    Botticella Ermelinda

    2011-11-01

    Full Text Available Abstract Background Manipulation of the amylose-amylopectin ratio in cereal starch has been identified as a major target for the production of starches with novel functional properties. In wheat, silencing of starch branching enzyme genes by a transgenic approach reportedly caused an increase of amylose content up to 70% of total starch, exhibiting novel and interesting nutritional characteristics. In this work, the functionality of starch branching enzyme IIa (SBEIIa has been targeted in bread wheat by TILLING. An EMS-mutagenised wheat population has been screened using High Resolution Melting of PCR products to identify functional SNPs in the three homoeologous genes encoding the target enzyme in the hexaploid genome. Results This analysis resulted in the identification of 56, 14 and 53 new allelic variants respectively for SBEIIa-A, SBEIIa-B and SBEIIa-D. The effects of the mutations on protein structure and functionality were evaluated by a bioinformatic approach. Two putative null alleles containing non-sense or splice site mutations were identified for each of the three homoeologous SBEIIa genes; qRT-PCR analysis showed a significant decrease of their gene expression and resulted in increased amylose content. Pyramiding of different single null homoeologous allowed to isolate double null mutants showing an increase of amylose content up to 21% compared to the control. Conclusion TILLING has successfully been used to generate novel alleles for SBEIIa genes known to control amylose content in wheat. Single and double null SBEIIa genotypes have been found to show a significant increase in amylose content.

  12. High resolution, high sensitivity imaging and analysis of minerals and inclusions (fluid and melt) using the new CSIRO-GEMOC nuclear microprobe

    International Nuclear Information System (INIS)

    Ryan, C.G.; McInnes, B.M.; Van Achterbergh, E.; Williams, P.J.; Dong, G.; Zaw, K.

    1999-01-01

    Full text: The new CSIRO-GEMOC Nuclear Microprobe (NMP) The instrument was designed specifically for minerals analysis and imaging and to achieve ppm to sub-ppm sensitivity at a spatial resolution of 1-2 μm using X-rays and y-rays induced by MeV energy ion beams. The key feature of the design is a unique magnetic quadrupole quintuplet ion focussing system that combines high current with high spatial resolution (Ryan et al., 1999). These design goals have been achieved or exceeded. On the first day of operation, a spot-size of 1.3 μm was obtained at a beam current of 0.5 nA, suitable for fluid inclusion analysis and imaging. The spot-size grows to just 1.8 μm at 10 nA (3 MeV protons), ideal for mineralogical samples with detection limits down to 0.2 ppm achieved in quantitative, high resolution, trace element images. Applications of the NMP include: research into ore deposit processes through trace element geochemistry, mineralogy and fluid inclusion analysis of ancient deposits and active sea-floor environments, ore characterization, and fundamental studies of mantle processes and extraterrestrial material. Quantitative True Elemental Imaging Dynamic Analysis is a method for projecting quantitative major and trace element images from proton-induced X-ray emission (PIXE) data obtained using the NMP (Ryan et al., 1995). The method un-mixes full elemental spectral signatures to produce quantitative images that can be directly interrogated for the concentrations of all elements in selected areas or line projections, etc. Fluid Inclusion Analysis and Imaging The analysis of fluids trapped as fluid inclusions in minerals holds the key to understanding ore metal pathways and ore formation processes. PIXE analysis using the NMP provides a direct non-destructive method to determine the composition of these trapped fluids with detection limits down to 20 ppm. However, some PIXE results have been controversial, such as the strong partitioning of Cu into the vapour phase (e

  13. True 3D kinematic analysis for slope instability assessment in the Siq of Petra (Jordan), from high resolution TLS

    Science.gov (United States)

    Gigli, Giovanni; Margottini, Claudio; Spizzichino, Daniele; Ruther, Heinz; Casagli, Nicola

    2016-04-01

    Most classifications of mass movements in rock slopes use relatively simple, idealized geometries for the basal sliding surface, like planar sliding, wedge sliding, toppling or columnar failures. For small volumes, the real sliding surface can be often well described by such simple geometries. Extended and complex rock surfaces, however, can exhibit a large number of mass movements, also showing various kind of kinematisms. As a consequence, the real situation in large rock surfaces with a complicate geometry is generally very complex and a site depending analysis, such as fieldwork and compass, cannot be comprehensive of the real situation. Since the outstanding development of terrestrial laser scanner (TLS) in recent years, rock slopes can now be investigated and mapped through high resolution point clouds, reaching the resolution of few mm's and accuracy less than a cm in most advanced instruments, even from remote surveying. The availability of slope surface digital data can offer a unique chance to determine potential kinematisms in a wide distributed area for all the investigated geomorphological processes. More in detail the proposed method is based on the definition of least squares fitting planes on clusters of points extracted by moving a sampling cube on the point cloud. If the associated standard deviation is below a defined threshold, the cluster is considered valid. By applying geometric criteria it is possible to join all the clusters lying on the same surface; in this way discontinuity planes can be reconstructed, rock mass geometrical properties are calculated and, finally, potential kinematisms established. The Siq of Petra (Jordan), is a 1.2 km naturally formed gorge, with an irregular horizontal shape and a complex vertical slope, that represents the main entrance to Nabatean archaeological site. In the Siq, discontinuities of various type (bedding, joints, faults), mainly related to geomorphological evolution of the slope, lateral stress

  14. High resolution Neutron and Synchrotron Powder Diffraction

    International Nuclear Information System (INIS)

    Hewat, A.W.

    1986-01-01

    The use of high-resolution powder diffraction has grown rapidly in the past years, with the development of Rietveld (1967) methods of data analysis and new high-resolution diffractometers and multidetectors. The number of publications in this area has increased from a handful per year until 1973 to 150 per year in 1984, with a ten-year total of over 1000. These papers cover a wide area of solid state-chemistry, physics and materials science, and have been grouped under 20 subject headings, ranging from catalysts to zeolites, and from battery electrode materials to pre-stressed superconducting wires. In 1985 two new high-resolution diffractometers are being commissioned, one at the SNS laboratory near Oxford, and one at the ILL in Grenoble. In different ways these machines represent perhaps the ultimate that can be achieved with neutrons and will permit refinement of complex structures with about 250 parameters and unit cell volumes of about 2500 Angstrom/sp3/. The new European Synchotron Facility will complement the Grenoble neutron diffractometers, and extend the role of high-resolution powder diffraction to the direct solution of crystal structures, pioneered in Sweden

  15. Detection of Schistosoma mansoni and Schistosoma haematobium by Real-Time PCR with High Resolution Melting Analysis

    Directory of Open Access Journals (Sweden)

    Hany Sady

    2015-07-01

    Full Text Available The present study describes a real-time PCR approach with high resolution melting-curve (HRM assay developed for the detection and differentiation of Schistosoma mansoni and S. haematobium in fecal and urine samples collected from rural Yemen. The samples were screened by microscopy and PCR for the Schistosoma species infection. A pair of degenerate primers were designed targeting partial regions in the cytochrome oxidase subunit I (cox1 gene of S. mansoni and S. haematobium using real-time PCR-HRM assay. The overall prevalence of schistosomiasis was 31.8%; 23.8% of the participants were infected with S. haematobium and 9.3% were infected with S. mansoni. With regards to the intensity of infections, 22.1% and 77.9% of S. haematobium infections were of heavy and light intensities, respectively. Likewise, 8.1%, 40.5% and 51.4% of S. mansoni infections were of heavy, moderate and light intensities, respectively. The melting points were distinctive for S. mansoni and S. haematobium, categorized by peaks of 76.49 ± 0.25 °C and 75.43 ± 0.26 °C, respectively. HRM analysis showed high detection capability through the amplification of Schistosoma DNA with as low as 0.0001 ng/µL. Significant negative correlations were reported between the real-time PCR-HRM cycle threshold (Ct values and microscopic egg counts for both S. mansoni in stool and S. haematobium in urine (p < 0.01. In conclusion, this closed-tube HRM protocol provides a potentially powerful screening molecular tool for the detection of S. mansoni and S. haematobium. It is a simple, rapid, accurate, and cost-effective method. Hence, this method is a good alternative approach to probe-based PCR assays.

  16. SNP discovery and High Resolution Melting Analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens.

    Science.gov (United States)

    Valenzuela-Muñoz, Valentina; Araya-Garay, José Miguel; Gallardo-Escárate, Cristian

    2013-06-01

    The California red abalone, Haliotis rufescens that belongs to the Haliotidae family, is the largest species of abalone in the world that has sustained the major fishery and aquaculture production in the USA and Mexico. This native mollusk has not been evaluated or assigned a conservation category even though in the last few decades it was heavily exploited until it disappeared in some areas along the California coast. In Chile, the red abalone was introduced in the 1970s from California wild abalone stocks for the purposes of aquaculture. Considering the number of years that the red abalone has been cultivated in Chile crucial genetic information is scarce and critical issues remain unresolved. This study reports and validates novel single nucleotide polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA pyrosequencing. A total of 622 high quality SNPs were identified in 146 sequences with an estimated frequency of 1 SNP each 1000bp. Forty-five SNPs markers with functional information for gene ontology were selected. Of these, 8 were polymorphic among the individuals screened: Heat shock protein 70 (HSP70), vitellogenin (VTG), lysin, alginate lyase enzyme (AL), Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme (ODC). Two additional sequences were also identified with polymorphisms but no similarities with known proteins were achieved. To validate the putative SNP markers, High Resolution Melting Analysis (HRMA) was conducted in a wild and hatchery-bred population. Additionally, SNP cross-amplifications were tested in two further native abalone species, Haliotis fulgens and Haliotis corrugata. This study provides novel candidate genes that could be used to evaluate loss of genetic diversity due to hatchery selection or inbreeding effects. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. High-resolution rovibrational analysis of CH281BrF in the range 920–980cm−1

    DEFF Research Database (Denmark)

    Visinoni, R.; Baldacci, A.; Stoppa, P.

    2013-01-01

    The high-resolution infrared spectrum of CH281BrF has been studied in part of the atmospheric window between 920 and 980cm−1, the region characterized by the v9 and v5+v6 absorptions. The v9 emerges as a pseudo a-type band, with selection rule ΔKa=ΔKc=0, ±2, and v5+v6 exhibits a predominant a...

  18. High-resolution-cone beam tomography analysis of bone microarchitecture in patients with acromegaly and radiological vertebral fractures.

    Science.gov (United States)

    Maffezzoni, Filippo; Maddalo, Michele; Frara, Stefano; Mezzone, Monica; Zorza, Ivan; Baruffaldi, Fabio; Doglietto, Francesco; Mazziotti, Gherardo; Maroldi, Roberto; Giustina, Andrea

    2016-11-01

    Vertebral fractures are an emerging complication of acromegaly but their prediction is still difficult occurring even in patients with normal bone mineral density. In this study we evaluated the ability of high-resolution cone-beam computed tomography to provide information on skeletal abnormalities associated with vertebral fractures in acromegaly. 40 patients (24 females, 16 males; median age 57 years, range 25-72) and 21 healthy volunteers (10 females, 11 males; median age 60 years, range: 25-68) were evaluated for trabecular (bone volume/trabecular volume ratio, mean trabecular separation, and mean trabecular thickness) and cortical (thickness and porosity) parameters at distal radius using a high-resolution cone-beam computed tomography system. All acromegaly patients were evaluated for morphometric vertebral fractures and for mineral bone density by dual-energy X-ray absorptiometry at lumbar spine, total hip, femoral neck, and distal radius. Acromegaly patients with vertebral fractures (15 cases) had significantly (p acromegaly patients did not have significant differences in bone density at either skeletal site. Patients with acromegaly showed lower bone volume/trabecular volume ratio (p = 0.003) and mean trabecular thickness (p acromegaly. High-resolution cone-beam computed tomography at the distal radius may be useful to evaluate and predict the effects of acromegaly on bone microstructure.

  19. Development of AMS high resolution injector system

    International Nuclear Information System (INIS)

    Bao Yiwen; Guan Xialing; Hu Yueming

    2008-01-01

    The Beijing HI-13 tandem accelerator AMS high resolution injector system was developed. The high resolution energy achromatic system consists of an electrostatic analyzer and a magnetic analyzer, which mass resolution can reach 600 and transmission is better than 80%. (authors)

  20. High resolution melting curve analysis as a new tool for rapid identification of canine parvovirus type 2 strains.

    Science.gov (United States)

    Bingga, Gali; Liu, Zhicheng; Zhang, Jianfeng; Zhu, Yujun; Lin, Lifeng; Ding, Shuangyang; Guo, Pengju

    2014-01-01

    A high resolution melting (HRM) curve method was developed to identify canine parvovirus type 2 (CPV-2) strains by nested PCR. Two sets of primers, CPV-426F/426R and CPV-87R/87F, were designed that amplified a 52 bp and 53 bp product from the viral VP2 capsid gene. The region amplified by CPV-426F/426R included the A4062G and T4064A mutations in CPV-2a, CPV-2b and CPV-2c. The region amplified by CPV-87F/87R included the A3045T mutation in the vaccine strains of CPV-2 and CPV-2a, CPV-2b and CPV-2c. Faecal samples were obtained from 30 dogs that were CPV antigen-positive. The DNA was isolated from the faecal samples and PCR-amplified using the two sets of primers, and genotyped by HRM curve analysis. The PCR-HRM assay was able to distinguish single nucleotide polymorphisms between CPV-2a, CPV-2b and CPV-2c using CPV-426F/426R. CPV-2a was distinguished from CPV-2b and CPV-2c by differences in the melting temperature. CPV-2b and CPV-2c could be distinguished based on the shape of the melting curve after generating heteroduplexes using a CPV-2b reference sample. The vaccine strains of CPV-2 were identified using CPV-87F/87R. Conventional methods for genotyping CPV strains are labor intensive, expensive or time consuming; the present PCR-based HRM assay might be an attractive alternative. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Diagnosis of asbestosis by a time expanded wave form analysis, auscultation and high resolution computed tomography: a comparative study.

    Science.gov (United States)

    al Jarad, N; Strickland, B; Bothamley, G; Lock, S; Logan-Sinclair, R; Rudd, R M

    1993-01-01

    BACKGROUND--Crackles are a prominent clinical feature of asbestosis and may be an early sign of the condition. Auscultation, however, is subjective and interexaminer disagreement is a problem. Computerised lung sound analysis can visualise, store, and analyse lung sounds and disagreement on the presence of crackles is minimal. High resolution computed tomography (HRCT) is superior to chest radiography in detecting early signs of asbestosis. The aim of this study was to compare clinical auscultation, time expanded wave form analysis (TEW), chest radiography, and HRCT in detecting signs of asbestosis in asbestos workers. METHODS--Fifty three asbestos workers (51 men and two women) were investigated. Chest radiography and HRCT were assessed by two independent readers for detection of interstitial opacities. HRCT was performed in the supine position with additional sections at the bases in the prone position. Auscultation for persistent fine inspiratory crackles was performed by two independent examiners unacquainted with the diagnosis. TEW analysis was obtained from a 33 second recording of lung sounds over the lung bases. TEW and auscultation were performed in a control group of 13 subjects who had a normal chest radiograph. There were 10 current smokers and three previous smokers. In asbestos workers the extent of pulmonary opacities on the chest radiograph was scored according to the International Labour Office (ILO) scale. Patients were divided into two groups: 21 patients in whom the chest radiograph was > 1/0 (group 1) and 32 patients in whom the chest radiograph was scored auscultation in seven (22%) patients and by TEW in 14 (44%). HRCT detected definite interstitial opacities in 11 (34%) and gravity dependent subpleural lines in two (6%) patients. All but two patients with evidence of interstitial disease or gravity dependent subpleural lines on HRCT had crackles detected by TEW. In patients with an ILO score of > 1/0 auscultation and TEW revealed mid to late

  2. High-resolution gas chromatography/mas spectrometry method for characterization and quantitative analysis of ginkgolic acids in ginkgo biloba plants, extracts, and dietary supplements

    Science.gov (United States)

    A high resolution GC/MS with Selected Ion Monitor (SIM) method focusing on the characterization and quantitative analysis of ginkgolic acids (GAs) in Ginkgo biloba L. plant materials, extracts and commercial products was developed and validated. The method involved sample extraction with (1:1) meth...

  3. Quantitative analysis of localized stresses in irradiated stainless steels using high resolution electron backscatter diffraction and molecular dynamics modeling

    International Nuclear Information System (INIS)

    Johnson, D.C.; Kuhr, B.; Farkas, D.; Was, G.S.

    2016-01-01

    Quantitative measurements of stress near dislocation channel–grain boundary (DC–GB) interaction sites were made using high resolution electron backscatter diffraction (HREBSD) and have been compared with molecular dynamics (MD) simulations. Tensile stress normal to the grain boundary was significantly elevated at discontinuous DC–GB intersections with peak magnitudes roughly an order of magnitude greater than at sites where slip transfer occurred. These results constitute the first measurement of stress amplification at DC–GB intersections and provide support to the theory that high normal stress at the grain boundary may be a key driver for the initiation of irradiation assisted stress corrosion cracks.

  4. Assessment of constituents in Allium by multivariate data analysis, high-resolution α-glucosidase inhibition assay and HPLC-SPE-NMR

    DEFF Research Database (Denmark)

    Schmidt, Jeppe Secher; Nyberg, Nils; Stærk, Dan

    2014-01-01

    Bulbs and leaves of 35 Allium species and cultivars bought or collected in 2010–2012 were investigated with multivariate data analysis, high-resolution α-glucosidase inhibition assays and HPLC-HRMS-SPE-NMR with the aim of exploring the potential of Allium as a future functional food for management...... of type 2 diabetes. It was found that 30 out of 106 crude extracts showed more than 80% inhibition of the α-glucosidase enzyme at a concentration of 40 mg/mL (dry sample) or 0.4 g/mL (fresh sample). High-resolution α-glucosidase biochromatograms of these extracts allowed fast identification of three...

  5. Factor analysis of combined organic and inorganic aerosol mass spectra from high resolution aerosol mass spectrometer measurements

    Directory of Open Access Journals (Sweden)

    Y. L. Sun

    2012-09-01

    Full Text Available Positive matrix factorization (PMF was applied to the merged high resolution mass spectra of organic and inorganic aerosols from aerosol mass spectrometer (AMS measurements to investigate the sources and evolution processes of submicron aerosols in New York City in summer 2009. This new approach is able to study the distribution of organic and inorganic species in different types of aerosols, the acidity of organic aerosol (OA factors, and the fragment ion patterns related to photochemical processing. In this study, PMF analysis of the unified AMS spectral matrix resolved 8 factors. The hydrocarbon-like OA (HOA and cooking OA (COA factors contain negligible amounts of inorganic species. The two factors that are primarily ammonium sulfate (SO4-OA and ammonium nitrate (NO3-OA, respectively, are overall neutralized. Among all OA factors the organic fraction of SO4-OA shows the highest degree of oxidation (O/C = 0.69. Two semi-volatile oxygenated OA (OOA factors, i.e., a less oxidized (LO-OOA and a more oxidized (MO-OOA, were also identified. MO-OOA represents local photochemical products with a diurnal profile exhibiting a pronounced noon peak, consistent with those of formaldehyde (HCHO and Ox(= O3 + NO2. The NO+/NO2+ ion ratio in MO-OOA is much higher than that in NO3-OA and in pure ammonium nitrate, indicating the formation of organic nitrates. The nitrogen-enriched OA (NOA factor contains ~25% of acidic inorganic salts, suggesting the formation of secondary OA via acid-base reactions of amines. The size distributions of OA factors derived from the size-resolved mass spectra show distinct diurnal evolving behaviors but overall a progressing evolution from smaller to larger particle mode as the oxidation degree of OA increases. Our results demonstrate that PMF analysis of the unified aerosol mass spectral matrix which contains both

  6. High resolution heart rate variability analysis in patients with angina pectoris during coronary artery bypass graft surgery

    Science.gov (United States)

    Mironov, V. A.; Mironova, T. F.; Kuvatov, V. A.; Nokhrina, O. Yu.; Kuvatova, E. V.

    2017-12-01

    The purpose of the study is approbation of the capabilities of high-resolution rhythmocardiography (RCG) for the determination of the actual cardiovascular status of operated patients with angina pectoris during coronary artery bypass graft surgery (CABGS) for myocardial revascularization. The research was done by means of a KAP-RK-02-Mikor hardware-software complex with a monitor record and the time- and frequency-domain analyses of heart rate variability (HRV). Monitor records were made at each stage of CABGS in 123 patients. As a result, HRV manifested itself as a fairly adequate and promising method for the determination of the cardiovascular status during CABGS. In addition, the data of the HRV study during CABGS testify to the capability of RCG to determine the high risk of life-threatening cardioarrhythmias before and during operation, to different changes in sinoatrial heart node (SN) dysregulation, and contain the HRV symptoms of a high death risk before, during and after shunting. The loss of the peripheral autonomic sympathetic and parasympathetic control in SN in the form of the autonomic cardioneuropathy syndrome is a predictor of the complications related to CABGS. The obtained data on RCG monitoring of HRV recording are suggestive of wide prospects of the high-resolution RCG method to be used in cardiac surgery as a whole. The actual multivariant dysregulations of SN pacemaker activity testify to its adequacy to the pathophysiology of each period of the cardiac operation, according to the initial ischemic damages and localization of cardiosurgical manipulations during CABGS.

  7. Analysis of a high-resolution regional climate simulation for Alpine temperature. Validation and influence of the NAO

    Energy Technology Data Exchange (ETDEWEB)

    Proemmel, K. [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Kuestenforschung

    2008-11-06

    To determine whether the increase in resolution of climate models improves the representation of climate is a crucial topic in regional climate modelling. An improvement over coarser-scale models is expected especially in areas with complex orography or along coastlines. However, some studies have shown no clear added value for regional climate models. In this study a high-resolution regional climate model simulation performed with REMO over the period 1958-1998 is analysed for 2m temperature over the orographically complex European Alps and their surroundings called the Greater Alpine Region (GAR). The model setup is in hindcast mode meaning that the simulation is driven with perfect boundary conditions by the ERA40 reanalysis through prescribing the values at the lateral boundaries and spectral nudging of the large-scale wind field inside the model domain. The added value is analysed between the regional climate simulation with a resolution of 1/6 and the driving reanalysis with a resolution of 1.125 . Before analysing the added value both the REMO simulation and the ERA40 reanalysis are validated against different station datasets of monthly and daily mean 2m temperature. The largest dataset is the dense, homogenised and quality controlled HISTALP dataset covering the whole GAR, which gave the opportunity for the validation undertaken in this study. The temporal variability of temperature, as quantified by correlation, is well represented by both REMO and ERA40. However, both show considerable biases. The REMO bias reaches 3 K in summer in regions known to experience a problem with summer drying in a number of regional models. In winter the bias is strongly influenced by the choice of the temperature lapse rate, which is applied to compare grid box and station data at different altitudes, and has the strongest influence on inner Alpine subregions where the altitude differences are largest. By applying a constant lapse rate the REMO bias in winter in the high

  8. Comparison of infrared spectroscopy techniques: developing an efficient method for high resolution analysis of sediment properties from long records

    Science.gov (United States)

    Hahn, Annette; Rosén, Peter; Kliem, Pierre; Ohlendorf, Christian; Persson, Per; Zolitschka, Bernd; Pasado Science Team

    2010-05-01

    The analysis of sediment samples in visible to mid-infrared spectra is ideal for high-resolution records. It requires only small amounts (0.01-0.1g dry weight) of sample material and facilitates rapid and cost efficient analysis of a wide variety of biogeochemical properties on minerogenic and organic substances (Kellner et al. 1998). One of these techniques, the Diffuse Reflectance Fourier Transform Infrared Spectrometry (DRIFTS), has already been successfully applied to lake sediment from very different settings and has shown to be a promising technique for high resolution analyses of long sedimentary records on glacial-interglacial timescales (Rosén et al. 2009). However, the DRIFTS technique includes a time-consuming step where sediment samples are mixed with KBr. To assess if alternative and more rapid infrared (IR) techniques can be used, four different IR spectroscopy techniques are compared for core catcher sediment samples from Laguna Potrok Aike - an ICDP site located in southernmost South America. Partial least square (PLS) calibration models were developed using the DRIFTS technique. The correlation coefficients (R) for correlations between DRIFTS-inferred and conventionally measured biogeochemical properties show values of 0.80 for biogenic silica (BSi), 0.95 for total organic carbon (TOC), 0.91 for total nitrogen (TN), and 0.92 for total inorganic carbon (TIC). Good statistical performance was also obtained by using the Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy ATR-FTIRS technique which requires less sample preparation. Two devices were used, the full-sized Bruker Equinox 252 and the smaller and less expensive Bruker Alpha. R for ATR-FTIRS-inferred and conventionally measured biogeochemical properties were 0.87 (BSi), 0.93 (TOC), 0.90 (TN), and 0.91 (TIC) for the Alpha, and 0.78 (TOC), 0.85 (TN), 0.79 (TIC) for the Equinox 252 device. As the penetration depth of the IR beam is frequency dependent, a firm surface contact of

  9. A method for generating high resolution satellite image time series

    Science.gov (United States)

    Guo, Tao

    2014-10-01

    There is an increasing demand for satellite remote sensing data with both high spatial and temporal resolution in many applications. But it still is a challenge to simultaneously improve spatial resolution and temporal frequency due to the technical limits of current satellite observation systems. To this end, much R&D efforts have been ongoing for years and lead to some successes roughly in two aspects, one includes super resolution, pan-sharpen etc. methods which can effectively enhance the spatial resolution and generate good visual effects, but hardly preserve spectral signatures and result in inadequate analytical value, on the other hand, time interpolation is a straight forward method to increase temporal frequency, however it increase little informative contents in fact. In this paper we presented a novel method to simulate high resolution time series data by combing low resolution time series data and a very small number of high resolution data only. Our method starts with a pair of high and low resolution data set, and then a spatial registration is done by introducing LDA model to map high and low resolution pixels correspondingly. Afterwards, temporal change information is captured through a comparison of low resolution time series data, and then projected onto the high resolution data plane and assigned to each high resolution pixel according to the predefined temporal change patterns of each type of ground objects. Finally the simulated high resolution data is generated. A preliminary experiment shows that our method can simulate a high resolution data with a reasonable accuracy. The contribution of our method is to enable timely monitoring of temporal changes through analysis of time sequence of low resolution images only, and usage of costly high resolution data can be reduces as much as possible, and it presents a highly effective way to build up an economically operational monitoring solution for agriculture, forest, land use investigation

  10. Global lateral transfer and evasion of C in freshwater systems - a revised high-resolution budget analysis

    Science.gov (United States)

    Lauerwald, Ronny; Laruelle, Goulven; Hartmann, Jens; Ciais, Philippe; Regnier, Pierre

    2016-04-01

    The net CO2 evasion from rivers (FCO2) is an important component when quantifying the lateral displacement of biologically fixed carbon from terrestrial systems and wetlands through the river network. Here, we present global maps of FCO2 from stream orders 3 and higher at 0.5° resolution (Lauerwald et al., 2015 - GBC). This resolution is comparable to that of Earth System Model simulations of vegetation and soil C dynamics and is also compatible with GlobalNEWS simulations of fluvial DOC and POC exports to the sea (Mayorga et al., 2010 - Environmental Modeling and Software). A GIS based approach was used to derive an empirical pCO2 model trained on data from 1182 sampling locations. While only few sampling data are available for Asia and Africa, the sampling locations cover the full spectrum from high to low latitudes. The empirical model predicts pCO2 from terrestrial net primary production, population density, and slope gradient within the river catchment and mean air temperature at the sampling location (r² = 0.47). The predicted pCO2 map was combined with spatially explicit estimates of stream surface area and gas exchange velocity calculated from published empirical equations and data sets to derive the FCO2 map. We used Monte Carlo simulations to assess the uncertainties of our estimates. At the global scale, we estimate an average river pCO2 of 2400 (2019-2826) μatm and a FCO2 of 650 (483-846) Tg C yr-1 (5th and 95th percentiles of confidence interval). Our maps reveal strong latitudinal gradients in pCO2, stream surface area, and FCO2. The zone between 10°N and 10°S contributes about half of the global CO2 evasion. Combining riverine FCO2 with the estimated fluvial DOC and POC exports from GlobalNEWS and FCO2 from lakes (downscaled from Raymond et al. 2013 - Nature), the total lateral transfer of biologically fixed C on land and in wetlands adds up to 1.3 Pg C yr-1. This estimate is likely conservative because CO2 evasion from smaller streams is not

  11. High-resolution spatial analysis of cholera patients reported in Artibonite department, Haiti in 2010–2011

    Directory of Open Access Journals (Sweden)

    Maya Allan

    2016-03-01

    Conclusion/significance: These findings demonstrate the value of high-resolution mapping for pinpointing locations most affected by cholera, and in the future could help prioritize the places in need of interventions such as improvement of sanitation and vaccination. The findings also describe spatio-temporal transmission patterns of the epidemic in a cholera-naïve country such as Haiti. By identifying transmission hubs, it is possible to target prevention strategies that, over time, could reduce transmission of the disease and eventually eliminate cholera in Haiti.

  12. High-resolution spatial analysis of cholera patients reported in Artibonite department, Haiti in 2010-2011.

    Science.gov (United States)

    Allan, Maya; Grandesso, Francesco; Pierre, Ronald; Magloire, Roc; Coldiron, Matthew; Martinez-Pino, Isabel; Goffeau, Thierry; Gitenet, Romain; François, Gwenola; Olson, David; Porten, Klaudia; Luquero, Francisco J

    2016-03-01

    Cholera is caused by Vibrio cholerae, and is transmitted through fecal-oral contact. Infection occurs after the ingestion of the bacteria and is usually asymptomatic. In a minority of cases, it causes acute diarrhea and vomiting, which can lead to potentially fatal severe dehydration, especially in the absence of appropriate medical care. Immunity occurs after infection and typically lasts 6-36 months. Cholera is responsible for outbreaks in many African and Asian developing countries, and caused localised and episodic epidemics in South America until the early 1990s. Haiti, despite its low socioeconomic status and poor sanitation, had never reported cholera before the recent outbreak that started in October 2010, with over 720,000 cases and over 8700 deaths (Case fatality rate: 1.2%) through 8 december 2014. So far, this outbreak has seen 3 epidemic peaks, and it is expected that cholera will remain in Haiti for some time. To trace the path of the early epidemic and to identify hot spots and potential transmission hubs during peaks, we examined the spatial distribution of cholera patients during the first two peaks in Artibonite, the second-most populous department of Haiti. We extracted the geographic origin of 84,000 patients treated in local health facilities between October 2010 and December 2011 and mapped these addresses to 63 rural communal sections and 9 urban cities. Spatial and cluster analysis showed that during the first peak, cholera spread along the Artibonite River and the main roads, and sub-communal attack rates ranged from 0.1% to 10.7%. During the second peak, remote mountain areas were most affected, although sometimes to very different degrees even in closely neighboring locations. Sub-communal attack rates during the second peak ranged from 0.2% to 13.7%. The relative risks at the sub-communal level during the second phase showed an inverse pattern compared to the first phase. These findings demonstrate the value of high-resolution mapping

  13. High resolution forecast of heavy precipitation with Lokal Modell: analysis of two case studies in the Alpine area

    Directory of Open Access Journals (Sweden)

    M. Elementi

    2005-01-01

    Full Text Available Northern Italy is frequently affected by severe precipitation conditions often inducing flood events with associated loss of properties, damages and casualties. The capability of correctly forecast these events, strongly required for an efficient support to civil protection actions, is still nowadays a challenge. This difficulty is also related with the complex structure of the precipitation field in the Alpine area and, more generally, over the Italian territory. Recently a new generation of non-hydrostatic meteorological models, suitable to be used at very high spatial resolution, has been developed. In this paper the performance of the non-hydrostatic Lokal Modell developed by the COSMO Consortium, is analysed with regard to a couple of intense precipitation events occurred in the Piemonte region in Northern Italy. These events were selected among the reference cases of the Hydroptimet/INTERREG IIIB project. LM run at the operational resolution of 7km provides a good forecast of the general rain structure, with an unsatisfactory representation of the precipitation distribution across the mountain ranges. It is shown that the inclusion of the new prognostic equations for cloud ice, rain and snow produces a remarkable improvement, reducing the precipitation in the upwind side and extending the intense rainfall area to the downwind side. The unrealistic maxima are decreased towards observed values. The use of very high horizontal resolution (2.8 km improves the general shape of the precipitation field in the flat area of the Piemonte region but, keeping active the moist convection scheme, sparse and more intense rainfall peaks are produced. When convective precipitation is not parametrised but explicitly represented by the model, this negative effect is removed.

  14. Chlorinated paraffin analysis by gas chromatography Orbitrap high-resolution mass spectrometry: Method performance, investigation of possible interferences and analysis of fish samples.

    Science.gov (United States)

    Krätschmer, Kerstin; Cojocariu, Cristian; Schächtele, Alexander; Malisch, Rainer; Vetter, Walter

    2018-03-02

    For decades, high quantities of short-chain chlorinated paraffins (SCCP) and medium-chain chlorinated paraffins (MCCP) have been widely used, for instance as plasticizers or flame retardants, leading to global pollution due to unintentional emissions from products or waste. Due to the high complexity of chlorinated paraffins with several thousand congeners there is no consensus on an analytical procedure for SCCPs and MCCPs in food samples. Amongst the multitude of methods currently in use, high-resolution mass spectrometry is particularly valuable for in-depth studies of homologue patterns. Here we analyse SCCPs and MCCPs with gas chromatography coupled to high-resolution Orbitrap mass spectrometry (GC-Orbitrap-HRMS) operated in full-scan acquisition in electron capture negative ion (ECNI) mode at 60,000 and 120,000 resolution (FWHM, m/z 200, equals roughly 30,000 and 60,000 at 5% peak height). Linear dynamic range, selectivity and sensitivity tests confirmed an excellent linearity in a concentration range of 25-15,000 pg/μL with very low limits of detection (LODs) in the low pg/μL range. Spiking experiments with high levels of native mono- and di-ortho-polychlorinated biphenyls (PCBs) and mixtures of MCCP and SCCP standards did not have a negative impact on isotope ratios of the examined homologues. Besides the [M-Cl] - fragment ions used for quantification, the mass spectra of homologues also featured [M-HCl] - ions whose abundance increased with decreasing chlorination degree. In addition, [M-HCl-Cl] - ions were detected with a relative abundance of 5-10%. Three salmon (Salmo salar) samples farmed in Norway showed a consistent CP homologue pattern which differed both from the CP pattern in a sample from Scottish aquaculture and a wild salmon sample. These measurements produce evidence that discretely different CP patterns may exist in different areas of origin. Our results demonstrate that GC/ECNI-Orbitrap-HRMS is well-suited for the analysis of CPs by

  15. High-resolution electron microscopy

    CERN Document Server

    Spence, John C H

    2013-01-01

    This new fourth edition of the standard text on atomic-resolution transmission electron microscopy (TEM) retains previous material on the fundamentals of electron optics and aberration correction, linear imaging theory (including wave aberrations to fifth order) with partial coherence, and multiple-scattering theory. Also preserved are updated earlier sections on practical methods, with detailed step-by-step accounts of the procedures needed to obtain the highest quality images of atoms and molecules using a modern TEM or STEM electron microscope. Applications sections have been updated - these include the semiconductor industry, superconductor research, solid state chemistry and nanoscience, and metallurgy, mineralogy, condensed matter physics, materials science and material on cryo-electron microscopy for structural biology. New or expanded sections have been added on electron holography, aberration correction, field-emission guns, imaging filters, super-resolution methods, Ptychography, Ronchigrams, tomogr...

  16. Ultra-high-performance liquid chromatography/tandem high-resolution mass spectrometry analysis of sixteen red beverages containing carminic acid: identification of degradation products by using principal component analysis/discriminant analysis.

    Science.gov (United States)

    Gosetti, Fabio; Chiuminatto, Ugo; Mazzucco, Eleonora; Mastroianni, Rita; Marengo, Emilio

    2015-01-15

    The study investigates the sunlight photodegradation process of carminic acid, a natural red colourant used in beverages. For this purpose, both carminic acid aqueous standard solutions and sixteen different commercial beverages, ten containing carminic acid and six containing E120 dye, were subjected to photoirradiation. The results show different patterns of degradation, not only between the standard solutions and the beverages, but also from beverage to beverage. Due to the different beverage recipes, unpredictable reactions take place between the dye and the other ingredients. To identify the dye degradation products in a very complex scenario, a methodology was used, based on the combined use of principal component analysis with discriminant analysis and ultra-high-performance liquid chromatography coupled with tandem high resolution mass spectrometry. The methodology is unaffected by beverage composition and allows the degradation products of carminic acid dye to be identified for each beverage. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Field-portable high-resolution EDXRF analysis with HgI2-detector-based instrumentation

    International Nuclear Information System (INIS)

    Berry, P.F.; Little, S.R.; Voots, G.R.

    1992-01-01

    Energy dispersive x-ray fluorescence (EDXRF) analysis is well known for its efficient use of x-ray detector technology for simultaneous multielement determination. Low-intensity excitation, such as from a radioisotope source, can thus be employed and has enabled the design of many types of truly portable EDXRF instrumentation. Portable design, however, has not been without significant compromise in analytical performance because of the limited x-ray resolving power of prior detection methods, except by the use of a cryogenically operated detector. The developments we refer to stem from the use of a comparatively new x-ray detection device fabricated from mercuric iodide (HgI 2 ). For this detector, only a modest degree of cooling is required to achieve an energy resolution of > 300 eV. Two field-portable instrument designs of different hand-held measurement probe configurations are available that have applications for industrial quality assurance and environmental screening

  18. High resolution extremity CT for biomechanics modeling

    International Nuclear Information System (INIS)

    Ashby, A.E.; Brand, H.; Hollerbach, K.; Logan, C.M.; Martz, H.E.

    1995-01-01

    With the advent of ever more powerful computing and finite element analysis (FEA) capabilities, the bone and joint geometry detail available from either commercial surface definitions or from medical CT scans is inadequate. For dynamic FEA modeling of joints, precise articular contours are necessary to get appropriate contact definition. In this project, a fresh cadaver extremity was suspended in parafin in a lucite cylinder and then scanned with an industrial CT system to generate a high resolution data set for use in biomechanics modeling

  19. High resolution extremity CT for biomechanics modeling

    Energy Technology Data Exchange (ETDEWEB)

    Ashby, A.E.; Brand, H.; Hollerbach, K.; Logan, C.M.; Martz, H.E.

    1995-09-23

    With the advent of ever more powerful computing and finite element analysis (FEA) capabilities, the bone and joint geometry detail available from either commercial surface definitions or from medical CT scans is inadequate. For dynamic FEA modeling of joints, precise articular contours are necessary to get appropriate contact definition. In this project, a fresh cadaver extremity was suspended in parafin in a lucite cylinder and then scanned with an industrial CT system to generate a high resolution data set for use in biomechanics modeling.

  20. A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC libraries using High Resolution Melt analysis

    Directory of Open Access Journals (Sweden)

    Caligari Peter DS

    2010-05-01

    Full Text Available Abstract Background The high-throughput anchoring of genetic markers into contigs is required for many ongoing physical mapping projects. Multidimentional BAC pooling strategies for PCR-based screening of large insert libraries is a widely used alternative to high density filter hybridisation of bacterial colonies. To date, concerns over reliability have led most if not all groups engaged in high throughput physical mapping projects to favour BAC DNA isolation prior to amplification by conventional PCR. Results Here, we report the first combined use of Multiplex Tandem PCR (MT-PCR and High Resolution Melt (HRM analysis on bacterial stocks of BAC library superpools as a means of rapidly anchoring markers to BAC colonies and thereby to integrate genetic and physical maps. We exemplify the approach using a BAC library of the model plant Arabidopsis thaliana. Super pools of twenty five 384-well plates and two-dimension matrix pools of the BAC library were prepared for marker screening. The entire procedure only requires around 3 h to anchor one marker. Conclusions A pre-amplification step during MT-PCR allows high multiplexing and increases the sensitivity and reliability of subsequent HRM discrimination. This simple gel-free protocol is more reliable, faster and far less costly than conventional PCR screening. The option to screen in parallel 3 genetic markers in one MT-PCR-HRM reaction using templates from directly pooled bacterial stocks of BAC-containing bacteria further reduces time for anchoring markers in physical maps of species with large genomes.

  1. Analysis of Properties of Reflectance Reference Targets for Permanent Radiometric Test Sites of High Resolution Airborne Imaging Systems

    Directory of Open Access Journals (Sweden)

    Eero Ahokas

    2010-08-01

    Full Text Available Reliable and optimal exploitation of rapidly developing airborne imaging methods requires geometric and radiometric quality assurance of production systems in operational conditions. Permanent test sites are the most promising approach for cost-efficient performance assessment. Optimal construction of permanent radiometric test sites for high resolution airborne imaging systems is an unresolved issue. The objective of this study was to assess the performance of commercially available gravels and painted and unpainted concrete targets for permanent, open-air radiometric test sites under sub-optimal climate conditions in Southern Finland. The reflectance spectrum and reflectance anisotropy and their stability were characterized during the summer of 2009. The management of reflectance anisotropy and stability were shown to be the key issues for better than 5% reflectance accuracy.

  2. High-resolution genomic fingerprinting of Campylobacter jejuni and Campylobacter coli by analysis of amplified fragment length polymorphisms

    DEFF Research Database (Denmark)

    Kokotovic, Branko; On, Stephen L.W.

    1999-01-01

    A method for high-resolution genomic fingerprinting of the enteric pathogens Campylobacter jejuni and Campylobacter coli, based on the determination of amplified fragment length polymorphism, is described. The potential of this method for molecular epidemiological studies of these species...... is evaluated with 50 type, reference, and well-characterised field strains. Amplified fragment length polymorphism fingerprints comprised over 60 bands detected in the size range 35-500 bp. Groups of outbreak strains, replicate subcultures, and 'genetically identical' strains from humans, poultry and cattle......, proved indistinguishable by amplified fragment length polymorphism fingerprinting, but were differentiated fi-om unrelated isolates. Previously unknown relationships between three hippurate-negative C. jejuni strains, and two C. coil var, hyoilei strains, were identified. These relationships corresponded...

  3. Species identification in meat products: A new screening method based on high resolution melting analysis of cyt b gene.

    Science.gov (United States)

    Lopez-Oceja, A; Nuñez, C; Baeta, M; Gamarra, D; de Pancorbo, M M

    2017-12-15

    Meat adulteration by substitution with lower value products and/or mislabeling involves economic, health, quality and socio-religious issues. Therefore, identification and traceability of meat species has become an important subject to detect possible fraudulent practices. In the present study the development of a high resolution melt (HRM) screening method for the identification of eight common meat species is reported. Samples from Bos taurus, Ovis aries, Sus scrofa domestica, Equus caballus, Oryctolagus cuniculus, Gallus gallus domesticus, Meleagris gallopavo and Coturnix coturnix were analyzed through the amplification of a 148 bp fragment from the cyt b gene with a universal primer pair in HRM analyses. Melting profiles from each species, as well as from several DNA mixtures of these species and blind samples, allowed a successful species differentiation. The results demonstrated that the HRM method here proposed is a fast, reliable, and low-cost screening technique. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Construction of a quartz spherical analyzer: application to high-resolution analysis of the Ni Kα emission spectrum

    International Nuclear Information System (INIS)

    Honnicke, Marcelo Goncalves; Cusatis, Cesar

    2016-01-01

    The construction and characterization of a focusing X-ray spherical analyzer based on α-quartz 44̄04 are presented. For this study, the performance of the analyzer was demonstrated by applying it to a high-resolution X-ray spectroscopy study of theKα_1_,_2emission spectrum of Ni. An analytical representation based on physical grounds was assumed to model the shape of the X-ray emission lines. Satellite structures assigned to 3dspectator hole transitions were resolved and determined as well as their relative contribution to the emission spectrum. The present results on 1s"-"13d"-"1shake probabilities support a recently proposed calculation framework based on a multi-configuration atomic model.

  5. High-resolution two-dimensional gel analysis of proteins in wing imaginal discs: A data base of Drosophila

    International Nuclear Information System (INIS)

    Santaren, J.F.; Garcia-Bellido, A.

    1990-01-01

    An improved method of high-resolution two-dimensional gel electrophoresis has been used to study the patterns of protein synthesis in wing imaginal discs of late instar larvae of Drosophila melanogaster. A small number of discs were radiolabeled with a mixture of 14 C-labeled amino acids or with [ 35 S]methionine and the pattern of labeled proteins was analyzed. One thousand and twenty-five polypeptides (787 acidic (IEF) and 238 basic (NEPHGE)) from wing discs of several wild-type strains have so far been separated and cataloged. All these polypeptides have been numbered and presented in a reference map for further studies. When comparing patterns of label we have found small quantitative differences in rate of synthesis between individuals of the same strain, not due to sexual differences, and very few quantitative and qualitative differences between groups of individuals of different strains

  6. Monitoring Oilfield Operations and GHG Emissions Sources Using Object-based Image Analysis of High Resolution Spatial Imagery

    Science.gov (United States)

    Englander, J. G.; Brodrick, P. G.; Brandt, A. R.

    2015-12-01

    Fugitive emissions from oil and gas extraction have become a greater concern with the recent increases in development of shale hydrocarbon resources. There are significant gaps in the tools and research used to estimate fugitive emissions from oil and gas extraction. Two approaches exist for quantifying these emissions: atmospheric (or 'top down') studies, which measure methane fluxes remotely, or inventory-based ('bottom up') studies, which aggregate leakage rates on an equipment-specific basis. Bottom-up studies require counting or estimating how many devices might be leaking (called an 'activity count'), as well as how much each device might leak on average (an 'emissions factor'). In a real-world inventory, there is uncertainty in both activity counts and emissions factors. Even at the well level there are significant disagreements in data reporting. For example, some prior studies noted a ~5x difference in the number of reported well completions in the United States between EPA and private data sources. The purpose of this work is to address activity count uncertainty by using machine learning algorithms to classify oilfield surface facilities using high-resolution spatial imagery. This method can help estimate venting and fugitive emissions sources from regions where reporting of oilfield equipment is incomplete or non-existent. This work will utilize high resolution satellite imagery to count well pads in the Bakken oil field of North Dakota. This initial study examines an area of ~2,000 km2 with ~1000 well pads. We compare different machine learning classification techniques, and explore the impact of training set size, input variables, and image segmentation settings to develop efficient and robust techniques identifying well pads. We discuss the tradeoffs inherent to different classification algorithms, and determine the optimal algorithms for oilfield feature detection. In the future, the results of this work will be leveraged to be provide activity

  7. A bi-ventricular cardiac atlas built from 1000+ high resolution MR images of healthy subjects and an analysis of shape and motion.

    Science.gov (United States)

    Bai, Wenjia; Shi, Wenzhe; de Marvao, Antonio; Dawes, Timothy J W; O'Regan, Declan P; Cook, Stuart A; Rueckert, Daniel

    2015-12-01

    Atlases encode valuable anatomical and functional information from a population. In this work, a bi-ventricular cardiac atlas was built from a unique data set, which consists of high resolution cardiac MR images of 1000+ normal subjects. Based on the atlas, statistical methods were used to study the variation of cardiac shapes and the distribution of cardiac motion across the spatio-temporal domain. We have shown how statistical parametric mapping (SPM) can be combined with a general linear model to study the impact of gender and age on regional myocardial wall thickness. Finally, we have also investigated the influence of the population size on atlas construction and atlas-based analysis. The high resolution atlas, the statistical models and the SPM method will benefit more studies on cardiac anatomy and function analysis in the future. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Integrated High Resolution Monitoring of Mediterranean vegetation

    Science.gov (United States)

    Cesaraccio, Carla; Piga, Alessandra; Ventura, Andrea; Arca, Angelo; Duce, Pierpaolo; Mereu, Simone

    2017-04-01

    The study of the vegetation features in a complex and highly vulnerable ecosystems, such as Mediterranean maquis, leads to the need of using continuous monitoring systems at high spatial and temporal resolution, for a better interpretation of the mechanisms of phenological and eco-physiological processes. Near-surface remote sensing techniques are used to quantify, at high temporal resolution, and with a certain degree of spatial integration, the seasonal variations of the surface optical and radiometric properties. In recent decades, the design and implementation of global monitoring networks involved the use of non-destructive and/or cheaper approaches such as (i) continuous surface fluxes measurement stations, (ii) phenological observation networks, and (iii) measurement of temporal and spatial variations of the vegetation spectral properties. In this work preliminary results from the ECO-SCALE (Integrated High Resolution Monitoring of Mediterranean vegetation) project are reported. The project was manly aimed to develop an integrated system for environmental monitoring based on digital photography, hyperspectral radiometry , and micrometeorological techniques during three years of experimentation (2013-2016) in a Mediterranean site of Italy (Capo Caccia, Alghero). The main results concerned the analysis of chromatic coordinates indices from digital images, to characterized the phenological patterns for typical shrubland species, determining start and duration of the growing season, and the physiological status in relation to different environmental drought conditions; then the seasonal patterns of canopy phenology, was compared to NEE (Net Ecosystem Exchange) patterns, showing similarities. However, maximum values of NEE and ER (Ecosystem respiration), and short term variation, seemed mainly tuned by inter annual pattern of meteorological variables, in particular of temperature recorded in the months preceding the vegetation green-up. Finally, green signals

  9. The EUV dayglow at high spectral resolution

    International Nuclear Information System (INIS)

    Morrison, M.D.; Bowers, C.W.; Feldman, P.D.; Meier, R.R.

    1990-01-01

    Rocket observations of the dayglow spectrum of the terrestrial atmosphere between 840 angstrom and 1860 angstrom at 2 angstrom resolution were obtained with a sounding rocket payload flown on January 17, 1985. Additionally, spectra were also obtained using a 0.125-m focal length scanning Ebert-Fastie monochromator covering the wavelength interval of 1150-1550 angstrom at 7 angstrom resolution on this flight and on a sounding rocket flight on August 29, 1983, under similar viewing geometries and solar zenith angles. Three bands of the N 2 c' 4 system are seen clearly resolved in the dayglow. Analysis of high-resolution N 2 Lyman-Birge-Hopfield data shows no anomalous vibrational distribution as has been reported from other observations. The altitude profiles of the observed O and N 2 emissions demonstrate that the MSIS-83 model O and N 2 densities are appropriate for the conditions of both the 1983 and 1985 rocket flights. A reduction of a factor of 2 in the model O 2 density is required for both flights to reproduce the low-altitude atomic oxygen emission profiles. The volume excitation rates calculated using the Hinteregger et al. (1981) SC number-sign 21REFW solar reference spectrum and the photoelectron flux model of Strickland and Meier (1982) need to be scaled upward by a factor of 1.4 for both fights to match the observations

  10. Food contaminant analysis at ultra-high mass resolution: application of hybrid linear ion trap - orbitrap mass spectrometry for the determination of the polyether toxins, azaspiracids, in shellfish.

    LENUS (Irish Health Repository)

    2010-10-30

    The biotoxins, azaspiracids (AZAs), from marine phytoplankton accumulate in shellfish and affect human health by causing severe gastrointestinal disturbance, diarrhea, nausea and vomiting. Specific and sensitive methods have been developed and validated for the determination of the most commonly occurring azaspiracid analogs. An LTQ Orbitrap mass spectrometer is a hybrid instrument that combines linear ion trap (LIT) mass spectrometry (MS) with high-resolution Fourier transform (FT) MS and this was exploited to perform simultaneous ultra-high-resolution full-scan MS analysis and collision-induced dissociation (CID) tandem mass spectrometry (MS\\/MS). Using the highest mass resolution setting (100,000 FWHM) in full-scan mode, the methodology was validated for the determination of six AZAs in mussel (Mytilus galloprovincialis) tissue extracts. Ultra-high mass resolution, together with a narrow mass tolerance window of ±2 mDa, dramatically improved detection sensitivity. In addition to employing chromatographic resolution to distinguish between the isomeric azaspiracid analogs, AZA1\\/AZA6 and AZA4\\/AZA5, higher energy collisionally induced dissociation (HCD) fragmentation on selected precursor ions were performed in parallel with full-scan FTMS. Using HCD MS\\/MS, most precursor and product ion masses were determined within 1 ppm of the theoretical m\\/z values throughout the mass spectral range and this enhanced the reliability of analyte identity.For the analysis of mussels (M. galloprovincialis), the method limit of quantitation (LOQ) was 0.010 µg\\/g using full-scan FTMS and this was comparable with the LOQ (0.007 µg\\/g) using CID MS\\/MS. The repeatability data were; intra-day RSD% (1.8-4.4%; n = 6) and inter-day RSD% (4.7-8.6%; n = 3). Application of these methods to the analysis of mussels (M. edulis) that were naturally contaminated with azaspiracids, using high-resolution full-scan Orbitrap MS and low-resolution CID MS\\/MS, produced

  11. Establishment and analysis of a High-Resolution Assimilation Dataset of the water-energy cycle in China

    Science.gov (United States)

    Zhu, X.; Wen, X.; Zheng, Z.

    2017-12-01

    For better prediction and understanding of land-atmospheric interaction, in-situ observed meteorological data acquired from the China Meteorological Administration (CMA) were assimilated in the Weather Research and Forecasting (WRF) model and the monthly Green Vegetation Coverage (GVF) data, which was calculated using the Normalized Difference Vegetation Index (NDVI) of the Earth Observing System Moderate-Resolution Imaging Spectroradiometer (EOS-MODIS) and Digital Elevation Model (DEM) data of the Shuttle Radar Topography Mission (SRTM) system. Furthermore, the WRF model produced a High-Resolution Assimilation Dataset of the water-energy cycle in China (HRADC). This dataset has a horizontal resolution of 25 km for near surface meteorological data, such as air temperature, humidity, wind vectors and pressure (19 levels); soil temperature and moisture (four levels); surface temperature; downward/upward short/long radiation; 3-h latent heat flux; sensible heat flux; and ground heat flux. In this study, we 1) briefly introduce the cycling 3D-Var assimilation method and 2) compare results of meteorological elements, such as 2 m temperature and precipitation generated by the HRADC with the gridded observation data from CMA, and surface temperature and specific humidity with Global LandData Assimilation System (GLDAS) output data from the National Aeronautics and Space Administration (NASA). We found that the satellite-derived GVF from MODIS increased over southeast China compared with the default model over the whole year. The simulated results of soil temperature, net radiation and surface energy flux from the HRADC are improved compared with the control simulation and are close to GLDAS outputs. The values of net radiation from HRADC are higher than the GLDAS outputs, and the differences in the simulations are large in the east region but are smaller in northwest China and on the Qinghai-Tibet Plateau. The spatial distribution of the sensible heat flux and the ground

  12. Cranial performance in the Komodo dragon (Varanus komodoensis) as revealed by high-resolution 3-D finite element analysis.

    Science.gov (United States)

    Moreno, Karen; Wroe, Stephen; Clausen, Philip; McHenry, Colin; D'Amore, Domenic C; Rayfield, Emily J; Cunningham, Eleanor

    2008-06-01

    The Komodo dragon (Varanus komodoensis) displays a unique hold and pull-feeding technique. Its delicate 'space-frame' skull morphology differs greatly from that apparent in most living large prey specialists and is suggestive of a high degree of optimization, wherein use of materials is minimized. Here, using high-resolution finite element modelling based on dissection and in vivo bite and pull data, we present results detailing the mechanical performance of the giant lizard's skull. Unlike most modern predators, V. komodoensis applies minimal input from the jaw muscles when butchering prey. Instead it uses series of actions controlled by postcranial muscles. A particularly interesting feature of the performance of the skull is that it reveals considerably lower overall stress when these additional extrinsic forces are added to those of the jaw adductors. This remarkable reduction in stress in response to additional force is facilitated by both internal and external bone anatomy. Functional correlations obtained from these analyses also provide a solid basis for the interpretation of feeding ecology in extinct species, including dinosaurs and sabre-tooth cats, with which V. komodoensis shares various cranial and dental characteristics.

  13. High resolution biostratigraphy of Oligo-Miocene Leon and Chama Formations: An integrated approach for sequence stratigraphy analysis

    Energy Technology Data Exchange (ETDEWEB)

    Pittelli, R.; Rull, V. (Maraven S.A., Caracas (Venezuela))

    1993-02-01

    Based on foraminiferal and palynological high resolution studies, a set of Sequence Boundaries (SB) and Maximum Flooding Surfaces (MSF) were identified for the Venezuelan Northwestern Andean Foothills Leon and Chama formations. Changes in abundance patterns of forminifera palynomorphs, in faunal/floral composition and distribution, together with quantitative studies of particulate organic matter allowed picking SB 30, 21 and 15.5 (very low values of fossil abundance and faunal discontinuities, recognized by a rapid stratigraphic change in biofacies and faunal assemblage and the associated mineralogical contents) and MFS 18.5, 16, and 15 (abundant fossils). The Leon Formation represents coastal plain and swamp deposits with some minor fluctuations in the seawater level. The top of the Leon Formation shaly unit is bounded by SB 30, according to Hag B.U. et al (version 1992), marked by a decrease in fossil abundance. An increase in faunal/floral content close to the top of the section coincides with the MFS 18.5. The upper part of the formation is marked by a sandy unit with SB 16.5, characterized again by a decrease in fossil abundance at its top. The Chama Formation was deposited in a transitional environment, with minor seawater level fluctuations. Climate type was tropical humid, with seasonal precipitations, except at the Early Miocene arid or semiarid phase. Mangrove and rain forest vegetation dominated throughout the Early to Middle Miocene. MFS 16 was picked on the basis of a high abundance of microforams and glauconite.

  14. High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia.

    Science.gov (United States)

    Arias, Leonardo; Barbieri, Chiara; Barreto, Guillermo; Stoneking, Mark; Pakendorf, Brigitte

    2018-02-01

    Northwestern Amazonia (NWA) is a center of high linguistic and cultural diversity. Several language families and linguistic isolates occur in this region, as well as different subsistence patterns, with some groups being foragers and others agriculturalists. In addition, speakers of Eastern Tukanoan languages are known for practicing linguistic exogamy, a marriage system in which partners are taken from different language groups. In this study, we use high-resolution mitochondrial DNA sequencing to investigate the impact of this linguistic and cultural diversity on the genetic relationships and population structure of NWA groups. We collected saliva samples from individuals representing 40 different NWA ethnolinguistic groups and sequenced 439 complete mitochondrial genomes to an average coverage of 1,030×. The mtDNA data revealed that NWA populations have high genetic diversity with extensive sharing of haplotypes among groups. Moreover, groups who practice linguistic exogamy have higher genetic diversity, while the foraging Nukak have lower genetic diversity. We also find that rivers play a more important role than either geography or language affiliation in structuring the genetic relationships of populations. Contrary to the view of NWA as a pristine area inhabited by small human populations living in isolation, our data support a view of high diversity and contact among different ethnolinguistic groups, with movement along rivers probably facilitating this contact. Additionally, we provide evidence for the impact of cultural practices, such as linguistic exogamy, on patterns of genetic variation. Overall, this study provides new data and insights into a remote and little-studied region of the world. © 2017 Wiley Periodicals, Inc.

  15. Mapping whole-brain activity with cellular resolution by light-sheet microscopy and high-throughput image analysis (Conference Presentation)

    Science.gov (United States)

    Silvestri, Ludovico; Rudinskiy, Nikita; Paciscopi, Marco; Müllenbroich, Marie Caroline; Costantini, Irene; Sacconi, Leonardo; Frasconi, Paolo; Hyman, Bradley T.; Pavone, Francesco S.

    2016-03-01

    Mapping neuronal activity patterns across the whole brain with cellular resolution is a challenging task for state-of-the-art imaging methods. Indeed, despite a number of technological efforts, quantitative cellular-resolution activation maps of the whole brain have not yet been obtained. Many techniques are limited by coarse resolution or by a narrow field of view. High-throughput imaging methods, such as light sheet microscopy, can be used to image large specimens with high resolution and in reasonable times. However, the bottleneck is then moved from image acquisition to image analysis, since many TeraBytes of data have to be processed to extract meaningful information. Here, we present a full experimental pipeline to quantify neuronal activity in the entire mouse brain with cellular resolution, based on a combination of genetics, optics and computer science. We used a transgenic mouse strain (Arc-dVenus mouse) in which neurons which have been active in the last hours before brain fixation are fluorescently labelled. Samples were cleared with CLARITY and imaged with a custom-made confocal light sheet microscope. To perform an automatic localization of fluorescent cells on the large images produced, we used a novel computational approach called semantic deconvolution. The combined approach presented here allows quantifying the amount of Arc-expressing neurons throughout the whole mouse brain. When applied to cohorts of mice subject to different stimuli and/or environmental conditions, this method helps finding correlations in activity between different neuronal populations, opening the possibility to infer a sort of brain-wide 'functional connectivity' with cellular resolution.

  16. GRANULOMETRIC MAPS FROM HIGH RESOLUTION SATELLITE IMAGES

    Directory of Open Access Journals (Sweden)

    Catherine Mering

    2011-05-01

    Full Text Available A new method of land cover mapping from satellite images using granulometric analysis is presented here. Discontinuous landscapes such as steppian bushes of semi arid regions and recently growing urban settlements are especially concerned by this study. Spatial organisations of the land cover are quantified by means of the size distribution analysis of the land cover units extracted from high resolution remotely sensed images. A granulometric map is built by automatic classification of every pixel of the image according to the granulometric density inside a sliding neighbourhood. Granulometric mapping brings some advantages over traditional thematic mapping by remote sensing by focusing on fine spatial events and small changes in one peculiar category of the landscape.

  17. FINOSEIS: A new approach to offshore-building foundation soil analysis using high resolution reflection seismic and Scholte-wave dispersion analysis

    Science.gov (United States)

    Wilken, Dennis; Wölz, Susanne; Müller, Christof; Rabbel, Wolfgang

    2009-05-01

    As part of the FINOSEIS project we present the development of new seismic acquisition and inversion concepts for offshore-building foundation soil analysis. FINOSEIS is a subproject of the FINO3 project, which is aimed at the construction of an offshore research platform based in 28 m water depth, hosting eight research projects dealing with offshore wind energy topics. Our investigations focus on the determination of seismic parameters and structural information of the building plot of FINO3. We infer the shear-wave velocity structure by exploiting the dispersive properties of Scholte-waves and use high resolution 2.5D reflection seismic acquisition to determine seismic stratigraphy in three dimensions. Our work is motivated regarding possible hazards to offshore foundations such as wind parks and the FINO3 platform itself, e.g. permanent mechanical load by wind- and wave-forces possibly leading to an impairment of the soil. We conducted a pre-investigation of the site of the future platform in order to help finding a suitable foundation soil by improving common site investigation methods. In May 2006 we did a survey covering an area of 2 km square employing high resolution 2.5D reflection seismic. Along three 2 km airgun profiles Scholte-waves were recorded with Ocean-Bottom-Seismometers. Spectral analysis of these led to pseudo-2D shear-wave velocity models along the profiles. The reflection seismic area is characterized by glacial stratigraphy and diffractions documented within the penetration range of 30 m. With respect to the topography of the identified horizons as well as to the distribution of diffracting objects, a suitable foundation area for the platform was suggested. The results of the Scholte-wave experiment provide valuable information for further inversion models as well as for the dimensioning of further measurements. We also implemented an inversion strategy using the particle swarm optimization method. The inverted layers of shear-wave velocity

  18. Planning for shallow high resolution seismic surveys

    CSIR Research Space (South Africa)

    Fourie, CJS

    2008-11-01

    Full Text Available of the input wave. This information can be used in conjunction with this spreadsheet to aid the geophysicist in designing shallow high resolution seismic surveys to achieve maximum resolution and penetration. This Excel spreadsheet is available free from...

  19. High-resolution continuous-flow analysis setup for water isotopic measurement from ice cores using laser spectroscopy

    Science.gov (United States)

    Emanuelsson, B. D.; Baisden, W. T.; Bertler, N. A. N.; Keller, E. D.; Gkinis, V.

    2015-07-01

    Here we present an experimental setup for water stable isotope (δ18O and δD) continuous-flow measurements and provide metrics defining the performance of the setup during a major ice core measurement campaign (Roosevelt Island Climate Evolution; RICE). We also use the metrics to compare alternate systems. Our setup is the first continuous-flow laser spectroscopy system that is using off-axis integrated cavity output spectroscopy (OA-ICOS; analyzer manufactured by Los Gatos Research, LGR) in combination with an evaporation unit to continuously analyze water samples from an ice core. A Water Vapor Isotope Standard Source (WVISS) calibration unit, manufactured by LGR, was modified to (1) enable measurements on several water standards, (2) increase the temporal resolution by reducing the response time and (3) reduce the influence from memory effects. While this setup was designed for the continuous-flow analysis (CFA) of ice cores, it can also continuously analyze other liquid or vapor sources. The custom setups provide a shorter response time (~ 54 and 18 s for 2013 and 2014 setup, respectively) compared to the original WVISS unit (~ 62 s), which is an improvement in measurement resolution. Another improvement compared to the original WVISS is that the custom setups have a reduced memory effect. Stability tests comparing the custom and WVISS setups were performed and Allan deviations (σAllan) were calculated to determine precision at different averaging times. For the custom 2013 setup the precision after integration times of 103 s is 0.060 and 0.070 ‰ for δ18O and δD, respectively. The corresponding σAllan values for the custom 2014 setup are 0.030, 0.060 and 0.043 ‰ for δ18O, δD and δ17O, respectively. For the WVISS setup the precision is 0.035, 0.070 and 0.042 ‰ after 103 s for δ18O, δD and δ17O, respectively. Both the custom setups and WVISS setup are influenced by instrumental drift with δ18O being more drift sensitive than δD. The

  20. The coupling of supercritical fluid chromatography and field ionization time-of-flight high-resolution mass spectrometry for rapid and quantitative analysis of petroleum middle distillates.

    Science.gov (United States)

    Qian, Kuangnan; Diehl, John W; Dechert, Gary J; DiSanzo, Frank P

    2004-01-01

    We report the first coupling of supercritical fluid chromatography (SFC) with field ionization time-of-flight high-resolution mass spectrometry (FI-ToF HRMS), in parallel with ultraviolet (UV) detection and flame ionization detection (FID), for rapid and quantitative analysis of petroleum middle distillates. SFC separates petroleum middle distillates into saturates and 1- to 3-ring aromatics. FI generates molecular ions for hydrocarbon species eluted from the SFC. The high resolution and exact mass measurements by ToF mass spectrometry provide elemental compositions of the molecules in the petroleum product. The amounts of saturates and aromatic ring types were quantified using the parallel SFC-FID assisted by SFC-UV. With a proper carbon-number calibration, the detailed composition of the petroleum middle distillate was rapidly determined.

  1. Noise reduction methods in the analysis of near infrared lunar occultation light curves for high angular resolution measurements

    International Nuclear Information System (INIS)

    Baug Tapas; Chandrasekhar Thyagarajan

    2013-01-01

    A lunar occultation (LO) technique in the near-infrared (NIR) provides angular resolution down to milliarcseconds for an occulted source, even with ground-based 1 m class telescopes. LO observations are limited to brighter objects because they require a high signal-to-noise ratio (S/N ∼40) for proper extraction of angular diameter values. Hence, methods to improve the S/N ratio by reducing noise using Fourier and wavelet transforms have been explored in this study. A sample of 54 NIR LO light curves observed with the IR camera at Mt Abu Observatory has been used. It is seen that both Fourier and wavelet methods have shown an improvement in S/N compared to the original data. However, the application of wavelet transforms causes a slight smoothing of the fringes and results in a higher value for angular diameter. Fourier transforms which reduce discrete noise frequencies do not distort the fringe. The Fourier transform method seems to be effective in improving the S/N, as well as improving the model fit, particularly in the fainter regime of our sample. These methods also provide a better model fit for brighter sources in some cases, though there may not be a significant improvement in S/N

  2. Analysis of high mass resolution PTR-TOF mass spectra from 1,3,5-trimethylbenzene (TMB) environmental chamber experiments

    Science.gov (United States)

    Müller, M.; Graus, M.; Wisthaler, A.; Hansel, A.; Metzger, A.; Dommen, J.; Baltensperger, U.

    2012-01-01

    A series of 1,3,5-trimethylbenzene (TMB) photo-oxidation experiments was performed in the 27-m3 Paul Scherrer Institute environmental chamber under various NOx conditions. A University of Innsbruck prototype high resolution Proton Transfer Reaction Time-of-Flight Mass Spectrometer (PTR-TOF) was used for measurements of gas and particulate phase organics. The gas phase mass spectrum displayed ~200 ion signals during the TMB photo-oxidation experiments. Molecular formulas CmHnNoOp were determined and ion signals were separated and grouped according to their C, O and N numbers. This allowed to determine the time evolution of the O:C ratio and of the average carbon oxidation state solid #000; color: #000;">OSC of the reaction mixture. Both quantities were compared with master chemical mechanism (MCMv3.1) simulations. The O:C ratio in the particle phase was about twice the O:C ratio in the gas phase. Average carbon oxidation states of secondary organic aerosol (SOA) samples solid #000; color: #000;">OSCSOA were in the range of -0.34 to -0.31, in agreement with expected average carbon oxidation states of fresh SOA (solid #000; color: #000;">OSC = -0.5-0).

  3. Quantitative analysis of multiple high-resolution mass spectrometry images using chemometric methods: quantitation of chlordecone in mouse liver.

    Science.gov (United States)

    Mohammadi, Saeedeh; Parastar, Hadi

    2018-05-15

    In this work, a chemometrics-based strategy is developed for quantitative mass spectrometry imaging (MSI). In this regard, quantification of chlordecone as a carcinogenic organochlorinated pesticide (C10Cll0O) in mouse liver using the matrix-assisted laser desorption ionization MSI (MALDI-MSI) method is used as a case study. The MSI datasets corresponded to 1, 5 and 10 days of mouse exposure to the standard chlordecone in the quantity range of 0 to 450 μg g-1. The binning approach in the m/z direction is used to group high resolution m/z values and to reduce the big data size. To consider the effect of bin size on the quality of results, three different bin sizes of 0.25, 0.5 and 1.0 were chosen. Afterwards, three-way MSI data arrays (two spatial and one m/z dimensions) for seven standards and four unknown samples were column-wise augmented with m/z values as the common mode. Then, these datasets were analyzed using multivariate curve resolution-alternating least squares (MCR-ALS) using proper constraints. The resolved mass spectra were used for identification of chlordecone in the presence of a complex background and interference. Additionally, the augmented spatial profiles were post-processed and 2D images for each component were obtained in calibration and unknown samples. The sum of these profiles was utilized to set the calibration curve and to obtain the analytical figures of merit (AFOMs). Inspection of the results showed that the lower bin size (i.e., 0.25) provides more accurate results. Finally, the obtained results by MCR for three datasets were compared with those of gas chromatography-mass spectrometry (GC-MS) and MALDI-MSI. The results showed that the MCR-assisted method gives a higher amount of chlordecone than MALDI-MSI and a lower amount than GC-MS. It is concluded that a combination of chemometric methods with MSI can be considered as an alternative way for MSI quantification.

  4. High resolution integral holography using Fourier ptychographic approach.

    Science.gov (United States)

    Li, Zhaohui; Zhang, Jianqi; Wang, Xiaorui; Liu, Delian

    2014-12-29

    An innovative approach is proposed for calculating high resolution computer generated integral holograms by using the Fourier Ptychographic (FP) algorithm. The approach initializes a high resolution complex hologram with a random guess, and then stitches together low resolution multi-view images, synthesized from the elemental images captured by integral imaging (II), to recover the high resolution hologram through an iterative retrieval with FP constrains. This paper begins with an analysis of the principle of hologram synthesis from multi-projections, followed by an accurate determination of the constrains required in the Fourier ptychographic integral-holography (FPIH). Next, the procedure of the approach is described in detail. Finally, optical reconstructions are performed and the results are demonstrated. Theoretical analysis and experiments show that our proposed approach can reconstruct 3D scenes with high resolution.

  5. Individual pore and interconnection size analysis of macroporous ceramic scaffolds using high-resolution X-ray tomography

    Energy Technology Data Exchange (ETDEWEB)

    Jerban, Saeed, E-mail: saeed.jerban@usherbrooke.ca; Elkoun, Saïd, E-mail: Said.Elkoun@usherbrooke.ca

    2016-08-15

    The pore interconnection size of β-tricalcium phosphate scaffolds plays an essential role in the bone repair process. Although, the μCT technique is widely used in the biomaterial community, it is rarely used to measure the interconnection size because of the lack of algorithms. In addition, discrete nature of the μCT introduces large systematic errors due to the convex geometry of interconnections. We proposed, verified and validated a novel pore-level algorithm to accurately characterize the individual pores and interconnections. Specifically, pores and interconnections were isolated, labeled, and individually analyzed with high accuracy. The technique was verified thoroughly by visually inspecting and verifying over 3474 properties of randomly selected pores. This extensive verification process has passed a one-percent accuracy criterion. Scanning errors inherent in the discretization, which lead to both dummy and significantly overestimated interconnections, have been examined using computer-based simulations and additional high-resolution scanning. Then accurate correction charts were developed and used to reduce the scanning errors. Only after the corrections, both the μCT and SEM-based results converged, and the novel algorithm was validated. Material scientists with access to all geometrical properties of individual pores and interconnections, using the novel algorithm, will have a more-detailed and accurate description of the substitute architecture and a potentially deeper understanding of the link between the geometric and biological interaction. - Highlights: •An algorithm is developed to analyze individually all pores and interconnections. •After pore isolating, the discretization errors in interconnections were corrected. •Dummy interconnections and overestimated sizes were due to thin material walls. •The isolating algorithm was verified through visual inspection (99% accurate). •After correcting for the systematic errors, algorithm was

  6. High resolution NMR spectroscopy of synthetic polymers in bulk

    International Nuclear Information System (INIS)

    Komorski, R.A.

    1986-01-01

    The contents of this book are: Overview of high-resolution NMR of solid polymers; High-resolution NMR of glassy amorphous polymers; Carbon-13 solid-state NMR of semicrystalline polymers; Conformational analysis of polymers of solid-state NMR; High-resolution NMR studies of oriented polymers; High-resolution solid-state NMR of protons in polymers; and Deuterium NMR of solid polymers. This work brings together the various approaches for high-resolution NMR studies of bulk polymers into one volume. Heavy emphasis is, of course, given to 13C NMR studies both above and below Tg. Standard high-power pulse and wide-line techniques are not covered

  7. HLA-A2 reactive antibodies in a patient who types as HLA-A2: The importance of high resolution typing and epitope-based antibody analysis.

    Science.gov (United States)

    Hahn, A B; Bravo-Egana, V; Jackstadt, J L; Conti, D J; Duquesnoy, R J

    2015-06-01

    This report describes a case of a highly sensitized patient who had serum antibodies reacting with HLA-A2 but whose phenotype included HLA-A2. The determination of HLA mismatch acceptability at the antigen level was problematic, but high-resolution HLA typing information and epitope-based antibody specificity analysis based on the nonself-self paradigm of HLA epitope immunogenicity have provided a solution. This case supports the concept that HLA typing at the allele level offers a better approach to identifying suitable donors for sensitized patients. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. SPARTAN high resolution solar studies

    Science.gov (United States)

    Bruner, Marilyn E.

    1993-01-01

    This report summarizes the work performed on Contract NAS5-29739, a sub-orbital research program directed toward the study of the geometry of and physical conditions in matter found in the upper layers of the solar atmosphere. The report describes a new sounding rocket payload developed under the contract, presents a guide to the contents of semiannual reports submitted during the contract, discusses the results of the first flight of the payload and the progress on scientific analysis. A bibliography of papers and publications is included.

  9. High-resolution dynamical downscaling of re-analysis data over the Kerguelen Islands using the WRF model

    Science.gov (United States)

    Fonseca, Ricardo; Martín-Torres, Javier

    2018-03-01

    We have used the Weather Research and Forecasting (WRF) model to simulate the climate of the Kerguelen Islands (49° S, 69° E) and investigate its inter-annual variability. Here, we have dynamically downscaled 30 years of the Climate Forecast System Reanalysis (CFSR) over these islands at 3-km horizontal resolution. The model output is found to agree well with the station and radiosonde data at the Port-aux-Français station, the only location in the islands for which observational data is available. An analysis of the seasonal mean WRF data showed a general increase in precipitation and decrease in temperature with elevation. The largest seasonal rainfall amounts occur at the highest elevations of the Cook Ice Cap in winter where the summer mean temperature is around 0 °C. Five modes of variability are considered: conventional and Modoki El Niño-Southern Oscillation (ENSO), Indian Ocean Dipole (IOD), Subtropical IOD (SIOD) and Southern Annular Mode (SAM). It is concluded that a key mechanism by which these modes impact the local climate is through interaction with the diurnal cycle in particular in the summer season when it has a larger magnitude. One of the most affected regions is the area just to the east of the Cook Ice Cap extending into the lower elevations between the Gallieni and Courbet Peninsulas. The WRF simulation shows that despite the small annual variability, the atmospheric flow in the Kerguelen Islands is rather complex which may also be the case for the other islands located in the Southern Hemisphere at similar latitudes.

  10. High-resolution numerical model of the middle and inner ear for a detailed analysis of radio frequency absorption

    International Nuclear Information System (INIS)

    Schmid, Gernot; Ueberbacher, Richard; Samaras, Theodoros; Jappel, Alexandra; Baumgartner, Wolf-Dieter; Tschabitscher, Manfred; Mazal, Peter R

    2007-01-01

    In order to enable a detailed analysis of radio frequency (RF) absorption in the human middle and inner ear organs, a numerical model of these organs was developed at a spatial resolution of 0.1 mm, based on a real human tissue sample. The dielectric properties of the liquids (perilymph and endolymph) inside the bony labyrinth were measured on samples of ten freshly deceased humans. After inserting this model into a commercially available numerical head model, FDTD-based computations for exposure scenarios with generic models of handheld devices operated close to the head in the frequency range 400-3700 MHz were carried out. For typical output power values of real handheld mobile communication devices the obtained results showed only very small amounts of absorbed RF power in the middle and inner ear organs. Highest absorption in the middle and inner ear was found for the 400 MHz irradiation. In this case, the RF power absorbed inside the labyrinth and the vestibulocochlear nerve was as low as 166 μW and 12 μW, respectively, when considering a device of 500 mW output power operated close to the ear. For typical mobile phone frequencies (900 MHz and 1850 MHz) and output power values (250 mW and 125 mW) the corresponding values of absorbed RF power were found to be more than one order of magnitude lower than the values given above. These results indicate that temperature-related biologically relevant effects on the middle and inner ear, induced by the RF emissions of typical handheld mobile communication devices, are unlikely

  11. High resolution NMR in zeolites

    Energy Technology Data Exchange (ETDEWEB)

    Diaz, Anix [INTEVEP, Filial de Petroleos de Venezuela, SA, Caracas (Venezuela). Dept. de Analisis y Evalucion

    1992-12-31

    In this work {sup 29} Si and {sup 27} Al NMR spectroscopy was used to study various types of zeolites. The corresponding spectra were used to measure the Si/Al ratios, to follow chemical modifications induced by acid and hydrothermal treatments, to determine non-equivalent crystallographic sites in highly dealuminated mordenites, and to detect modifications of faujasites due to the insertion of titanium atoms in the lattice. (author) 7 refs., 7 figs., 2 tabs.

  12. High resolution NMR in zeolites

    International Nuclear Information System (INIS)

    Diaz, Anix

    1991-01-01

    In this work 29 Si and 27 Al NMR spectroscopy was used to study various types of zeolites. The corresponding spectra were used to measure the Si/Al ratios, to follow chemical modifications induced by acid and hydrothermal treatments, to determine non-equivalent crystallographic sites in highly dealuminated mordenites, and to detect modifications of faujasites due to the insertion of titanium atoms in the lattice. (author)

  13. High resolution sequence stratigraphy in China

    International Nuclear Information System (INIS)

    Zhang Shangfeng; Zhang Changmin; Yin Yanshi; Yin Taiju

    2008-01-01

    Since high resolution sequence stratigraphy was introduced into China by DENG Hong-wen in 1995, it has been experienced two development stages in China which are the beginning stage of theory research and development of theory research and application, and the stage of theoretical maturity and widely application that is going into. It is proved by practices that high resolution sequence stratigraphy plays more and more important roles in the exploration and development of oil and gas in Chinese continental oil-bearing basin and the research field spreads to the exploration of coal mine, uranium mine and other strata deposits. However, the theory of high resolution sequence stratigraphy still has some shortages, it should be improved in many aspects. The authors point out that high resolution sequence stratigraphy should be characterized quantitatively and modelized by computer techniques. (authors)

  14. High resolution CT of the chest

    Energy Technology Data Exchange (ETDEWEB)

    Barneveld Binkhuysen, F H [Eemland Hospital (Netherlands), Dept. of Radiology

    1996-12-31

    Compared to conventional CT high resolution CT (HRCT) shows several extra anatomical structures which might effect both diagnosis and therapy. The extra anatomical structures were discussed briefly in this article. (18 refs.).

  15. High-resolution spectrometer at PEP

    International Nuclear Information System (INIS)

    Weiss, J.M.; HRS Collaboration.

    1982-01-01

    A description is presented of the High Resolution Spectrometer experiment (PEP-12) now running at PEP. The advanced capabilities of the detector are demonstrated with first physics results expected in the coming months

  16. Ultra-high resolution coded wavefront sensor

    KAUST Repository

    Wang, Congli

    2017-06-08

    Wavefront sensors and more general phase retrieval methods have recently attracted a lot of attention in a host of application domains, ranging from astronomy to scientific imaging and microscopy. In this paper, we introduce a new class of sensor, the Coded Wavefront Sensor, which provides high spatio-temporal resolution using a simple masked sensor under white light illumination. Specifically, we demonstrate megapixel spatial resolution and phase accuracy better than 0.1 wavelengths at reconstruction rates of 50 Hz or more, thus opening up many new applications from high-resolution adaptive optics to real-time phase retrieval in microscopy.

  17. Structure of high-resolution NMR spectra

    CERN Document Server

    Corio, PL

    2012-01-01

    Structure of High-Resolution NMR Spectra provides the principles, theories, and mathematical and physical concepts of high-resolution nuclear magnetic resonance spectra.The book presents the elementary theory of magnetic resonance; the quantum mechanical theory of angular momentum; the general theory of steady state spectra; and multiple quantum transitions, double resonance and spin echo experiments.Physicists, chemists, and researchers will find the book a valuable reference text.

  18. High Resolution Powder Diffraction and Structure Determination

    International Nuclear Information System (INIS)

    Cox, D. E.

    1999-01-01

    It is clear that high-resolution synchrotrons X-ray powder diffraction is a very powerful and convenient tool for material characterization and structure determination. Most investigations to date have been carried out under ambient conditions and have focused on structure solution and refinement. The application of high-resolution techniques to increasingly complex structures will certainly represent an important part of future studies, and it has been seen how ab initio solution of structures with perhaps 100 atoms in the asymmetric unit is within the realms of possibility. However, the ease with which temperature-dependence measurements can be made combined with improvements in the technology of position-sensitive detectors will undoubtedly stimulate precise in situ structural studies of phase transitions and related phenomena. One challenge in this area will be to develop high-resolution techniques for ultra-high pressure investigations in diamond anvil cells. This will require highly focused beams and very precise collimation in front of the cell down to dimensions of 50 (micro)m or less. Anomalous scattering offers many interesting possibilities as well. As a means of enhancing scattering contrast it has applications not only to the determination of cation distribution in mixed systems such as the superconducting oxides discussed in Section 9.5.3, but also to the location of specific cations in partially occupied sites, such as the extra-framework positions in zeolites, for example. Another possible application is to provide phasing information for ab initio structure solution. Finally, the precise determination of f as a function of energy through an absorption edge can provide useful information about cation oxidation states, particularly in conjunction with XANES data. In contrast to many experiments at a synchrotron facility, powder diffraction is a relatively simple and user-friendly technique, and most of the procedures and software for data analysis

  19. Ultra high-resolution gene centric genomic structural analysis of a non-syndromic congenital heart defect, Tetralogy of Fallot.

    Directory of Open Access Journals (Sweden)

    Douglas C Bittel

    Full Text Available Tetralogy of Fallot (TOF is one of the most common severe congenital heart malformations. Great progress has been made in identifying key genes that regulate heart development, yet approximately 70% of TOF cases are sporadic and nonsyndromic with no known genetic cause. We created an ultra high-resolution gene centric comparative genomic hybridization (gcCGH microarray based on 591 genes with a validated association with cardiovascular development or function. We used our gcCGH array to analyze the genomic structure of 34 infants with sporadic TOF without a deletion on chromosome 22q11.2 (n male = 20; n female = 14; age range of 2 to 10 months. Using our custom-made gcCGH microarray platform, we identified a total of 613 copy number variations (CNVs ranging in size from 78 base pairs to 19.5 Mb. We identified 16 subjects with 33 CNVs that contained 13 different genes which are known to be directly associated with heart development. Additionally, there were 79 genes from the broader list of genes that were partially or completely contained in a CNV. All 34 individuals examined had at least one CNV involving these 79 genes. Furthermore, we had available whole genome exon arrays from right ventricular tissue in 13 of our subjects. We analyzed these for correlations between copy number and gene expression level. Surprisingly, we could detect only one clear association between CNVs and expression (GSTT1 for any of the 591 focal genes on the gcCGH array. The expression levels of GSTT1 were correlated with copy number in all cases examined (r = 0.95, p = 0.001. We identified a large number of small CNVs in genes with varying associations with heart development. Our results illustrate the complexity of human genome structural variation and underscore the need for multifactorial assessment of potential genetic/genomic factors that contribute to congenital heart defects.

  20. Methyl jasmonate-induced emission of biogenic volatiles is biphasic in cucumber: a high-resolution analysis of dose dependence.

    Science.gov (United States)

    Jiang, Yifan; Ye, Jiayan; Li, Shuai; Niinemets, Ülo

    2017-07-20

    Methyl jasmonate (MeJA) is a key airborne elicitor activating jasmonate-dependent signaling pathways, including induction of stress-related volatile emissions, but how the magnitude and timing of these emissions scale with MeJA dose is not known. Treatments with exogenous MeJA concentrations ranging from mild (0.2 mM) to lethal (50 mM) were used to investigate quantitative relationships among MeJA dose and the kinetics and magnitude of volatile release in Cucumis sativus by combining high-resolution measurements with a proton-transfer reaction time-of-flight mass spectrometer (PTR-TOF-MS) and GC-MS. The results highlighted biphasic kinetics of elicitation of volatiles. The early phase, peaking in 0.1-1 h after the MeJA treatment, was characterized by emissions of lipoxygenase (LOX) pathway volatiles and methanol. In the subsequent phase, starting in 6-12 h and reaching a maximum in 15-25 h after the treatment, secondary emissions of LOX compounds as well as emissions of monoterpenes and sesquiterpenes were elicited. For both phases, the maximum emission rates and total integrated emissions increased with applied MeJA concentration. Furthermore, the rates of induction and decay, and the duration of emission bursts were positively, and the timing of emission maxima were negatively associated with MeJA dose for LOX compounds and terpenoids, except for the duration of the first LOX burst. These results demonstrate major effects of MeJA dose on the kinetics and magnitude of volatile response, underscoring the importance of biotic stress severity in deciphering the downstream events of biological impacts. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  1. High Resolution Melting Analysis for Detecting p53 Gene Mutations in Patients with Non-small Cell Lung Cancer

    Directory of Open Access Journals (Sweden)

    Zhihong CHEN

    2011-10-01

    Full Text Available Background and objective It has been proven that p53 gene was related to many human cancers. The mutations in p53 gene play an important role in carcinogensis and mostly happened in exon 5-8. The aim of this study is to establish a high resolution melting (HRM assay to detect p53 mutations from patients with non-small cell lung cancer (NSCLC, to investigate the characteristics of p53 gene mutations, and to analyze the relationship between p53 mutations and evolution regularity of pathogenesis. Methods p53 mutations in exon 5-8 were detected by HRM assay on DNA insolated from 264 NSCLC samples derived from tumor tissues and 54 control samples from pericancerous pulmonary tissues. The mutation samples by the HRM assay were confirmed by sequencing technique. Samples which were positive by HRM but wild type by sequencing were further confirmed by sub-clone and sequencing. Results No mutation was found in 54 pericancerous pulmonary samples by HRM assay. 104 of the 264 tumor tissues demonstrated mutation curves by HRM assay, 102 samples were confirmed by sequencing, including 95 point mutations and 7 frame shift mutations by insertion or deletion. The mutation rate of p53 gene was 39.4%. The mutation rate from exon 5-8 were 11.7%, 8%, 12.5% and 10.6%, respectively and there was no statistically significant difference between them (P=0.35. p53 mutations were significantly more frequent in males than that in females, but not related to the other clinicopathologic characteristics. Conclusion The results indicate that HRM is a sensitive in-tube methodology to detect for mutations in clinical samples. The results suggest that the arising p53 mutations in NSCLC may be due to spontaneous error in DNA synthesis and repair.

  2. High-resolution Thomson scattering system on the COMPASS tokamak: Evaluation of plasma parameters and error analysis

    Czech Academy of Sciences Publication Activity Database

    Aftanas, Milan; Böhm, Petr; Bílková, Petra; Weinzettl, Vladimír; Zajac, Jaromír; Žáček, František; Stöckel, Jan; Hron, Martin; Pánek, Radomír; Scannell, R.; Walsh, M.

    2012-01-01

    Roč. 83, č. 10 (2012), 10E350-10E350 ISSN 0034-6748. [Topical Conference High-Temperature Plasma Diagnostics/19./. Monterey, 06.05.2012-10.05.2012] R&D Projects: GA ČR GA202/09/1467; GA MŠk 7G10072 Institutional research plan: CEZ:AV0Z20430508 Keywords : error analysis * Monte Carlo methods * plasma density * plasma diagnostics * plasma temperature * plasma toroidal confinement * Tokamak devices Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 1.602, year: 2012 http://dx.doi.org/10.1063/1.4743956

  3. High Resolution Melting (HRM) analysis for mutation screening of RGSL1,RGS16 and RGS8 in breast cancer

    DEFF Research Database (Denmark)

    Wiechec, Emilia; Wiuf, Carsten Henrik; Overgaard, Jens

    2011-01-01

    coding exons of RGSL1, RGS16, and RGS8 in tumors from 200 breast cancer patients. All sequence variants detected by HRM resulted in abnormal shape of the melting curves. The identified mutations and known single nucleotide polymorphisms (SNP) were subsequently confirmed by sequencing, and distribution...... cancer patients. In addition, a total of seven known SNPs were identified in this study. Genotype distributions were not significantly different between breast cancer patients and controls. CONCLUSIONS AND IMPACT: Identification of novel mutations within RGSL1 provides a new insight...... into the pathophysiology of breast cancer. Moreover, the HRM analysis represents a reliable and highly sensitive method for mutation scanning of multiple exons....

  4. Comparison of laser fluorimetry, high resolution gamma-ray spectrometry and neutron activation analysis techniques for determination of uranium content in soil samples

    International Nuclear Information System (INIS)

    Ghods, A.; Asgharizadeh, F.; Salimi, B.; Abbasi, A.

    2004-01-01

    Much more concern is given nowadays for exposure of the world population to natural radiation especially to uranium since 57% of that exposure is due to radon-222, which is a member of uranium decay series. Most of the methods used for uranium determination is low concentration require either tedious separation and preconcentration or the accessibility to special instrumentation for detection of uranium at this low level. this study compares three techniques and methods for uranium analysis among different soil sample with variable uranium contents. Two of these techniques, neutron activation analysis and high resolution gamma-ray spectrometry , are non-destructive while the other, laser fluorimetry is done via chemical extraction of uranium. Analysis of standard materials is done also to control the quality and accuracy of the work. In spite of having quite variable ranges of detection limit, results obtained by high resolution gamma-ray spectrometry based on the assumption of having secular equilibrium between uranium and its daughters, which causes deviation whenever this condition was missed. For samples with reasonable uranium content, neutron activation analysis would be a rapid and reliable technique, while for low uranium content laser fluorimetry would be the most appropriate and accurate technique

  5. High tracking resolution detectors. Final Technical Report

    International Nuclear Information System (INIS)

    Vasile, Stefan; Li, Zheng

    2010-01-01

    High-resolution tracking detectors based on Active Pixel Sensor (APS) have been valuable tools in Nuclear Physics and High-Energy Physics research, and have contributed to major discoveries. Their integration time, radiation length and readout rate is a limiting factor for the planed luminosity upgrades in nuclear and high-energy physics collider-based experiments. The goal of this program was to demonstrate and develop high-gain, high-resolution tracking detector arrays with faster readout, and shorter radiation length than APS arrays. These arrays may operate as direct charged particle detectors or as readouts of high resolution scintillating fiber arrays. During this program, we developed in CMOS large, high-resolution pixel sensor arrays with integrated readout, and reset at pixel level. Their intrinsic gain, high immunity to surface and moisture damage, will allow operating these detectors with minimal packaging/passivation requirements and will result in radiation length superior to APS. In Phase I, we designed and fabricated arrays with calorimetric output capable of sub-pixel resolution and sub-microsecond readout rate. The technical effort was dedicated to detector and readout structure development, performance verification, as well as to radiation damage and damage annealing.

  6. Using texture analysis to improve per-pixel classification of very high resolution images for mapping plastic greenhouses

    Science.gov (United States)

    Agüera, Francisco; Aguilar, Fernando J.; Aguilar, Manuel A.

    The area occupied by plastic-covered greenhouses has undergone rapid growth in recent years, currently exceeding 500,000 ha worldwide. Due to the vast amount of input (water, fertilisers, fuel, etc.) required, and output of different agricultural wastes (vegetable, plastic, chemical, etc.), the environmental impact of this type of production system can be serious if not accompanied by sound and sustainable territorial planning. For this, the new generation of satellites which provide very high resolution imagery, such as QuickBird and IKONOS can be useful. In this study, one QuickBird and one IKONOS satellite image have been used to cover the same area under similar circumstances. The aim of this work was an exhaustive comparison of QuickBird vs. IKONOS images in land-cover detection. In terms of plastic greenhouse mapping, comparative tests were designed and implemented, each with separate objectives. Firstly, the Maximum Likelihood Classification (MLC) was applied using five different approaches combining R, G, B, NIR, and panchromatic bands. The combinations of the bands used, significantly influenced some of the indexes used to classify quality in this work. Furthermore, the quality classification of the QuickBird image was higher in all cases than that of the IKONOS image. Secondly, texture features derived from the panchromatic images at different window sizes and with different grey levels were added as a fifth band to the R, G, B, NIR images to carry out the MLC. The inclusion of texture information in the classification did not improve the classification quality. For classifications with texture information, the best accuracies were found in both images for mean and angular second moment texture parameters. The optimum window size in these texture parameters was 3×3 for IK images, while for QB images it depended on the quality index studied, but the optimum window size was around 15×15. With regard to the grey level, the optimum was 128. Thus, the

  7. Earthquake source imaging by high-resolution array analysis at regional distances: the 2010 M7 Haiti earthquake as seen by the Venezuela National Seismic Network

    Science.gov (United States)

    Meng, L.; Ampuero, J. P.; Rendon, H.

    2010-12-01

    Back projection of teleseismic waves based on array processing has become a popular technique for earthquake source imaging,in particular to track the areas of the source that generate the strongest high frequency radiation. The technique has been previously applied to study the rupture process of the Sumatra earthquake and the supershear rupture of the Kunlun earthquakes. Here we attempt to image the Haiti earthquake using the data recorded by Venezuela National Seismic Network (VNSN). The network is composed of 22 broad-band stations with an East-West oriented geometry, and is located approximately 10 degrees away from Haiti in the perpendicular direction to the Enriquillo fault strike. This is the first opportunity to exploit the privileged position of the VNSN to study large earthquake ruptures in the Caribbean region. This is also a great opportunity to explore the back projection scheme of the crustal Pn phase at regional distances,which provides unique complementary insights to the teleseismic source inversions. The challenge in the analysis of the 2010 M7.0 Haiti earthquake is its very compact source region, possibly shorter than 30km, which is below the resolution limit of standard back projection techniques based on beamforming. Results of back projection analysis using the teleseismic USarray data reveal little details of the rupture process. To overcome the classical resolution limit we explored the Multiple Signal Classification method (MUSIC), a high-resolution array processing technique based on the signal-noise orthognality in the eigen space of the data covariance, which achieves both enhanced resolution and better ability to resolve closely spaced sources. We experiment with various synthetic earthquake scenarios to test the resolution. We find that MUSIC provides at least 3 times higher resolution than beamforming. We also study the inherent bias due to the interferences of coherent Green’s functions, which leads to a potential quantification

  8. Analysis of multiple quaternary ammonium compounds in the brain using tandem capillary column separation and high resolution mass spectrometric detection.

    Science.gov (United States)

    Falasca, Sara; Petruzziello, Filomena; Kretz, Robert; Rainer, Gregor; Zhang, Xiaozhe

    2012-06-08

    Endogenous quaternary ammonium compounds are involved in various physiological processes in the central nervous system. In the present study, eleven quaternary ammonium compounds, including acetylcholine, choline, carnitine, acetylcarnitine and seven other acylcarnitines of low polarity, were analyzed from brain extracts using a two dimension capillary liquid chromatography-Fourier transform mass spectrometry method. To deal with their large difference in hydrophobicities, tandem coupling between reversed phase and hydrophilic interaction chromatography columns was used to separate all the targeted quaternary ammonium compounds. Using high accuracy mass spectrometry in selected ion monitoring mode, all the compounds could be detected from each brain sample with high selectivity. The developed method was applied for the relative quantification of these quaternary ammonium compounds in three different brain regions of tree shrews: prefrontal cortex, striatum, and hippocampus. The comparative analysis showed that quaternary ammonium compounds were differentially distributed across the three brain areas. The analytical method proved to be highly sensitive and reliable for simultaneous determination of all the targeted analytes from brain samples. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Dislocation density and Burgers vector population in fiber-textured Ni thin films determined by high-resolution X-ray line profile analysis

    DEFF Research Database (Denmark)

    Csiszár, Gábor; Pantleon, Karen; Alimadadi, Hossein

    2012-01-01

    distribution are determined by high-resolution X-ray diffraction line profile analysis. The substructure parameters are correlated with the strength of the films by using the combined Taylor and Hall-Petch relations. The convolutional multiple whole profile method is used to obtain the substructure parameters......Nanocrystalline Ni thin films have been produced by direct current electrodeposition with different additives and current density in order to obtain 〈100〉, 〈111〉 and 〈211〉 major fiber textures. The dislocation density, the Burgers vector population and the coherently scattering domain size...

  10. Sensitivity analysis of high resolution gamma-ray detection for safeguards monitoring at natural uranium conversion facilities

    Energy Technology Data Exchange (ETDEWEB)

    Dewji, S.A., E-mail: dewjisa@ornl.gov [Oak Ridge National Laboratory, PO Box 2008 MS-6335, Oak Ridge TN 37831 (United States); Georgia Institute of Technology, 770 State Street, Atlanta, GA 30332-0745 (United States); Croft, S. [Oak Ridge National Laboratory, PO Box 2008 MS-6335, Oak Ridge TN 37831 (United States); Hertel, N.E. [Oak Ridge National Laboratory, PO Box 2008 MS-6335, Oak Ridge TN 37831 (United States); Georgia Institute of Technology, 770 State Street, Atlanta, GA 30332-0745 (United States)

    2017-03-11

    Under the policies proposed by recent International Atomic Energy Agency (IAEA) circulars and policy papers, implementation of safeguards exists when any purified aqueous uranium solution or uranium oxides suitable for isotopic enrichment or fuel fabrication exists. Under IAEA Policy Paper 18, the starting point for nuclear material under safeguards was reinterpreted, suggesting that purified uranium compounds should be subject to safeguards procedures no later than the first point in the conversion process. In response to this technical need, a combination of simulation models and experimental measurements were employed in previous work to develop and validate gamma-ray nondestructive assay monitoring systems in a natural uranium conversion plant (NUCP). In particular, uranyl nitrate (UO{sub 2}(NO{sub 3}){sub 2}) solution exiting solvent extraction was identified as a key measurement point (KMP). Passive nondestructive assay techniques using high resolution gamma-ray spectroscopy were evaluated to determine their viability as a technical means for drawing safeguards conclusions at NUCPs, and if the IAEA detection requirements of 1 significant quantity (SQ) can be met in a timely manner. Building upon the aforementioned previous validation work on detector sensitivity to varying concentrations of uranyl nitrate via a series of dilution measurements, this work investigates detector response parameter sensitivities to gamma-ray signatures of uranyl nitrate. The full energy peak efficiency of a detection system is dependent upon the sample, geometry, absorption, and intrinsic efficiency parameters. Perturbation of these parameters translates into corresponding variations of the 185.7 keV peak area of the {sup 235}U in uranyl nitrate. Such perturbations in the assayed signature impact the quality or versatility of the safeguards conclusions drawn. Given the potentially high throughput of uranyl nitrate in NUCPs, the ability to assay 1 SQ of material requires

  11. Ultra-high resolution protein crystallography

    International Nuclear Information System (INIS)

    Takeda, Kazuki; Hirano, Yu; Miki, Kunio

    2010-01-01

    Many protein structures have been determined by X-ray crystallography and deposited with the Protein Data Bank. However, these structures at usual resolution (1.5< d<3.0 A) are insufficient in their precision and quantity for elucidating the molecular mechanism of protein functions directly from structural information. Several studies at ultra-high resolution (d<0.8 A) have been performed with synchrotron radiation in the last decade. The highest resolution of the protein crystals was achieved at 0.54 A resolution for a small protein, crambin. In such high resolution crystals, almost all of hydrogen atoms of proteins and some hydrogen atoms of bound water molecules are experimentally observed. In addition, outer-shell electrons of proteins can be analyzed by the multipole refinement procedure. However, the influence of X-rays should be precisely estimated in order to derive meaningful information from the crystallographic results. In this review, we summarize refinement procedures, current status and perspectives for ultra high resolution protein crystallography. (author)

  12. Normalization to specific gravity prior to analysis improves information recovery from high resolution mass spectrometry metabolomic profiles of human urine.

    Science.gov (United States)

    Edmands, William M B; Ferrari, Pietro; Scalbert, Augustin

    2014-11-04

    Extraction of meaningful biological information from urinary metabolomic profiles obtained by liquid-chromatography coupled to mass spectrometry (MS) necessitates the control of unwanted sources of variability associated with large differences in urine sample concentrations. Different methods of normalization either before analysis (preacquisition normalization) through dilution of urine samples to the lowest specific gravity measured by refractometry, or after analysis (postacquisition normalization) to urine volume, specific gravity and median fold change are compared for their capacity to recover lead metabolites for a potential future use as dietary biomarkers. Twenty-four urine samples of 19 subjects from the European Prospective Investigation into Cancer and nutrition (EPIC) cohort were selected based on their high and low/nonconsumption of six polyphenol-rich foods as assessed with a 24 h dietary recall. MS features selected on the basis of minimum discriminant selection criteria were related to each dietary item by means of orthogonal partial least-squares discriminant analysis models. Normalization methods ranked in the following decreasing order when comparing the number of total discriminant MS features recovered to that obtained in the absence of normalization: preacquisition normalization to specific gravity (4.2-fold), postacquisition normalization to specific gravity (2.3-fold), postacquisition median fold change normalization (1.8-fold increase), postacquisition normalization to urinary volume (0.79-fold). A preventative preacquisition normalization based on urine specific gravity was found to be superior to all curative postacquisition normalization methods tested for discovery of MS features discriminant of dietary intake in these urinary metabolomic datasets.

  13. High resolution molecular and histological analysis of renal disease progression in ZSF1 fa/faCP rats, a model of type 2 diabetic nephropathy.

    Science.gov (United States)

    Dower, Ken; Zhao, Shanrong; Schlerman, Franklin J; Savary, Leigh; Campanholle, Gabriela; Johnson, Bryce G; Xi, Li; Nguyen, Vuong; Zhan, Yutian; Lech, Matthew P; Wang, Ju; Nie, Qing; Karsdal, Morten A; Genovese, Federica; Boucher, Germaine; Brown, Thomas P; Zhang, Baohong; Homer, Bruce L; Martinez, Robert V

    2017-01-01

    ZSF1 rats exhibit spontaneous nephropathy secondary to obesity, hypertension, and diabetes, and have gained interest as a model system with potentially high translational value to progressive human disease. To thoroughly characterize this model, and to better understand how closely it recapitulates human disease, we performed a high resolution longitudinal analysis of renal disease progression in ZSF1 rats spanning from early disease to end stage renal disease. Analyses included metabolic endpoints, renal histology and ultrastructure, evaluation of a urinary biomarker of fibrosis, and transcriptome analysis of glomerular-enriched tissue over the course of disease. Our findings support the translational value of the ZSF1 rat model, and are provided here to assist researchers in the determination of the model's suitability for testing a particular mechanism of interest, the design of therapeutic intervention studies, and the identification of new targets and biomarkers for type 2 diabetic nephropathy.

  14. High-Resolution Sonars: What Resolution Do We Need for Target Recognition?

    Directory of Open Access Journals (Sweden)

    Pailhas Yan

    2010-01-01

    Full Text Available Target recognition in sonar imagery has long been an active research area in the maritime domain, especially in the mine-counter measure context. Recently it has received even more attention as new sensors with increased resolution have been developed; new threats to critical maritime assets and a new paradigm for target recognition based on autonomous platforms have emerged. With the recent introduction of Synthetic Aperture Sonar systems and high-frequency sonars, sonar resolution has dramatically increased and noise levels decreased. Sonar images are distance images but at high resolution they tend to appear visually as optical images. Traditionally algorithms have been developed specifically for imaging sonars because of their limited resolution and high noise levels. With high-resolution sonars, algorithms developed in the image processing field for natural images become applicable. However, the lack of large datasets has hampered the development of such algorithms. Here we present a fast and realistic sonar simulator enabling development and evaluation of such algorithms.We develop a classifier and then analyse its performances using our simulated synthetic sonar images. Finally, we discuss sensor resolution requirements to achieve effective classification of various targets and demonstrate that with high resolution sonars target highlight analysis is the key for target recognition.

  15. Hybrid analysis (barcode-high resolution melting) for authentication of Thai herbal products, Andrographis paniculata (Burm.f.) Wall.ex Nees.

    Science.gov (United States)

    Osathanunkul, Maslin; Suwannapoom, Chatmongkon; Khamyong, Nuttaluck; Pintakum, Danupol; Lamphun, Santisuk Na; Triwitayakorn, Kanokporn; Osathanunkul, Kitisak; Madesis, Panagiotis

    2016-01-01

    Andrographis paniculata Nees is a medicinal plant with multiple pharmacological properties. It has been used over many centuries as a household remedy. A. paniculata products sold on the markets are in processed forms so it is difficult to authenticate. Therefore buying the herbal products poses a high-risk of acquiring counterfeited, substituted and/or adulterated products. Due to these issues, a reliable method to authenticate products is needed. High resolution melting analysis coupled with DNA barcoding (Bar-HRM) was applied to detect adulteration in commercial herbal products. The rbcL barcode was selected to use in primers design for HRM analysis to produce standard melting profile of A. paniculata species. DNA of the tested commercial products was isolated and their melting profiles were then generated and compared with the standard A. paniculata. The melting profiles of the rbcL amplicons of the three closely related herbal species (A. paniculata, Acanthus ebracteatus and Rhinacanthus nasutus) are clearly separated so that they can be distinguished by the developed method. The method was then used to authenticate commercial herbal products. HRM curves of all 10 samples tested are similar to A. paniculata which indicated that all tested products were contained the correct species as labeled. The method described in this study has been proved to be useful in aiding identification and/or authenticating A. paniculata. This Bar-HRM analysis has allowed us easily to determine the A. paniculata species in herbal products on the markets even they are in processed forms. We propose the use of DNA barcoding combined with High Resolution Melting analysis for authenticating of Andrographis paniculata products.The developed method can be used regardless of the type of the DNA template (fresh or dried tissue, leaf, and stem).rbcL region was chosen for the analysis and work well with our samplesWe can easily determine the A. paniculata species in herbal products tested

  16. High-Resolution PET Detector. Final report

    International Nuclear Information System (INIS)

    Karp, Joel

    2014-01-01

    The objective of this project was to develop an understanding of the limits of performance for a high resolution PET detector using an approach based on continuous scintillation crystals rather than pixelated crystals. The overall goal was to design a high-resolution detector, which requires both high spatial resolution and high sensitivity for 511 keV gammas. Continuous scintillation detectors (Anger cameras) have been used extensively for both single-photon and PET scanners, however, these instruments were based on NaI(Tl) scintillators using relatively large, individual photo-multipliers. In this project we investigated the potential of this type of detector technology to achieve higher spatial resolution through the use of improved scintillator materials and photo-sensors, and modification of the detector surface to optimize the light response function.We achieved an average spatial resolution of 3-mm for a 25-mm thick, LYSO continuous detector using a maximum likelihood position algorithm and shallow slots cut into the entrance surface

  17. Fast and sensitive analysis of beta blockers by ultra-high-performance liquid chromatography coupled with ultra-high-resolution TOF mass spectrometry.

    Science.gov (United States)

    Tomková, Jana; Ondra, Peter; Kocianová, Eva; Václavík, Jan

    2017-07-01

    This paper presents a method for the determination of acebutolol, betaxolol, bisoprolol, metoprolol, nebivolol and sotalol in human serum by liquid-liquid extraction and ultra-high-performance liquid chromatography coupled with ultra-high-resolution TOF mass spectrometry. After liquid-liquid extraction, beta blockers were separated on a reverse-phase analytical column (Acclaim RS 120; 100 × 2.1 mm, 2.2 μm). The total run time was 6 min for each sample. Linearity, limit of detection, limit of quantification, matrix effects, specificity, precision, accuracy, recovery and sample stability were evaluated. The method was successfully applied to the therapeutic drug monitoring of 108 patients with hypertension. This method was also used for determination of beta blockers in 33 intoxicated patients. Copyright © 2016 John Wiley & Sons, Ltd.

  18. A high resolution portable spectroscopy system

    International Nuclear Information System (INIS)

    Kulkarni, C.P.; Vaidya, P.P.; Paulson, M.; Bhatnagar, P.V.; Pande, S.S.; Padmini, S.

    2003-01-01

    Full text: This paper describes the system details of a High Resolution Portable Spectroscopy System (HRPSS) developed at Electronics Division, BARC. The system can be used for laboratory class, high-resolution nuclear spectroscopy applications. The HRPSS consists of a specially designed compact NIM bin, with built-in power supplies, accommodating a low power, high resolution MCA, and on-board embedded computer for spectrum building and communication. A NIM based spectroscopy amplifier and a HV module for detector bias are integrated (plug-in) in the bin. The system communicates with a host PC via a serial link. Along-with a laptop PC, and a portable HP-Ge detector, the HRPSS offers a laboratory class performance for portable applications

  19. Combining pixel and object based image analysis of ultra-high resolution multibeam bathymetry and backscatter for habitat mapping in shallow marine waters

    Science.gov (United States)

    Ierodiaconou, Daniel; Schimel, Alexandre C. G.; Kennedy, David; Monk, Jacquomo; Gaylard, Grace; Young, Mary; Diesing, Markus; Rattray, Alex

    2018-06-01

    Habitat mapping data are increasingly being recognised for their importance in underpinning marine spatial planning. The ability to collect ultra-high resolution (cm) multibeam echosounder (MBES) data in shallow waters has facilitated understanding of the fine-scale distribution of benthic habitats in these areas that are often prone to human disturbance. Developing quantitative and objective approaches to integrate MBES data with ground observations for predictive modelling is essential for ensuring repeatability and providing confidence measures for habitat mapping products. Whilst supervised classification approaches are becoming more common, users are often faced with a decision whether to implement a pixel based (PB) or an object based (OB) image analysis approach, with often limited understanding of the potential influence of that decision on final map products and relative importance of data inputs to patterns observed. In this study, we apply an ensemble learning approach capable of integrating PB and OB Image Analysis from ultra-high resolution MBES bathymetry and backscatter data for mapping benthic habitats in Refuge Cove, a temperate coastal embayment in south-east Australia. We demonstrate the relative importance of PB and OB seafloor derivatives for the five broad benthic habitats that dominate the site. We found that OB and PB approaches performed well with differences in classification accuracy but not discernible statistically. However, a model incorporating elements of both approaches proved to be significantly more accurate than OB or PB methods alone and demonstrate the benefits of using MBES bathymetry and backscatter combined for class discrimination.

  20. High-resolution whole-genome analysis of skull base chordomas implicates FHIT loss in chordoma pathogenesis.

    Science.gov (United States)

    Diaz, Roberto Jose; Guduk, Mustafa; Romagnuolo, Rocco; Smith, Christian A; Northcott, Paul; Shih, David; Berisha, Fitim; Flanagan, Adrienne; Munoz, David G; Cusimano, Michael D; Pamir, M Necmettin; Rutka, James T

    2012-09-01

    Chordoma is a rare tumor arising in the sacrum, clivus, or vertebrae. It is often not completely resectable and shows a high incidence of recurrence and progression with shortened patient survival and impaired quality of life. Chemotherapeutic options are limited to investigational therapies at present. Therefore, adjuvant therapy for control of tumor recurrence and progression is of great interest, especially in skull base lesions where complete tumor resection is often not possible because of the proximity of cranial nerves. To understand the extent of genetic instability and associated chromosomal and gene losses or gains in skull base chordoma, we undertook whole-genome single-nucleotide polymorphism microarray analysis of flash frozen surgical chordoma specimens, 21 from the clivus and 1 from C1 to C2 vertebrae. We confirm the presence of a deletion at 9p involving CDKN2A, CDKN2B, and MTAP but at a much lower rate (22%) than previously reported for sacral chordoma. At a similar frequency (21%), we found aneuploidy of chromosome 3. Tissue microarray immunohistochemistry demonstrated absent or reduced fragile histidine triad (FHIT) protein expression in 98% of sacral chordomas and 67%of skull base chordomas. Our data suggest that chromosome 3 aneuploidy and epigenetic regulation of FHIT contribute to loss of the FHIT tumor suppressor in chordoma. The finding that FHIT is lost in a majority of chordomas provides new insight into chordoma pathogenesis and points to a potential new therapeutic target for this challenging neoplasm.

  1. High-resolution Whole-Genome Analysis of Skull Base Chordomas Implicates FHIT Loss in Chordoma Pathogenesis

    Directory of Open Access Journals (Sweden)

    Roberto Jose Diaz

    2012-09-01

    Full Text Available Chordoma is a rare tumor arising in the sacrum, clivus, or vertebrae. It is often not completely resectable and shows a high incidence of recurrence and progression with shortened patient survival and impaired quality of life. Chemotherapeutic options are limited to investigational therapies at present. Therefore, adjuvant therapy for control of tumor recurrence and progression is of great interest, especially in skull base lesions where complete tumor resection is often not possible because of the proximity of cranial nerves. To understand the extent of genetic instability and associated chromosomal and gene losses or gains in skull base chordoma, we undertook whole-genome single-nucleotide polymorphism microarray analysis of flash frozen surgical chordoma specimens, 21 from the clivus and 1 from C1 to C2 vertebrae. We confirm the presence of a deletion at 9p involving CDKN2A, CDKN2B, and MTAP but at a much lower rate (22% than previously reported for sacral chordoma. At a similar frequency (21%, we found aneuploidy of chromosome 3. Tissue microarray immunohistochemistry demonstrated absent or reduced fragile histidine triad (FHIT protein expression in 98% of sacral chordomas and 67%of skull base chordomas. Our data suggest that chromosome 3 aneuploidy and epigenetic regulation of FHIT contribute to loss of the FHIT tumor suppressor in chordoma. The finding that FHIT is lost in a majority of chordomas provides new insight into chordoma pathogenesis and points to a potential new therapeutic target for this challenging neoplasm.

  2. High-resolution multi-slice PET

    International Nuclear Information System (INIS)

    Yasillo, N.J.; Chintu Chen; Ordonez, C.E.; Kapp, O.H.; Sosnowski, J.; Beck, R.N.

    1992-01-01

    This report evaluates the progress to test the feasibility and to initiate the design of a high resolution multi-slice PET system. The following specific areas were evaluated: detector development and testing; electronics configuration and design; mechanical design; and system simulation. The design and construction of a multiple-slice, high-resolution positron tomograph will provide substantial improvements in the accuracy and reproducibility of measurements of the distribution of activity concentrations in the brain. The range of functional brain research and our understanding of local brain function will be greatly extended when the development of this instrumentation is completed

  3. High resolution neutron spectroscopy for helium isotopes

    International Nuclear Information System (INIS)

    Abdel-Wahab, M.S.; Klages, H.O.; Schmalz, G.; Haesner, B.H.; Kecskemeti, J.; Schwarz, P.; Wilczynski, J.

    1992-01-01

    A high resolution fast neutron time-of-flight spectrometer is described, neutron time-of-flight spectra are taken using a specially designed TDC in connection to an on-line computer. The high time-of-flight resolution of 5 ps/m enabled the study of the total cross section of 4 He for neutrons near the 3/2 + resonance in the 5 He nucleus. The resonance parameters were determined by a single level Breit-Winger fit to the data. (orig.)

  4. Smartphone microendoscopy for high resolution fluorescence imaging

    Directory of Open Access Journals (Sweden)

    Xiangqian Hong

    2016-09-01

    Full Text Available High resolution optical endoscopes are increasingly used in diagnosis of various medical conditions of internal organs, such as the cervix and gastrointestinal (GI tracts, but they are too expensive for use in resource-poor settings. On the other hand, smartphones with high resolution cameras and Internet access have become more affordable, enabling them to diffuse into most rural areas and developing countries in the past decade. In this paper, we describe a smartphone microendoscope that can take fluorescence images with a spatial resolution of 3.1 μm. Images collected from ex vivo, in vitro and in vivo samples using the device are also presented. The compact and cost-effective smartphone microendoscope may be envisaged as a powerful tool for detecting pre-cancerous lesions of internal organs in low and middle-income countries (LMICs.

  5. High-resolution Kendrick Mass Defect Analysis of Poly(ethylene oxide)-based Non-ionic Surfactants and Their Degradation Products.

    Science.gov (United States)

    Fouquet, Thierry; Shimada, Haruo; Maeno, Katsuyuki; Ito, Kanako; Ozeki, Yuka; Kitagawa, Shinya; Ohtani, Hajime; Sato, Hiroaki

    2017-09-01

    Matrix assisted laser desorption ionization (MALDI) high-resolution mass spectrometry (HRMS) and the recently introduced high-resolution Kendrick mass defect (HRKMD) analysis are combined to thoroughly characterize non-ionic surfactants made of a poly(ethylene oxide) (PEO) core capped by esters of fatty acids. A PEO monostearate surfactant is first analyzed as a proof of principle of the HRKMD analysis conducted with a fraction of EO as the base unit (EO/X with X being an integer) in lieu of EO for a regular KMD analysis. Data visualization is greatly enhanced and the distributions detected in the MALDI mass spectrum are assigned to a pristine (H, OH)-PEO as well as mono- and di-esterified PEO chains with palmitate and stearate end-groups in HRKMD plots computed with EO/45. The MALDI-HRMS/HRKMD analysis is then successfully applied to the more complex case of ethoxylated hydrogenated castor oil (EHCO) found to contain a large number of hydrogenated ricinoleate moieties (up to 14) in its HRKMD plot computed with EO/43, departing from the expected triglyceride structure. The exhaustiveness of the MALDI-HRMS/HRKMD strategy is validated by comparing the so-obtained fingerprints with results from alternative techniques (electrospray ionization MS, size exclusion and liquid adsorption chromatography, ion mobility spectrometry). Finally, aged non-ionic surfactants formed upon hydrolytic degradation are analyzed by MALDI-HRMS/HRKMD to easily assign the degradation products and infer the associated degradation routes. In addition to the hydrolysis of the ester groups observed for EHCO, chain scissions and new polar end-groups are observed in the HRKMD plot of PEO monostearate arising from a competitive oxidative ageing.

  6. High resolution CT in diffuse lung disease

    International Nuclear Information System (INIS)

    Webb, W.R.

    1995-01-01

    High resolution CT (computerized tomography) was discussed in detail. The conclusions were HRCT is able to define lung anatomy at the secondary lobular level and define a variety of abnormalities in patients with diffuse lung diseases. Evidence from numerous studies indicates that HRCT can play a major role in the assessment of diffuse infiltrative lung disease and is indicate clinically (95 refs.)

  7. Classification of high resolution satellite images

    OpenAIRE

    Karlsson, Anders

    2003-01-01

    In this thesis the Support Vector Machine (SVM)is applied on classification of high resolution satellite images. Sveral different measures for classification, including texture mesasures, 1st order statistics, and simple contextual information were evaluated. Additionnally, the image was segmented, using an enhanced watershed method, in order to improve the classification accuracy.

  8. High resolution CT in diffuse lung disease

    Energy Technology Data Exchange (ETDEWEB)

    Webb, W R [California Univ., San Francisco, CA (United States). Dept. of Radiology

    1996-12-31

    High resolution CT (computerized tomography) was discussed in detail. The conclusions were HRCT is able to define lung anatomy at the secondary lobular level and define a variety of abnormalities in patients with diffuse lung diseases. Evidence from numerous studies indicates that HRCT can play a major role in the assessment of diffuse infiltrative lung disease and is indicate clinically (95 refs.).

  9. High-resolution clean-sc

    NARCIS (Netherlands)

    Sijtsma, P.; Snellen, M.

    2016-01-01

    In this paper a high-resolution extension of CLEAN-SC is proposed: HR-CLEAN-SC. Where CLEAN-SC uses peak sources in “dirty maps” to define so-called source components, HR-CLEAN-SC takes advantage of the fact that source components can likewise be derived from points at some distance from the peak,

  10. A High-Resolution Stopwatch for Cents

    Science.gov (United States)

    Gingl, Z.; Kopasz, K.

    2011-01-01

    A very low-cost, easy-to-make stopwatch is presented to support various experiments in mechanics. The high-resolution stopwatch is based on two photodetectors connected directly to the microphone input of a sound card. Dedicated free open-source software has been developed and made available to download. The efficiency is demonstrated by a free…

  11. Source analysis of beta-synchronisation and cortico-muscular coherence after movement termination based on high resolution electroencephalography.

    Directory of Open Access Journals (Sweden)

    Muthuraman Muthuraman

    Full Text Available We hypothesized that post-movement beta synchronization (PMBS and cortico-muscular coherence (CMC during movement termination relate to each other and have similar role in sensorimotor integration. We calculated the parameters and estimated the sources of these phenomena.We measured 64-channel EEG simultaneously with surface EMG of the right first dorsal interosseus muscle in 11 healthy volunteers. In Task1, subjects kept a medium-strength contraction continuously; in Task2, superimposed on this movement, they performed repetitive self-paced short contractions. In Task3 short contractions were executed alone. Time-frequency analysis of the EEG and CMC was performed with respect to the offset of brisk movements and averaged in each subject. Sources of PMBS and CMC were also calculated.High beta power in Task1, PMBS in Task2-3, and CMC in Task1-2 could be observed in the same individual frequency bands. While beta synchronization in Task1 and PMBS in Task2-3 appeared bilateral with contralateral predominance, CMC in Task1-2 was strictly a unilateral phenomenon; their main sources did not differ contralateral to the movement in the primary sensorimotor cortex in 7 of 11 subjects in Task1, and in 6 of 9 subjects in Task2. In Task2, CMC and PMBS had the same latency but their amplitudes did not correlate with each other. In Task2, weaker PMBS source was found bilaterally within the secondary sensory cortex, while the second source of CMC was detected in the premotor cortex, contralateral to the movement. In Task3, weaker sources of PMBS could be estimated in bilateral supplementary motor cortex and in the thalamus. PMBS and CMC appear simultaneously at the end of a phasic movement possibly suggesting similar antikinetic effects, but they may be separate processes with different active functions. Whereas PMBS seems to reset the supraspinal sensorimotor network, cortico-muscular coherence may represent the recalibration of cortico-motoneuronal and

  12. Source analysis of beta-synchronisation and cortico-muscular coherence after movement termination based on high resolution electroencephalography.

    Science.gov (United States)

    Muthuraman, Muthuraman; Tamás, Gertrúd; Hellriegel, Helge; Deuschl, Günther; Raethjen, Jan

    2012-01-01

    We hypothesized that post-movement beta synchronization (PMBS) and cortico-muscular coherence (CMC) during movement termination relate to each other and have similar role in sensorimotor integration. We calculated the parameters and estimated the sources of these phenomena.We measured 64-channel EEG simultaneously with surface EMG of the right first dorsal interosseus muscle in 11 healthy volunteers. In Task1, subjects kept a medium-strength contraction continuously; in Task2, superimposed on this movement, they performed repetitive self-paced short contractions. In Task3 short contractions were executed alone. Time-frequency analysis of the EEG and CMC was performed with respect to the offset of brisk movements and averaged in each subject. Sources of PMBS and CMC were also calculated.High beta power in Task1, PMBS in Task2-3, and CMC in Task1-2 could be observed in the same individual frequency bands. While beta synchronization in Task1 and PMBS in Task2-3 appeared bilateral with contralateral predominance, CMC in Task1-2 was strictly a unilateral phenomenon; their main sources did not differ contralateral to the movement in the primary sensorimotor cortex in 7 of 11 subjects in Task1, and in 6 of 9 subjects in Task2. In Task2, CMC and PMBS had the same latency but their amplitudes did not correlate with each other. In Task2, weaker PMBS source was found bilaterally within the secondary sensory cortex, while the second source of CMC was detected in the premotor cortex, contralateral to the movement. In Task3, weaker sources of PMBS could be estimated in bilateral supplementary motor cortex and in the thalamus. PMBS and CMC appear simultaneously at the end of a phasic movement possibly suggesting similar antikinetic effects, but they may be separate processes with different active functions. Whereas PMBS seems to reset the supraspinal sensorimotor network, cortico-muscular coherence may represent the recalibration of cortico-motoneuronal and spinal systems.

  13. The High Resolution Stereo Camera (HRSC) of Mars Express and its approach to science analysis and mapping for Mars and its satellites

    Science.gov (United States)

    Gwinner, K.; Jaumann, R.; Hauber, E.; Hoffmann, H.; Heipke, C.; Oberst, J.; Neukum, G.; Ansan, V.; Bostelmann, J.; Dumke, A.; Elgner, S.; Erkeling, G.; Fueten, F.; Hiesinger, H.; Hoekzema, N. M.; Kersten, E.; Loizeau, D.; Matz, K.-D.; McGuire, P. C.; Mertens, V.; Michael, G.; Pasewaldt, A.; Pinet, P.; Preusker, F.; Reiss, D.; Roatsch, T.; Schmidt, R.; Scholten, F.; Spiegel, M.; Stesky, R.; Tirsch, D.; van Gasselt, S.; Walter, S.; Wählisch, M.; Willner, K.

    2016-07-01

    The High Resolution Stereo Camera (HRSC) of ESA's Mars Express is designed to map and investigate the topography of Mars. The camera, in particular its Super Resolution Channel (SRC), also obtains images of Phobos and Deimos on a regular basis. As HRSC is a push broom scanning instrument with nine CCD line detectors mounted in parallel, its unique feature is the ability to obtain along-track stereo images and four colors during a single orbital pass. The sub-pixel accuracy of 3D points derived from stereo analysis allows producing DTMs with grid size of up to 50 m and height accuracy on the order of one image ground pixel and better, as well as corresponding orthoimages. Such data products have been produced systematically for approximately 40% of the surface of Mars so far, while global shape models and a near-global orthoimage mosaic could be produced for Phobos. HRSC is also unique because it bridges between laser altimetry and topography data derived from other stereo imaging instruments, and provides geodetic reference data and geological context to a variety of non-stereo datasets. This paper, in addition to an overview of the status and evolution of the experiment, provides a review of relevant methods applied for 3D reconstruction and mapping, and respective achievements. We will also review the methodology of specific approaches to science analysis based on joint analysis of DTM and orthoimage information, or benefitting from high accuracy of co-registration between multiple datasets, such as studies using multi-temporal or multi-angular observations, from the fields of geomorphology, structural geology, compositional mapping, and atmospheric science. Related exemplary results from analysis of HRSC data will be discussed. After 10 years of operation, HRSC covered about 70% of the surface by panchromatic images at 10-20 m/pixel, and about 97% at better than 100 m/pixel. As the areas with contiguous coverage by stereo data are increasingly abundant, we also

  14. Comparison of performance of object-based image analysis techniques available in open source software (Spring and Orfeo Toolbox/Monteverdi) considering very high spatial resolution data

    Science.gov (United States)

    Teodoro, Ana C.; Araujo, Ricardo

    2016-01-01

    The use of unmanned aerial vehicles (UAVs) for remote sensing applications is becoming more frequent. However, this type of information can result in several software problems related to the huge amount of data available. Object-based image analysis (OBIA) has proven to be superior to pixel-based analysis for very high-resolution images. The main objective of this work was to explore the potentialities of the OBIA methods available in two different open source software applications, Spring and OTB/Monteverdi, in order to generate an urban land cover map. An orthomosaic derived from UAVs was considered, 10 different regions of interest were selected, and two different approaches were followed. The first one (Spring) uses the region growing segmentation algorithm followed by the Bhattacharya classifier. The second approach (OTB/Monteverdi) uses the mean shift segmentation algorithm followed by the support vector machine (SVM) classifier. Two strategies were followed: four classes were considered using Spring and thereafter seven classes were considered for OTB/Monteverdi. The SVM classifier produces slightly better results and presents a shorter processing time. However, the poor spectral resolution of the data (only RGB bands) is an important factor that limits the performance of the classifiers applied.

  15. Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies.

    Science.gov (United States)

    Kjeldsen, Eigil

    2015-01-01

    The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies. Copyright© 2015, International Institute of Anticancer Research (Dr. John G. Delinasios), All rights reserved.

  16. Detectors for high resolution dynamic pet

    International Nuclear Information System (INIS)

    Derenzo, S.E.; Budinger, T.F.; Huesman, R.H.

    1983-05-01

    This report reviews the motivation for high spatial resolution in dynamic positron emission tomography of the head and the technical problems in realizing this objective. We present recent progress in using small silicon photodiodes to measure the energy deposited by 511 keV photons in small BGO crystals with an energy resolution of 9.4% full-width at half-maximum. In conjunction with a suitable phototube coupled to a group of crystals, the photodiode signal to noise ratio is sufficient for the identification of individual crystals both for conventional and time-of-flight positron tomography

  17. Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene

    DEFF Research Database (Denmark)

    Candiloro, Ida Lm; Mikeska, Thomas; Hokland, Peter

    2008-01-01

    ABSTRACT: BACKGROUND: Methylation-sensitive high resolution melting (MS-HRM) methodology is able to recognise heterogeneously methylated sequences by their characteristic melting profiles. To further analyse heterogeneously methylated sequences, we adopted a digital approach to MS-HRM (dMS-HRM) t......ABSTRACT: BACKGROUND: Methylation-sensitive high resolution melting (MS-HRM) methodology is able to recognise heterogeneously methylated sequences by their characteristic melting profiles. To further analyse heterogeneously methylated sequences, we adopted a digital approach to MS-HRM (d......MS-HRM) that involves the amplification of single templates after limiting dilution to quantify and to determine the degree of methylation. We used this approach to study methylation of the CDKN2B (p15) cell cycle progression inhibitor gene which is inactivated by DNA methylation in haematological malignancies...... the methylated alleles and assess the degree of methylation. Direct sequencing of selected dMS-HRM products was used to determine the exact DNA methylation pattern and confirmed the degree of methylation estimated by dMS-HRM. CONCLUSION: dMS-HRM is a powerful technique for the analysis of methylation in CDKN2B...

  18. The diagnosis of small solitary pulmonary nodule: comparison of standard and inverse digital images on a high resolution monitor using ROC analysis

    International Nuclear Information System (INIS)

    Choi, Byeong Kyoo; Lee, In Sun; Seo, Joon Beom; Lee, Jin Seong; Song, Koun Sik; Lim, Tae Hwan

    2002-01-01

    To study the impact of inversion of soft-copy chest radiographs on the detection of small solitary pulmonary nodules using a high-resolution monitor. The study group consisted of 80 patients who had undergone posterior chest radiography; 40 had a solitary noncalcified pulmonary nodule approximately 1 cm in diameter, and 40 were control subjects. Standard and inverse digital images using the inversion tool on a PACS system were displayed on high-resolution monitors (2048x2560x8 bit). Ten radiologists were requested to rank each image using a five-point scale (1=definitely negative, 3=equivocal or indeterminate, 5=definite nodule), and the data were interpreted using receiver operating characteristic (ROC) analysis. The area under the ROC curve for pooled data of standard image sets was significantly larger than that of inverse image sets (0.8893 and 0.8095, respectively; p 0.05). For detecting small solitary pulmonary nodules, inverse digital images were significantly inferior to standard digital images

  19. Flux Analysis of Free Amino Sugars and Amino Acids in Soils by Isotope Tracing with a Novel Liquid Chromatography/High Resolution Mass Spectrometry Platform.

    Science.gov (United States)

    Hu, Yuntao; Zheng, Qing; Wanek, Wolfgang

    2017-09-05

    Soil fluxomics analysis can provide pivotal information for understanding soil biochemical pathways and their regulation, but direct measurement methods are rare. Here, we describe an approach to measure soil extracellular metabolite (amino sugar and amino acid) concentrations and fluxes based on a 15 N isotope pool dilution technique via liquid chromatography and high-resolution mass spectrometry. We produced commercially unavailable 15 N and 13 C labeled amino sugars and amino acids by hydrolyzing peptidoglycan isolated from isotopically labeled bacterial biomass and used them as tracers ( 15 N) and internal standards ( 13 C). High-resolution (Orbitrap Exactive) MS with a resolution of 50 000 allowed us to separate different stable isotope labeled analogues across a large range of metabolites. The utilization of 13 C internal standards greatly improved the accuracy and reliability of absolute quantification. We successfully applied this method to two types of soils and quantified the extracellular gross fluxes of 2 amino sugars, 18 amino acids, and 4 amino acid enantiomers. Compared to the influx and efflux rates of most amino acids, similar ones were found for glucosamine, indicating that this amino sugar is released through peptidoglycan and chitin decomposition and serves as an important nitrogen source for soil microorganisms. d-Alanine and d-glutamic acid derived from peptidoglycan decomposition exhibited similar turnover rates as their l-enantiomers. This novel approach offers new strategies to advance our understanding of the production and transformation pathways of soil organic N metabolites, including the unknown contributions of peptidoglycan and chitin decomposition to soil organic N cycling.

  20. Flux Analysis of Free Amino Sugars and Amino Acids in Soils by Isotope Tracing with a Novel Liquid Chromatography/High Resolution Mass Spectrometry Platform

    Science.gov (United States)

    2017-01-01

    Soil fluxomics analysis can provide pivotal information for understanding soil biochemical pathways and their regulation, but direct measurement methods are rare. Here, we describe an approach to measure soil extracellular metabolite (amino sugar and amino acid) concentrations and fluxes based on a 15N isotope pool dilution technique via liquid chromatography and high-resolution mass spectrometry. We produced commercially unavailable 15N and 13C labeled amino sugars and amino acids by hydrolyzing peptidoglycan isolated from isotopically labeled bacterial biomass and used them as tracers (15N) and internal standards (13C). High-resolution (Orbitrap Exactive) MS with a resolution of 50 000 allowed us to separate different stable isotope labeled analogues across a large range of metabolites. The utilization of 13C internal standards greatly improved the accuracy and reliability of absolute quantification. We successfully applied this method to two types of soils and quantified the extracellular gross fluxes of 2 amino sugars, 18 amino acids, and 4 amino acid enantiomers. Compared to the influx and efflux rates of most amino acids, similar ones were found for glucosamine, indicating that this amino sugar is released through peptidoglycan and chitin decomposition and serves as an important nitrogen source for soil microorganisms. d-Alanine and d-glutamic acid derived from peptidoglycan decomposition exhibited similar turnover rates as their l-enantiomers. This novel approach offers new strategies to advance our understanding of the production and transformation pathways of soil organic N metabolites, including the unknown contributions of peptidoglycan and chitin decomposition to soil organic N cycling. PMID:28776982

  1. Constructing a WISE High Resolution Galaxy Atlas

    Science.gov (United States)

    Jarrett, T. H.; Masci, F.; Tsai, C. W.; Petty, S.; Cluver, M.; Assef, Roberto J.; Benford, D.; Blain, A.; Bridge, C.; Donoso, E.; hide

    2012-01-01

    After eight months of continuous observations, the Wide-field Infrared Survey Explorer (WISE) mapped the entire sky at 3.4 micron, 4.6 micron, 12 micron, and 22 micron. We have begun a dedicated WISE High Resolution Galaxy Atlas project to fully characterize large, nearby galaxies and produce a legacy image atlas and source catalog. Here we summarize the deconvolution techniques used to significantly improve the spatial resolution of WISE imaging, specifically designed to study the internal anatomy of nearby galaxies. As a case study, we present results for the galaxy NGC 1566, comparing the WISE enhanced-resolution image processing to that of Spitzer, Galaxy Evolution Explorer, and ground-based imaging. This is the first paper in a two-part series; results for a larger sample of nearby galaxies are presented in the second paper.

  2. Photoionization of Ar2 at high resolution

    International Nuclear Information System (INIS)

    Dehmer, P.M.

    1982-01-01

    The relative photoionization cross section of Ar 2 was determined at a resolution of 0.07 A in the wavelength region from 800 to 850 A using a new photoionization mass spectrometer that combines a high intensity helium continuum lamp with a free supersonic molecular beam source. In the region studied, the photoionization cross section is dominated by autoionization of molecular Rydberg states, and the structure is diffuse owing to the combined effects of autoionization and predissociation. The molecular photoionization spectrum is extremely complex and shows little resemblence either to the corresponding atomic spectrum (indicating that the spectrum of the dimer is not simply a perturbed atomic spectrum) or to the molecular absorption spectrum at longer wavelengths. The regular vibrational progressions seen at longer wavelengths are absent above the first ionization potential. Detailed spectroscopic analysis is possible for only a small fraction of the observed features; however, vibrational intervals of 50--100 cm -1 suggest that some of the Rydberg states have B 2 Pi/sub 3/2g/ ionic cores. A comparison of the absorption and photoionization spectra shows that, at wavelengths shorter than approx.835 A, many of the excited states decay via mechanisms other than autoionization

  3. High resolution imaging of boron carbide microstructures

    International Nuclear Information System (INIS)

    MacKinnon, I.D.R.; Aselage, T.; Van Deusen, S.B.

    1986-01-01

    Two samples of boron carbide have been examined using high resolution transmission electron microscopy (HRTEM). A hot-pressed B 13 C 2 sample shows a high density of variable width twins normal to (10*1). Subtle shifts or offsets of lattice fringes along the twin plane and normal to approx.(10*5) were also observed. A B 4 C powder showed little evidence of stacking disorder in crystalline regions

  4. A Combined Approach to Classifying Land Surface Cover of Urban Domestic Gardens Using Citizen Science Data and High Resolution Image Analysis

    Directory of Open Access Journals (Sweden)

    Fraser Baker

    2018-03-01

    Full Text Available Domestic gardens are an important component of cities, contributing significantly to urban green infrastructure (GI and its associated ecosystem services. However, domestic gardens are incredibly heterogeneous which presents challenges for quantifying their GI contribution and associated benefits for sustainable urban development. This study applies an innovative methodology that combines citizen science data with high resolution image analysis to create a garden dataset in the case study city of Manchester, UK. An online Citizen Science Survey (CSS collected estimates of proportional coverage for 10 garden land surface types from 1031 city residents. High resolution image analysis was conducted to validate the CSS estimates, and to classify 7 land surface cover categories for all garden parcels in the city. Validation of the CSS land surface estimations revealed a mean accuracy of 76.63% (s = 15.24%, demonstrating that citizens are able to provide valid estimates of garden surface coverage proportions. An Object Based Image Analysis (OBIA classification achieved an estimated overall accuracy of 82%, with further processing required to classify shadow objects. CSS land surface estimations were then extrapolated across the entire classification through calculation of within image class proportions, to provide the proportional coverage of 10 garden land surface types (buildings, hard impervious surfaces, hard pervious surfaces, bare soil, trees, shrubs, mown grass, rough grass, cultivated land, water within every garden parcel in the city. The final dataset provides a better understanding of the composition of GI in domestic gardens and how this varies across the city. An average garden in Manchester has 50.23% GI, including trees (16.54%, mown grass (14.46%, shrubs (9.19%, cultivated land (7.62%, rough grass (1.97% and water (0.45%. At the city scale, Manchester has 49.0% GI, and around one fifth (20.94% of this GI is contained within domestic

  5. Mutation analysis of SLC26A4 for Pendred syndrome and nonsyndromic hearing loss by high-resolution melting

    DEFF Research Database (Denmark)

    Chen, Neng; Tranebjærg, Lisbeth; Rendtorff, Nanna Dahl

    2011-01-01

    Pendred syndrome and DFNB4 (autosomal recessive nonsyndromic congenital deafness, locus 4) are associated with autosomal recessive congenital sensorineural hearing loss and mutations in the SLC26A4 gene. Extensive allelic heterogeneity, however, necessitates analysis of all exons and splice sites...

  6. Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

    International Nuclear Information System (INIS)

    Zeng, Ying-Xu; Mjøs, Svein Are; David, Fabrice P.A.; Schmid, Adrien W.

    2016-01-01

    Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

  7. Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Ying-Xu [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); Mjøs, Svein Are, E-mail: svein.mjos@kj.uib.no [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); David, Fabrice P.A. [Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne (Switzerland); Schmid, Adrien W. [Proteomics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne (Switzerland)

    2016-03-31

    Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

  8. Challenges in Resolution for IC Failure Analysis

    Science.gov (United States)

    Martinez, Nick

    1999-10-01

    Resolution is becoming more and more of a challenge in the world of Failure Analysis in integrated circuits. This is a result of the ongoing size reduction in microelectronics. Determining the cause of a failure depends upon being able to find the responsible defect. The time it takes to locate a given defect is extremely important so that proper corrective actions can be taken. The limits of current microscopy tools are being pushed. With sub-micron feature sizes and even smaller killing defects, optical microscopes are becoming obsolete. With scanning electron microscopy (SEM), the resolution is high but the voltage involved can make these small defects transparent due to the large mean-free path of incident electrons. In this presentation, I will give an overview of the use of inspection methods in Failure Analysis and show example studies of my work as an Intern student at Texas Instruments. 1. Work at Texas Instruments, Stafford, TX, was supported by TI. 2. Work at Texas Tech University, was supported by NSF Grant DMR9705498.

  9. High resolution fire risk mapping in Italy

    Science.gov (United States)

    Fiorucci, Paolo; Biondi, Guido; Campo, Lorenzo; D'Andrea, Mirko

    2014-05-01

    extinguishing actions, leaving more resources to improve safety in areas at risk. With the availability of fire perimeters mapped over a period spanning from 5 to 10 years, depending by the region, a procedure was defined in order to assess areas at risk with high spatial resolution (900 m2) based on objective criteria by observing past fire events. The availability of fire perimeters combined with a detailed knowledge of topography and land cover allowed to understand which are the main features involved in forest fire occurrences and their behaviour. The seasonality of the fire regime was also considered, partitioning the analysis in two macro season (November- April and May- October). In addition, the total precipitation obtained from the interpolation of 30 years-long time series from 460 raingauges and the average air temperature obtained downscaling 30 years ERA-INTERIM data series were considered. About 48000 fire perimeters which burnt about 5500 km2 were considered in the analysis. The analysis has been carried out at 30 m spatial resolution. Some important considerations relating to climate and the territorial features that characterize the fire regime at national level contribute to better understand the forest fire phenomena. These results allow to define new strategies for forest fire prevention and management extensible to other geographical areas.

  10. High resolution SETI: Experiences and prospects

    Science.gov (United States)

    Horowitz, Paul; Clubok, Ken

    Megachannel spectroscopy with sub-Hertz resolution constitutes an attractive strategy for a microwave search for extraterrestrial intelligence (SETI), assuming the transmission of a narrowband radiofrequency beacon. Such resolution matches the properties of the interstellar medium, and the necessary Doppler corrections provide a high degree of interference rejection. We have constructed a frequency-agile receiver with an FFT-based 8 megachannel digital spectrum analyzer, on-line signal recognition, and multithreshold archiving. We are using it to conduct a meridian transit search of the northern sky at the Harvard-Smithsonian 26-m antenna, with a second identical system scheduled to begin observations in Argentina this month. Successive 400 kHz spectra, at 0.05 Hz resolution, are searched for features characteristic of an intentional narrowband beacon transmission. These spectra are centered on guessable frequencies (such as λ21 cm), referenced successively to the local standard of rest, the galactic barycenter, and the cosmic blackbody rest frame. This search has rejected interference admirably, but is greatly limited both in total frequency coverage and sensitivity to signals other than carriers. We summarize five years of high resolution SETI at Harvard, in the context of answering the questions "How useful is narrowband SETI, how serious are its limitations, what can be done to circumvent them, and in what direction should SETI evolve?" Increasingly powerful signal processing hardware, combined with ever-higher memory densities, are particularly relevant, permitting the construction of compact and affordable gigachannel spectrum analyzers covering hundreds of megahertz of instantaneous bandwidth.

  11. First high resolution analysis of the 3ν2 and 3ν2 -ν2 bands of 32S16O2

    Science.gov (United States)

    Ulenikov, O. N.; Bekhtereva, E. S.; Gromova, O. V.; Berezkin, K. B.; Horneman, V.-M.; Sydow, C.; Maul, C.; Bauerecker, S.

    2017-11-01

    The second bending overtone band 3ν2 of sulfur dioxide has been studied for the first time with high resolution rotation-vibration spectroscopy. The 1530 transitions involving 728 upper state energy levels with Jmax.= 53 and Kamax . = 15 have been assigned to the 3ν2 band. The 746 transitions belonging to the 3ν2 -ν2 "hot" band have been also assigned in the region of 950-1100 cm-1. For the analysis of the assigned transitions, an effective Hamiltonian of an isolated (030) vibrational state (the Watson operator in A-reduction and Ir representation) was used. Set of 9 varied parameters was determined which reproduce the initial experimental data with the drms deviations of 9.0 ×10-4 cm-1 and 9.8 ×10-4 cm-1 for the 3ν2 and 3ν2 -ν2 bands, which are comparable with the experimental uncertainties.

  12. Detection of plant oil DNA using high resolution melting (HRM) post PCR analysis: a tool for disclosure of olive oil adulteration.

    Science.gov (United States)

    Vietina, Michelangelo; Agrimonti, Caterina; Marmiroli, Nelson

    2013-12-15

    Extra virgin olive oil is frequently subjected to adulterations with addition of oils obtained from plants other than olive. DNA analysis is a fast and economic tool to identify plant components in oils. Extraction and amplification of DNA by PCR was tested in olives, in milled seeds and in oils, to investigate its use in olive oil traceability. DNA was extracted from different oils made of hazelnut, maize, sunflower, peanut, sesame, soybean, rice and pumpkin. Comparing the DNA melting profiles in reference plant materials and in the oils, it was possible to identify any plant components in oils and mixtures of oils. Real-Time PCR (RT-PCR) platform has been added of the new methodology of high resolution melting (HRM), both were used to analyse olive oils mixed with different percentage of other oils. Results showed HRM a cost effective method for efficient detection of adulterations in olive oils. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. High Resolution and Differential PIXE combined with RBS, EBS and AFM analysis of magnesium titanate (MgTiO3) multilayer structures

    International Nuclear Information System (INIS)

    Reis, M.A.; Alves, L.C.; Barradas, N.P.; Chaves, P.C.; Nunes, B.; Taborda, A.; Surendran, K.P.; Wu, A.; Vilarinho, P.M.; Alves, E.

    2010-01-01

    Thorough structural characterization of deep laying thin film, including the inference of interdiffusion profiles is frequently a complex problem. The use of RBS/PIXE holistic approaches, already shown to represent a powerful method, sometimes faces difficulties if standard experimental procedures are used. In this work, following a series of 4 He Rutherford backscattering and 1 H elastic backscattering experiments, carried out to study the influence of SrTiO 3 as a possible cladding layer between Pt/TiO 2 /SiO 2 /(1 0 0)Si substrates and MgTiO 3 films, a simple holistic RBS-PIXE is shown to be not enough for the solution of such a problem. Establishing of the Sr depth profile, was only possible after AFM, High-Resolution EDS PIXE and differential PIXE analysis were carried out. Results, problems faced and conclusions obtained are presented.

  14. A method for volume determination of the orbit and its contents by high resolution axial tomography and quantitative digital image analysis.

    Science.gov (United States)

    Cooper, W C

    1985-01-01

    The various congenital and acquired conditions which alter orbital volume are reviewed. Previous investigative work to determine orbital capacity is summarized. Since these studies were confined to postmortem evaluations, the need for a technique to measure orbital volume in the living state is presented. A method for volume determination of the orbit and its contents by high-resolution axial tomography and quantitative digital image analysis is reported. This procedure has proven to be accurate (the discrepancy between direct and computed measurements ranged from 0.2% to 4%) and reproducible (greater than 98%). The application of this method to representative clinical problems is presented and discussed. The establishment of a diagnostic system versatile enough to expand the usefulness of computerized axial tomography and polytomography should add a new dimension to ophthalmic investigation and treatment.

  15. Enhanced Isotopic Ratio Outlier Analysis (IROA Peak Detection and Identification with Ultra-High Resolution GC-Orbitrap/MS: Potential Application for Investigation of Model Organism Metabolomes

    Directory of Open Access Journals (Sweden)

    Yunping Qiu

    2018-01-01

    Full Text Available Identifying non-annotated peaks may have a significant impact on the understanding of biological systems. In silico methodologies have focused on ESI LC/MS/MS for identifying non-annotated MS peaks. In this study, we employed in silico methodology to develop an Isotopic Ratio Outlier Analysis (IROA workflow using enhanced mass spectrometric data acquired with the ultra-high resolution GC-Orbitrap/MS to determine the identity of non-annotated metabolites. The higher resolution of the GC-Orbitrap/MS, together with its wide dynamic range, resulted in more IROA peak pairs detected, and increased reliability of chemical formulae generation (CFG. IROA uses two different 13C-enriched carbon sources (randomized 95% 12C and 95% 13C to produce mirror image isotopologue pairs, whose mass difference reveals the carbon chain length (n, which aids in the identification of endogenous metabolites. Accurate m/z, n, and derivatization information are obtained from our GC/MS workflow for unknown metabolite identification, and aids in silico methodologies for identifying isomeric and non-annotated metabolites. We were able to mine more mass spectral information using the same Saccharomyces cerevisiae growth protocol (Qiu et al. Anal. Chem 2016 with the ultra-high resolution GC-Orbitrap/MS, using 10% ammonia in methane as the CI reagent gas. We identified 244 IROA peaks pairs, which significantly increased IROA detection capability compared with our previous report (126 IROA peak pairs using a GC-TOF/MS machine. For 55 selected metabolites identified from matched IROA CI and EI spectra, using the GC-Orbitrap/MS vs. GC-TOF/MS, the average mass deviation for GC-Orbitrap/MS was 1.48 ppm, however, the average mass deviation was 32.2 ppm for the GC-TOF/MS machine. In summary, the higher resolution and wider dynamic range of the GC-Orbitrap/MS enabled more accurate CFG, and the coupling of accurate mass GC/MS IROA methodology with in silico fragmentation has great

  16. Enhanced Isotopic Ratio Outlier Analysis (IROA) Peak Detection and Identification with Ultra-High Resolution GC-Orbitrap/MS: Potential Application for Investigation of Model Organism Metabolomes.

    Science.gov (United States)

    Qiu, Yunping; Moir, Robyn D; Willis, Ian M; Seethapathy, Suresh; Biniakewitz, Robert C; Kurland, Irwin J

    2018-01-18

    Identifying non-annotated peaks may have a significant impact on the understanding of biological systems. In silico methodologies have focused on ESI LC/MS/MS for identifying non-annotated MS peaks. In this study, we employed in silico methodology to develop an Isotopic Ratio Outlier Analysis (IROA) workflow using enhanced mass spectrometric data acquired with the ultra-high resolution GC-Orbitrap/MS to determine the identity of non-annotated metabolites. The higher resolution of the GC-Orbitrap/MS, together with its wide dynamic range, resulted in more IROA peak pairs detected, and increased reliability of chemical formulae generation (CFG). IROA uses two different 13 C-enriched carbon sources (randomized 95% 12 C and 95% 13 C) to produce mirror image isotopologue pairs, whose mass difference reveals the carbon chain length (n), which aids in the identification of endogenous metabolites. Accurate m/z, n, and derivatization information are obtained from our GC/MS workflow for unknown metabolite identification, and aids in silico methodologies for identifying isomeric and non-annotated metabolites. We were able to mine more mass spectral information using the same Saccharomyces cerevisiae growth protocol (Qiu et al. Anal. Chem 2016) with the ultra-high resolution GC-Orbitrap/MS, using 10% ammonia in methane as the CI reagent gas. We identified 244 IROA peaks pairs, which significantly increased IROA detection capability compared with our previous report (126 IROA peak pairs using a GC-TOF/MS machine). For 55 selected metabolites identified from matched IROA CI and EI spectra, using the GC-Orbitrap/MS vs. GC-TOF/MS, the average mass deviation for GC-Orbitrap/MS was 1.48 ppm, however, the average mass deviation was 32.2 ppm for the GC-TOF/MS machine. In summary, the higher resolution and wider dynamic range of the GC-Orbitrap/MS enabled more accurate CFG, and the coupling of accurate mass GC/MS IROA methodology with in silico fragmentation has great potential in

  17. High-resolution Whole-Genome Analysis of Skull Base Chordomas Implicates FHIT Loss in Chordoma Pathogenesis12

    OpenAIRE

    Diaz, Roberto Jose; Guduk, Mustafa; Romagnuolo, Rocco; Smith, Christian A; Northcott, Paul; Shih, David; Berisha, Fitim; Flanagan, Adrienne; Munoz, David G; Cusimano, Michael D; Pamir, M Necmettin; Rutka, James T

    2012-01-01

    Chordoma is a rare tumor arising in the sacrum, clivus, or vertebrae. It is often not completely resectable and shows a high incidence of recurrence and progression with shortened patient survival and impaired quality of life. Chemotherapeutic options are limited to investigational therapies at present. Therefore, adjuvant therapy for control of tumor recurrence and progression is of great interest, especially in skull base lesions where complete tumor resection is often not possible because ...

  18. Development of a High Resolution, Real Time, Distribution-Level Metering System and Associated Visualization, Modeling, and Data Analysis Functions

    Energy Technology Data Exchange (ETDEWEB)

    Bank, J.; Hambrick, J.

    2013-05-01

    NREL is developing measurement devices and a supporting data collection network specifically targeted at electrical distribution systems to support research in this area. This paper describes the measurement network which is designed to apply real-time and high speed (sub-second) measurement principles to distribution systems that are already common for the transmission level in the form of phasor measurement units and related technologies.

  19. Wide-scope analysis of pesticide and veterinary drug residues in meat matrices by high resolution MS: detection and identification using Exactive-Orbitrap.

    Science.gov (United States)

    Gómez-Pérez, María Luz; Romero-González, Roberto; Plaza-Bolaños, Patricia; Génin, Eric; Martínez Vidal, José Luis; Garrido Frenich, Antonia

    2014-01-01

    A multiresidue and multiclass method for the simultaneous determination of more than 350 compounds including pesticides, biopesticides and veterinary drugs in different meat matrices (beef, pork and chicken) by ultra-high performance liquid chromatography coupled to Orbitrap MS has been developed. In the present study, the determination of fragments was accomplished as an essential tool for a reliable identification of compounds using high resolution MS. To obtain these fragments, different strategies have been carried out in order to ensure an appropriate fragment assignment and identification. The analytical method is suitable for qualitative analysis, and it was also evaluated for quantitative analysis. Generic extraction conditions were optimized, obtaining adequate recovery and precision values for most of the studied analytes (>290). The limits of detection ranged from 2 to 16 µg kg(-1). Limits of quantification were 10 µg kg(-1) with the exception of few compounds with a higher value (50 or 100 µg kg(-1)). Limits of identification were also established, and they ranged from 2 to 150 µg kg(-1). This method was applied to the analysis of 18 meat samples and some veterinary drugs as enrofloxacin and sulfadiazine were detected and further identified/quantified (with triple quadrupole) in two different samples at 33 µg kg(-1) and trace levels, respectively. No pesticides were detected in the analyzed samples. Copyright © 2014 John Wiley & Sons, Ltd.

  20. Near Infrared Microspectroscopy, Fluorescence Microspectroscopy, Infrared Chemical Imaging and High Resolution Nuclear Magnetic Resonance Analysis of Soybean Seeds, Somatic Embryos and Single Cells

    CERN Document Server

    Baianu, I C; Hofmann, N E; Korban, S S; Lozano, P; You, T; AOCS 94th Meeting, Kansas

    2002-01-01

    Novel methodologies are currently being developed and established for the chemical analysis of soybean seeds, embryos and single cells by Fourier Transform Infrared (FT-IR), Fourier Transform Near Infrared (FT-NIR) Microspectroscopy, Fluorescence and High-Resolution NMR (HR-NMR). The first FT-NIR chemical images of biological systems approaching one micron resolution are presented here. Chemical images obtained by FT-NIR and FT-IR Microspectroscopy are presented for oil in soybean seeds and somatic embryos under physiological conditions. FT-NIR spectra of oil and proteins were obtained for volumes as small as two cubic microns. Related, HR-NMR analyses of oil contents in somatic embryos are also presented here with nanoliter precision. Such 400 MHz 1H NMR analyses allowed the selection of mutagenized embryos with higher oil content (e.g. ~20%) compared to non-mutagenized control embryos. Moreover, developmental changes in single soybean seeds and/or somatic embryos may be monitored by FT-NIR with a precision ...

  1. In-Situ Sampling Analysis of a Jupiter Trojan Asteroid by High Resolution Mass Spectrometry in the Solar Power Sail Mission

    Science.gov (United States)

    Kebukawa, Y.; Aoki, J.; Ito, M.; Kawai, Y.; Okada, T.; Matsumoto, J.; Yano, H.; Yurimoto, H.; Terada, K.; Toyoda, M.; Yabuta, H.; Nakamura, R.; Cottin, H.; Grand, N.; Mori, O.

    2017-12-01

    The Solar Power Sail (SPS) mission is one of candidates for the upcoming strategic middle-class space exploration to demonstrate the first outer Solar System journey of Japan. The mission concept includes in-situ sampling analysis of the surface and subsurface (up to 1 m) materials of a Jupiter Trojan asteroid using high resolution mass spectrometry (HRMS). The candidates for the HRMS are multi-turn time-of-flight mass spectrometer (MULTUM) type and Cosmorbitrap type. We plan to analyze isotopic and elemental compositions of volatile materials from organic matter, hydrated minerals, and ice (if any), in order to understand origin and evolution of the Jupiter Trojan asteroids. It will provide insights into planet formation/migration theories, evolution and distribution of volatiles in the Solar System, and missing link between asteroids and comets on evolutional. The HRMS system allows to measure H, N, C, O isotopic compositions and elemental compositions of molecules prepared by various pre-MS procedures including stepwise heating up to 600ºC, gas chromatography (GC), and high-temperature pyrolysis with catalyst to decompose the samples into simple gaseous molecules (e.g., H2, CO, and N2) for isotopic ratio analysis. The required mass resolution should be at least 30,000 for analyzing isotopic ratios for simple gaseous molecules. For elemental compositions, mass accuracy of 10 ppm is required to determine elemental compositions for molecules with m/z up to 300 (as well as compound specific isotopic compositions for smaller molecules). Our planned analytical sequences consist of three runs for both surface and subsurface samples. In addition, `sniff mode' which simply introduces environmental gaseous molecules into a HRMS will be done by the system.

  2. High-resolution computed tomography to differentiate chronic diffuse interstitial lung diseases with predominant ground-glass pattern using logical analysis of data

    International Nuclear Information System (INIS)

    Martin, Sophie Grivaud; Brauner, Michel W.; Rety, Frederique; Kronek, Louis-Philippe; Brauner, Nadia; Valeyre, Dominique; Nunes, Hilario; Brillet, Pierre-Yves

    2010-01-01

    We evaluated the performance of high-resolution computed tomography (HRCT) to differentiate chronic diffuse interstitial lung diseases (CDILD) with predominant ground-glass pattern by using logical analysis of data (LAD). A total of 162 patients were classified into seven categories: sarcoidosis (n = 38), connective tissue disease (n = 32), hypersensitivity pneumonitis (n = 18), drug-induced lung disease (n = 15), alveolar proteinosis (n = 12), idiopathic non-specific interstitial pneumonia (n = 10) and miscellaneous (n = 37). First, 40 CT attributes were investigated by the LAD to build up patterns characterising a category. From the association of patterns, LAD determined models specific to each CDILD. Second, data were recomputed by adding eight clinical attributes to the analysis. The 20 x 5 cross-folding method was used for validation. Models could be individualised for sarcoidosis, hypersensitivity pneumonitis, connective tissue disease and alveolar proteinosis. An additional model was individualised for drug-induced lung disease by adding clinical data. No model was demonstrated for idiopathic non-specific interstitial pneumonia and the miscellaneous category. The results showed that HRCT had a good sensitivity (≥64%) and specificity (≥78%) and a high negative predictive value (≥93%) for diseases with a model. Higher sensitivity (≥78%) and specificity (≥89%) were achieved by adding clinical data. The diagnostic performance of HRCT is high and can be increased by adding clinical data. (orig.)

  3. High-resolution analysis of a QTL for resistance to Stagonospora nodorum glume blotch in wheat reveals presence of two distinct resistance loci in the target interval.

    Science.gov (United States)

    Shatalina, Margarita; Messmer, Monika; Feuillet, Catherine; Mascher, Fabio; Paux, Etienne; Choulet, Frédéric; Wicker, Thomas; Keller, Beat

    2014-03-01

    Stagonospora nodorum glume blotch (SNG), caused by the necrotrophic fungus Stagonospora nodorum, is one of the economically important diseases of bread wheat (Triticum aestivum L.). Resistance to SNG is known to be quantitative and previous studies of a recombinant inbred line (RIL) population identified a major quantitative trait locus (QTL) for resistance to SNG on the short arm of chromosome 3B. To localize this QTL (QSng.sfr-3BS) with high resolution, we constructed a genetic map for the QTL target region using information from sequenced flow-sorted chromosomes 3B of the two parental cultivars 'Arina' and 'Forno', the physical map of chromosome 3B of cultivar 'Chinese Spring' and BAC-clone sequences. The mapping population of near-isogenic lines (NIL) was evaluated for SNG resistance in field infection tests. NILs segregated for disease resistance as well as for plant height; additionally, we observed a high environmental influence on the trait. Our analysis detected a strong negative correlation of SNG resistance and plant height. Further analysis of the target region identified two linked loci associated with SNG resistance. One of them was also associated with plant height, revealing an effect of QSng.sfr-3BS on plant height that was hidden in the RIL population. This result demonstrates an unexpectedly high genetic complexity of resistance controlled by QSng.sfr-3BS and shows the importance of the study of QTL in mendelized form in NILs.

  4. Analysis of visual appearance of retinal nerve fibers in high resolution fundus images: a study on normal subjects.

    Science.gov (United States)

    Kolar, Radim; Tornow, Ralf P; Laemmer, Robert; Odstrcilik, Jan; Mayer, Markus A; Gazarek, Jiri; Jan, Jiri; Kubena, Tomas; Cernosek, Pavel

    2013-01-01

    The retinal ganglion axons are an important part of the visual system, which can be directly observed by fundus camera. The layer they form together inside the retina is the retinal nerve fiber layer (RNFL). This paper describes results of a texture RNFL analysis in color fundus photographs and compares these results with quantitative measurement of RNFL thickness obtained from optical coherence tomography on normal subjects. It is shown that local mean value, standard deviation, and Shannon entropy extracted from the green and blue channel of fundus images are correlated with corresponding RNFL thickness. The linear correlation coefficients achieved values 0.694, 0.547, and 0.512 for respective features measured on 439 retinal positions in the peripapillary area from 23 eyes of 15 different normal subjects.

  5. Analysis of Visual Appearance of Retinal Nerve Fibers in High Resolution Fundus Images: A Study on Normal Subjects

    Directory of Open Access Journals (Sweden)

    Radim Kolar

    2013-01-01

    Full Text Available The retinal ganglion axons are an important part of the visual system, which can be directly observed by fundus camera. The layer they form together inside the retina is the retinal nerve fiber layer (RNFL. This paper describes results of a texture RNFL analysis in color fundus photographs and compares these results with quantitative measurement of RNFL thickness obtained from optical coherence tomography on normal subjects. It is shown that local mean value, standard deviation, and Shannon entropy extracted from the green and blue channel of fundus images are correlated with corresponding RNFL thickness. The linear correlation coefficients achieved values 0.694, 0.547, and 0.512 for respective features measured on 439 retinal positions in the peripapillary area from 23 eyes of 15 different normal subjects.

  6. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    2012-01-01

    High Resolution NMR: Theory and Chemical Applications discusses the principles and theory of nuclear magnetic resonance and how this concept is used in the chemical sciences. This book is written at an intermediate level, with mathematics used to augment verbal descriptions of the phenomena. This text pays attention to developing and interrelating four approaches - the steady state energy levels, the rotating vector picture, the density matrix, and the product operator formalism. The style of this book is based on the assumption that the reader has an acquaintance with the general principles of quantum mechanics, but no extensive background in quantum theory or proficiency in mathematics is required. This book begins with a description of the basic physics, together with a brief account of the historical development of the field. It looks at the study of NMR in liquids, including high resolution NMR in the solid state and the principles of NMR imaging and localized spectroscopy. This book is intended to assis...

  7. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    1999-01-01

    High Resolution NMR provides a broad treatment of the principles and theory of nuclear magnetic resonance (NMR) as it is used in the chemical sciences. It is written at an "intermediate" level, with mathematics used to augment, rather than replace, clear verbal descriptions of the phenomena. The book is intended to allow a graduate student, advanced undergraduate, or researcher to understand NMR at a fundamental level, and to see illustrations of the applications of NMR to the determination of the structure of small organic molecules and macromolecules, including proteins. Emphasis is on the study of NMR in liquids, but the treatment also includes high resolution NMR in the solid state and the principles of NMR imaging and localized spectroscopy. Careful attention is given to developing and interrelating four approaches - steady state energy levels, the rotating vector picture, the density matrix, and the product operator formalism. The presentation is based on the assumption that the reader has an acquaintan...

  8. High-resolution flurescence spectroscopy in immunoanalysis

    Energy Technology Data Exchange (ETDEWEB)

    Grubor, Nenad M. [Iowa State Univ., Ames, IA (United States)

    2005-01-01

    The work presented in this dissertation combines highly sensitive and selective fluorescence line-narrowing spectroscopy (FLNS) detection with various modes of immunoanalytical techniques. It has been shown that FLNS is capable of directly probing molecules immunocomplexed with antibodies, eliminating analytical ambiguities that may arise from interferences that accompany traditional immunochemical techniques. Moreover, the utilization of highly cross-reactive antibodies for highly specific analyte determination has been demonstrated. Finally, they demonstrate the first example of the spectral resolution of diastereomeric analytes based on their interaction with a cross-reactive antibody.

  9. Instantaneous Shoreline Extraction Utilizing Integrated Spectrum and Shadow Analysis From LiDAR Data and High-resolution Satellite Imagery

    Science.gov (United States)

    Lee, I.-Chieh

    manually connected, for its length was less than 3% of the total shoreline length in our dataset. Secondly, the parameters for satellite image classification needed to be manually determined. The need for manpower was significantly less compared to the ground surveying or aerial photogrammetry. The first phase of shoreline extraction was to utilize Normalized Difference Vegetation Index (NDVI), Mean-Shift segmentation on the coordinate (X, Y, Z), and attributes (multispectral bands from satellite images) of the LiDAR points to classify each LiDAR point into land or water surface. Boundary of the land points were then traced to create the shoreline. The second phase of shoreline extraction solely from satellite images utilized spectrum, NDVI, and shadow analysis to classify the satellite images into classes. These classes were then refined by mean-shift segmentation on the panchromatic band. By tracing the boundary of the water surface, the shoreline can be created. Since these two shorelines may represent different shoreline instances in time, evaluating the changes of shoreline was the first to be done. Then an independent scenario analysis and a procedure are performed for the shoreline of each of the three conditions: in the process of erosion, in the process of accession, and remaining the same. With these three conditions, we could analysis the actual terrain type and correct the classification errors to obtain a more accurate shoreline. Meanwhile, methods of evaluating the quality of shorelines had also been discussed. The experiment showed that there were three indicators could best represent the quality of the shoreline. These indicators were: (1) shoreline accuracy, (2) land area difference between extracted shoreline and ground truth shoreline, and (3) bias factor from shoreline quality metrics.

  10. Study of exhaled breath condensate sample preparation for metabolomics analysis by LC-MS/MS in high resolution mode.

    Science.gov (United States)

    Fernández-Peralbo, M A; Calderón Santiago, M; Priego-Capote, F; Luque de Castro, M D

    2015-11-01

    Metabolomic analysis of exhaled breath condensate (EBC) requires an unavoidable sample preparation step because of the low concentration of its components, and potential cleanup for possible interferents. Sample preparation based on protein precipitation (PP), solid-phase extraction (SPE) by hydrophilic and lipophilic sorbents or lyophilization has demonstrated that the analytical sample from the last is largely the best because lyophilization allows reconstitution in a volume as small as required (preconcentration factors up to 80-times with respect to the original sample), thus doubling the number of detected compounds as compared with the other alternatives (47 versus 25). In addition, PP and/or SPE cleanup are unnecessary as no effect from the EBC components removed by these steps appears in the chromatograms. The total 49 EBC compounds tentatively identified and confirmed by MS/MS in this research include amino acids, fatty acids, fatty amides, fatty aldehydes, sphingoid bases, oxoanionic compounds, imidazoles, hydroxy acids and aliphatic acyclic acids. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Analysis of polychlorinated dibenzo-p-dioxins and dibenzofurans using simultaneous dual gas chromatography-high resolution mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Tirler, W.; Voto, G.; Donega, M. [Eco-Research, Bolzano (Italy)

    2004-09-15

    Polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/F) are two classes of environmental contaminants. Seventeen congeners exist that are substituted in the 2,3,7,8 position and are considered to be the most toxic. Due to the large number (210) of compounds of the PCDD/F family, gas chromatographic (GC) separation of these from the cluster of less toxic isomers is a difficult task. At present no commercially available column can separate all 2,3,7,8 substituted congeners from the remaining PCDD/F. The co elution of less toxic with toxic congeners can cause false TEQ related results, because mass spectrometry cannot differentiate between toxic and non toxic congeners within the same homologous group. To overcome this, the analysis is performed using at least two capillary GC columns, of different polarity. Non polar columns can separate chlorine homologous groups and all toxic congeners from each other but not from all nontoxic congeners. Thus, a polar column should be used in addition for specific separation. Exchange of a GC column on a HRGC-HRMS system is usually a time consuming procedure. Significant time saving can be achieved using a mass spectrometer coupled to two GCs, that allows switching between two different GC columns, without disturbing the measurement conditions of the mass spectrometer. The aim of the present work was to develop a method that permits to work simultaneously with both GCs in order to further improve time savings.

  12. CtGEM typing: Discrimination of Chlamydia trachomatis ocular and urogenital strains and major evolutionary lineages by high resolution melting analysis of two amplified DNA fragments.

    Science.gov (United States)

    Giffard, Philip M; Andersson, Patiyan; Wilson, Judith; Buckley, Cameron; Lilliebridge, Rachael; Harris, Tegan M; Kleinecke, Mariana; O'Grady, Kerry-Ann F; Huston, Wilhelmina M; Lambert, Stephen B; Whiley, David M; Holt, Deborah C

    2018-01-01

    Chlamydia trachomatis infects the urogenital tract (UGT) and eyes. Anatomical tropism is correlated with variation in the major outer membrane protein encoded by ompA. Strains possessing the ocular ompA variants A, B, Ba and C are typically found within the phylogenetically coherent "classical ocular lineage". However, variants B, Ba and C have also been found within three distinct strains in Australia, all associated with ocular disease in children and outside the classical ocular lineage. CtGEM genotyping is a method for detecting and discriminating ocular strains and also the major phylogenetic lineages. The rationale was facilitation of surveillance to inform responses to C. trachomatis detection in UGT specimens from young children. CtGEM typing is based on high resolution melting analysis (HRMA) of two PCR amplified fragments with high combinatorial resolving power, as defined by computerised comparison of 65 whole genomes. One fragment is from the hypothetical gene defined by Jali-1891 in the C. trachomatis B_Jali20 genome, while the other is from ompA. Twenty combinatorial CtGEM types have been shown to exist, and these encompass unique genotypes for all known ocular strains, and also delineate the TI and T2 major phylogenetic lineages, identify LGV strains and provide additional resolution beyond this. CtGEM typing and Sanger sequencing were compared with 42 C. trachomatis positive clinical specimens, and there were no disjunctions. CtGEM typing is a highly efficient method designed and tested using large scale comparative genomics. It divides C. trachomatis into clinically and biologically meaningful groups, and may have broad application in surveillance.

  13. High-Resolution MRI in Rectal Cancer

    International Nuclear Information System (INIS)

    Dieguez, Adriana

    2010-01-01

    High-resolution MRI is the best method of assessing the relation of the rectal tumor with the potential circumferential resection margin (CRM). Therefore it is currently considered the method of choice for local staging of rectal cancer. The primary surgery of rectal cancer is total mesorectal excision (TME), which plane of dissection is formed by the mesorectal fascia surrounding mesorectal fat and rectum. This fascia will determine the circumferential margin of resection. At the same time, high resolution MRI allows adequate pre-operative identification of important prognostic risk factors, improving the selection and indication of therapy for each patient. This information includes, besides the circumferential margin of resection, tumor and lymph node staging, extramural vascular invasion and the description of lower rectal tumors. All these should be described in detail in the report, being part of the discussion in the multidisciplinary team, the place where the decisions involving the patient with rectal cancer will take place. The aim of this study is to provide the information necessary to understand the use of high resolution MRI in the identification of prognostic risk factors in rectal cancer. The technical requirements and standardized report for this study will be describe, as well as the anatomical landmarks of importance for the total mesorectal excision (TME), as we have said is the surgery of choice for rectal cancer. (authors) [es

  14. High-resolution spectroscopy of gases for industrial applications

    DEFF Research Database (Denmark)

    Fateev, Alexander; Clausen, Sønnik

    High-resolution spectroscopy of gases is a powerful technique which has various fundamental and practical applications: in situ simultaneous measurements of gas temperature and gas composition, radiative transfer modeling, validation of existing and developing of new databases and etc. Existing...... databases (e.g. HITRAN, HITEMP or CDSD) can normally be used for absorption spectra calculations at limited temperature/pressure ranges. Therefore experimental measurements of absorption/transmission spectra gases (e.g. CO2, H2O or SO2) at high-resolution and elevated temperatures are essential both...... for analysis of complex experimental data and further development of the databases. High-temperature gas cell facilities available at DTU Chemical Engineering are presented and described. The gas cells and high-resolution spectrometers allow us to perform high-quality reference measurements of gases relevant...

  15. Atmospheric methane at Cape Meares - Analysis of a high-resolution data base and its environmental implications

    Science.gov (United States)

    Khalil, M. A. K.; Rasmussen, R. A.; Moraes, F.

    1993-01-01

    Between 1979 and 1992 we took some 120,000 measurements of atmospheric methane at Cape Meares on the Oregon coast. The site is representative of methane concentrations in the northern latitudes (from 30 deg N to 90 deg N). The average concentration during the experiment was 1698 parts per billion by volume (ppbv). Methane concentration increased by 190 ppbv (or 11.9 percent) during the 13-year span of the experiment. The rate of increase was about 20 +/- 4 ppbv/yr in the first 2 yr and 10 +/- 2 ppbv/yr in the last 2 yr of the experiment, suggesting a substantial decline in the trend at northern middle and high latitudes. Prominent seasonal cycles were observed. During the year, the concentration stays more or less constant until May and then starts falling, reaching lowest levels in July and August, then rises rapidly to nearly maximum concentrations in October. Interannual variations with small amplitudes of 2-3 ppbv occur with periods of 1.4 and 6.5 yr.

  16. USGS High Resolution Orthoimagery Collection - Historical - National Geospatial Data Asset (NGDA) High Resolution Orthoimagery

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — USGS high resolution orthorectified images from The National Map combine the image characteristics of an aerial photograph with the geometric qualities of a map. An...

  17. Ultra high resolution X-ray detectors

    International Nuclear Information System (INIS)

    Hess, U.; Buehler, M.; Hentig, R. von; Hertrich, T.; Phelan, K.; Wernicke, D.; Hoehne, J.

    2001-01-01

    CSP Cryogenic Spectrometers GmbH is developing cryogenic energy dispersive X-ray spectrometers based on superconducting detector technology. Superconducting sensors exhibit at least a 10-fold improvement in energy resolution due to their low energy gap compared to conventional Si(Li) or Ge detectors. These capabilities are extremely valuable for the analysis of light elements and in general for the analysis of the low energy range of the X-ray spectrum. The spectrometer is based on a mechanical cooler needing no liquid coolants and an adiabatic demagnetization refrigerator (ADR) stage which supplies the operating temperature of below 100 mK for the superconducting sensor. Applications include surface analysis in semiconductor industry as well material analysis for material composition e.g. in ceramics or automobile industry

  18. Quantitative and Qualitative Assessment of Soil Erosion Risk in Małopolska (Poland), Supported by an Object-Based Analysis of High-Resolution Satellite Images

    Science.gov (United States)

    Drzewiecki, Wojciech; Wężyk, Piotr; Pierzchalski, Marcin; Szafrańska, Beata

    2014-06-01

    In 2011 the Marshal Office of Małopolska Voivodeship decided to evaluate the vulnerability of soils to water erosion for the entire region. The quantitative and qualitative assessment of the erosion risk for the soils of the Małopolska region was done based on the USLE approach. The special work-flow of geoinformation technologies was used to fulfil this goal. A high-resolution soil map, together with rainfall data, a detailed digital elevation model and statistical information about areas sown with particular crops created the input information for erosion modelling in GIS environment. The satellite remote sensing technology and the object-based image analysis (OBIA) approach gave valuable support to this study. RapidEye satellite images were used to obtain the essential up-to-date data about land use and vegetation cover for the entire region (15,000 km2). The application of OBIA also led to defining the direction of field cultivation and the mapping of contour tillage areas. As a result, the spatially differentiated values of erosion control practice factor were used. Both, the potential and the actual soil erosion risk were assessed quantificatively and qualitatively. The results of the erosion assessment in the Małopolska Voivodeship reveal the fact that a majority of its agricultural lands is characterized by moderate or low erosion risk levels. However, high-resolution erosion risk maps show its substantial spatial diversity. According to our study, average or higher actual erosion intensity levels occur for 10.6 % of agricultural land, i.e. 3.6 % of the entire voivodeship area. In 20 % of the municipalities there is a very urgent demand for erosion control. In the next 23 % an urgent erosion control is needed. Our study showed that even a slight improvement of P-factor estimation may have an influence on modeling results. In our case, despite a marginal change of erosion assessment figures on a regional scale, the influence on the final prioritization of

  19. Assessment of genetic mutations in the XRCC2 coding region by high resolution melting curve analysis and the risk of differentiated thyroid carcinoma in Iran

    Directory of Open Access Journals (Sweden)

    Shima Fayaz

    2012-01-01

    Full Text Available Homologous recombination (HR is the major pathway for repairing double strand breaks (DSBs in eukaryotes and XRCC2 is an essential component of the HR repair machinery. To evaluate the potential role of mutations in gene repair by HR in individuals susceptible to differentiated thyroid carcinoma (DTC we used high resolution melting (HRM analysis, a recently introduced method for detecting mutations, to examine the entire XRCC2 coding region in an Iranian population. HRM analysis was used to screen for mutations in three XRCC2 coding regions in 50 patients and 50 controls. There was no variation in the HRM curves obtained from the analysis of exons 1 and 2 in the case and control groups. In exon 3, an Arg188His polymorphism (rs3218536 was detected as a new melting curve group (OR: 1.46; 95%CI: 0.432-4.969; p = 0.38 compared with the normal melting curve. We also found a new Ser150Arg polymorphism in exon 3 of the control group. These findings suggest that genetic variations in the XRCC2 coding region have no potential effects on susceptibility to DTC. However, further studies with larger populations are required to confirm this conclusion.

  20. High-resolution melting analysis (HRM) for differentiation of four major Taeniidae species in dogs Taenia hydatigena, Taenia multiceps, Taenia ovis, and Echinococcus granulosus sensu stricto.

    Science.gov (United States)

    Dehghani, Mansoureh; Mohammadi, Mohammad Ali; Rostami, Sima; Shamsaddini, Saeedeh; Mirbadie, Seyed Reza; Harandi, Majid Fasihi

    2016-07-01

    Tapeworms of the genus Taenia include several species of important parasites with considerable medical and veterinary significance. Accurate identification of these species in dogs is the prerequisite of any prevention and control program. Here, we have applied an efficient method for differentiating four major Taeniid species in dogs, i.e., Taenia hydatigena, T. multiceps, T. ovis, and Echinococcus granulosus sensu stricto. High-resolution melting (HRM) analysis is simpler, less expensive, and faster technique than conventional DNA-based assays and enables us to detect PCR amplicons in a closed system. Metacestode samples were collected from local abattoirs from sheep. All the isolates had already been identified by PCR-sequencing, and their sequence data were deposited in the GenBank. Real-time PCR coupled with HRM analysis targeting mitochondrial cox1 and ITS1 genes was used to differentiate taeniid species. Distinct melting curves were obtained from ITS1 region enabling accurate differentiation of three Taenia species and E. granulosus in dogs. The HRM curves of Taenia species and E .granulosus were clearly separated at Tm of 85 to 87 °C. In addition, double-pick melting curves were produced in mixed infections. Cox1 melting curves were not decisive enough to distinguish four taeniids. In this work, the efficiency of HRM analysis to differentiate four major taeniid species in dogs has been demonstrated using ITS1 gene.

  1. Introducing AAA-MS, a rapid and sensitive method for amino acid analysis using isotope dilution and high-resolution mass spectrometry.

    Science.gov (United States)

    Louwagie, Mathilde; Kieffer-Jaquinod, Sylvie; Dupierris, Véronique; Couté, Yohann; Bruley, Christophe; Garin, Jérôme; Dupuis, Alain; Jaquinod, Michel; Brun, Virginie

    2012-07-06

    Accurate quantification of pure peptides and proteins is essential for biotechnology, clinical chemistry, proteomics, and systems biology. The reference method to quantify peptides and proteins is amino acid analysis (AAA). This consists of an acidic hydrolysis followed by chromatographic separation and spectrophotometric detection of amino acids. Although widely used, this method displays some limitations, in particular the need for large amounts of starting material. Driven by the need to quantify isotope-dilution standards used for absolute quantitative proteomics, particularly stable isotope-labeled (SIL) peptides and PSAQ proteins, we developed a new AAA assay (AAA-MS). This method requires neither derivatization nor chromatographic separation of amino acids. It is based on rapid microwave-assisted acidic hydrolysis followed by high-resolution mass spectrometry analysis of amino acids. Quantification is performed by comparing MS signals from labeled amino acids (SIL peptide- and PSAQ-derived) with those of unlabeled amino acids originating from co-hydrolyzed NIST standard reference materials. For both SIL peptides and PSAQ standards, AAA-MS quantification results were consistent with classical AAA measurements. Compared to AAA assay, AAA-MS was much faster and was 100-fold more sensitive for peptide and protein quantification. Finally, thanks to the development of a labeled protein standard, we also extended AAA-MS analysis to the quantification of unlabeled proteins.

  2. Moderate resolution spectrophotometry of high redshift quasars

    Science.gov (United States)

    Schneider, Donald P.; Schmidt, Maarten; Gunn, James E.

    1991-01-01

    A uniform set of photometry and high signal-to-noise moderate resolution spectroscopy of 33 quasars with redshifts larger than 3.1 is presented. The sample consists of 17 newly discovered quasars (two with redshifts in excess of 4.4) and 16 sources drawn from the literature. The objects in this sample have r magnitudes between 17.4 and 21.4; their luminosities range from -28.8 to -24.9. Three of the 33 objects are broad absorption line quasars. A number of possible high redshift damped Ly-alpha systems were found.

  3. SPIRAL2/DESIR high resolution mass separator

    Energy Technology Data Exchange (ETDEWEB)

    Kurtukian-Nieto, T., E-mail: kurtukia@cenbg.in2p3.fr [Centre d’Études Nucléaires de Bordeaux Gradignan, Université Bordeaux 1-CNRS/IN2P3, BP 120, F-33175 Gradignan Cedex (France); Baartman, R. [TRIUMF, 4004 Wesbrook Mall, Vancouver B.C., V6T 2A3 (Canada); Blank, B.; Chiron, T. [Centre d’Études Nucléaires de Bordeaux Gradignan, Université Bordeaux 1-CNRS/IN2P3, BP 120, F-33175 Gradignan Cedex (France); Davids, C. [Physics Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Delalee, F. [Centre d’Études Nucléaires de Bordeaux Gradignan, Université Bordeaux 1-CNRS/IN2P3, BP 120, F-33175 Gradignan Cedex (France); Duval, M. [GANIL, CEA/DSM-CNRS/IN2P3, Bd Henri Becquerel, BP 55027, F-14076 Caen Cedex 5 (France); El Abbeir, S.; Fournier, A. [Centre d’Études Nucléaires de Bordeaux Gradignan, Université Bordeaux 1-CNRS/IN2P3, BP 120, F-33175 Gradignan Cedex (France); Lunney, D. [CSNSM-IN2P3-CNRS, Université de Paris Sud, F-91405 Orsay (France); Méot, F. [BNL, Upton, Long Island, New York (United States); Serani, L. [Centre d’Études Nucléaires de Bordeaux Gradignan, Université Bordeaux 1-CNRS/IN2P3, BP 120, F-33175 Gradignan Cedex (France); Stodel, M.-H.; Varenne, F. [GANIL, CEA/DSM-CNRS/IN2P3, Bd Henri Becquerel, BP 55027, F-14076 Caen Cedex 5 (France); and others

    2013-12-15

    DESIR is the low-energy part of the SPIRAL2 ISOL facility under construction at GANIL. DESIR includes a high-resolution mass separator (HRS) with a designed resolving power m/Δm of 31,000 for a 1 π-mm-mrad beam emittance, obtained using a high-intensity beam cooling device. The proposed design consists of two 90-degree magnetic dipoles, complemented by electrostatic quadrupoles, sextupoles, and a multipole, arranged in a symmetric configuration to minimize aberrations. A detailed description of the design and results of extensive simulations are given.

  4. Processing method for high resolution monochromator

    International Nuclear Information System (INIS)

    Kiriyama, Koji; Mitsui, Takaya

    2006-12-01

    A processing method for high resolution monochromator (HRM) has been developed at Japanese Atomic Energy Agency/Quantum Beam Science Directorate/Synchrotron Radiation Research unit at SPring-8. For manufacturing a HRM, a sophisticated slicing machine and X-ray diffractometer have been installed for shaping a crystal ingot and orienting precisely the surface of a crystal ingot, respectively. The specification of the slicing machine is following; Maximum size of a diamond blade is φ 350mm in diameter, φ 38.1mm in the spindle diameter, and 2mm in thickness. A large crystal such as an ingot with 100mm in diameter, 200mm in length can be cut. Thin crystal samples such as a wafer can be also cut using by another sample holder. Working distance of a main shaft with the direction perpendicular to working table in the machine is 350mm at maximum. Smallest resolution of the main shaft with directions of front-and-back and top-and-bottom are 0.001mm read by a digital encoder. 2mm/min can set for cutting samples in the forward direction. For orienting crystal faces relative to the blade direction adjustment, a one-circle goniometer and 2-circle segment are equipped on the working table in the machine. A rotation and a tilt of the stage can be done by manual operation. Digital encoder in a turn stage is furnished and has angle resolution of less than 0.01 degrees. In addition, a hand drill as a supporting device for detailed processing of crystal is prepared. Then, an ideal crystal face can be cut from crystal samples within an accuracy of about 0.01 degrees. By installation of these devices, a high energy resolution monochromator crystal for inelastic x-ray scattering and a beam collimator are got in hand and are expected to be used for nanotechnology studies. (author)

  5. Automated data processing of high-resolution mass spectra

    DEFF Research Database (Denmark)

    Hansen, Michael Adsetts Edberg; Smedsgaard, Jørn

    of the massive amounts of data. We present an automated data processing method to quantitatively compare large numbers of spectra from the analysis of complex mixtures, exploiting the full quality of high-resolution mass spectra. By projecting all detected ions - within defined intervals on both the time...... infusion of crude extracts into the source taking advantage of the high sensitivity, high mass resolution and accuracy and the limited fragmentation. Unfortunately, there has not been a comparable development in the data processing techniques to fully exploit gain in high resolution and accuracy...... infusion analyses of crude extract to find the relationship between species from several species terverticillate Penicillium, and also that the ions responsible for the segregation can be identified. Furthermore the process can automate the process of detecting unique species and unique metabolites....

  6. High-resolution melting analysis for detection of a single-nucleotide polymorphism and the genotype of the myostatin gene in warmblood horses.

    Science.gov (United States)

    Serpa, Priscila B S; Garbade, Petra; Natalini, Cláudio C; Pires, Ananda R; Tisotti, Tainor M

    2017-01-01

    OBJECTIVE To develop a high-resolution melting (HRM) assay to detect the g.66493737C>T polymorphism in the myostatin gene (MSTN) and determine the frequency of 3 previously defined g.66493737 genotypes (T/T, T/C, and C/C) in warmblood horses. SAMPLES Blood samples from 23 horses. PROCEDURES From each blood sample, DNA was extracted and analyzed by standard PCR methods and an HRM assay to determine the MSTN genotype. Three protocols (standard protocol, protocol in which a high-salt solution was added to the reaction mixture before the first melting cycle, and protocol in which an unlabeled probe was added to the reaction mixture before analysis) for the HRM assay were designed and compared. Genotype results determined by the HRM protocol that generated the most consistent melting curves were compared with those determined by sequencing. RESULTS The HRM protocol in which an unlabeled probe was added to the reaction mixture generated the most consistent melting curves. The genotypes of the g.66493737C>T polymorphism were determined for 22 horses (16 by HRM analysis and 20 by sequencing); 14, 7, and 1 had the T/T, T/C, and C/C genotypes, respectively. The genotype determined by HRM analysis agreed with that determined by sequencing for 14 of 16 horses. The frequency of alleles T and C was 79.5% and 20.5%, respectively. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that HRM analysis may be a faster and more economical alternative than PCR methods for genotyping. Genotyping results might be useful as predictors of athletic performance for horses.

  7. Easy, Fast, and Reproducible Quantification of Cholesterol and Other Lipids in Human Plasma by Combined High Resolution MSX and FTMS Analysis

    Science.gov (United States)

    Gallego, Sandra F.; Højlund, Kurt; Ejsing, Christer S.

    2018-01-01

    Reliable, cost-effective, and gold-standard absolute quantification of non-esterified cholesterol in human plasma is of paramount importance in clinical lipidomics and